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Conserved domains on  [gi|808376393|ref|XP_012193020|]
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U3 snoRNP-associated protein Rrp5 [Pseudozyma hubeiensis SY62]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1062-1138 3.92e-37

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 134.38  E-value: 3.92e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLKPSYF 1138
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 961-1028 1.67e-32

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 120.86  E-value: 1.67e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
RpsA super family cl33936
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 762-1134 1.33e-25

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


The actual alignment was detected with superfamily member COG0539:

Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 110.13  E-value: 1.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  762 NVDAVDVGEKVTGKVAAVHKEVVVLTlVPSGVRALLSLSVLASMRGStaeellESLEEDQEIDDLVVSVKNpAKGIVIV- 840
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVD-IGYKSEGIIPLSEFSDEPGE------LEVKVGDEVEVYVEKVED-GEGEIVLs 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  841 ---ADKVRSSKNADDgtnglvsgQVKQGNVVQGRVIQKNDKYLdcIVALGTAtRATLHMTDLADGFSSNvalPSP--GQT 915
Cdd:COG0539    84 kkkADREKAWEELEE--------AFENGEPVEGKVKGVVKGGL--IVDIGGV-RAFLPASQVDVRPVRD---LDEyvGKT 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  916 LQCYIVSLKSNGKNAVISTRpsrvnpsasaEVTDPEITS-----IADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQV 990
Cdd:COG0539   150 LEFKIIKLDRKRNNVVVSRR----------AVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHI 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  991 RELfdefvrDWKtR-------FTVGQVVSGTIMDTNPSNNEIEMSLKST---PgsikprAERLEERhadadkkrakrltd 1060
Cdd:COG0539   219 SEI------SWG-RvkhpsevLKVGDEVEVKVLKIDREKERISLSLKQLqpdP------WENIAEK-------------- 271

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1061 FKVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGK----ADEALKafrVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:COG0539   272 YPVGDVVKGKVTRLTDFGAFVELE-PGVEGLVHISEMSWTKrvahPSDVVK---VGDEVEVKVLDIDPEERRISLSIK 345
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 596-661 2.67e-25

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 100.39  E-value: 2.67e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393  596 TANIIKLGlPNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:cd05697     5 KGTIRKLR-PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 501-574 7.86e-19

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05696:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 71  Bit Score: 81.93  E-value: 7.86e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  501 GATLEVTVVQT-INDWGLIVSIHEtDLRGFVHISQVSDDHVVSLPpssGPFAKETVHKARVVGHSPTDRTLQLSL 574
Cdd:cd05696     1 GAVVDSVKVTKvEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDT---GPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 144-288 3.33e-17

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05693:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 100  Bit Score: 78.41  E-value: 3.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  144 LIPGSRLLCSVLAIHPLAVVVSLPNQMLGHIPVTQISPQFTRRLQaaadasaedddedesmdedsdsdddddeaQTNGTS 223
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLE-----------------------------ELDEES 51

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  224 SKRAKNDakKVPELRDLFHVGQWLVASVlqVRSGDVAKGRpsreggeyekesRRVELSLAPHLVN 288
Cdd:cd05693    52 EEEDDEE--ELPDLEDLFSVGQLVRCKV--VSLDKSKSGK------------KRIELSLEPELVN 100
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 295-378 4.76e-14

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05694:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 74  Bit Score: 68.43  E-value: 4.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  295 DLDVGATLSATISSVEDHGYMLDSGVSEFSGFVPFTDAAklpdsfhagkNGKSLQVGSVVFAKITKVPDNKRSFEATLDP 374
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG----------NFSKLKVGQLLLCVVEKVKDDGRVVSLSADP 70


                  ....
gi 808376393  375 KTVS 378
Cdd:cd05694    71 SKVS 74
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 682-751 1.44e-09

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05698:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 70  Bit Score: 55.69  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1288-1532 2.42e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 60.13  E-value: 2.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1288 FERLLLSSPNSSFLWIQFMSFSLQLSDVDRARSIARRALKvinyREEQERMnvwiALLNLENTY---GSEETLESTFREA 1364
Cdd:COG2956    31 LEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGLLDRAEELLEKL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1365 IQAN-DGFTMYLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQAleKRDHTST 1443
Cdd:COG2956   103 LELDpDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL--DPDCARA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1444 ITAFAINEFKLGDPERGRTIFEGLVDSYPKRLDLwWQYLDQESRLEGNETQVRNLFERAMTLKLTAKKgksLLKKWLDYE 1523
Cdd:COG2956   181 LLLLAELYLEQGDYEEAIAALERALEQDPDYLPA-LPRLAELYEKLGDPEEALELLRKALELDPSDDL---LLALADLLE 256


                  ....*....
gi 808376393 1524 KREGDAKSQ 1532
Cdd:COG2956   257 RKEGLEAAL 265
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 394-451 1.86e-05

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05695:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 66  Bit Score: 43.80  E-value: 1.86e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  394 GTLTKVLITAALPTGLNVNLFGMFDATIDRFHlpeLPEGKDIPDVYKEGSKHVARVLW 451
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLH---LDPEKSSKSTYKEGQKVRARILY 55
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1062-1138 3.92e-37

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 134.38  E-value: 3.92e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLKPSYF 1138
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 961-1028 1.67e-32

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 120.86  E-value: 1.67e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 762-1134 1.33e-25

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 110.13  E-value: 1.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  762 NVDAVDVGEKVTGKVAAVHKEVVVLTlVPSGVRALLSLSVLASMRGStaeellESLEEDQEIDDLVVSVKNpAKGIVIV- 840
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVD-IGYKSEGIIPLSEFSDEPGE------LEVKVGDEVEVYVEKVED-GEGEIVLs 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  841 ---ADKVRSSKNADDgtnglvsgQVKQGNVVQGRVIQKNDKYLdcIVALGTAtRATLHMTDLADGFSSNvalPSP--GQT 915
Cdd:COG0539    84 kkkADREKAWEELEE--------AFENGEPVEGKVKGVVKGGL--IVDIGGV-RAFLPASQVDVRPVRD---LDEyvGKT 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  916 LQCYIVSLKSNGKNAVISTRpsrvnpsasaEVTDPEITS-----IADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQV 990
Cdd:COG0539   150 LEFKIIKLDRKRNNVVVSRR----------AVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHI 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  991 RELfdefvrDWKtR-------FTVGQVVSGTIMDTNPSNNEIEMSLKST---PgsikprAERLEERhadadkkrakrltd 1060
Cdd:COG0539   219 SEI------SWG-RvkhpsevLKVGDEVEVKVLKIDREKERISLSLKQLqpdP------WENIAEK-------------- 271

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1061 FKVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGK----ADEALKafrVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:COG0539   272 YPVGDVVKGKVTRLTDFGAFVELE-PGVEGLVHISEMSWTKrvahPSDVVK---VGDEVEVKVLDIDPEERRISLSIK 345
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 596-661 2.67e-25

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 100.39  E-value: 2.67e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393  596 TANIIKLGlPNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:cd05697     5 KGTIRKLR-PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
758-1134 2.59e-22

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 103.87  E-value: 2.59e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  758 LAKLNVDAVDVGEKVTGKVAAV-HKEVVVLtlVPSGVRALLSLSVLASMRGSTAEELLESLeedQEIDDLVVSVKNpAKG 836
Cdd:PRK00087  292 YMNELEKQIRRGDIVKGTVVSVnENEVFVD--VGYKSEGVIPLRELTLDEISSLKESVKVG---DEIEVKVLKLED-EDG 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  837 IVIVADKVRSSKNADDGtngLVSGQvKQGNVVQGRVIQKNDKYLDCIVALgtaTRATLHMTDLADGFSSNvaLPS-PGQT 915
Cdd:PRK00087  366 YVVLSKKEADREKAWKE---LEEAF-ENGEPVKGKVKEVVKGGLLVDYGG---VRAFLPASHVELGYVED--LSEyKGQE 436

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  916 LQCYIVSLKSNGKNAVISTRPSRVNPSASAEvtdpEITSIADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQVRELFD 995
Cdd:PRK00087  437 LEVKIIEFNRKRRKKVVLSRKAILEEEKEKK----KEETWNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISW 511

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  996 EFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKstpgsikpraERLEERHADADKKrakrltdFKVGDKVKGFVKNVI 1075
Cdd:PRK00087  512 GRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLK----------KLLPDPWENVEEK-------YPVGSIVLGKVVRIA 574

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393 1076 DFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK00087  575 PFGAFVELE-PGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 501-574 7.86e-19

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 81.93  E-value: 7.86e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  501 GATLEVTVVQT-INDWGLIVSIHEtDLRGFVHISQVSDDHVVSLPpssGPFAKETVHKARVVGHSPTDRTLQLSL 574
Cdd:cd05696     1 GAVVDSVKVTKvEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDT---GPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1062-1134 6.33e-18

