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Conserved domains on  [gi|1918012629|gb|KAF8058454|]
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esf2 [Scenedesmus sp. PABB004]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 1067-1164 3.59e-56

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 189.33  E-value: 3.59e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1067 GIVYVSRLPPHMKPAKLRQLLSPYGEVGRIYCTPEDAAARKQRKKNGGNSGKNFTEGWVEFEDKAVAKRVAGALNGQPMG 1146
Cdd:cd12263      1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                           90
                   ....*....|....*...
gi 1918012629 1147 GSRRSAYHYDLWALRYLP 1164
Cdd:cd12263     81 GKKRSRFRDDLWNIKYLP 98
lipoyl_domain cd06849
Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. ...
 47-134 8.27e-20

Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue.


:

Pssm-ID: 133458 [Multi-domain]  Cd Length: 74  Bit Score: 84.76  E-value: 8.27e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   47 IVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVP 126
Cdd:cd06849      1 TEIKMPDLGESMTEGTIVEWLVKEGDSVEEGDVLAEVETD--------------KATVEVEAPAAGVLAKILVEEGDTVP 66


                   ....*...
gi 1918012629  127 VGAPIALL 134
Cdd:cd06849     67 VGQVIAVI 74
PLN03192 super family cl33658
Voltage-dependent potassium channel; Provisional
 261-706 5.26e-09

Voltage-dependent potassium channel; Provisional


The actual alignment was detected with superfamily member PLN03192:

Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 60.65  E-value: 5.26e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  261 DALTGDIVTDHRSIARRYLCGWFAIDLLATLPVDYVVRAVEVTPRRAAgvpprgavgarsrarpraraaqgtwACSLRGd 340
Cdd:PLN03192   119 DPRTQLLVRDRKKIAVRYLSTWFLMDVASTIPFQALAYLITGTVKLNL-------------------------SYSLLG- 172

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  341 cswsvvgdgsvsvvgLLRLLRFFRVVWIL----KHVKFMHFSVvlgdfaddlyailpllSILELVIILLYLGHVSGCFFY 416
Cdd:PLN03192   173 ---------------LLRFWRLRRVKQLFtrleKDIRFSYFWI----------------RCARLLSVTLFLVHCAGCLYY 221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  417 LLSTP-PWQTKheqaliasgemtTWMshafggdkvlmmptpleppppagappprgaaldaatgrwwlcpdwgyaatpcpG 495
Cdd:PLN03192   222 LIADRyPHQGK------------TWI-----------------------------------------------------G 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  496 CAGPRLRCAShygLAFRYVTSMYWAYTTMTTVGSTTL-----AEKLWAITTMIVSGFFFSFVVGRMASLVAKlDSHRT-A 569
Cdd:PLN03192   237 AVIPNFRETS---LWIRYISAIYWSITTMTTVGYGDLhavntIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE-GTRRTmE 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  570 VNEKLEVVTTFLKDVELPRHLARRVLD-MFRKQKIKPYDRGAVLAALPFELRAKVLRHLYAGAIASVPLLRALSHDELFL 648
Cdd:PLN03192   313 FRNSIEAASNFVGRNRLPPRLKDQILAyMCLRFKAESLNQQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLL 392

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  649 sdACSRLQPYNCSAETYVYQRGESGGDVFILLRGELHVLDLDAT--TCLAKIPEGSVFGE 706
Cdd:PLN03192   393 --LVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEkeRVVGTLGCGDIFGE 450
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 1067-1164 3.59e-56

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 189.33  E-value: 3.59e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1067 GIVYVSRLPPHMKPAKLRQLLSPYGEVGRIYCTPEDAAARKQRKKNGGNSGKNFTEGWVEFEDKAVAKRVAGALNGQPMG 1146
Cdd:cd12263      1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                           90
                   ....*....|....*...
gi 1918012629 1147 GSRRSAYHYDLWALRYLP 1164
Cdd:cd12263     81 GKKRSRFRDDLWNIKYLP 98
lipoyl_domain cd06849
Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. ...
 47-134 8.27e-20

Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue.


