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Conserved domains on  [gi|1907070772|ref|XP_036010348|]
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splicing factor 3B subunit 1 isoform X1 [Mus musculus]

Protein Classification

CTD and SF3b1 domain-containing protein( domain architecture ID 12225364)

protein containing domains CTD, SF3b1, and HSH155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HSH155 super family cl26678
U2 snRNP spliceosome subunit [RNA processing and modification];
300-1158 0e+00

U2 snRNP spliceosome subunit [RNA processing and modification];


The actual alignment was detected with superfamily member COG5181:

Pssm-ID: 227508 [Multi-domain]  Cd Length: 975  Bit Score: 1207.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  300 MQTEDRTMKSVNDQPS-GNLPFLKPDDIQYFDKLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAR 378
Cdd:COG5181    118 MCLPARGYKALTDFHGyADLGFFKVEDLKYFADDEKDFFMPLLEDREGDERDVYRLLLKVKNGGKRMRMEGLRILTDKAV 197

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  379 EFGAGPLFNQILPLLMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAA 458
Cdd:COG5181    198 NFGAAAVFNKVLPMLMSRELEDQERHLVVKLIDRLLYGLDDLKVPYVHKILVVVGPLLIDEDLKRRCMGREIILNLVYRC 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  459 GLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLR 538
Cdd:COG5181    278 GLGFSVSSMRPDITSKDEYVRNVTGRAVGVVADALGVEELLPFLEALCGSRKSWEARHTGIRIAQQICELLGRSRLSHLG 357

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  539 SLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANY 618
Cdd:COG5181    358 PLLKCISKLLKDRSRFVRIDTANALSYLAELVGPYGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACH 437

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  619 YTREVMLILIREFQSPDEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVELANKV 698
Cdd:COG5181    438 DTREHMEIVFREFKSPDEEMKKDLLVVERICDKVGTDTPWKLRDQVSPEFFSPFWRRRSAGDRRSYKQVVLTTVILAKMG 517

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  699 GAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKR 778
Cdd:COG5181    518 GDPRVSRKILEYYSDEPEPYRKMNAGLVSRIFSRLGRLGFDERLEERLYDSILNAFQEQDTTVGLILPCFSTVLVSLEFR 597

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  779 VKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVI 858
Cdd:COG5181    598 GKPHLSMIVSTILKLLRSKPPDVRIRAADLMGSLAKVLKACGETKELAKLGNILYENLGEDYPEVLGSILKAICSIYSVH 677

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  859 GMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYI 938
Cdd:COG5181    678 RFRSMQPPISGILPSLTPILRNKHQKVVANTIALVGTICMNSPEYIGVREWMRICFELVDSLKSWNKEIRRNATETFGCI 757

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  939 AKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKD 1018
Cdd:COG5181    758 SRAIGPQDVLDILLNNLKVQERQQRVCTSVAISIVAEYCGPFSVLPTLMSDYETPEANVQNGVLKAMCFMFEYIGQASLD 837

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1019 YIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPC 1098
Cdd:COG5181    838 YVYSITPLLEDALTDRDPVHRQTAMNVIRHLVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEGMESFATVLGSG 917

                          810       820       830       840       850       860
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1099 RMLQYCLQGLFHPARKVRDVYWKIYNSIYIGSQDALIAHYPrIYNDDKNTYIRyELDYIL 1158
Cdd:COG5181    918 AMMKYVQQGLFHPSSTVRKRYWTVYNIMYVFDSDAMVPCYP-VEEDLNPELAR-TLHICI 975
SF3b1 pfam08920
Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B ...
 186-296 7.46e-67

Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly.


