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Conserved domains on  [gi|308254576|gb|EFO98528|]
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CRE-EMB-5 protein [Caenorhabditis remanei]

Protein Classification

DLD and SH2_Nterm_SPT6_like domain-containing protein( domain architecture ID 13390031)

protein containing domains DLD, S1_like, SH2_Nterm_SPT6_like, and SH2_Cterm_SPT6_like

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1274-1482 2.00e-78

SH2 domain;


:

Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 257.46  E-value: 2.00e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1274 EDDLTDMKNETKKKESNTRVKRVIAHPNFHNVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHNFFVKES 1353
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1354 AKDQVFSIGRQLSVGGEDFEDLDELIARFVQPLIQVSHDITTHKYFFtRGTCEDseaVEAFVH-EKKRELGRSPYVFSAS 1432
Cdd:pfam14633   81 DKENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFK-DGTKEE---VEEWLReEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576  1433 YRQPCQFCISYMFDNTNRIRHEYFKIVPGGVRFRHQNFDSLERMLVWFKR 1482
Cdd:pfam14633  157 HKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_5 super family cl22429
Helix-hairpin-helix domain;
905-1008 3.46e-34

Helix-hairpin-helix domain;


The actual alignment was detected with superfamily member pfam14635:

Pssm-ID: 473956  Cd Length: 104  Bit Score: 126.89  E-value: 3.46e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   905 EDIFCLSLHPLQREIDQEQLALVLNHELVNKVNEEGVDINKCAEFPHYTNMLQFTCGLGPRKATALLKSIKANDNLIESR 984
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 308254576   985 SKLVVGCKLGPKVFMNCAGFIRID 1008
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 750-900 6.28e-23

Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


The actual alignment was detected with superfamily member pfam14639:

Pssm-ID: 473878  Cd Length: 150  Bit Score: 96.47  E-value: 6.28e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   750 RIMAVCYSTVR-EEASFGVMVDENGSIVDYLRMVhftkrtmAQGNTGALKRESMDLFKKFVQRRRPHAIGLNIEDMDCTR 828
Cdd:pfam14639    6 RVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKLA-------WREFDRENKAQFEETLKKFLLSKKPHVIGVSGENRDAQK 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308254576   829 LKRDLEEAVQELySQNMIIRQIPVFLMDNEAAKVYMRSNISVAENPDHPPTLRQAVSLARILLDPIPEYAHL 900
Cdd:pfam14639   79 FYEDVQRVLHEL-EQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQV 149
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1191-1251 1.04e-13

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


:

Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 67.31  E-value: 1.04e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 308254576  1191 CPGTAVGIRVRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSC 1251
Cdd:pfam00575   12 TRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
Tex_N super family cl46305
Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss: ...
 295-410 9.22e-12

Tex-like protein N-terminal domain; This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors.


The actual alignment was detected with superfamily member pfam14641:

Pssm-ID: 480645  Cd Length: 115  Bit Score: 63.35  E-value: 9.22e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   295 EADEDELEREAQWImkfafeetsvTNQSSFDMNDklecmmnmdnsNQEERKRAVIDAIKAVLRFIRVrsNSFEVPFIGFY 374
Cdd:pfam14641    3 DLTDEELEEEANWI----------SNRLLVEKND-----------DFERLLEPFKEAVGNVLEFISK--DNLEVPFIWQH 59

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576   375 RKESI-----------DNLLTLNNLWTVYDFDEKWCHLSEKK---TKLYD 410
Cdd:pfam14641   60 RRDYLlhsekdgfeigHKLLNEDDLWRIVQLDIKFHSLIEKRnnlEKLYE 109
HHH_9 super family cl40179
HHH domain;
1021-1105 2.23e-07

HHH domain;


The actual alignment was detected with superfamily member pfam17674:

Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.46  E-value: 2.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1021 EVLDGSRVHPETYEWARKMAVDaLEVDdsadptaaLQEIMESPDRLRDLDLDAFADElnrqGFGEkkSTLYDISSELSAR 1100
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKD-LGLD--------LKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEELAKP 65


                   ....*
gi 308254576  1101 YKDLR 1105
Cdd:pfam17674   66 GRDPR 70
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1274-1482 2.00e-78