Pssm-ID: 133458 [Multi-domain]  Cd Length: 74  Bit Score: 84.76  E-value: 8.27e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   47 IVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVP 126
Cdd:cd06849      1 TEIKMPDLGESMTEGTIVEWLVKEGDSVEEGDVLAEVETD--------------KATVEVEAPAAGVLAKILVEEGDTVP 66


                   ....*...
gi 1918012629  127 VGAPIALL 134
Cdd:cd06849     67 VGQVIAVI 74
AceF COG0508
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component ...
 46-135 4.37e-19

Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component [Energy production and conversion]; Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440274 [Multi-domain]  Cd Length: 77  Bit Score: 82.81  E-value: 4.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASV 125
Cdd:COG0508      2 AIEIKMPDLGESMTEGTIVEWLVKEGDTVKEGDPLAEVETD--------------KATMEVPAPAAGVLLEILVKEGDTV 67

                           90
                   ....*....|
gi 1918012629  126 PVGAPIALLA 135
Cdd:COG0508     68 PVGAVIAVIA 77
PDHac_trf_mito TIGR01349
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
 48-139 6.24e-17

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score. [Energy metabolism, Pyruvate dehydrogenase]


Pssm-ID: 273567 [Multi-domain]  Cd Length: 436  Bit Score: 84.85  E-value: 6.24e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   48 VLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGA-SVP 126
Cdd:TIGR01349    1 KITMPALSPTMTTGNLAKWLKKEGDKVNPGDVIAEIETD--------------KATMEFEAVEEGYLAKILVPEGTkDVP 66

                           90
                   ....*....|...
gi 1918012629  127 VGAPIALLAEEPG 139
Cdd:TIGR01349   67 VNKPIAVLVEEKE 79
PRK11856 PRK11856
branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed
 45-137 3.60e-16

branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed


Pssm-ID: 237001 [Multi-domain]  Cd Length: 411  Bit Score: 82.53  E-value: 3.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   45 GAIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTE-SLVEegyrndefagevvlsLEAQEEAVVAALLVPEGA 123
Cdd:PRK11856     1 MMFEFKMPDLGEGMTEGEIVEWLVKVGDTVKEGQPLAEVETDkATVE---------------IPSPVAGTVAKLLVEEGD 65

                           90
                   ....*....|....
gi 1918012629  124 SVPVGAPIALLAEE 137
Cdd:PRK11856    66 VVPVGSVIAVIEEE 79
Biotin_lipoyl pfam00364
Biotin-requiring enzyme; This family covers two Prosite entries, the conserved lysine residue ...
 48-134 1.68e-09

Biotin-requiring enzyme; This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognize the Glycine cleavage system H proteins.


Pssm-ID: 395290 [Multi-domain]  Cd Length: 73  Bit Score: 55.30  E-value: 1.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   48 VLPMPALSPSMTHGrVARWLKAVGDSVAEYDLLLEVGTESLVEEgyrndefagevvlsLEAQEEAVVAALLVPEGASVPV 127
Cdd:pfam00364    2 EIKSPMIGESVREG-VVEWLVKVGDKVKAGQPLAEVEAMKMEME--------------IPAPVAGVVKEILVPEGDTVEV 66


                   ....*..
gi 1918012629  128 GAPIALL 134
Cdd:pfam00364   67 GDPLAKI 73
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 261-706 5.26e-09

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 60.65  E-value: 5.26e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  261 DALTGDIVTDHRSIARRYLCGWFAIDLLATLPVDYVVRAVEVTPRRAAgvpprgavgarsrarpraraaqgtwACSLRGd 340
Cdd:PLN03192   119 DPRTQLLVRDRKKIAVRYLSTWFLMDVASTIPFQALAYLITGTVKLNL-------------------------SYSLLG- 172