:

Pssm-ID: 462634 [Multi-domain]  Cd Length: 114  Bit Score: 220.32  E-value: 7.46e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  186 SKRKSRWDETPASQM---GGSTPVLTPGK-TPIGtpAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAM 261
Cdd:pfam08920    1 SKRRSRWDETPANAGsgpGGATPGETPGRqTPVG--AMGMATPTPGALGPMTPEQMQAFRWEKEIDERNRPLTDEELDAM 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907070772  262 FP-EGYKVLPPPAGYVPIRTPARKLTATPTPLGGMT 296
Cdd:pfam08920   79 LPgEGYKILDPPAGYVPIRTPARKLLATPTPMGGTG 114
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 95-236 1.50e-11

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 62.54  E-value: 1.50e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772    95 GSETPGatpgskiWDPTPSHTPA-GAATPGRGDTPGHATPGHGGATssarknrwdetpkterdTPGHGSGWAETPRTDRG 173
Cdd:smart01104    1 GGRTPA-------WGASGSKTPAwGSRTPGTAAGGAPTARGGSGSR-----------------TPAWGGAGSRTPAWGGA 56

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907070772   174 GDSIGETPTPGAS---KRKSRWDET--PASQMGGSTPVLTPGKTPIGTPamnMATPTPGHIMSMTPEQ 236
Cdd:smart01104   57 GPTGSRTPAWGGAsawGNKSSEGSAssWAAGPGGAYGAPTPGYGGTPSA---YGPATPGGGAMAGSAS 121
 
Name Accession Description Interval E-value
HSH155 COG5181
U2 snRNP spliceosome subunit [RNA processing and modification];
300-1158 0e+00

U2 snRNP spliceosome subunit [RNA processing and modification];


Pssm-ID: 227508 [Multi-domain]  Cd Length: 975  Bit Score: 1207.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  300 MQTEDRTMKSVNDQPS-GNLPFLKPDDIQYFDKLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAR 378
Cdd:COG5181    118 MCLPARGYKALTDFHGyADLGFFKVEDLKYFADDEKDFFMPLLEDREGDERDVYRLLLKVKNGGKRMRMEGLRILTDKAV 197

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  379 EFGAGPLFNQILPLLMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAA 458
Cdd:COG5181    198 NFGAAAVFNKVLPMLMSRELEDQERHLVVKLIDRLLYGLDDLKVPYVHKILVVVGPLLIDEDLKRRCMGREIILNLVYRC 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  459 GLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLR 538
Cdd:COG5181    278 GLGFSVSSMRPDITSKDEYVRNVTGRAVGVVADALGVEELLPFLEALCGSRKSWEARHTGIRIAQQICELLGRSRLSHLG 357

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  539 SLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANY 618
Cdd:COG5181    358 PLLKCISKLLKDRSRFVRIDTANALSYLAELVGPYGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACH 437

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  619 YTREVMLILIREFQSPDEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVELANKV 698
Cdd:COG5181    438 DTREHMEIVFREFKSPDEEMKKDLLVVERICDKVGTDTPWKLRDQVSPEFFSPFWRRRSAGDRRSYKQVVLTTVILAKMG 517

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  699 GAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKR 778
Cdd:COG5181    518 GDPRVSRKILEYYSDEPEPYRKMNAGLVSRIFSRLGRLGFDERLEERLYDSILNAFQEQDTTVGLILPCFSTVLVSLEFR 597

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  779 VKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVI 858
Cdd:COG5181    598 GKPHLSMIVSTILKLLRSKPPDVRIRAADLMGSLAKVLKACGETKELAKLGNILYENLGEDYPEVLGSILKAICSIYSVH 677

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  859 GMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYI 938
Cdd:COG5181    678 RFRSMQPPISGILPSLTPILRNKHQKVVANTIALVGTICMNSPEYIGVREWMRICFELVDSLKSWNKEIRRNATETFGCI 757

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  939 AKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKD 1018
Cdd:COG5181    758 SRAIGPQDVLDILLNNLKVQERQQRVCTSVAISIVAEYCGPFSVLPTLMSDYETPEANVQNGVLKAMCFMFEYIGQASLD 837

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1019 YIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPC 1098
Cdd:COG5181    838 YVYSITPLLEDALTDRDPVHRQTAMNVIRHLVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEGMESFATVLGSG 917

                          810       820       830       840       850       860
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1099 RMLQYCLQGLFHPARKVRDVYWKIYNSIYIGSQDALIAHYPrIYNDDKNTYIRyELDYIL 1158
Cdd:COG5181    918 AMMKYVQQGLFHPSSTVRKRYWTVYNIMYVFDSDAMVPCYP-VEEDLNPELAR-TLHICI 975
SF3b1 pfam08920
Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B ...
 186-296 7.46e-67

Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly.