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 257.46  E-value: 2.00e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1274 EDDLTDMKNETKKKESNTRVKRVIAHPNFHNVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHNFFVKES 1353
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1354 AKDQVFSIGRQLSVGGEDFEDLDELIARFVQPLIQVSHDITTHKYFFtRGTCEDseaVEAFVH-EKKRELGRSPYVFSAS 1432
Cdd:pfam14633   81 DKENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFK-DGTKEE---VEEWLReEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576  1433 YRQPCQFCISYMFDNTNRIRHEYFKIVPGGVRFRHQNFDSLERMLVWFKR 1482
Cdd:pfam14633  157 HKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_7 pfam14635
Helix-hairpin-helix motif;
905-1008 3.46e-34

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 126.89  E-value: 3.46e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   905 EDIFCLSLHPLQREIDQEQLALVLNHELVNKVNEEGVDINKCAEFPHYTNMLQFTCGLGPRKATALLKSIKANDNLIESR 984
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 308254576   985 SKLVVGCKLGPKVFMNCAGFIRID 1008
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
 1298-1382 8.30e-34

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 125.04  E-value: 8.30e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576 1298 AHPNFHNVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHNFFVKESAKDQVFSIGRQLSVGGEDFEDLDE 1377
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDE 80


                  ....*
gi 308254576 1378 LIARF 1382
Cdd:cd09918    81 IIARF 85
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 750-900 6.28e-23

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 96.47  E-value: 6.28e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   750 RIMAVCYSTVR-EEASFGVMVDENGSIVDYLRMVhftkrtmAQGNTGALKRESMDLFKKFVQRRRPHAIGLNIEDMDCTR 828
Cdd:pfam14639    6 RVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKLA-------WREFDRENKAQFEETLKKFLLSKKPHVIGVSGENRDAQK 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308254576   829 LKRDLEEAVQELySQNMIIRQIPVFLMDNEAAKVYMRSNISVAENPDHPPTLRQAVSLARILLDPIPEYAHL 900
Cdd:pfam14639   79 FYEDVQRVLHEL-EQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQV 149
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
831-1140 6.56e-19

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 93.17  E-value: 6.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  831 RDLEEAVQELYSQnmIIRQIPVFlMDNEA-AKVYMRSNISVAENPDHPPTLRQAVSLARILLDPIPE------------- 896
Cdd:COG2183   384 RETEQFVAELIKE--LDLKVQYV-IVSEAgASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAElvkidpksigvgq 460

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  897 YAHlwnsdedifclslhplqrEIDQEQLALVLNHELVNKVNEEGVDINKcAEFPhytnMLQFTCGLGPRKAtallKSIKA 976
Cdd:COG2183   461 YQH------------------DVNQKKLKRSLDAVVEDCVNAVGVDLNT-ASAP----LLSYVSGLNPTLA----KNIVA 513

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  977 --NDN-LIESRSKL--VVGckLGPKVFMNCAGFIRIDTHKvsdkteayvEVLDGSRVHPETYEWARKMAvDALEVDdsad 1051
Cdd:COG2183   514 yrDENgAFKSRKELlkVPR--LGPKAFEQAAGFLRIRDGD---------NPLDNSAVHPESYPVVEKIL-KDLGVS---- 577

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576 1052 ptaaLQEIMESPDRLRDLDLDAFADELnrqgFGEKksTLYDISSELSARYKDLREPFLEPR-GEDLYNLlarcgKEIKEG 1130
Cdd:COG2183   578 ----VKDLIGNKELLKKLDPEKYADEL----FGLP--TLRDILKELEKPGRDPRPEFKTPTfREGVLKI-----EDLKPG 642

                         330
                  ....*....|
gi 308254576 1131 SKVLGTVQSV 1140
Cdd:COG2183   643 MILEGTVTNV 652
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 749-864 4.56e-16

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 74.91  E-value: 4.56e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576    749 RRIMAVCYSTVReeaSFGVMVDENGSIVDYLRMVHFTKRTMAQgntgalkresmDLFKKFVQRRRPHAIGLNIEDMDCTR 828
Cdd:smart00732    1 KRVLGLDPGRKG---IGVAVVDETGKLADPLEVIPRTNKEADA-----------ARLKKLIKKYQPDLIVIGLPLNMNGT 66

                            90       100       110
                    ....*....|....*....|....*....|....*.
gi 308254576    829 LKRDLEEAVQELYSQNMiirQIPVFLMDNEAAKVYM 864
Cdd:smart00732   67 ASRETEEAFAELLKERF---NLPVVLVDERLATVYA 99
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1191-1251 1.04e-13

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 67.31  E-value: 1.04e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 308254576  1191 CPGTAVGIRVRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSC 1251
Cdd:pfam00575   12 TRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 295-410 9.22e-12

Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.