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.57  E-value: 6.33e-18
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393   1062 KVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 682-1134 6.37e-18

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 89.02  E-value: 6.37e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREvseddFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQA----SPEY 757
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLSREKAqrheLWIK 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   758 LAKLNVDAVDVGEKVTGKVAAVhkevvvLTLVPSGVRALLSLSvLASMRgsTAEELLESLEEDQEIDDLVVSVKNPAkgi 837
Cdd:TIGR00717   94 LEKAYEEGSIVEGKIVGKVKGG------FIVDLNGVEAFLPGS-QVDVK--PIKDLDSLIGKTLKFKIIKLDQKRNN--- 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   838 VIVADK----VRSSKNADDGTNGLVSGQVKQGNVVQgrvIQKNDKYLDcivaLGtATRATLHMTDLADGfssNVALPSP- 912
Cdd:TIGR00717  162 IVVSRRayleEERSQAREELLENLKEGDVVKGVVKN---ITDFGAFVD----LG-GVDGLLHITDMSWK---RVKHPSEy 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   913 ---GQTLQCYIVSLKSNGKNAVISTRPSRVNPSASAEVTDPEitsiadlakGQKVRGFVKAITNVGLFVTIGRKLDARVQ 989
Cdd:TIGR00717  231 vkvGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPV---------GDKITGRVTNLTDYGVFVEIEEGIEGLVH 301

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   990 VREL-FDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKSTpgsiKPRA-ERLEERH-------------------- 1047
Cdd:TIGR00717  302 VSEMsWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQC----KANPwEQFEEKHpvgdrvtgkikkitdfgafv 377

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1048 ----------------------------------------ADADKKR----AKRLTD---------FKVGDKVKGFVKNV 1074
Cdd:TIGR00717  378 eleggidglihlsdiswdkdgreadhlykkgdeieavvlaVDKEKKRislgVKQLTEnpwekfaakYKVGSVVKGKVTEI 457

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1075 IDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:TIGR00717  458 KDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 144-288 3.33e-17

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 78.41  E-value: 3.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  144 LIPGSRLLCSVLAIHPLAVVVSLPNQMLGHIPVTQISPQFTRRLQaaadasaedddedesmdedsdsdddddeaQTNGTS 223
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLE-----------------------------ELDEES 51

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  224 SKRAKNDakKVPELRDLFHVGQWLVASVlqVRSGDVAKGRpsreggeyekesRRVELSLAPHLVN 288
Cdd:cd05693    52 EEEDDEE--ELPDLEDLFSVGQLVRCKV--VSLDKSKSGK------------KRIELSLEPELVN 100
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 498-767 5.51e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 86.37  E-value: 5.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  498 YPIGATLEVTVVqTINDWGLIVSIhETDLRGFVHISQVS-DDHVVSlppssgpfAKETVHK-----ARVVGHSPTDRTLQ 571
Cdd:PRK06299  284 YPVGSKVKGKVT-NITDYGAFVEL-EEGIEGLVHVSEMSwTKKNKH--------PSKVVSVgqeveVMVLEIDEEKRRIS 353

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  572 LSLK----------------ASVLERKfmrvsevevgevvTANIIKLGlpnaIFLQLQGHVDGVVfsnHFAD----VKLT 631
Cdd:PRK06299  354 LGLKqckenpweefaekypvGDVVEGK-------------VKNITDFG----AFVGLEGGIDGLV---HLSDiswdKKGE 413

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  632 QPEKRFKPGLQVRARVIDVDPNRNRIVLTLKkSLVKSdlPIVASMQDARVGVVTNATVFRVQTNSLVVSLFGGLKALIPG 711
Cdd:PRK06299  414 EAVELYKKGDEVEAVVLKVDVEKERISLGIK-QLEED--PFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  712 REVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK----QASPEYLAKLNVDAVD 767
Cdd:PRK06299  491 SELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKaldeAEEKEAIAEYNSASDS 550
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 498-751 1.16e-14

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 78.62  E-value: 1.16e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   498 YPIGATLEVTVVQtINDWGLIVSIHEtDLRGFVHISQVSDDHVVSLPpsSGPFAKETVHKARVVGHSPTDRTLQLSLKaS 577
Cdd:TIGR00717  270 FPVGDKITGRVTN-LTDYGVFVEIEE-GIEGLVHVSEMSWVKKNSHP--SKVVKKGDEVEVMILDIDPERRRLSLGLK-Q 344

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   578 VLERKFMRVSEVEVG-EVVTANIIKLgLPNAIFLQLQGHVDGVV-FSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRN 655
Cdd:TIGR00717  345 CKANPWEQFEEKHPVgDRVTGKIKKI-TDFGAFVELEGGIDGLIhLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKK 423

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   656 RIVLTLKKsLVKSDLPIVASMQdaRVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMR 735
Cdd:TIGR00717  424 RISLGVKQ-LTENPWEKFAAKY--KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAK 500

                          250
                   ....*....|....*.
gi 808376393   736 ITEVDYENQKLVGSIK 751
Cdd:TIGR00717  501 VVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 295-378 4.76e-14

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 68.43  E-value: 4.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  295 DLDVGATLSATISSVEDHGYMLDSGVSEFSGFVPFTDAAklpdsfhagkNGKSLQVGSVVFAKITKVPDNKRSFEATLDP 374
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG----------NFSKLKVGQLLLCVVEKVKDDGRVVSLSADP 70


                  ....
gi 808376393  375 KTVS 378
Cdd:cd05694    71 SKVS 74
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
960-1030 5.08e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 62.62  E-value: 5.08e-12
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393    960 KGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLK 1030
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1060-1134 3.63e-10

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 59.42  E-value: 3.63e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1060 DFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDG---KADEALKafrVGDKVRAIVLRINEEKrKISFGLK 1134
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGyvkDINDYLK---VGDEVKVKVLSIDEDG-KISLSIK 74
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1061-1133 5.92e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.91  E-value: 5.92e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393  1061 FKVGDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGL 1133
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 682-751 1.44e-09

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 55.69  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1288-1532 2.42e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 60.13  E-value: 2.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1288 FERLLLSSPNSSFLWIQFMSFSLQLSDVDRARSIARRALKvinyREEQERMnvwiALLNLENTY---GSEETLESTFREA 1364
Cdd:COG2956    31 LEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGLLDRAEELLEKL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1365 IQAN-DGFTMYLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQAleKRDHTST 1443
Cdd:COG2956   103 LELDpDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL--DPDCARA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1444 ITAFAINEFKLGDPERGRTIFEGLVDSYPKRLDLwWQYLDQESRLEGNETQVRNLFERAMTLKLTAKKgksLLKKWLDYE 1523
Cdd:COG2956   181 LLLLAELYLEQGDYEEAIAALERALEQDPDYLPA-LPRLAELYEKLGDPEEALELLRKALELDPSDDL---LLALADLLE 256


                  ....*....
gi 808376393 1524 KREGDAKSQ 1532
Cdd:COG2956   257 RKEGLEAAL 265
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
680-751 1.68e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.68e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393    680 RVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
604-662 9.76e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 9.76e-08
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393    604 LPNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLK 662
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1408-1528 1.33e-05

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 48.91  E-value: 1.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1408 WIEYARFYLRTDQPDSARALLPRAMqalEKRDHTSTI-TAFAINEFKLG-DPERGRTIFE-GLvDSYPKRLDLWWQYLDQ 1484
Cdd:pfam05843    4 WIQYMRAMRRAEGIKGARKVFKKAR---KRPRLTYHVyVASALMEYYCSkDPAVAFKIFElGL-KLFPEDEEFVLKYLDY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 808376393  1485 ESRLEgNETQVRNLFERAMTlKLTAKKG-KSLLKKWLDYEKREGD 1528
Cdd:pfam05843   80 LISLN-DDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGD 122
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 394-451 1.86e-05

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 43.80  E-value: 1.86e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  394 GTLTKVLITAALPTGLNVNLFGMFDATIDRFHlpeLPEGKDIPDVYKEGSKHVARVLW 451
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLH---LDPEKSSKSTYKEGQKVRARILY 55
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 949-1030 9.28e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 47.08  E-value: 9.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  949 DPEITSIADLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:PRK06299  449 DPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528


                  ..
gi 808376393 1029 LK 1030
Cdd:PRK06299  529 IK 530
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 958-1029 2.16e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 41.12  E-value: 2.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393   958 LAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSL 1029
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
500-575 3.43e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 3.43e-04
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393    500 IGATLEVTVVQtINDWGLIVSIhETDLRGFVHISQVSDDHVVSLPPSsgpFAKETVHKARVVGHSPTDRTLQLSLK 575
Cdd:smart00316    2 VGDVVEGTVTE-ITPGGAFVDL-GNGVEGLIPISELSDKRVKDPEEV---LKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 508-573 3.43e-04