Pssm-ID: 462634 [Multi-domain]  Cd Length: 114  Bit Score: 220.32  E-value: 7.46e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  186 SKRKSRWDETPASQM---GGSTPVLTPGK-TPIGtpAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAM 261
Cdd:pfam08920    1 SKRRSRWDETPANAGsgpGGATPGETPGRqTPVG--AMGMATPTPGALGPMTPEQMQAFRWEKEIDERNRPLTDEELDAM 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907070772  262 FP-EGYKVLPPPAGYVPIRTPARKLTATPTPLGGMT 296
Cdd:pfam08920   79 LPgEGYKILDPPAGYVPIRTPARKLLATPTPMGGTG 114
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 95-236 1.50e-11

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 62.54  E-value: 1.50e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772    95 GSETPGatpgskiWDPTPSHTPA-GAATPGRGDTPGHATPGHGGATssarknrwdetpkterdTPGHGSGWAETPRTDRG 173
Cdd:smart01104    1 GGRTPA-------WGASGSKTPAwGSRTPGTAAGGAPTARGGSGSR-----------------TPAWGGAGSRTPAWGGA 56

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907070772   174 GDSIGETPTPGAS---KRKSRWDET--PASQMGGSTPVLTPGKTPIGTPamnMATPTPGHIMSMTPEQ 236
Cdd:smart01104   57 GPTGSRTPAWGGAsawGNKSSEGSAssWAAGPGGAYGAPTPGYGGTPSA---YGPATPGGGAMAGSAS 121
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 30-226 3.20e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.79  E-value: 3.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   30 AKAGELKVVNGAAASQPPSKRKRRWDQTADQTPGATPKK-------LSSWDQAETPGhtPSLRWDETPGRAKGSETPGAT 102
Cdd:PHA03307   188 SPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRsaaddagASSSDSSSSES--SGCGWGPENECPLPRPAPITL 265

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  103 PGSkIW--------DPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRW------DETPKTERD------------ 156
Cdd:PHA03307   266 PTR-IWeasgwngpSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSssssreSSSSSTSSSsessrgaavspg 344

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  157 -------TPGHGSGWAETPRTDRGGDSIGETPTPGASK-----RKSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATP 224
Cdd:PHA03307   345 pspsrspSPSRPPPPADPSSPRKRPRPSRAPSSPAASAgrptrRRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASG 424


                   ..
gi 1907070772  225 TP 226
Cdd:PHA03307   425 AF 426
HEAT_EZ pfam13513
HEAT-like repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats ...
 841-896 1.22e-03

HEAT-like repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). These EZ repeats are found in subunits of cyanobacterial phycocyanin lyase and other proteins and probably carry out a scaffolding role.


Pssm-ID: 463906 [Multi-domain]  Cd Length: 55  Bit Score: 38.12  E-value: 1.22e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907070772  841 PEVLGSILGALKAIVNViGMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRI 896
Cdd:pfam13513    1 WRVREAAALALGSLAEG-GPDLLAPAVPELLPALLPLLNDDSDLVREAAAWALGRL 55
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 87-291 1.35e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.05  E-value: 1.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   87 DETPGRAKGSETP---GATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTERDTPGHGSG 163
Cdd:PRK07764   589 GPAPGAAGGEGPPapaSSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  164 WAEtprtdRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATPTPGhimsmtpeqlqAWRWE 243
Cdd:PRK07764   669 WPA-----KAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQG-----------ASAPS 732

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1907070772  244 REIDERNRPLSDEELDAMFPEGYKVLPPPAGYVPIRTPARKLTATPTP 291
Cdd:PRK07764   733 PAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS 780
 
Name Accession Description Interval E-value
HSH155 COG5181
U2 snRNP spliceosome subunit [RNA processing and modification];
300-1158 0e+00

U2 snRNP spliceosome subunit [RNA processing and modification];


Pssm-ID: 227508 [Multi-domain]  Cd Length: 975  Bit Score: 1207.09  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  300 MQTEDRTMKSVNDQPS-GNLPFLKPDDIQYFDKLLVDVDESTLSPEEQKERKIMKLLLKIKNGTPPMRKAALRQITDKAR 378
Cdd:COG5181    118 MCLPARGYKALTDFHGyADLGFFKVEDLKYFADDEKDFFMPLLEDREGDERDVYRLLLKVKNGGKRMRMEGLRILTDKAV 197