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  341 cswsvvgdgsvsvvgLLRLLRFFRVVWIL----KHVKFMHFSVvlgdfaddlyailpllSILELVIILLYLGHVSGCFFY 416
Cdd:PLN03192   173 ---------------LLRFWRLRRVKQLFtrleKDIRFSYFWI----------------RCARLLSVTLFLVHCAGCLYY 221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  417 LLSTP-PWQTKheqaliasgemtTWMshafggdkvlmmptpleppppagappprgaaldaatgrwwlcpdwgyaatpcpG 495
Cdd:PLN03192   222 LIADRyPHQGK------------TWI-----------------------------------------------------G 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  496 CAGPRLRCAShygLAFRYVTSMYWAYTTMTTVGSTTL-----AEKLWAITTMIVSGFFFSFVVGRMASLVAKlDSHRT-A 569
Cdd:PLN03192   237 AVIPNFRETS---LWIRYISAIYWSITTMTTVGYGDLhavntIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE-GTRRTmE 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  570 VNEKLEVVTTFLKDVELPRHLARRVLD-MFRKQKIKPYDRGAVLAALPFELRAKVLRHLYAGAIASVPLLRALSHDELFL 648
Cdd:PLN03192   313 FRNSIEAASNFVGRNRLPPRLKDQILAyMCLRFKAESLNQQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLL 392

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  649 sdACSRLQPYNCSAETYVYQRGESGGDVFILLRGELHVLDLDAT--TCLAKIPEGSVFGE 706
Cdd:PLN03192   393 --LVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEkeRVVGTLGCGDIFGE 450
RRM smart00360
RNA recognition motif;
1069-1149 2.32e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.21  E-value: 2.32e-08
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaaRKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFGKVESV---------RLVRDKETGKS-KGF--AFVEFESEEDAEKALEALNGKELDGR 69


                    .
gi 1918012629  1149 R 1149
Cdd:smart00360   70 P 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 1069-1149 2.74e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.07  E-value: 2.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaarKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSI----------RLVRDETGRS-KGF--AFVEFEDEEDAEKAIEALNGKELGGR 67


                   .
gi 1918012629 1149 R 1149
Cdd:pfam00076   68 E 68
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1070-1149 6.58e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 42.78  E-value: 6.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1070 YVSRLPPHMKPAKLRQLLSPYGEVgriyctpedAAARKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGSR 1149
Cdd:COG0724      5 YVGNLPYSVTEEDLRELFSEYGEV---------TSVKLITDRETGRS-RGF--GFVEMPDDEEAQAAIEALNGAELMGRT 72
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 637-719 2.77e-04

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 42.00  E-value: 2.77e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   637 LLRALshDELFLSDACSRLQPYNCSAETYVYQRGESGGDVFILLRGEL---HVLDLDATTCLAKIPEGSVFGEGTVLRHM 713
Cdd:smart00100    1 LFKNL--DAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVevyKVLEDGEEQIVGTLGPGDFFGELALLTNS 78


                    ....*..
gi 1918012629   714 E-ARHAA 719
Cdd:smart00100   79 RrAASAA 85
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 637-720 3.69e-03

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 38.46  E-value: 3.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  637 LLRALSHDELflSDACSRLQPYNCSAETYVYQRGESGGDVFILLRGELHVLDLDA---TTCLAKIPEGSVFGEGTVLRHM 713
Cdd:cd00038      1 LFSGLDDEEL--EELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgrEQIVGFLGPGDLFGELALLGNG 78


                   ....*..
gi 1918012629  714 EARHAAQ 720
Cdd:cd00038     79 PRSATVR 85
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 1067-1164 3.59e-56

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 189.33  E-value: 3.59e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1067 GIVYVSRLPPHMKPAKLRQLLSPYGEVGRIYCTPEDAAARKQRKKNGGNSGKNFTEGWVEFEDKAVAKRVAGALNGQPMG 1146
Cdd:cd12263      1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                           90
                   ....*....|....*...
gi 1918012629 1147 GSRRSAYHYDLWALRYLP 1164
Cdd:cd12263     81 GKKRSRFRDDLWNIKYLP 98
lipoyl_domain cd06849
Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. ...
 47-134 8.27e-20

Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue.


