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Conserved domains on  [gi|29337008|sp|Q9UXC4|]
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RecName: Full=Exosome complex component Rrp4

Protein Classification

Rrp4 family protein( domain architecture ID 11437793)

Rrp4 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 8-243 1.39e-118

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


:

Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 337.98  E-value: 1.39e-118
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   8 KIVLQPRSIVVPGELLAEGEFQipWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSfYYPKINDIVIGLVEDVEIYG 87
Cdd:COG1097   1 KIYVEDRKIVVPGDLLAEGEYK--PGSGTYVEGGKIYSTVLGLVEIKDDKVSVIPLEGK-YIPKVGDLVIGKVTDVGPSN 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008  88 WVVDIKAPYKAYLPASNLLGRSINV-GEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPR 166
Cdd:COG1097  78 WEVDINSPYQALLPVSEVPGRPFNVeSDDLRKYLDIGDYILAKVKNFDRTRDPLLTMKDKGLGKIEGGRIVEISPSKVPR 157

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29337008 167 VIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSG 243
Cdd:COG1097 158 VIGKKGSMINMLKKETGCEIIVGQNGRIWIKGPDEEGEELAIEAIKKIEREAHTSGLTDRIKEFLEEEKGERGVSSE 234
 
Name Accession Description Interval E-value
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 8-243 1.39e-118

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 337.98  E-value: 1.39e-118
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   8 KIVLQPRSIVVPGELLAEGEFQipWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSfYYPKINDIVIGLVEDVEIYG 87
Cdd:COG1097   1 KIYVEDRKIVVPGDLLAEGEYK--PGSGTYVEGGKIYSTVLGLVEIKDDKVSVIPLEGK-YIPKVGDLVIGKVTDVGPSN 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008  88 WVVDIKAPYKAYLPASNLLGRSINV-GEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPR 166
Cdd:COG1097  78 WEVDINSPYQALLPVSEVPGRPFNVeSDDLRKYLDIGDYILAKVKNFDRTRDPLLTMKDKGLGKIEGGRIVEISPSKVPR 157

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29337008 167 VIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSG 243
Cdd:COG1097 158 VIGKKGSMINMLKKETGCEIIVGQNGRIWIKGPDEEGEELAIEAIKKIEREAHTSGLTDRIKEFLEEEKGERGVSSE 234
PRK04163 PRK04163
exosome complex protein Rrp4;
8-242 4.92e-118

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 336.48  E-value: 4.92e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008    8 KIVLQPRSIVVPGELLAEGEFQIPWSPYilKINSKYYSTVVGLFDVKDTQFEVIPLEGSfYYPKINDIVIGLVEDVEIYG 87
Cdd:PRK04163   2 KIFVEDRKIVVPGDLLAEGEFKAGRGTY--KENGKIYSTVVGLVDIKDDKVRVIPLEGK-YIPKVGDLVIGKVTDVTFSG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   88 WVVDIKAPYKAYLPASNLLGRSIN-VGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPR 166
Cdd:PRK04163  79 WEVDINSPYKAYLPVSEVLGRPVNvEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29337008  167 VIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASS 242
Cdd:PRK04163 159 VIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSGLTDRIKEFLEEELGERGESS 234
KH-I_Rrp4_prokar cd22524
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from ...
 154-235 7.06e-39

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from archaea; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from archaea. It is a non-catalytic component of the exosome, which is a phosphorolytic 3'-5' exoribonuclease complex involved in RNA degradation and processing. Rrp4 increases the RNA binding and the efficiency of RNA degradation and confers strong poly(A) specificity to the exosome.


Pssm-ID: 411952 [Multi-domain]  Cd Length: 82  Bit Score: 130.01  E-value: 7.06e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008 154 GIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEE 233
Cdd:cd22524   1 GILVEISPSKVPRVIGKKGSMINMLKKKTNCDIFVGQNGRIWVKGPSPEDEEIAIKAIRMIEEEAHTSGLTDRVKEFLEE 80


                ..
gi 29337008 234 KL 235
Cdd:cd22524  81 EL 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
71-136 3.98e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 3.98e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29337008     71 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLlgrSINVGEDLRRYLDVGDYVIARIENFDRS 136
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISEL---SDKRVKDPEEVLKVGDEVKVKVLSVDEE 63
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 154-200 3.08e-04

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 37.42  E-value: 3.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 29337008   154 GIVIDIMPVKVPRVIGKNksMYETLTSKSGCSIFVANNGRIWATCPS 200
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSH--FLHELGKKGPFEIAVGLNGRIWIKSET 45
 
Name Accession Description Interval E-value
Rrp4 COG1097
Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular ...
 8-243 1.39e-118

Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440714 [Multi-domain]  Cd Length: 234  Bit Score: 337.98  E-value: 1.39e-118
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   8 KIVLQPRSIVVPGELLAEGEFQipWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSfYYPKINDIVIGLVEDVEIYG 87
Cdd:COG1097   1 KIYVEDRKIVVPGDLLAEGEYK--PGSGTYVEGGKIYSTVLGLVEIKDDKVSVIPLEGK-YIPKVGDLVIGKVTDVGPSN 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008  88 WVVDIKAPYKAYLPASNLLGRSINV-GEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPR 166
Cdd:COG1097  78 WEVDINSPYQALLPVSEVPGRPFNVeSDDLRKYLDIGDYILAKVKNFDRTRDPLLTMKDKGLGKIEGGRIVEISPSKVPR 157

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29337008 167 VIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASSG 243
Cdd:COG1097 158 VIGKKGSMINMLKKETGCEIIVGQNGRIWIKGPDEEGEELAIEAIKKIEREAHTSGLTDRIKEFLEEEKGERGVSSE 234
PRK04163 PRK04163
exosome complex protein Rrp4;
8-242 4.92e-118