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  379 EFGAGPLFNQILPLLMSPTLEDQERHLLVKVIDRILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAA 458
Cdd:COG5181    198 NFGAAAVFNKVLPMLMSRELEDQERHLVVKLIDRLLYGLDDLKVPYVHKILVVVGPLLIDEDLKRRCMGREIILNLVYRC 277

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  459 GLATMISTMRPDIDNMDEYVRNTTARAFAVVASALGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCAILPHLR 538
Cdd:COG5181    278 GLGFSVSSMRPDITSKDEYVRNVTGRAVGVVADALGVEELLPFLEALCGSRKSWEARHTGIRIAQQICELLGRSRLSHLG 357

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  539 SLVEIIEHGLVDEQQKVRTISALAIAALAEAATPYGIESFDSVLKPLWKGIRQHRGKGLAAFLKAIGYLIPLMDAEYANY 618
Cdd:COG5181    358 PLLKCISKLLKDRSRFVRIDTANALSYLAELVGPYGIEQFDEVLCPLWEGASQHRGKELVSFLKAMGFIIPLMSPEYACH 437

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  619 YTREVMLILIREFQSPDEEMKKIVLKVVKQCCGTDGVEANYIKTEILPPFFKHFWQHRMALDRRNYRQLVDTTVELANKV 698
Cdd:COG5181    438 DTREHMEIVFREFKSPDEEMKKDLLVVERICDKVGTDTPWKLRDQVSPEFFSPFWRRRSAGDRRSYKQVVLTTVILAKMG 517

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  699 GAAEIISRIVDDLKDEAEQYRKMVMETIEKIMGNLGAADIDHKLEEQLIDGILYAFQEQTTEDSVMLNGFGTVVNALGKR 778
Cdd:COG5181    518 GDPRVSRKILEYYSDEPEPYRKMNAGLVSRIFSRLGRLGFDERLEERLYDSILNAFQEQDTTVGLILPCFSTVLVSLEFR 597

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  779 VKPYLPQICGTVLWRLNNKSAKVRQQAADLISRTAVVMKTCQEEKLMGHLGVVLYEYLGEEYPEVLGSILGALKAIVNVI 858
Cdd:COG5181    598 GKPHLSMIVSTILKLLRSKPPDVRIRAADLMGSLAKVLKACGETKELAKLGNILYENLGEDYPEVLGSILKAICSIYSVH 677

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  859 GMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRIADRGAEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYI 938
Cdd:COG5181    678 RFRSMQPPISGILPSLTPILRNKHQKVVANTIALVGTICMNSPEYIGVREWMRICFELVDSLKSWNKEIRRNATETFGCI 757

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  939 AKAIGPHDVLATLLNNLKVQERQNRVCTTVAIAIVAETCSPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYIGEMGKD 1018
Cdd:COG5181    758 SRAIGPQDVLDILLNNLKVQERQQRVCTSVAISIVAEYCGPFSVLPTLMSDYETPEANVQNGVLKAMCFMFEYIGQASLD 837

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1019 YIYAVTPLLEDALMDRDLVHRQTASAVVQHMSLGVYGFGCEDSLNHLLNYVWPNVFETSPHVIQAVMGALEGLRVAIGPC 1098
Cdd:COG5181    838 YVYSITPLLEDALTDRDPVHRQTAMNVIRHLVLNCPGTGDEDAAIHLLNLLWPNILEPSPHVIQSFDEGMESFATVLGSG 917

                          810       820       830       840       850       860
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772 1099 RMLQYCLQGLFHPARKVRDVYWKIYNSIYIGSQDALIAHYPrIYNDDKNTYIRyELDYIL 1158
Cdd:COG5181    918 AMMKYVQQGLFHPSSTVRKRYWTVYNIMYVFDSDAMVPCYP-VEEDLNPELAR-TLHICI 975
SF3b1 pfam08920
Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B ...
 186-296 7.46e-67

Splicing factor 3B subunit 1; This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly.