Pssm-ID: 133458 [Multi-domain]  Cd Length: 74  Bit Score: 84.76  E-value: 8.27e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   47 IVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVP 126
Cdd:cd06849      1 TEIKMPDLGESMTEGTIVEWLVKEGDSVEEGDVLAEVETD--------------KATVEVEAPAAGVLAKILVEEGDTVP 66


                   ....*...
gi 1918012629  127 VGAPIALL 134
Cdd:cd06849     67 VGQVIAVI 74
AceF COG0508
Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component ...
 46-135 4.37e-19

Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component [Energy production and conversion]; Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 440274 [Multi-domain]  Cd Length: 77  Bit Score: 82.81  E-value: 4.37e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASV 125
Cdd:COG0508      2 AIEIKMPDLGESMTEGTIVEWLVKEGDTVKEGDPLAEVETD--------------KATMEVPAPAAGVLLEILVKEGDTV 67

                           90
                   ....*....|
gi 1918012629  126 PVGAPIALLA 135
Cdd:COG0508     68 PVGAVIAVIA 77
PDHac_trf_mito TIGR01349
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
 48-139 6.24e-17

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score. [Energy metabolism, Pyruvate dehydrogenase]


Pssm-ID: 273567 [Multi-domain]  Cd Length: 436  Bit Score: 84.85  E-value: 6.24e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   48 VLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGA-SVP 126
Cdd:TIGR01349    1 KITMPALSPTMTTGNLAKWLKKEGDKVNPGDVIAEIETD--------------KATMEFEAVEEGYLAKILVPEGTkDVP 66

                           90
                   ....*....|...
gi 1918012629  127 VGAPIALLAEEPG 139
Cdd:TIGR01349   67 VNKPIAVLVEEKE 79
PRK11856 PRK11856
branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed
 45-137 3.60e-16

branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed


Pssm-ID: 237001 [Multi-domain]  Cd Length: 411  Bit Score: 82.53  E-value: 3.60e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   45 GAIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTE-SLVEegyrndefagevvlsLEAQEEAVVAALLVPEGA 123
Cdd:PRK11856     1 MMFEFKMPDLGEGMTEGEIVEWLVKVGDTVKEGQPLAEVETDkATVE---------------IPSPVAGTVAKLLVEEGD 65

                           90
                   ....*....|....
gi 1918012629  124 SVPVGAPIALLAEE 137
Cdd:PRK11856    66 VVPVGSVIAVIEEE 79
PRK11892 PRK11892
pyruvate dehydrogenase subunit beta; Provisional
 46-137 3.03e-14

pyruvate dehydrogenase subunit beta; Provisional


Pssm-ID: 237011 [Multi-domain]  Cd Length: 464  Bit Score: 76.88  E-value: 3.03e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTeslveegyrnDEFAGEVvlslEAQEEAVVAALLVPEGAS- 124
Cdd:PRK11892     2 AIEILMPALSPTMEEGTLAKWLKKEGDKVKSGDVIAEIET----------DKATMEV----EAVDEGTLGKILVPEGTEg 67

                           90
                   ....*....|...
gi 1918012629  125 VPVGAPIALLAEE 137
Cdd:PRK11892    68 VKVNTPIAVLLEE 80
PLN02744 PLN02744
dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
 51-139 2.20e-10

dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Pssm-ID: 215397 [Multi-domain]  Cd Length: 539  Bit Score: 64.87  E-value: 2.20e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   51 MPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGA-SVPVGA 129
Cdd:PLN02744   117 MPSLSPTMTEGNIARWLKKEGDKVSPGEVLCEVETD--------------KATVEMECMEEGYLAKIVKGDGAkEIKVGE 182

                           90
                   ....*....|
gi 1918012629  130 PIALLAEEPG 139
Cdd:PLN02744   183 VIAITVEEEE 192
sucB TIGR01347
2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component); This ...
 52-137 5.93e-10

2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component); This model describes the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase. [Energy metabolism, TCA cycle]


Pssm-ID: 273565 [Multi-domain]  Cd Length: 403  Bit Score: 62.83  E-value: 5.93e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   52 PALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVPVGAPI 131
Cdd:TIGR01347    6 PELAESITEGTVAEWHKKVGDTVKRDENIVEIETD--------------KVVLEVPSPADGVLQEILFKEGDTVESGQVL 71


                   ....*.
gi 1918012629  132 ALLAEE 137
Cdd:TIGR01347   72 AILEEG 77
Biotin_lipoyl pfam00364
Biotin-requiring enzyme; This family covers two Prosite entries, the conserved lysine residue ...
 48-134 1.68e-09

Biotin-requiring enzyme; This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognize the Glycine cleavage system H proteins.