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 43.28  E-value: 3.43e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393  508 VVQTINDWGLIVSIHETDlrGFVHISQVSDDHVVSLPPSSGPFAKET--------VHKARVVGHSPTDRTLQLS 573
Cdd:PRK08563   88 EVVEVVEFGAFVRIGPVD--GLLHISQIMDDYISYDPKNGRLIGKESkrvlkvgdVVRARIVAVSLKERRPRGS 159
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 961-1072 1.05e-03

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 40.55  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNeIEMSLKSTpgsiKPRA 1040
Cdd:COG1098     6 GDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGK-ISLSIKQA----EEKP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 808376393 1041 ERlEERHADADKKRAKRLtDFKvgDKVKGFVK 1072
Cdd:COG1098    81 KR-PPRPRRNSRPKAGFE-SFE--DKLSKFLK 108
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 607-661 2.09e-03

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 38.42  E-value: 2.09e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 808376393   607 AIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 680-750 2.15e-03

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 38.42  E-value: 2.15e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393   680 RVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSI 750
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 640-776 2.74e-03

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 41.95  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  640 GLQVRARVIDVDPNRNRIVLTLK------KSLVKSDLpiVASMQ--DARVGVVTNAT---VFrvqtnslvVSLfGGLKAL 708
Cdd:COG0539   147 GKTLEFKIIKLDRKRNNVVVSRRavleeeREEKREEL--LEKLEegDVVEGTVKNITdfgAF--------VDL-GGVDGL 215

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393  709 IPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASP----EYLAKLNvdavdVGEKVTGKV 776
Cdd:COG0539   216 LHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQPdpweNIAEKYP-----VGDVVKGKV 282
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1062-1138 3.92e-37

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 134.38  E-value: 3.92e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLKPSYF 1138
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 961-1028 1.67e-32

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 120.86  E-value: 1.67e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 762-1134 1.33e-25

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 110.13  E-value: 1.33e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  762 NVDAVDVGEKVTGKVAAVHKEVVVLTlVPSGVRALLSLSVLASMRGStaeellESLEEDQEIDDLVVSVKNpAKGIVIV- 840
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVD-IGYKSEGIIPLSEFSDEPGE------LEVKVGDEVEVYVEKVED-GEGEIVLs 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  841 ---ADKVRSSKNADDgtnglvsgQVKQGNVVQGRVIQKNDKYLdcIVALGTAtRATLHMTDLADGFSSNvalPSP--GQT 915
Cdd:COG0539    84 kkkADREKAWEELEE--------AFENGEPVEGKVKGVVKGGL--IVDIGGV-RAFLPASQVDVRPVRD---LDEyvGKT 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  916 LQCYIVSLKSNGKNAVISTRpsrvnpsasaEVTDPEITS-----IADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQV 990
Cdd:COG0539   150 LEFKIIKLDRKRNNVVVSRR----------AVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHI 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  991 RELfdefvrDWKtR-------FTVGQVVSGTIMDTNPSNNEIEMSLKST---PgsikprAERLEERhadadkkrakrltd 1060
Cdd:COG0539   219 SEI------SWG-RvkhpsevLKVGDEVEVKVLKIDREKERISLSLKQLqpdP------WENIAEK-------------- 271

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1061 FKVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGK----ADEALKafrVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:COG0539   272 YPVGDVVKGKVTRLTDFGAFVELE-PGVEGLVHISEMSWTKrvahPSDVVK---VGDEVEVKVLDIDPEERRISLSIK 345
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 596-661 2.67e-25

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 100.39  E-value: 2.67e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393  596 TANIIKLGlPNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:cd05697     5 KGTIRKLR-PSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
758-1134 2.59e-22

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 103.87  E-value: 2.59e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  758 LAKLNVDAVDVGEKVTGKVAAV-HKEVVVLtlVPSGVRALLSLSVLASMRGSTAEELLESLeedQEIDDLVVSVKNpAKG 836
Cdd:PRK00087  292 YMNELEKQIRRGDIVKGTVVSVnENEVFVD--VGYKSEGVIPLRELTLDEISSLKESVKVG---DEIEVKVLKLED-EDG 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  837 IVIVADKVRSSKNADDGtngLVSGQvKQGNVVQGRVIQKNDKYLDCIVALgtaTRATLHMTDLADGFSSNvaLPS-PGQT 915
Cdd:PRK00087  366 YVVLSKKEADREKAWKE---LEEAF-ENGEPVKGKVKEVVKGGLLVDYGG---VRAFLPASHVELGYVED--LSEyKGQE 436

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  916 LQCYIVSLKSNGKNAVISTRPSRVNPSASAEvtdpEITSIADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQVRELFD 995
Cdd:PRK00087  437 LEVKIIEFNRKRRKKVVLSRKAILEEEKEKK----KEETWNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISW 511

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  996 EFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKstpgsikpraERLEERHADADKKrakrltdFKVGDKVKGFVKNVI 1075
Cdd:PRK00087  512 GRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLK----------KLLPDPWENVEEK-------YPVGSIVLGKVVRIA 574

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393 1076 DFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK00087  575 PFGAFVELE-PGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 961-1134 2.67e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 100.24  E-value: 2.67e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELfdefvrDWKTR-------FTVGQVVSGTIMDTNPSNNEIEMSLKSTp 1033
Cdd:PRK06299  287 GSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM------SWTKKnkhpskvVSVGQEVEVMVLEIDEEKRRISLGLKQC- 359

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1034 gsiKPRA-ERLEERHadadkkrakrltdfKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELS-DGKADEALKAFRV 1111
Cdd:PRK06299  360 ---KENPwEEFAEKY--------------PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISwDKKGEEAVELYKK 421

                         170       180
                  ....*....|....*....|...
gi 808376393 1112 GDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK06299  422 GDEVEAVVLKVDVEKERISLGIK 444
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 960-1134 3.06e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 93.69  E-value: 3.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  960 KGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELF-DEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIemSLkstpgSIKp 1038
Cdd:PRK06299  373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI--SL-----GIK- 444

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1039 raeRLEERHADadkkraKRLTDFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAI 1118
Cdd:PRK06299  445 ---QLEEDPFE------EFAKKHKKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVLKVGDEVEAK 514

                         170
                  ....*....|....*.
gi 808376393 1119 VLRINEEKRKISFGLK 1134
Cdd:PRK06299  515 VINIDRKNRRISLSIK 530
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 501-574 7.86e-19

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 81.93  E-value: 7.86e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  501 GATLEVTVVQT-INDWGLIVSIHEtDLRGFVHISQVSDDHVVSLPpssGPFAKETVHKARVVGHSPTDRTLQLSL 574
Cdd:cd05696     1 GAVVDSVKVTKvEPDLGAVFELKD-GLLGFVHISHLSDDKVPSDT---GPFKAGTTHKARIIGYSPMDGLLQLSL 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 766-1134 3.87e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.39  E-value: 3.87e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  766 VDVGEKVTGKVAAVHKEVVVLTLVPSGVRALLSLSVLASMRGSTAEELLESleeDQEIDDLVVSVKNPAKGIVIVADKVR 845
Cdd:PRK06676   15 VEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKV---GDELEVYVLKVEDGEGNLLLSKRRLE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  846 SSKNADDgtnglVSGQVKQGNVVQGRVIQkndkyldcIVALGTATR---------ATLHMTDLADGFSSNValpspGQTL 916
Cdd:PRK06676   92 AEKAWDK-----LEEKFEEGEVVEVKVTE--------VVKGGLVVDvegvrgfipASLISTRFVEDFSDFK-----GKTL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  917 QCYIVSLKSNGKNAVISTRpsrvnpsasaEVTDPEITS-----IADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQVR 991
Cdd:PRK06676  154 EVKIIELDPEKNRVILSRR----------AVVEEERAAkkeelLSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHIS 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  992 ELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKST-PGSIkpraERLEERhadadkkrakrltdFKVGDKVKGF 1070
Cdd:PRK06676  223 ELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTlPGPW----EGVEEK--------------LPEGDVIEGT 284

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1071 VKNVIDFGVFVQIEGtNVSGLAHMNELSD---GKADEALKafrVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK06676  285 VKRLTDFGAFVEVLP-GVEGLVHISQISHkhiATPSEVLE---EGQEVKVKVLEVNEEEKRISLSIK 347
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1062-1134 6.33e-18

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 79.57  E-value: 6.33e-18
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393   1062 KVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 682-1134 6.37e-18