Pssm-ID: 464230  Cd Length: 115  Bit Score: 63.35  E-value: 9.22e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   295 EADEDELEREAQWImkfafeetsvTNQSSFDMNDklecmmnmdnsNQEERKRAVIDAIKAVLRFIRVrsNSFEVPFIGFY 374
Cdd:pfam14641    3 DLTDEELEEEANWI----------SNRLLVEKND-----------DFERLLEPFKEAVGNVLEFISK--DNLEVPFIWQH 59

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576   375 RKESI-----------DNLLTLNNLWTVYDFDEKWCHLSEKK---TKLYD 410
Cdd:pfam14641   60 RRDYLlhsekdgfeigHKLLNEDDLWRIVQLDIKFHSLIEKRnnlEKLYE 109
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1299-1385 2.46e-10

Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.


Pssm-ID: 214585 [Multi-domain]  Cd Length: 84  Bit Score: 58.39  E-value: 2.46e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   1299 HPNFH-NVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHnfFVKESAKDQVFSIGrqlsvGGEDFEDLDE 1377
Cdd:smart00252    1 QPWYHgFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVKH--YRIRRNEDGKFYLE-----GGRKFPSLVE 73


                    ....*...
gi 308254576   1378 LIARFVQP 1385
Cdd:smart00252   74 LVEHYQKN 81
HHH_9 pfam17674
HHH domain;
1021-1105 2.23e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.46  E-value: 2.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1021 EVLDGSRVHPETYEWARKMAVDaLEVDdsadptaaLQEIMESPDRLRDLDLDAFADElnrqGFGEkkSTLYDISSELSAR 1100
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKD-LGLD--------LKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEELAKP 65


                   ....*
gi 308254576  1101 YKDLR 1105
Cdd:pfam17674   66 GRDPR 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1197-1252 4.38e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 48.75  E-value: 4.38e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 308254576   1197 GIRVRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSCK 1252
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1192-1252 2.11e-04

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 41.06  E-value: 2.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 308254576 1192 PGTAVGIR-----VRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSCK 1252
Cdd:cd05698     5 HGTIVKVKpngciVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
 
Name Accession Description Interval E-value
SH2_2 pfam14633
SH2 domain;
1274-1482 2.00e-78

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 257.46  E-value: 2.00e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1274 EDDLTDMKNETKKKESNTRVKRVIAHPNFHNVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHNFFVKES 1353
Cdd:pfam14633    1 DADKEELKKKKKAKARKTYVKRVIKHPLFHNFNYAQAEEYLASQDRGDVVIRPSSKGPDHLTVTWKVADGVYQHIDVLEL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1354 AKDQVFSIGRQLSVGGEDFEDLDELIARFVQPLIQVSHDITTHKYFFtRGTCEDseaVEAFVH-EKKRELGRSPYVFSAS 1432
Cdd:pfam14633   81 DKENEFSLGKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFK-DGTKEE---VEEWLReEKKANPKRSPYAFCLS 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576  1433 YRQPCQFCISYMFDNTNRIRHEYFKIVPGGVRFRHQNFDSLERMLVWFKR 1482
Cdd:pfam14633  157 HKHPGYFLLSFKANKNSRVHHWYVKVTPDGFRLRGQQFPDVDALCNGFKK 206
HHH_7 pfam14635
Helix-hairpin-helix motif;
905-1008 3.46e-34

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 126.89  E-value: 3.46e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   905 EDIFCLSLHPLQREIDQEQLALVLNHELVNKVNEEGVDINKCAEFPHYTNMLQFTCGLGPRKATALLKSIKANDNLIESR 984
Cdd:pfam14635    1 EDILSLSFHPLQELLPKEELLKALETAFVDIVNLVGVDVNEAIANKYEAAILPYIAGLGPRKADHLLKILAANNGRLDNR 80

