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Conserved domains on  [gi|1207107270|ref|XP_021332434|]
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transcription elongation factor A N-terminal and central domain-containing protein [Danio rerio]

Protein Classification

transcription factor S-II family protein( domain architecture ID 13520976)

transcription factor S-II (TFS II) family protein similar to Drosophila melanogaster transcription elongation factor S-II, which is necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
214-324 4.29e-30

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


:

Pssm-ID: 462184  Cd Length: 112  Bit Score: 111.91  E-value: 4.29e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 214 ALRSKCVHLILQALSTNQQTDPGHmnKLKALAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTP 293
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEE--DALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISP 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1207107270 294 DAFAQMSVEEMAGEKLRRLRETYTSLAISEH 324
Cdd:pfam07500  82 EKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII super family cl36890
transcription elongation factor S-II; This model represents eukaryotic transcription ...
5-386 8.39e-30

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


The actual alignment was detected with superfamily member TIGR01385:

Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 116.48  E-value: 8.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270   5 EIIYCATQIERLHEDGSYEDVISLLTELDITSVTLEQIQTTDIVKVLyRLLKSCPVLSAKTKAKSLLTKWKKLYNlshai 84
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKVVD----- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270  85 llKNNDKNTREDKELETHnmsnvelplefpfltngfqplhekvnesqacntkqlditkdanqgkcnnlcfnasskklciA 164
Cdd:TIGR01385  77 --KNKSDHPGGNPEDKTT-------------------------------------------------------------V 93
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 165 TESAESLQtqleQESITPAVESNRS-DTEESAQTSVPQNTNQHTTNcDSTalRSKCVHLILQALSTNQQTDPGHMNKlKA 243
Cdd:TIGR01385  94 GESVNSVK----QEAKSQSDKIEQPkYVSSSPRNAKNDFVPTAVTN-DKV--RDKCRELLYDALAKDSDHPPQSIDP-EA 165
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 244 LAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTPDAFAQMSVEEMAGEKLRRLRETYTSLAISE 323
Cdd:TIGR01385 166 KAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFE 245
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207107270 324 HQLpETVKGTPTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:TIGR01385 246 AQG-AKIQKAVTDLFTCGKCKQKKCTYYQ-----------LQTRSADEPMTTFVTCEECGNRW 296
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
214-324 4.29e-30

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 111.91  E-value: 4.29e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 214 ALRSKCVHLILQALSTNQQTDPGHmnKLKALAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTP 293
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEE--DALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISP 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1207107270 294 DAFAQMSVEEMAGEKLRRLRETYTSLAISEH 324
Cdd:pfam07500  82 EKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
5-386 8.39e-30

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 116.48  E-value: 8.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270   5 EIIYCATQIERLHEDGSYEDVISLLTELDITSVTLEQIQTTDIVKVLyRLLKSCPVLSAKTKAKSLLTKWKKLYNlshai 84
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKVVD----- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270  85 llKNNDKNTREDKELETHnmsnvelplefpfltngfqplhekvnesqacntkqlditkdanqgkcnnlcfnasskklciA 164
Cdd:TIGR01385  77 --KNKSDHPGGNPEDKTT-------------------------------------------------------------V 93
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 165 TESAESLQtqleQESITPAVESNRS-DTEESAQTSVPQNTNQHTTNcDSTalRSKCVHLILQALSTNQQTDPGHMNKlKA 243
Cdd:TIGR01385  94 GESVNSVK----QEAKSQSDKIEQPkYVSSSPRNAKNDFVPTAVTN-DKV--RDKCRELLYDALAKDSDHPPQSIDP-EA 165
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 244 LAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTPDAFAQMSVEEMAGEKLRRLRETYTSLAISE 323
Cdd:TIGR01385 166 KAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFE 245
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207107270 324 HQLpETVKGTPTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:TIGR01385 246 AQG-AKIQKAVTDLFTCGKCKQKKCTYYQ-----------LQTRSADEPMTTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
214-315 5.52e-16

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 73.12  E-value: 5.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270  214 ALRSKCVHLILQALSTNQQTdPGHMNKLKALAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTP 293
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDP-EEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80
                           90       100
                   ....*....|....*....|..
gi 1207107270  294 DAFAQMSVEEMAGEKLRRLRET 315
Cdd:smart00510  81 EKLATMTAEELASAELKEKREK 102
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
28-77 6.37e-10