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 89.02  E-value: 6.37e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREvseddFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQA----SPEY 757
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLSREKAqrheLWIK 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   758 LAKLNVDAVDVGEKVTGKVAAVhkevvvLTLVPSGVRALLSLSvLASMRgsTAEELLESLEEDQEIDDLVVSVKNPAkgi 837
Cdd:TIGR00717   94 LEKAYEEGSIVEGKIVGKVKGG------FIVDLNGVEAFLPGS-QVDVK--PIKDLDSLIGKTLKFKIIKLDQKRNN--- 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   838 VIVADK----VRSSKNADDGTNGLVSGQVKQGNVVQgrvIQKNDKYLDcivaLGtATRATLHMTDLADGfssNVALPSP- 912
Cdd:TIGR00717  162 IVVSRRayleEERSQAREELLENLKEGDVVKGVVKN---ITDFGAFVD----LG-GVDGLLHITDMSWK---RVKHPSEy 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   913 ---GQTLQCYIVSLKSNGKNAVISTRPSRVNPSASAEVTDPEitsiadlakGQKVRGFVKAITNVGLFVTIGRKLDARVQ 989
Cdd:TIGR00717  231 vkvGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPV---------GDKITGRVTNLTDYGVFVEIEEGIEGLVH 301

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   990 VREL-FDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKSTpgsiKPRA-ERLEERH-------------------- 1047
Cdd:TIGR00717  302 VSEMsWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQC----KANPwEQFEEKHpvgdrvtgkikkitdfgafv 377

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1048 ----------------------------------------ADADKKR----AKRLTD---------FKVGDKVKGFVKNV 1074
Cdd:TIGR00717  378 eleggidglihlsdiswdkdgreadhlykkgdeieavvlaVDKEKKRislgVKQLTEnpwekfaakYKVGSVVKGKVTEI 457

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1075 IDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:TIGR00717  458 KDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 144-288 3.33e-17

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 78.41  E-value: 3.33e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  144 LIPGSRLLCSVLAIHPLAVVVSLPNQMLGHIPVTQISPQFTRRLQaaadasaedddedesmdedsdsdddddeaQTNGTS 223
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLE-----------------------------ELDEES 51

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  224 SKRAKNDakKVPELRDLFHVGQWLVASVlqVRSGDVAKGRpsreggeyekesRRVELSLAPHLVN 288
Cdd:cd05693    52 EEEDDEE--ELPDLEDLFSVGQLVRCKV--VSLDKSKSGK------------KRIELSLEPELVN 100
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 498-767 5.51e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 86.37  E-value: 5.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  498 YPIGATLEVTVVqTINDWGLIVSIhETDLRGFVHISQVS-DDHVVSlppssgpfAKETVHK-----ARVVGHSPTDRTLQ 571
Cdd:PRK06299  284 YPVGSKVKGKVT-NITDYGAFVEL-EEGIEGLVHVSEMSwTKKNKH--------PSKVVSVgqeveVMVLEIDEEKRRIS 353

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  572 LSLK----------------ASVLERKfmrvsevevgevvTANIIKLGlpnaIFLQLQGHVDGVVfsnHFAD----VKLT 631
Cdd:PRK06299  354 LGLKqckenpweefaekypvGDVVEGK-------------VKNITDFG----AFVGLEGGIDGLV---HLSDiswdKKGE 413

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  632 QPEKRFKPGLQVRARVIDVDPNRNRIVLTLKkSLVKSdlPIVASMQDARVGVVTNATVFRVQTNSLVVSLFGGLKALIPG 711
Cdd:PRK06299  414 EAVELYKKGDEVEAVVLKVDVEKERISLGIK-QLEED--PFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  712 REVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK----QASPEYLAKLNVDAVD 767
Cdd:PRK06299  491 SELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKaldeAEEKEAIAEYNSASDS 550
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 861-1134 2.25e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 83.00  E-value: 2.25e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  861 QVKQGNVVQGRVIQKNDKYLDcIVALGTATRATLHMTDLADGFSSNVALP-SPGQTLQCYIVSLKSNGKNAVISTRpsrv 939
Cdd:PRK06676   14 EVEVGDVVTGEVLKVEDKQVF-VNIEGYKVEGVIPISELSNDHIEDINDVvKVGDELEVYVLKVEDGEGNLLLSKR---- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  940 npSASAEVTDPEITsiADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQVRELFDEFVRDWKTrfTVGQVVSGTIMDTN 1019
Cdd:PRK06676   89 --RLEAEKAWDKLE--EKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELD 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1020 PSNNEIEMSlkstpgsikpRAERLEERHAdadKKRAKRLTDFKVGDKVKGFVKNVIDFGVFVQIEGtnVSGLAHMNELSD 1099
Cdd:PRK06676  162 PEKNRVILS----------RRAVVEEERA---AKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGG--VDGLVHISELSH 226

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 808376393 1100 GKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK06676  227 ERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 955-1134 1.60e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 81.75  E-value: 1.60e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  955 IADLAKGQKVRGFVKAITNVGLFVTIGrKLDARVQVRELfdefvrDWKtR-------FTVGQVVSGTIMDTNPSNNEIEM 1027
Cdd:PRK06299  196 LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDI------SWK-RvnhpsevVNVGDEVKVKVLKFDKEKKRVSL 267

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1028 SLKStpgsikpraerLEERHADADKKRakrltdFKVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELS-DGKADEAL 1106
Cdd:PRK06299  268 GLKQ-----------LGEDPWEAIEKK------YPVGSKVKGKVTNITDYGAFVELE-EGIEGLVHVSEMSwTKKNKHPS 329

                         170       180
                  ....*....|....*....|....*...
gi 808376393 1107 KAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK06299  330 KVVSVGQEVEVMVLEIDEEKRRISLGLK 357
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 910-1134 2.96e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 80.47  E-value: 2.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  910 PSPGQTLQCYIVSLKSNGKNAVISTRpsrvnpsASAEVTDPEITS--IADLAKGQKVRGFVKAITNVGLFVTIGrKLDAR 987
Cdd:PRK07899  163 PYIGQEIEAKIIELDKNRNNVVLSRR-------AWLEQTQSEVRSefLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGL 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  988 VQVRELfdefvrDWK------TRFTVGQVVSGTIMDTNPSNNEIEMSLKST---PGSIKPRAerleerHAdadkkrakrl 1058
Cdd:PRK07899  235 VHVSEL------SWKhidhpsEVVEVGQEVTVEVLDVDMDRERVSLSLKATqedPWQQFART------HA---------- 292

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393 1059 tdfkVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK07899  293 ----IGQIVPGKVTKLVPFGAFVRVE-EGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1063-1132 8.25e-15

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 70.35  E-value: 8.25e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1063 VGDKVKGFVKNVIDFGVFVQIEGtnVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFG 1132
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 498-751 1.16e-14

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 78.62  E-value: 1.16e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   498 YPIGATLEVTVVQtINDWGLIVSIHEtDLRGFVHISQVSDDHVVSLPpsSGPFAKETVHKARVVGHSPTDRTLQLSLKaS 577
Cdd:TIGR00717  270 FPVGDKITGRVTN-LTDYGVFVEIEE-GIEGLVHVSEMSWVKKNSHP--SKVVKKGDEVEVMILDIDPERRRLSLGLK-Q 344

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   578 VLERKFMRVSEVEVG-EVVTANIIKLgLPNAIFLQLQGHVDGVV-FSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRN 655
Cdd:TIGR00717  345 CKANPWEQFEEKHPVgDRVTGKIKKI-TDFGAFVELEGGIDGLIhLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKK 423

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   656 RIVLTLKKsLVKSDLPIVASMQdaRVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMR 735
Cdd:TIGR00717  424 RISLGVKQ-LTENPWEKFAAKY--KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAK 500

                          250
                   ....*....|....*.
gi 808376393   736 ITEVDYENQKLVGSIK 751
Cdd:TIGR00717  501 VVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 295-378 4.76e-14

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 68.43  E-value: 4.76e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  295 DLDVGATLSATISSVEDHGYMLDSGVSEFSGFVPFTDAAklpdsfhagkNGKSLQVGSVVFAKITKVPDNKRSFEATLDP 374
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG----------NFSKLKVGQLLLCVVEKVKDDGRVVSLSADP 70


                  ....
gi 808376393  375 KTVS 378
Cdd:cd05694    71 SKVS 74
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1043-1134 1.07e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.97  E-value: 1.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1043 LEERHAdadKKRAKRLTDFKVGDKVKGFVKNVIDFGVFVQIEGtnVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRI 1122
Cdd:PRK06299  184 LEEERA---EEREELLENLEEGQVVEGVVKNITDYGAFVDLGG--VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKF 258

                          90
                  ....*....|..
gi 808376393 1123 NEEKRKISFGLK 1134
Cdd:PRK06299  259 DKEKKRVSLGLK 270
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1064-1132 1.77e-13