Pssm-ID: 462634 [Multi-domain]  Cd Length: 114  Bit Score: 220.32  E-value: 7.46e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  186 SKRKSRWDETPASQM---GGSTPVLTPGK-TPIGtpAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDAM 261
Cdd:pfam08920    1 SKRRSRWDETPANAGsgpGGATPGETPGRqTPVG--AMGMATPTPGALGPMTPEQMQAFRWEKEIDERNRPLTDEELDAM 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907070772  262 FP-EGYKVLPPPAGYVPIRTPARKLTATPTPLGGMT 296
Cdd:pfam08920   79 LPgEGYKILDPPAGYVPIRTPARKLLATPTPMGGTG 114
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 95-236 1.50e-11

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 62.54  E-value: 1.50e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772    95 GSETPGatpgskiWDPTPSHTPA-GAATPGRGDTPGHATPGHGGATssarknrwdetpkterdTPGHGSGWAETPRTDRG 173
Cdd:smart01104    1 GGRTPA-------WGASGSKTPAwGSRTPGTAAGGAPTARGGSGSR-----------------TPAWGGAGSRTPAWGGA 56

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907070772   174 GDSIGETPTPGAS---KRKSRWDET--PASQMGGSTPVLTPGKTPIGTPamnMATPTPGHIMSMTPEQ 236
Cdd:smart01104   57 GPTGSRTPAWGGAsawGNKSSEGSAssWAAGPGGAYGAPTPGYGGTPSA---YGPATPGGGAMAGSAS 121
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 60-185 3.16e-07

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 50.21  E-value: 3.16e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772    60 QTP--GATPKKLSSWdqaetPGHTPSLRWDETPGRAKGSetpgatpGSKiwdpTPSHTPAGAATPGRGDTPGH--ATPGH 135
Cdd:smart01104    3 RTPawGASGSKTPAW-----GSRTPGTAAGGAPTARGGS-------GSR----TPAWGGAGSRTPAWGGAGPTgsRTPAW 66

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|
gi 1907070772   136 GGATSSARKNRWDeTPKTERDTPGHGSGwAETPrtdrGGDSIGETPTPGA 185
Cdd:smart01104   67 GGASAWGNKSSEG-SASSWAAGPGGAYG-APTP----GYGGTPSAYGPAT 110
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 30-226 3.20e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.79  E-value: 3.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   30 AKAGELKVVNGAAASQPPSKRKRRWDQTADQTPGATPKK-------LSSWDQAETPGhtPSLRWDETPGRAKGSETPGAT 102
Cdd:PHA03307   188 SPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRsaaddagASSSDSSSSES--SGCGWGPENECPLPRPAPITL 265

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  103 PGSkIW--------DPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRW------DETPKTERD------------ 156
Cdd:PHA03307   266 PTR-IWeasgwngpSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSssssreSSSSSTSSSsessrgaavspg 344

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  157 -------TPGHGSGWAETPRTDRGGDSIGETPTPGASK-----RKSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATP 224
Cdd:PHA03307   345 pspsrspSPSRPPPPADPSSPRKRPRPSRAPSSPAASAgrptrRRARAAVAGRARRRDATGRFPAGRPRPSPLDAGAASG 424


                   ..
gi 1907070772  225 TP 226
Cdd:PHA03307   425 AF 426
PHA03247 PHA03247
large tegument protein UL36; Provisional
 40-297 2.18e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.17  E-value: 2.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   40 GAAASQPPSKRKRRWDQTADQTPGATPKKlsSWDQAETPGH-TPSLRWDETPGRA---------KGSETPGATPGSkiwD 109
Cdd:PHA03247  2476 GAPVYRRPAEARFPFAAGAAPDPGGGGPP--DPDAPPAPSRlAPAILPDEPVGEPvhprmltwiRGLEELASDDAG---D 2550

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  110 PTPSHTPAG-AATPGRGDTPGHATPGHGGATSSARKNRWDETPKTERdtpghgsgwAETPRTDRGgDSIGETPTPGASKR 188
Cdd:PHA03247  2551 PPPPLPPAApPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSAR---------PRAPVDDRG-DPRGPAPPSPLPPD 2620

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  189 KSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATPTPGHImSMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKV 268
Cdd:PHA03247  2621 THAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRV-SRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLA 2699