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 54.44  E-value: 6.37e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207107270  28 LLTELDITSVTLEQIQTTDIVKVLYRLLKSCPVLSAKTKAKSLLTKWKKL 77
Cdd:pfam08711   2 LLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENPEIKKLAKELVKKWKRL 51
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
331-386 1.15e-04

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 39.51  E-value: 1.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1207107270 331 KGTPTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:cd13749     1 EGTTTDLFKCGKCKKRKCTYYQ-----------LQTRSADEPMTTFVTCLNCGNRW 45
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
214-324 4.29e-30

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 111.91  E-value: 4.29e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 214 ALRSKCVHLILQALSTNQQTDPGHmnKLKALAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTP 293
Cdd:pfam07500   4 KVRDKCRELLYDALAKDSTEASEE--DALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISP 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1207107270 294 DAFAQMSVEEMAGEKLRRLRETYTSLAISEH 324
Cdd:pfam07500  82 EKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
5-386 8.39e-30

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 116.48  E-value: 8.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270   5 EIIYCATQIERLHEDGSYEDVISLLTELDITSVTLEQIQTTDIVKVLyRLLKSCPVLSAKTKAKSLLTKWKKLYNlshai 84
Cdd:TIGR01385   3 EVASHAKALDKNKSSKNVEQCLDILHQLKEFPPTEELLQETKVGVKV-NKLRKHPNEDISKLAKKIIKSWKKVVD----- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270  85 llKNNDKNTREDKELETHnmsnvelplefpfltngfqplhekvnesqacntkqlditkdanqgkcnnlcfnasskklciA 164
Cdd:TIGR01385  77 --KNKSDHPGGNPEDKTT-------------------------------------------------------------V 93
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 165 TESAESLQtqleQESITPAVESNRS-DTEESAQTSVPQNTNQHTTNcDSTalRSKCVHLILQALSTNQQTDPGHMNKlKA 243
Cdd:TIGR01385  94 GESVNSVK----QEAKSQSDKIEQPkYVSSSPRNAKNDFVPTAVTN-DKV--RDKCRELLYDALAKDSDHPPQSIDP-EA 165
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270 244 LAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTPDAFAQMSVEEMAGEKLRRLRETYTSLAISE 323
Cdd:TIGR01385 166 KAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFE 245
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207107270 324 HQLpETVKGTPTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:TIGR01385 246 AQG-AKIQKAVTDLFTCGKCKQKKCTYYQ-----------LQTRSADEPMTTFVTCEECGNRW 296
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
214-315 5.52e-16

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 73.12  E-value: 5.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207107270  214 ALRSKCVHLILQALSTNQQTdPGHMNKLKALAENIELHVHALHGRNQHKYKFHIRSKVANLKNPNNPHLRQGLISGQLTP 293
Cdd:smart00510   2 KVRDKCQEMLYKALQKISDP-EEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80
                           90       100
                   ....*....|....*....|..
gi 1207107270  294 DAFAQMSVEEMAGEKLRRLRET 315
Cdd:smart00510  81 EKLATMTAEELASAELKEKREK 102
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
28-77 6.37e-10

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 54.44  E-value: 6.37e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207107270  28 LLTELDITSVTLEQIQTTDIVKVLYRLLKSCPVLSAKTKAKSLLTKWKKL 77
Cdd:pfam08711   2 LLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENPEIKKLAKELVKKWKRL 51
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
331-386 1.15e-04

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 39.51  E-value: 1.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1207107270 331 KGTPTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:cd13749     1 EGTTTDLFKCGKCKKRKCTYYQ-----------LQTRSADEPMTTFVTCLNCGNRW 45
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
338-386 2.27e-03

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 35.66  E-value: 2.27e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1207107270 338 VRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:pfam01096   1 AKCPKCGNREAYFFQ-----------LQTRSADEPMTVFYVCTKCGHRW 38
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
334-386 3.67e-03

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


Pssm-ID: 259791  Cd Length: 45  Bit Score: 34.98  E-value: 3.67e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1207107270 334 PTNKVRCRQCDSMDCRVTQisrgtlflpswVQSGSADNDSMTFMTCANCGEQW 386
Cdd:cd00656     3 PTTDRTCPKCGHDEAYWWM-----------LQTRSADEPPTRFYKCTKCGHTW 44
 
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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