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 66.75  E-value: 1.77e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKA-DEALKAFRVGDKVRAIVLRINEEKRKISFG 1132
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWTQRvRHPSEIYKKGQEVEAVVLNIDVERERISLG 69
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 866-1134 5.21e-13

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 74.36  E-value: 5.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  866 NVVQGRVIQKNDkyLDCIVALGTATRATLHMTDLAdgFSSNVALPSP----GQTLQCYIVSLKSNGKNAVISTRPSRVNP 941
Cdd:PRK12269  580 DVVKGRVTKIAD--FGAFIELAEGIEGLAHISEFS--WVKKTSKPSDmvkiGDEVECMILGYDIQAGRVSLGLKQVTANP 655

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  942 SASAEVTDPeitsiadlAKGQKVRGFVKaITNVGLFVTIGRKLDARVQVREL-FDEFVRDWKTRFTVGQVVSGTIMDTNP 1020
Cdd:PRK12269  656 WEEIEARYP--------VGARFTRRIVK-VTNAGAFIEMEEGIDGFLHVDDLsWVKRTRPADHELEVGKEIECMVIECDP 726

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1021 SNNEIEMSLKSTpgsikpraerleerhadADKKRAKRLTDFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLA---HMNEL 1097
Cdd:PRK12269  727 QARRIRLGVKQL-----------------SDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPG-GVEGLVrkqHLVEN 788

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 808376393 1098 SDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK12269  789 RDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825
rpsA PRK13806
30S ribosomal protein S1; Provisional
 861-1132 1.47e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 72.06  E-value: 1.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  861 QVKQGNVVQGRVIQKNDkyLDCIVALGTATRATLHMTDLAdgfSSNVALP----SPGQTLQCYIVSLKSNGKNAVIstrp 936
Cdd:PRK13806  199 TVKEGDVVEGTVTRLAP--FGAFVELAPGVEGMVHISELS---WSRVQKAdeavSVGDTVRVKVLGIERAKKGKGL---- 269

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  937 sRVNPSASAEVTDPEITSIADLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELfdefvrDWKTRF-------TVGQ 1009
Cdd:PRK13806  270 -RISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEM------SWTRRVnkpedvvAPGD 342

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1010 VVSGTIMDTNPSNNEIEMSLKSTPGSikPRAErLEERhadadkkrakrltdFKVGDKVKGFVKNVIDFGVFVQIEgTNVS 1089
Cdd:PRK13806  343 AVAVKIKDIDPAKRRISLSLRDAEGD--PWAD-VAER--------------FAPGTTVTGTVEKRAQFGLFVNLA-PGVT 404

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 808376393 1090 GLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFG 1132
Cdd:PRK13806  405 GLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1067-1130 2.39e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 63.55  E-value: 2.39e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393 1067 VKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKIS 1130
Cdd:cd00164     1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 1063-1133 4.21e-12

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 63.19  E-value: 4.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1063 VGDKVKGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDG-----KADEAL------KAFRVGDKVRAIVLRINEEKRKISF 1131
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDyyefdEENHALvgertgKVFRLGDKVKVRVVRVDLDRRKIDF 80


                  ..
gi 808376393 1132 GL 1133
Cdd:cd04471    81 EL 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
960-1030 5.08e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 62.62  E-value: 5.08e-12
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393    960 KGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLK 1030
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1058-1129 1.01e-11

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 62.22  E-value: 1.01e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393 1058 LTDFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKI 1129
Cdd:cd04461     9 FSDLKPGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 1064-1131 2.51e-11

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 60.71  E-value: 2.51e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISF 1131
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
494-756 1.65e-10

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 65.74  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  494 LQHAYPIGATLEVTVVQTINDwGLIVSIheTDLRGFVHISQVSDDHVVSLPPssgpFAKETVhKARVVGHSPTDRtlqls 573
Cdd:PRK00087  383 LEEAFENGEPVKGKVKEVVKG-GLLVDY--GGVRAFLPASHVELGYVEDLSE----YKGQEL-EVKIIEFNRKRR----- 449

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  574 lKASVLERKFMRVSEVEVGEVVTANIIKLG----------LPNAIFLQLQGhVDGVVfsnHFADV---KLTQPEKRFKPG 640
Cdd:PRK00087  450 -KKVVLSRKAILEEEKEKKKEETWNSLEEGdvvegevkrlTDFGAFVDIGG-VDGLL---HVSEIswgRVEKPSDVLKVG 524

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  641 LQVRARVIDVDPNRNRIVLTLKKsLVKSDLPIVAsmQDARVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFN 720
Cdd:PRK00087  525 DEIKVYILDIDKENKKLSLSLKK-LLPDPWENVE--EKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID 601

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 808376393  721 DVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASPE 756
Cdd:PRK00087  602 KPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEE 637
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1060-1134 3.63e-10

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 59.42  E-value: 3.63e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1060 DFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDG---KADEALKafrVGDKVRAIVLRINEEKrKISFGLK 1134
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGyvkDINDYLK---VGDEVKVKVLSIDEDG-KISLSIK 74
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1061-1133 5.92e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.91  E-value: 5.92e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393  1061 FKVGDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGL 1133
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 964-1028 9.75e-10

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 55.85  E-value: 9.75e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393  964 VRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 682-751 1.44e-09

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 55.69  E-value: 1.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1288-1532 2.42e-09

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 60.13  E-value: 2.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1288 FERLLLSSPNSSFLWIQFMSFSLQLSDVDRARSIARRALKvinyREEQERMnvwiALLNLENTY---GSEETLESTFREA 1364
Cdd:COG2956    31 LEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGLLDRAEELLEKL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1365 IQAN-DGFTMYLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQAleKRDHTST 1443
Cdd:COG2956   103 LELDpDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL--DPDCARA 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1444 ITAFAINEFKLGDPERGRTIFEGLVDSYPKRLDLwWQYLDQESRLEGNETQVRNLFERAMTLKLTAKKgksLLKKWLDYE 1523
Cdd:COG2956   181 LLLLAELYLEQGDYEEAIAALERALEQDPDYLPA-LPRLAELYEKLGDPEEALELLRKALELDPSDDL---LLALADLLE 256


                  ....*....
gi 808376393 1524 KREGDAKSQ 1532
Cdd:COG2956   257 RKEGLEAAL 265
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1064-1132 3.52e-09

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 54.51  E-value: 3.52e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELS-DGKADEALKAFRVGDKVRAIVLRINEEKRKISFG 1132
Cdd:cd05689     4 GTRLFGKVTNLTDYGCFVELE-EGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISLG 72
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1288-1547 5.62e-09

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 60.80  E-value: 5.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1288 FERLLLSSPNSSFLWIQFMSFSLQLSDVDRARSIARRALK-----VINYREEQERMNvwiallnlentygSEETLESTFR 1362
Cdd:COG5107   291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspslTMFLSEYYELVN-------------DEEAVYGCFD 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1363 EAIQAndgftmYLKMINILEKSS------KTEEAEELFVKAKAKYSVLpefWIEYARFYLRTDQPDSARALLPRAMQALE 1436
Cdd:COG5107   358 KCTQD------LKRKYSMGESESaskvdnNFEYSKELLLKRINKLTFV---FCVHLNYVLRKRGLEAARKLFIKLRKEGI 428

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1437 KRDHTSTITAFaINEFKLGDPERGRTIFEGLVDSYPKRLDLWWQYLDQESRLeGNETQVRNLFERAMTlKLTAKKGKSLL 1516
Cdd:COG5107   429 VGHHVYIYCAF-IEYYATGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRI-NDEENARALFETSVE-RLEKTQLKRIY 505

                         250       260       270
                  ....*....|....*....|....*....|.
gi 808376393 1517 KKWLDYEKREGDAKSQGKVLMRAKKFVDEIN 1547
Cdd:COG5107   506 DKMIEYESMVGSLNNVYSLEERFRELVPQEN 536
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 640-1030 1.57e-08

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 58.98  E-value: 1.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   640 GLQVRARVIDVDPNRNRIVLTLKKSLVKSDLPIVASM------QDARVGVVTNATVFRVqtnslVVSLfGGLKALIPGRE 713
Cdd:TIGR00717  145 GKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELlenlkeGDVVKGVVKNITDFGA-----FVDL-GGVDGLLHITD 218

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   714 VSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASPEYLAKLNvDAVDVGEKVTGKVAAV-HKEVVVLtlVPSG 792
Cdd:TIGR00717  219 MSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE-KKFPVGDKITGRVTNLtDYGVFVE--IEEG 295

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   793 VRALLSLSvlasmrgstaeellesleedqEIDdLVVSVKNPAKgIVIVADKVRSSKNADDGTNGLVSGQVKQ-------- 864
Cdd:TIGR00717  296 IEGLVHVS---------------------EMS-WVKKNSHPSK-VVKKGDEVEVMILDIDPERRRLSLGLKQckanpweq 352