                           90       100
                   ....*....|....*....|....
gi 308254576   985 SKLVVGCKLGPKVFMNCAGFIRID 1008
Cdd:pfam14635   81 SQLITKCIMGPKVFMNCAGFLIID 104
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
 1298-1382 8.30e-34

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 125.04  E-value: 8.30e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576 1298 AHPNFHNVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHNFFVKESAKDQVFSIGRQLSVGGEDFEDLDE 1377
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLDE 80


                  ....*
gi 308254576 1378 LIARF 1382
Cdd:cd09918    81 IIARF 85
SH2_Cterm_SPT6_like cd09928
C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription ...
 1391-1484 3.83e-27

C-terminal Src homology 2 (SH2) domain found in Spt6; Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198182  Cd Length: 89  Bit Score: 106.16  E-value: 3.83e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576 1391 HDITTHKYFftRGTCEDSEavEAFVHEKKRELGRSPYVFSASYRQPCQFCISYMFDNTnRIRHEYFKIVPGGVRFRHQNF 1470
Cdd:cd09928     1 EMLNHHKYF--RGTKEEVE--KLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPANT-RVRHEYVKVTPDGFRFRGQVF 75

                          90
                  ....*....|....
gi 308254576 1471 DSLERMLVWFKRHF 1484
Cdd:cd09928    76 PSVDSLLNWFKEHF 89
YqgF pfam14639
Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to ...
 750-900 6.28e-23

Holliday-junction resolvase-like of SPT6; The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage


Pssm-ID: 258777  Cd Length: 150  Bit Score: 96.47  E-value: 6.28e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   750 RIMAVCYSTVR-EEASFGVMVDENGSIVDYLRMVhftkrtmAQGNTGALKRESMDLFKKFVQRRRPHAIGLNIEDMDCTR 828
Cdd:pfam14639    6 RVLGVAFGSGRfDDAIICVLVNGEGEVTDFLKLA-------WREFDRENKAQFEETLKKFLLSKKPHVIGVSGENRDAQK 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 308254576   829 LKRDLEEAVQELySQNMIIRQIPVFLMDNEAAKVYMRSNISVAENPDHPPTLRQAVSLARILLDPIPEYAHL 900
Cdd:pfam14639   79 FYEDVQRVLHEL-EQDSRLHTIGVILVDDEVAILYQNSKRAEAEFPDYPPLLRYCVALARYIQDPLLEYAQV 149
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
831-1140 6.56e-19

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 93.17  E-value: 6.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  831 RDLEEAVQELYSQnmIIRQIPVFlMDNEA-AKVYMRSNISVAENPDHPPTLRQAVSLARILLDPIPE------------- 896
Cdd:COG2183   384 RETEQFVAELIKE--LDLKVQYV-IVSEAgASVYSASELAREEFPDLDVTVRGAVSIARRLQDPLAElvkidpksigvgq 460

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  897 YAHlwnsdedifclslhplqrEIDQEQLALVLNHELVNKVNEEGVDINKcAEFPhytnMLQFTCGLGPRKAtallKSIKA 976
Cdd:COG2183   461 YQH------------------DVNQKKLKRSLDAVVEDCVNAVGVDLNT-ASAP----LLSYVSGLNPTLA----KNIVA 513

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  977 --NDN-LIESRSKL--VVGckLGPKVFMNCAGFIRIDTHKvsdkteayvEVLDGSRVHPETYEWARKMAvDALEVDdsad 1051
Cdd:COG2183   514 yrDENgAFKSRKELlkVPR--LGPKAFEQAAGFLRIRDGD---------NPLDNSAVHPESYPVVEKIL-KDLGVS---- 577

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576 1052 ptaaLQEIMESPDRLRDLDLDAFADELnrqgFGEKksTLYDISSELSARYKDLREPFLEPR-GEDLYNLlarcgKEIKEG 1130
Cdd:COG2183   578 ----VKDLIGNKELLKKLDPEKYADEL----FGLP--TLRDILKELEKPGRDPRPEFKTPTfREGVLKI-----EDLKPG 642

                         330
                  ....*....|
gi 308254576 1131 SKVLGTVQSV 1140
Cdd:COG2183   643 MILEGTVTNV 652
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 749-864 4.56e-16