Pssm-ID: 395290 [Multi-domain]  Cd Length: 73  Bit Score: 55.30  E-value: 1.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   48 VLPMPALSPSMTHGrVARWLKAVGDSVAEYDLLLEVGTESLVEEgyrndefagevvlsLEAQEEAVVAALLVPEGASVPV 127
Cdd:pfam00364    2 EIKSPMIGESVREG-VVEWLVKVGDKVKAGQPLAEVEAMKMEME--------------IPAPVAGVVKEILVPEGDTVEV 66


                   ....*..
gi 1918012629  128 GAPIALL 134
Cdd:pfam00364   67 GDPLAKI 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1069-1149 3.25e-09

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 54.60  E-value: 3.25e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaarKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:cd00590      1 LFVGNLPPDTTEEDLRELFSKFGEVVSV----------RIVRDRDGKS-KGF--AFVEFESPEDAEKALEALNGTELGGR 67


                   .
gi 1918012629 1149 R 1149
Cdd:cd00590     68 P 68
PRK14875 PRK14875
acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional
 51-137 3.25e-09

acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional


Pssm-ID: 184875 [Multi-domain]  Cd Length: 371  Bit Score: 60.34  E-value: 3.25e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   51 MPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTeslveegyrnDEFAGEVvlslEAQEEAVVAALLVPEGASVPVGAP 130
Cdd:PRK14875     7 MPKWGLSMTEGKVAGWLVQEGDEVEKGDELLDVET----------DKITNEV----EAPAAGTLRRQVAQEGETLPVGAL 72


                   ....*..
gi 1918012629  131 IALLAEE 137
Cdd:PRK14875    73 LAVVADA 79
PLN03192 PLN03192
Voltage-dependent potassium channel; Provisional
 261-706 5.26e-09

Voltage-dependent potassium channel; Provisional


Pssm-ID: 215625 [Multi-domain]  Cd Length: 823  Bit Score: 60.65  E-value: 5.26e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  261 DALTGDIVTDHRSIARRYLCGWFAIDLLATLPVDYVVRAVEVTPRRAAgvpprgavgarsrarpraraaqgtwACSLRGd 340
Cdd:PLN03192   119 DPRTQLLVRDRKKIAVRYLSTWFLMDVASTIPFQALAYLITGTVKLNL-------------------------SYSLLG- 172

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  341 cswsvvgdgsvsvvgLLRLLRFFRVVWIL----KHVKFMHFSVvlgdfaddlyailpllSILELVIILLYLGHVSGCFFY 416
Cdd:PLN03192   173 ---------------LLRFWRLRRVKQLFtrleKDIRFSYFWI----------------RCARLLSVTLFLVHCAGCLYY 221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  417 LLSTP-PWQTKheqaliasgemtTWMshafggdkvlmmptpleppppagappprgaaldaatgrwwlcpdwgyaatpcpG 495
Cdd:PLN03192   222 LIADRyPHQGK------------TWI-----------------------------------------------------G 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  496 CAGPRLRCAShygLAFRYVTSMYWAYTTMTTVGSTTL-----AEKLWAITTMIVSGFFFSFVVGRMASLVAKlDSHRT-A 569
Cdd:PLN03192   237 AVIPNFRETS---LWIRYISAIYWSITTMTTVGYGDLhavntIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE-GTRRTmE 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  570 VNEKLEVVTTFLKDVELPRHLARRVLD-MFRKQKIKPYDRGAVLAALPFELRAKVLRHLYAGAIASVPLLRALSHDELFL 648
Cdd:PLN03192   313 FRNSIEAASNFVGRNRLPPRLKDQILAyMCLRFKAESLNQQQLIDQLPKSICKSICQHLFLPVVEKVYLFKGVSREILLL 392