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   865 -------GNVVQGRVIQKNDkyLDCIVALGTATRATLHMTDLA--DGFSSNVALPSPGQTLQCYIVSLKSNGKnavistr 935
Cdd:TIGR00717  353 feekhpvGDRVTGKIKKITD--FGAFVELEGGIDGLIHLSDISwdKDGREADHLYKKGDEIEAVVLAVDKEKK------- 423

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393   936 psRVNPSASAEVTDPEITSIADLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTI 1015
Cdd:TIGR00717  424 --RISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKV 501

                          410
                   ....*....|....*
gi 808376393  1016 MDTNPSNNEIEMSLK 1030
Cdd:TIGR00717  502 VDIDKKNRKVSLSVK 516
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
680-751 1.68e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.68e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393    680 RVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 952-1029 1.75e-08

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 52.98  E-value: 1.75e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  952 ITSIADLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSL 1029
Cdd:cd04461     6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 957-1134 2.10e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 58.58  E-value: 2.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  957 DLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEfvrDWKTRFTVGQVVSGTIMDTNpsNNEIEMSlKSTPGS- 1035
Cdd:PRK13806   31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDA---DGELTVAVGDEVELYVVSVN--GQEIRLS-KALSGQg 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1036 -------------------------------IKPRA---------------------------ERLEE--------RHAD 1049
Cdd:PRK13806  105 gaamleeayengvpvegkvtgtckggfnvevLGRRAfcpvsqidlryvedpesyvgqtfqfliTRVEEngrnivvsRRAL 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1050 ADKKRAKRLTDF----KVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEE 1125
Cdd:PRK13806  185 LEREQKEALEAFmetvKEGDVVEGTVTRLAPFGAFVELA-PGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERA 263

                         250
                  ....*....|...
gi 808376393 1126 KR----KISFGLK 1134
Cdd:PRK13806  264 KKgkglRISLSIK 276
PRK08059 PRK08059
general stress protein 13; Validated
 1057-1134 2.41e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 53.90  E-value: 2.41e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393 1057 RLTDFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK08059    1 MMSQYEVGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 1062-1134 3.03e-08

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 52.20  E-value: 3.03e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQI-EGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:cd04452     2 EEGELVVVTVKSIADMGAYVSLlEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 1068-1134 4.45e-08

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 51.86  E-value: 4.45e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1068 KGFVKNVIDFGVFVQIEGT--NVSGLAHMNELS-DGKADEALKAFRVGDKVRAIVLRIneEKRKISFGLK 1134
Cdd:cd05684     5 KGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISI--QNGKISLSMK 72
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1064-1130 7.10e-08

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 50.76  E-value: 7.10e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKIS 1130
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTL-GRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIE 66
PRK05807 PRK05807
RNA-binding protein S1;
1061-1134 8.31e-08

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 52.83  E-value: 8.31e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393 1061 FKVGDKVKGFVKNVIDFGVFVQIEGTnvSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRInEEKRKISFGLK 1134
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGK--TGLVHISEVADTYVKDIREHLKEQDKVKVKVISI-DDNGKISLSIK 73
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
604-662 9.76e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 9.76e-08
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393    604 LPNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLK 662
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1310-1434 1.19e-07

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 52.50  E-value: 1.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1310 LQLSDVDRARSIARRALKvinyrEEQERMNVWIALLNLENTYGSEETLESTFREAIQANDGFTMYLKMI-NILEKSSKTE 1388
Cdd:COG4783    15 LLAGDYDEAEALLEKALE-----LDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLgLALLKAGDYD 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 808376393 1389 EAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQA 1434
Cdd:COG4783    90 EALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 484-754 3.01e-07

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 54.28  E-value: 3.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  484 KAPVAKDEQLLQHAYPIGATLEVTVVQTINDwGLIVSIHetDLRGFVHISQVSDDHVVSLppssGPFAKETVhKARVVGH 563
Cdd:COG0539    86 KADREKAWEELEEAFENGEPVEGKVKGVVKG-GLIVDIG--GVRAFLPASQVDVRPVRDL----DEYVGKTL-EFKIIKL 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  564 SPTDRTLQLSLKAsVLE--RKFMRVsevevgevvtaniiklglpnAIFLQLQ---------------------GHVDGVV 620
Cdd:COG0539   158 DRKRNNVVVSRRA-VLEeeREEKRE--------------------ELLEKLEegdvvegtvknitdfgafvdlGGVDGLL 216

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  621 fsnHFADV---KLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLKKslVKSDlPIVASMQDARVGVVTNATVFRVQTNSL 697
Cdd:COG0539   217 ---HISEIswgRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQ--LQPD-PWENIAEKYPVGDVVKGKVTRLTDFGA 290

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393  698 VVSLFGGLKALIPgreVSE-------DDFNDVksgFAEGKVIKMRITEVDYENQKLVGSIKQAS 754
Cdd:COG0539   291 FVELEPGVEGLVH---ISEmswtkrvAHPSDV---VKVGDEVEVKVLDIDPEERRISLSIKQLA 348
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1064-1129 3.78e-07

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 48.77  E-value: 3.78e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKI 1129
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKL-SDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRL 65
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 863-1134 4.37e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 54.72  E-value: 4.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  863 KQGNVVQGRVIQKNDKYLDCIVALGTATRATLHMTDlADGFSSNVALPSPGQTLQCYIVSLKSNGK-----NAVISTRPS 937
Cdd:PRK12269  397 RDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQ-SDCQKVDAPESLIGLTSKFYIERISQSKQhrgndNIVINRRRY 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  938 RVNPSASAEVTDPEITSIADlakgqKVRGFVKAITNVGLFVTIGrKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMD 1017
Cdd:PRK12269  476 LEERARQAREEFFNSVHIED-----SVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIR 549

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1018 TNPSNNEIEMSLKstpgsikpraerleerHADADKkRAKRLTDFKVGDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNEL 1097
Cdd:PRK12269  550 LDQAEKRINLSLK----------------HFQPDP-WLEFENKFGVNDVVKGRVTKIADFGAFIEL-AEGIEGLAHISEF 611

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 808376393 1098 S-DGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK12269  612 SwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1064-1134 2.38e-06

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 46.45  E-value: 2.38e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1062-1134 2.90e-06

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 47.77  E-value: 2.90e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQIEgTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK07252    2 KIGDKLKGTITGIKPYGAFVALE-NGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 508-573 3.81e-06

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 46.90  E-value: 3.81e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393  508 VVQTINDWGLIVSIHETDlrGFVHISQVSDDHVVSLPPSSGPFAKET--------VHKARVVGHSPTDRTLQLS 573
Cdd:cd04460     6 EVVEVVDFGAFVRIGPVD--GLLHISQIMDDYISYDPKNKRLIGEETkrvlkvgdVVRARIVAVSLKERRPRES 77
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1056-1126 4.04e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 51.03  E-value: 4.04e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393 1056 KRLTDFKVGDKVKGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEK 1126
Cdd:PRK06676   10 NSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGE 80
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1064-1134 4.54e-06

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 45.74  E-value: 4.54e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRkISFGLK 1134
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR-ISLSIK 69
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1310-1541 5.01e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 49.62  E-value: 5.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1310 LQLSDVDRARSIARRALKvINYreeqermNVWIALLNLENTYGS----EETLEStFREAIQANDGF-TMYLKMINILEKS 1384
Cdd:COG0457    19 RRLGRYEEAIEDYEKALE-LDP-------DDAEALYNLGLAYLRlgryEEALAD-YEQALELDPDDaEALNNLGLALQAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1385 SKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQAleKRDHTSTITAFAINEFKLGDPERGRTIF 1464
Cdd:COG0457    90 GRYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERALEL--DPDDADALYNLGIALEKLGRYEEALELL 167

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1465 EGLVDSYPKRLDLWWQYLDQESRLEGNETQVRNLFERAMTLKLTAKKGKSLLKKWLDYEKREGDAKSQGKVLMRAKK 1541
Cdd:COG0457   168 EKLEAAALAALLAAALGEAALALAAAEVLLALLLALEQALRKKLAILTLAALAELLLLALALLLALRLAALALYQYR 244
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 482-756 5.67e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 50.64  E-value: 5.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  482 ALKAPVAKDEqlLQHAYPIGATLEVTVVQTINDwGLIVSIheTDLRGFVHISQVSDDHVVSLPPSSGpfakeTVHKARVV 561
Cdd:PRK06676   89 RLEAEKAWDK--LEEKFEEGEVVEVKVTEVVKG-GLVVDV--EGVRGFIPASLISTRFVEDFSDFKG-----KTLEVKII 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  562 GHSPTDRTLQLSLKASV-LERKFMRVSEVEVGEV------VTANIIKLGlpnaIFLQLqGHVDGVVfsnHFADV---KLT 631
Cdd:PRK06676  159 ELDPEKNRVILSRRAVVeEERAAKKEELLSSLKEgdvvegTVARLTDFG----AFVDI-GGVDGLV---HISELsheRVE 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  632 QPEKRFKPGLQVRARVIDVDPNRNRIVLTLKKSL------VKSDLPivasmqdarVGVVTNATVFRVQTNSLVVSLFGGL 705
Cdd:PRK06676  231 KPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKLP---------EGDVIEGTVKRLTDFGAFVEVLPGV 301