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 336.48  E-value: 4.92e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008    8 KIVLQPRSIVVPGELLAEGEFQIPWSPYilKINSKYYSTVVGLFDVKDTQFEVIPLEGSfYYPKINDIVIGLVEDVEIYG 87
Cdd:PRK04163   2 KIFVEDRKIVVPGDLLAEGEFKAGRGTY--KENGKIYSTVVGLVDIKDDKVRVIPLEGK-YIPKVGDLVIGKVTDVTFSG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   88 WVVDIKAPYKAYLPASNLLGRSIN-VGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKDLGRVSNGIVIDIMPVKVPR 166
Cdd:PRK04163  79 WEVDINSPYKAYLPVSEVLGRPVNvEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTLKGKGLGKIEGGTIVEIKPVKVPR 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29337008  167 VIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEEKLGERNASS 242
Cdd:PRK04163 159 VIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHTSGLTDRIKEFLEEELGERGESS 234
KH-I_Rrp4_prokar cd22524
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from ...
 154-235 7.06e-39

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from archaea; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from archaea. It is a non-catalytic component of the exosome, which is a phosphorolytic 3'-5' exoribonuclease complex involved in RNA degradation and processing. Rrp4 increases the RNA binding and the efficiency of RNA degradation and confers strong poly(A) specificity to the exosome.


Pssm-ID: 411952 [Multi-domain]  Cd Length: 82  Bit Score: 130.01  E-value: 7.06e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008 154 GIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENESHIKGLTDRIKQFIEE 233
Cdd:cd22524   1 GILVEISPSKVPRVIGKKGSMINMLKKKTNCDIFVGQNGRIWVKGPSPEDEEIAIKAIRMIEEEAHTSGLTDRVKEFLEE 80


                ..
gi 29337008 234 KL 235
Cdd:cd22524  81 EL 82
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 68-151 1.00e-28

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 104.17  E-value: 1.00e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008  68 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGE-DLRRYLDVGDYVIARIENFDRSIDPVLSVKGK 146
Cdd:cd05789   2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDElNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSL 81


                ....*
gi 29337008 147 DLGRV 151
Cdd:cd05789  82 KYGKL 86
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 154-232 1.95e-09

type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins; The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411873 [Multi-domain]  Cd Length: 78  Bit Score: 53.03  E-value: 1.95e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29337008 154 GIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPSRFSEEILIEAIRKIENEsHIKGLTDRIKQFIE 232
Cdd:cd22445   1 GLLVKVTPGLVRRLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTRQQTSILANIIEACEHM-HTSDQRKQIFSRLA 78
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 68-151 1.27e-06

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 45.23  E-value: 1.27e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008  68 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLGRSinvGEDLRRYLDVGDYVIARIENFDRSIDPVLSVKGKD 147
Cdd:cd04454   2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKD---KKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNE 78


                ....
gi 29337008 148 LGRV 151
Cdd:cd04454  79 LGVI 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
71-136 3.98e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 3.98e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29337008     71 KINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLlgrSINVGEDLRRYLDVGDYVIARIENFDRS 136
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISEL---SDKRVKDPEEVLKVGDEVKVKVLSVDEE 63
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 15-152 4.37e-05

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 43.04  E-value: 4.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   15 SIVVPGELLAEGEFQIPwSPYILKINSKYYSTVVGLFDVKDTQFE--VIPLEGSFYYPKINDIVIGLVEDVEIYGWVVDI 92
Cdd:PRK09521   6 DLVLPGDYLAVIEEYLP-GEGTYEDNGEVYASVVGKVFIDDINRKisVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRI 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   93 KA----------PYKAYLPASNllgRSINVGEDLRRYLDVGDYVIARIENFDRSIDpvLSVKGKDLGRVS 152
Cdd:PRK09521  85 VSiegserelatSKLAYIHISQ---VSDGYVESLTDAFKIGDIVRAKVISYTDPLQ--LSTKGKDLGVIY 149
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 73-147 5.65e-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: 40.33  E-value: 5.65e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29337008  73 NDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLlgrSINVGEDLRRYLDVGDYVIARIENFDRSIDPV-LSVKGKD 147
Cdd:cd05691   1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAEL---SRDRVEDATERFKVGDEVEAKITNVDRKNRKIsLSIKAKE 73
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 154-200 3.08e-04

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 37.42  E-value: 3.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 29337008   154 GIVIDIMPVKVPRVIGKNksMYETLTSKSGCSIFVANNGRIWATCPS 200
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSH--FLHELGKKGPFEIAVGLNGRIWIKSET 45
S1_Rrp40 cd05790
S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 68-142 5.03e-04

S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240216  Cd Length: 86  Bit Score: 38.01  E-value: 5.03e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29337008  68 YYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPASNLLG---RSinvgedlRRYLDVGDYVIARIENFDRSIDPVLS 142
Cdd:cd05790   2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGatkRN-------RPNLNVGDLVYARVVKANRDMEPELS 72
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 55-130 7.39e-04

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 39.42  E-value: 7.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29337008   55 DTQFEVIplegsFYYPKINDIVIGLVEDVEIYGWVVDIKA------------PYKAYLPAsnllgRSINVGEDLRRYLDV 122
Cdd:PRK08563  69 EVEFDAL-----VFKPELQEVVEGEVVEVVEFGAFVRIGPvdgllhisqimdDYISYDPK-----NGRLIGKESKRVLKV 138


                 ....*...
gi 29337008  123 GDYVIARI 130
Cdd:PRK08563 139 GDVVRARI 146
 
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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