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  649 sdACSRLQPYNCSAETYVYQRGESGGDVFILLRGELHVLDLDAT--TCLAKIPEGSVFGE 706
Cdd:PLN03192   393 --LVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEIIDSEGEkeRVVGTLGCGDIFGE 450
RRM smart00360
RNA recognition motif;
1069-1149 2.32e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.21  E-value: 2.32e-08
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaaRKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:smart00360    2 LFVGNLPPDTTEEELRELFSKFGKVESV---------RLVRDKETGKS-KGF--AFVEFESEEDAEKALEALNGKELDGR 69


                    .
gi 1918012629  1149 R 1149
Cdd:smart00360   70 P 70
PRK05704 PRK05704
2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase;
52-137 5.93e-08

2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase;


Pssm-ID: 235571 [Multi-domain]  Cd Length: 407  Bit Score: 56.38  E-value: 5.93e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   52 PALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVPVGAPI 131
Cdd:PRK05704     8 PTLPESVTEATIATWHKKPGDAVKRDEVLVEIETD--------------KVVLEVPAPAAGVLSEILAEEGDTVTVGQVL 73


                   ....*.
gi 1918012629  132 ALLAEE 137
Cdd:PRK05704    74 GRIDEG 79
Biotinyl_lipoyl_domains cd06663
Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the ...
 50-131 1.67e-07

Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue.


Pssm-ID: 133456 [Multi-domain]  Cd Length: 73  Bit Score: 49.75  E-value: 1.67e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   50 PMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVPVGA 129
Cdd:cd06663      3 LIPDLAQHLGDGTVVKWLKKVGDKVKKGDVLAEIEAM--------------KATSDVEAPKSGTVKKVLVKEGTKVEGDT 68


                   ..
gi 1918012629  130 PI 131
Cdd:cd06663     69 PL 70
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
 1068-1142 4.05e-07

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 48.72  E-value: 4.05e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1918012629 1068 IVYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaaRKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNG 1142
Cdd:cd12307      1 VVYIGHLPHGFYEPELRKYFSQFGTVTRL---------RLSRSKKTGKS-KGY--AFVEFEDPEVAKIVAETMNN 63
SucB_Actino TIGR02927
2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; This model ...
 46-137 5.71e-07

2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817).


Pssm-ID: 200219 [Multi-domain]  Cd Length: 579  Bit Score: 53.86  E-value: 5.71e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTESLVEEgyrndefagevvlsLEAQEEAVVAALLVPEGASV 125
Cdd:TIGR02927    2 AESVKMPALGESVTEGTVTSWLKAVGDTVEADEPLLEVSTDKVDTE--------------IPSPAAGVLLEIRAPEDDTV 67

                           90
                   ....*....|..
gi 1918012629  126 PVGAPIALLAEE 137
Cdd:TIGR02927   68 EVGGVLAIIGEP 79
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 1069-1149 2.74e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.07  E-value: 2.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaarKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSI----------RLVRDETGRS-KGF--AFVEFEDEEDAEKAIEALNGKELGGR 67


                   .
gi 1918012629 1149 R 1149
Cdd:pfam00076   68 E 68
SucB_Actino TIGR02927
2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; This model ...
 51-136 1.17e-05

2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817).


Pssm-ID: 200219 [Multi-domain]  Cd Length: 579  Bit Score: 49.63  E-value: 1.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   51 MPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTESLVEEgyrndefagevvlsLEAQEEAVVAALLVPEGASVPVGAP 130
Cdd:TIGR02927  131 MPELGESVTEGTVTSWLKAVGDTVEVDEPLLEVSTDKVDTE--------------IPSPVAGTLLEIRAPEDDTVEVGTV 196


                   ....*.
gi 1918012629  131 IALLAE 136
Cdd:TIGR02927  197 LAIIGD 202
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 1069-1147 4.81e-05

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 42.93  E-value: 4.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVgriyctpedAAARKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGG 1147
Cdd:cd21608      2 LYVGNLSWDTTEDDLRDLFSEFGEV---------ESAKVITDRETGRS-RGF--GFVTFSTAEAAEAAIDALNGKELDG 68
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1070-1149 6.58e-05

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 42.78  E-value: 6.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1070 YVSRLPPHMKPAKLRQLLSPYGEVgriyctpedAAARKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGSR 1149
Cdd:COG0724      5 YVGNLPYSVTEEDLRELFSEYGEV---------TSVKLITDRETGRS-RGF--GFVEMPDDEEAQAAIEALNGAELMGRT 72
biotinyl_domain cd06850
The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all ...
 46-134 1.26e-04

The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.