                          250       260
                   ....*....|....*....|....*....
gi 1907070772  269 LPPPAGYVPIRTPARKLTATPTPLGGMTG 297
Cdd:PHA03247  2700 DPPPPPPTPEPAPHALVSATPLPPGPAAA 2728
dnaA PRK14086
chromosomal replication initiator protein DnaA;
45-210 9.46e-05

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 46.74  E-value: 9.46e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   45 QPPSKRKRRWDQtADQTPGATPKKLSSWDQAEtPGHTPSLRWDETPGRAKGSETPGATPGSKIWDPTPSHTPAGAATPGR 124
Cdd:PRK14086   124 PRADDRPPGLPR-QDQLPTARPAYPAYQQRPE-PGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGR 201

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  125 GDTPGHATPGHGGATSSARKNRWDetpkTERDTPGHGSGWAEtprtdRGGDSIGETPTPGASKRKSRWDETPASQmggST 204
Cdd:PRK14086   202 PEYDQRRRDYDHPRPDWDRPRRDR----TDRPEPPPGAGHVH-----RGGPGPPERDDAPVVPIRPSAPGPLAAQ---PA 269


                   ....*.
gi 1907070772  205 PVLTPG 210
Cdd:PRK14086   270 PAPGPG 275
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 91-205 3.32e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 44.67  E-value: 3.32e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   91 GRAKGSETPGATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGG-ATSSARKNRWDETPKterdTPGHGSGWAetpr 169
Cdd:PRK14959   379 SAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSSAAPATPApSAAPSPRVPWDDAPP----APPRSGIPP---- 450

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1907070772  170 tdRGGDSIGET-PTPGASKRKSRWDETPASQMGGSTP 205
Cdd:PRK14959   451 --RPAPRMPEAsPVPGAPDSVASASDAPPTLGDPSDT 485
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 42-260 9.05e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.44  E-value: 9.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   42 AASQPPSKRKRRWDQTADQTPGATPKklsswdqAETPGHTPSLRWDETPGRAKGSETPGATPGSKIWDPTPSHTPAGAAT 121
Cdd:PRK07764   616 AAPAAPAAPAAPAPAGAAAAPAEASA-------APAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPA 688

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  122 PGRGDTPGHATPGHGGATSSARKNRWDETPkterdTPGHGSGWAETPRTDRGGDSIGETPTPGAskrksrwDETPASQMG 201
Cdd:PRK07764   689 APAAPAGAAPAQPAPAPAATPPAGQADDPA-----AQPPQAAQGASAPSPAADDPVPLPPEPDD-------PPDPAGAPA 756

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907070772  202 GSTPVLTPGKTPIGTPAMNMATPTPGHIMSMTPEQLQAWRWEREIDERNRPLSDEELDA 260
Cdd:PRK07764   757 QPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAEEVAMELLEEELGA 815
HEAT_EZ pfam13513
HEAT-like repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats ...
 841-896 1.22e-03

HEAT-like repeat; The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). These EZ repeats are found in subunits of cyanobacterial phycocyanin lyase and other proteins and probably carry out a scaffolding role.


Pssm-ID: 463906 [Multi-domain]  Cd Length: 55  Bit Score: 38.12  E-value: 1.22e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907070772  841 PEVLGSILGALKAIVNViGMHKMTPPIKDLLPRLTPILKNRHEKVQENCIDLVGRI 896
Cdd:pfam13513    1 WRVREAAALALGSLAEG-GPDLLAPAVPELLPALLPLLNDDSDLVREAAAWALGRL 55
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 87-291 1.35e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.05  E-value: 1.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772   87 DETPGRAKGSETP---GATPGSKIWDPTPSHTPAGAATPGRGDTPGHATPGHGGATSSARKNRWDETPKTERDTPGHGSG 163
Cdd:PRK07764   589 GPAPGAAGGEGPPapaSSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907070772  164 WAEtprtdRGGDSIGETPTPGASKRKSRWDETPASQMGGSTPVLTPGKTPIGTPAMNMATPTPGhimsmtpeqlqAWRWE 243
Cdd:PRK07764   669 WPA-----KAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQG-----------ASAPS 732

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1907070772  244 REIDERNRPLSDEELDAMFPEGYKVLPPPAGYVPIRTPARKLTATPTP 291
Cdd:PRK07764   733 PAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS 780
 
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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