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 74.91  E-value: 4.56e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576    749 RRIMAVCYSTVReeaSFGVMVDENGSIVDYLRMVHFTKRTMAQgntgalkresmDLFKKFVQRRRPHAIGLNIEDMDCTR 828
Cdd:smart00732    1 KRVLGLDPGRKG---IGVAVVDETGKLADPLEVIPRTNKEADA-----------ARLKKLIKKYQPDLIVIGLPLNMNGT 66

                            90       100       110
                    ....*....|....*....|....*....|....*.
gi 308254576    829 LKRDLEEAVQELYSQNMiirQIPVFLMDNEAAKVYM 864
Cdd:smart00732   67 ASRETEEAFAELLKERF---NLPVVLVDERLATVYA 99
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1191-1251 1.04e-13

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 67.31  E-value: 1.04e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 308254576  1191 CPGTAVGIRVRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSC 1251
Cdd:pfam00575   12 TRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
HTH_44 pfam14641
Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two ...
 295-410 9.22e-12

Helix-turn-helix DNA-binding domain of SPT6; This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.


Pssm-ID: 464230  Cd Length: 115  Bit Score: 63.35  E-value: 9.22e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   295 EADEDELEREAQWImkfafeetsvTNQSSFDMNDklecmmnmdnsNQEERKRAVIDAIKAVLRFIRVrsNSFEVPFIGFY 374
Cdd:pfam14641    3 DLTDEELEEEANWI----------SNRLLVEKND-----------DFERLLEPFKEAVGNVLEFISK--DNLEVPFIWQH 59

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 308254576   375 RKESI-----------DNLLTLNNLWTVYDFDEKWCHLSEKK---TKLYD 410
Cdd:pfam14641   60 RRDYLlhsekdgfeigHKLLNEDDLWRIVQLDIKFHSLIEKRnnlEKLYE 109
SH2 smart00252
Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides ...
 1299-1385 2.46e-10

Src homology 2 domains; Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.


Pssm-ID: 214585 [Multi-domain]  Cd Length: 84  Bit Score: 58.39  E-value: 2.46e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   1299 HPNFH-NVSYESATKMLDGMDWTDCIIRPSANKDSGLSVTWKICDRVYHnfFVKESAKDQVFSIGrqlsvGGEDFEDLDE 1377
Cdd:smart00252    1 QPWYHgFISREEAEKLLKNEGDGDFLVRDSESSPGDYVLSVRVKGKVKH--YRIRRNEDGKFYLE-----GGRKFPSLVE 73


                    ....*...
gi 308254576   1378 LIARFVQP 1385
Cdd:smart00252   74 LVEHYQKN 81
HHH_9 pfam17674
HHH domain;
1021-1105 2.23e-07

HHH domain;


Pssm-ID: 465451 [Multi-domain]  Cd Length: 70  Bit Score: 49.46  E-value: 2.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576  1021 EVLDGSRVHPETYEWARKMAVDaLEVDdsadptaaLQEIMESPDRLRDLDLDAFADElnrqGFGEkkSTLYDISSELSAR 1100
Cdd:pfam17674    1 NPLDNTAIHPESYPLAEKILKD-LGLD--------LKDLIGNSALLKKLDPKKLAEE----EVGL--PTLKDILEELAKP 65


                   ....*
gi 308254576  1101 YKDLR 1105
Cdd:pfam17674   66 GRDPR 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1197-1252 4.38e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 48.75  E-value: 4.38e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 308254576   1197 GIRVRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSCK 1252
Cdd:smart00316   17 GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1192-1252 2.11e-04

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 41.06  E-value: 2.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 308254576 1192 PGTAVGIR-----VRFDNGMTGFCPNKNISSSHIDNPLTRVKINQPYYFKVLKLDKERFSLFLSCK 1252
Cdd:cd05698     5 HGTIVKVKpngciVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
HHH_3 pfam12836
Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.
 938-1005 4.24e-03

Helix-hairpin-helix motif; The HhH domain is a short DNA-binding domain.


Pssm-ID: 463723 [Multi-domain]  Cd Length: 62  Bit Score: 37.08  E-value: 4.24e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 308254576   938 EEGVDINKCAEfphytNMLQFTCGLGPRKATALLKSIKANdNLIESRS--KLVVGckLGPKVFMNCAGFI 1005
Cdd:pfam12836    1 AVGVDINTASA-----ELLSRVPGLGPKLAKNIVEYREEN-GPFRSREdlLKVKG--LGPKTFEQLAGFL 62
 
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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