Pssm-ID: 133459 [Multi-domain]  Cd Length: 67  Bit Score: 41.25  E-value: 1.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPalspsmthGRVARWLKAVGDSVAeydlllevgteslveegyrndefAGEVVLSLEA---------QEEAVVAA 116
Cdd:cd06850      1 EVTAPMP--------GTVVKVLVKEGDKVE-----------------------AGQPLAVLEAmkmenevtaPVAGVVKE 49

                           90
                   ....*....|....*...
gi 1918012629  117 LLVPEGASVPVGAPIALL 134
Cdd:cd06850     50 ILVKEGDQVEAGQLLVVI 67
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
 1069-1149 1.70e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 41.34  E-value: 1.70e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVgriycTPEDAAARKQRKKNGGNSGKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:cd21620      4 LYVGNLPQTCQSEDLIILFEPYGNV-----CGAHIASRKKVKVSWVKPSKLF--AFVEFETKEAATTAIVLLNGITYMGC 76


                   .
gi 1918012629 1149 R 1149
Cdd:cd21620     77 Q 77
PTZ00144 PTZ00144
dihydrolipoamide succinyltransferase; Provisional
 47-132 2.07e-04

dihydrolipoamide succinyltransferase; Provisional


Pssm-ID: 240289 [Multi-domain]  Cd Length: 418  Bit Score: 45.44  E-value: 2.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   47 IVLPMPALSPSMTHGRVARWLKAVGDSVAEYDLLLEVGTEslveegyrndefagEVVLSLEAQEEAVVAALLVPEGASVP 126
Cdd:PTZ00144    45 KVIKVPTMGDSISEGTVVEWKKKVGDYVKEDEVICIIETD--------------KVSVDIRAPASGVITKIFAEEGDTVE 110


                   ....*.
gi 1918012629  127 VGAPIA 132
Cdd:PTZ00144   111 VGAPLS 116
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
 1068-1142 2.60e-04

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 40.62  E-value: 2.60e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1918012629 1068 IVYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaaRKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNG 1142
Cdd:cd12552      1 IIYVSHLPHGFHEKELKKYFAQFGDLKNV---------RLARSKKTGNS-KHY--GFLEFVNPEDAMIAQKSMNN 63
cNMP smart00100
Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a ...
 637-719 2.77e-04

Cyclic nucleotide-monophosphate binding domain; Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.


Pssm-ID: 197516 [Multi-domain]  Cd Length: 120  Bit Score: 42.00  E-value: 2.77e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   637 LLRALshDELFLSDACSRLQPYNCSAETYVYQRGESGGDVFILLRGEL---HVLDLDATTCLAKIPEGSVFGEGTVLRHM 713
Cdd:smart00100    1 LFKNL--DAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVevyKVLEDGEEQIVGTLGPGDFFGELALLTNS 78


                    ....*..
gi 1918012629   714 E-ARHAA 719
Cdd:smart00100   79 RrAASAA 85
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 1069-1149 1.72e-03

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 38.37  E-value: 1.72e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVgriyctpedAAARKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGGS 1148
Cdd:cd12362      1 LFVYHLPNEFTDQDLYQLFAPFGNV---------VSAKVFVDKNTGRS-KGF--GFVSYDNPLSAQAAIKAMNGFQVGGK 68


                   .
gi 1918012629 1149 R 1149
Cdd:cd12362     69 R 69
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
 1070-1151 2.44e-03