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 808376393  706 KALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASPE 756
Cdd:PRK06676  302 EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEA 352
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 629-830 6.03e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.93  E-value: 6.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  629 KLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLKKSLVKsdlPIVASMQDARVG-----VVTNATVFRVqtnslVVSLFG 703
Cdd:PRK06299  324 KNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKEN---PWEEFAEKYPVGdvvegKVKNITDFGA-----FVGLEG 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  704 GLKALIPGREVS-EDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASP----EYLAKlnvdaVDVGEKVTGKVAA 778
Cdd:PRK06299  396 GIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEdpfeEFAKK-----HKKGSIVTGTVTE 470

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 808376393  779 V-HKEVVVltLVPSGVRALLSLSVLASMRGSTAeelLESLEEDQEIDDLVVSV 830
Cdd:PRK06299  471 VkDKGAFV--ELEDGVEGLIRASELSRDRVEDA---TEVLKVGDEVEAKVINI 518
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1374-1506 9.12e-06

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 47.11  E-value: 9.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1374 YLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPRAMQAleKRDHTSTITAFAINEFK 1453
Cdd:COG4783     7 LYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPEARLNLGLALLK 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 808376393 1454 LGDPERGRTIFEGLVDSYPKRLDLWWQYLDQESRLeGNETQVRNLFERAMTLK 1506
Cdd:COG4783    85 AGDYDEALALLEKALKLDPEHPEAYLRLARAYRAL-GRPDEAIAALEKALELD 136
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1064-1134 1.01e-05

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 44.95  E-value: 1.01e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKL-GDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 961-1030 1.15e-05

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 44.52  E-value: 1.15e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLK 1030
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 1048-1134 1.22e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 50.05  E-value: 1.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1048 ADADKKRAKRLT-DFKVGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSD---GKADEALKafrVGDKVRAIVLRIN 1123
Cdd:PRK11824  605 AEAAKERIEGITaEPEVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADervEKVEDVLK---EGDEVKVKVLEID 680

                          90
                  ....*....|.
gi 808376393 1124 eEKRKISFGLK 1134
Cdd:PRK11824  681 -KRGRIRLSRK 690
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1408-1528 1.33e-05

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 48.91  E-value: 1.33e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  1408 WIEYARFYLRTDQPDSARALLPRAMqalEKRDHTSTI-TAFAINEFKLG-DPERGRTIFE-GLvDSYPKRLDLWWQYLDQ 1484
Cdd:pfam05843    4 WIQYMRAMRRAEGIKGARKVFKKAR---KRPRLTYHVyVASALMEYYCSkDPAVAFKIFElGL-KLFPEDEEFVLKYLDY 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 808376393  1485 ESRLEgNETQVRNLFERAMTlKLTAKKG-KSLLKKWLDYEKREGD 1528
Cdd:pfam05843   80 LISLN-DDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGD 122
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 1275-1433 1.51e-05

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 49.61  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1275 ADLATKAPSSATDFERLLLSSPNSSFLWIQFMSFSLQLSDVDRARSIARRALKVINyreeqermNVWIALLNLENTYGSE 1354
Cdd:COG3914    54 AAAAALLALAAGEAAAAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNP--------DNAEALFNLGNLLLAL 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1355 ETLES---TFREAIQANDGFT-MYLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLPR 1430
Cdd:COG3914   126 GRLEEalaALRRALALNPDFAeAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNALQDLGRLEEAIAAYRR 205


                  ...
gi 808376393 1431 AMQ 1433
Cdd:COG3914   206 ALE 208
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 394-451 1.86e-05

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 43.80  E-value: 1.86e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  394 GTLTKVLITAALPTGLNVNLFGMFDATIDRFHlpeLPEGKDIPDVYKEGSKHVARVLW 451
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLH---LDPEKSSKSTYKEGQKVRARILY 55
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 958-1028 2.23e-05

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 43.92  E-value: 2.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393  958 LAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRD---WKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDpslYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
PRK08582 PRK08582
RNA-binding protein S1;
1063-1134 3.69e-05

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 45.02  E-value: 3.69e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393 1063 VGDKVKGFVKNVIDFGVFVQIEGtNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRInEEKRKISFGLK 1134
Cdd:PRK08582    5 VGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNV-EDDGKIGLSIK 74
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 592-777 5.37e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 47.56  E-value: 5.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  592 GEVVTANIIKLGlPNAIFLQLQGH-VDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLKKSLVKSDL 670
Cdd:PRK06676   18 GDVVTGEVLKVE-DKQVFVNIEGYkVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAW 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  671 pivASMQDA-RVGVVTNATVFRVQTNSLVVSlFGGLKALIPGREVSE---DDFNDVKsgfaeGKVIKMRITEVDYENQKL 746
Cdd:PRK06676   97 ---DKLEEKfEEGEVVEVKVTEVVKGGLVVD-VEGVRGFIPASLISTrfvEDFSDFK-----GKTLEVKIIELDPEKNRV 167

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 808376393  747 VGSIK--------QASPEYLAKLNvdavdVGEKVTGKVA 777
Cdd:PRK06676  168 ILSRRavveeeraAKKEELLSSLK-----EGDVVEGTVA 201
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1068-1134 5.92e-05

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 42.85  E-value: 5.92e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1068 KGFVKNVIDFGVFVQIEGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRInEEKRKISFGLK 1134
Cdd:cd05686     8 KGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR-EMKDKMKLSLS 73
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1362-1472 6.18e-05

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 44.95  E-value: 6.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1362 REAIQANDGFTMYLKMINILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLpraMQALE-KRDH 1440
Cdd:COG5010    45 AGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYY---EKALAlSPDN 121

                          90       100       110
                  ....*....|....*....|....*....|..
gi 808376393 1441 TSTITAFAINEFKLGDPERGRTIFEGLVDSYP 1472
Cdd:COG5010   122 PNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 1056-1134 6.85e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 46.72  E-value: 6.85e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393 1056 KRLTDFKVGDKVKGFVKNVIDFGVFVQIEGtnVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK07400  189 RKMNRLEVGEVVVGTVRGIKPYGAFIDIGG--VSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK 265
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 605-661 7.34e-05

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 42.57  E-value: 7.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393  605 PNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:cd04461    27 PYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1380-1476 7.67e-05

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 43.24  E-value: 7.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1380 ILEKSSKTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLpramQALE-KRDHTSTITAFAINEFKLGDPE 1458
Cdd:COG3063     1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIALE----KALKlDPNNAEALLNLAELLLELGDYD 76

                          90
                  ....*....|....*...
gi 808376393 1459 RGRTIFEGLVDSYPKRLD 1476
Cdd:COG3063    77 EALAYLERALELDPSALR 94
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 682-752 8.84e-05

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 42.26  E-value: 8.84e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393  682 GVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQ 752
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 949-1030 9.28e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 47.08  E-value: 9.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  949 DPEITSIADLAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:PRK06299  449 DPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLS 528


                  ..
gi 808376393 1029 LK 1030
Cdd:PRK06299  529 IK 530
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 509-777 1.48e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 46.02  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  509 VQTINDWGLIVSIHETDLRGFVHISQVSDDHVVSlppssgpfAKETVH-----KARVVGHSPTDRTLQLSLKA------- 576
Cdd:PRK06676   25 VLKVEDKQVFVNIEGYKVEGVIPISELSNDHIED--------INDVVKvgdelEVYVLKVEDGEGNLLLSKRRleaekaw 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  577 SVLERKFmrvSEVEVGEVVTANIIKLGLpnaiflqlQGHVDGV-VF------SNHFADvkltqPEKRFKpGLQVRARVID 649
Cdd:PRK06676   97 DKLEEKF---EEGEVVEVKVTEVVKGGL--------VVDVEGVrGFipasliSTRFVE-----DFSDFK-GKTLEVKIIE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  650 VDPNRNRIVLTlKKSLVKSDLpivASMQDA-----RVGVVTNATVFRVQTNSLVVSLfGGLKALIPGREVSEDDFNDVKS 724
Cdd:PRK06676  160 LDPEKNRVILS-RRAVVEEER---AAKKEEllsslKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSE 234