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 38.13  E-value: 2.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1070 YVSRLPPHMKPAKLRQLLSPYGEVgriyctpedAAARKQRKKNGGNSGKNFTegwvEFEDKAVAKRVAGALNGQPMGGSR 1149
Cdd:cd12244      4 YISNLPLDMDEQDLENMLKPFGQV---------ISTRILRDSKGQSRGVGFA----RMESREKCEDVISKFNGKVLKTPS 70


                   ..
gi 1918012629 1150 RS 1151
Cdd:cd12244     71 AS 72
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
 1069-1148 2.79e-03

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 38.16  E-value: 2.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRiyctpedaaARKQRKKN-----GGNSGKNFTEGWVEFEDKAVAKRVAGALNGQ 1143
Cdd:cd12280      1 IFVSGLPPDVTIDELADLFGQIGIIKR---------YKDTWPPKikiytDKETGKPKGEATLTYEDPSAAKAAIEWFNGK 71


                   ....*
gi 1918012629 1144 PMGGS 1148
Cdd:cd12280     72 EFRGN 76
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 1070-1147 3.58e-03

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 37.28  E-value: 3.58e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1918012629 1070 YVSRLPPHMKPAKLRQLLSPYGEVGRIYCtpedaaarkqrkknggNSGKNFteGWVEFEDKAVAKRVAGALNGQPMGG 1147
Cdd:cd12332      5 FVGNLPNDITEEEFKELFQKYGEVSEVFL----------------NKGKGF--GFIRLDTRANAEAAKAELDGTPRKG 64
CAP_ED cd00038
effector domain of the CAP family of transcription factors; members include CAP (or cAMP ...
 637-720 3.69e-03

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels


Pssm-ID: 237999 [Multi-domain]  Cd Length: 115  Bit Score: 38.46  E-value: 3.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629  637 LLRALSHDELflSDACSRLQPYNCSAETYVYQRGESGGDVFILLRGELHVLDLDA---TTCLAKIPEGSVFGEGTVLRHM 713
Cdd:cd00038      1 LFSGLDDEEL--EELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgrEQIVGFLGPGDLFGELALLGNG 78


                   ....*..
gi 1918012629  714 EARHAAQ 720
Cdd:cd00038     79 PRSATVR 85
aceF PRK11854
pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated
 46-139 5.85e-03

pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated


Pssm-ID: 236999 [Multi-domain]  Cd Length: 633  Bit Score: 40.76  E-value: 5.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1918012629   46 AIVLPMPALSpsMTHGRVARWLKAVGDSVAEYDLLLEVGTeslveegyrnDEFAGEVvlslEAQEEAVVAALLVPEGASV 125
Cdd:PRK11854     2 AIEIKVPDIG--ADEVEVTEILVKVGDKVEAEQSLITVEG----------DKASMEV----PSPQAGVVKEIKVKVGDKV 65

                           90
                   ....*....|....
gi 1918012629  126 PVGAPIALLAEEPG 139
Cdd:PRK11854    66 ETGALIMIFESADG 79
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 1069-1147 7.65e-03

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 36.77  E-value: 7.65e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1918012629 1069 VYVSRLPPHMKPAKLRQLLSPYGEVGRIyctpedaaarKQRKKNGGNSgKNFteGWVEFEDKAVAKRVAGALNGQPMGG 1147
Cdd:cd12380      4 VYVKNFGEDVDDDELKELFEKYGKITSA----------KVMKDDSGKS-KGF--GFVNFENHEAAQKAVEELNGKELNG 69
PRK11855 PRK11855
dihydrolipoamide acetyltransferase; Reviewed
 63-134 9.48e-03

dihydrolipoamide acetyltransferase; Reviewed


Pssm-ID: 237000 [Multi-domain]  Cd Length: 547  Bit Score: 40.19  E-value: 9.48e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1918012629   63 VARWLKAVGDSVAEYDLLLEVGTESLVEEgyrndefagevVLSLEAqeeAVVAALLVPEGASVPVGAPIALL 134
Cdd:PRK11855   135 VIEWLVKVGDTVEEDQSLITVETDKATME-----------IPSPVA---GVVKEIKVKVGDKVSVGSLLVVI 192
 
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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