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393  725 GFAEGKVIKMRITEVDYENQKLVGSIKQASPE----YLAKLNVDAVdvgekVTGKVA 777
Cdd:PRK06676  235 VVSVGQEVEVKVLSIDWETERISLSLKDTLPGpwegVEEKLPEGDV-----IEGTVK 286
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 605-660 2.04e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.83  E-value: 2.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393  605 PNAIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLT 660
Cdd:cd00164    10 KFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 958-1029 2.16e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 41.12  E-value: 2.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393   958 LAKGQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSL 1029
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
500-575 3.43e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 3.43e-04
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393    500 IGATLEVTVVQtINDWGLIVSIhETDLRGFVHISQVSDDHVVSLPPSsgpFAKETVHKARVVGHSPTDRTLQLSLK 575
Cdd:smart00316    2 VGDVVEGTVTE-ITPGGAFVDL-GNGVEGLIPISELSDKRVKDPEEV---LKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 508-573 3.43e-04

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 43.28  E-value: 3.43e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 808376393  508 VVQTINDWGLIVSIHETDlrGFVHISQVSDDHVVSLPPSSGPFAKET--------VHKARVVGHSPTDRTLQLS 573
Cdd:PRK08563   88 EVVEVVEFGAFVRIGPVD--GLLHISQIMDDYISYDPKNGRLIGKESkrvlkvgdVVRARIVAVSLKERRPRGS 159
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 1063-1134 4.64e-04

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 43.66  E-value: 4.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1063 VGDKVKGFVKNVIDFGVFVQI-EGTNVSGLAHMNELSDGkadeALKAFR----VGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVTLdEYPGKEGFIHISEVASG----WVKNIRdhvkEGQKVVCKVIRVDPRKGHIDLSLK 80
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 667-750 5.52e-04

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 40.26  E-value: 5.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  667 KSDLPIVASmqDARVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKL 746
Cdd:cd04461     2 EGTLPTNFS--DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 808376393  747 VGSI 750
Cdd:cd04461    80 LLSL 83
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1064-1129 6.43e-04

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 39.82  E-value: 6.43e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 808376393 1064 GDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKI 1129
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNV 65
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 961-1072 1.05e-03

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 40.55  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNeIEMSLKSTpgsiKPRA 1040
Cdd:COG1098     6 GDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGK-ISLSIKQA----EEKP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 808376393 1041 ERlEERHADADKKRAKRLtDFKvgDKVKGFVK 1072
Cdd:COG1098    81 KR-PPRPRRNSRPKAGFE-SFE--DKLSKFLK 108
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 630-663 1.52e-03

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 38.71  E-value: 1.52e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 808376393  630 LTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLKK 663
Cdd:cd05703    40 LEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 608-665 1.70e-03

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 38.85  E-value: 1.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393  608 IFLQLQG-HVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTLKKSL 665
Cdd:cd05708    18 VFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASY 76
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 1059-1124 1.71e-03

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 42.96  E-value: 1.71e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1059 TDFKVGDKVKGF-VKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINE 1124
Cdd:PLN00207  749 MVPTVGDIYRNCeIKSIAPYGAFVEI-APGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND 814
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 607-661 2.09e-03

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 38.42  E-value: 2.09e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 808376393   607 AIFLQLQGHVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLTL 661
Cdd:pfam00575   18 GAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 680-750 2.15e-03

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 38.42  E-value: 2.15e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393   680 RVGVVTNATVFRVQTNSLVVSLFGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSI 750
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 682-751 2.33e-03

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 37.82  E-value: 2.33e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  682 GVVTNATVFRVQTNSLVVSLfGGLKALIPGREVSEDDFNDVKSgfAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSRR 67
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 961-1028 2.66e-03

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 37.98  E-value: 2.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMS 1028
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 640-776 2.74e-03

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 41.95  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  640 GLQVRARVIDVDPNRNRIVLTLK------KSLVKSDLpiVASMQ--DARVGVVTNAT---VFrvqtnslvVSLfGGLKAL 708
Cdd:COG0539   147 GKTLEFKIIKLDRKRNNVVVSRRavleeeREEKREEL--LEKLEegDVVEGTVKNITdfgAF--------VDL-GGVDGL 215

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 808376393  709 IPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIKQASP----EYLAKLNvdavdVGEKVTGKV 776
Cdd:COG0539   216 LHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQPdpweNIAEKYP-----VGDVVKGKV 282
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 1058-1136 4.09e-03

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 37.59  E-value: 4.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 808376393 1058 LTDFKVGDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELsdgkadeaLKAFRVGDKVraIVlRINEEKRKISFGLKPS 1136
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDL-NDHVRGLIHRSNL--------LRDYEVGDEV--IV-QVTDIPENGNIDLIPV 77
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 961-1031 4.66e-03

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 37.17  E-value: 4.66e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEF--VRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKS 1031
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVsvLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 961-1031 4.95e-03

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 37.25  E-value: 4.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKS 1031
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71
PRK08582 PRK08582
RNA-binding protein S1;
961-1072 5.54e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 38.86  E-value: 5.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNpSNNEIEMSLKS---TPGSIK 1037
Cdd:PRK08582    6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSIKKakdRPKRQH 84

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 808376393 1038 PRAERLEERHADADKKRAKrltDFKvgDKVKGFVK 1072
Cdd:PRK08582   85 DRPRHEDNRGGGNDVAPKE---DFE--QKMSRFLK 114
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1062-1134 5.70e-03

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 37.23  E-value: 5.70e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 808376393 1062 KVGDKVKGFVKNVIDFGVFVQIeGTNVSGLAHMNELSDGKADEALKAFRVGDKVRAIVLRINEEKRKISFGLK 1134
Cdd:cd05706     2 KVGDILPGRVTKVNDRYVLVQL-GNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 611-756 6.38e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.55  E-value: 6.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  611 QLQGHvDGVVFSNHFADVK---LTQPE--KRFKPGLQVRARV--------------IDVDPNRNRIVLTLKKSLVKSdlp 671
Cdd:PRK07400  114 QLQKE-DATVRSEVFATNRggaLVRIEglRGFIPGSHISTRKpkeelvgeelplkfLEVDEERNRLVLSHRRALVER--- 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  672 ivaSMQDARVGVVTNATVFRVQTNSLVVSLfGGLKALIPGREVSEDDFNDVKSGFAEGKVIKMRITEVDYENQKLVGSIK 751
Cdd:PRK07400  190 ---KMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK 265


                  ....*
gi 808376393  752 QASPE 756
Cdd:PRK07400  266 QLEPE 270
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1386-1483 7.24e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 40.10  E-value: 7.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393 1386 KTEEAEELFVKAKAKYSVLPEFWIEYARFYLRTDQPDSARALLpramQALEKRDHTSTITAFAINE--FKLGDPERGRTI 1463
Cdd:COG2956    23 QPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIH----QKLLERDPDRAEALLELAQdyLKAGLLDRAEEL 98

                          90       100
                  ....*....|....*....|
gi 808376393 1464 FEGLVDSYPKRLDLWWQYLD 1483
Cdd:COG2956    99 LEKLLELDPDDAEALRLLAE 118
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 615-660 7.25e-03

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 36.44  E-value: 7.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 808376393  615 HVDGVVFSNHFADVKLTQPEKRFKPGLQVRARVIDVDPNRNRIVLT 660
Cdd:cd05685    23 KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 1067-1130 8.37e-03

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 39.04  E-value: 8.37e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 808376393 1067 VKGFVKNVIDFGVFVQIeGTnVSGLAHMNELSDGKA--DEALKAF---------RVGDKVRA-IV-LRINEEKRKIS 1130
Cdd:PRK08563   85 VEGEVVEVVEFGAFVRI-GP-VDGLLHISQIMDDYIsyDPKNGRLigkeskrvlKVGDVVRArIVaVSLKERRPRGS 159
PRK08059 PRK08059
general stress protein 13; Validated
 961-1042 9.14e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 37.72  E-value: 9.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 808376393  961 GQKVRGFVKAITNVGLFVTIGRKLDARVQVRELFDEFVRDWKTRFTVGQVVSGTIMDTNPSNNEIEMSLKSTPGSIKPRA 1040
Cdd:PRK08059    8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAPEAKR 87


                  ..
gi 808376393 1041 ER 1042
Cdd:PRK08059   88 KK 89
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 1067-1130 9.81e-03

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 37.27  E-value: 9.81e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 808376393 1067 VKGFVKNVIDFGVFVQIegTNVSGLAHMNELSDG--KADEALKAF---------RVGDKVRAIVLRINEEKRKIS 1130
Cdd:cd04460     3 VEGEVVEVVDFGAFVRI--GPVDGLLHISQIMDDyiSYDPKNKRLigeetkrvlKVGDVVRARIVAVSLKERRPR 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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