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Conserved domains on  [gi|1864461801|ref|XP_035140417|]
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protein capicua homolog isoform X3 [Callithrix jacchus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 1110-1187 2.24e-59

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


:

Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 198.45  E-value: 2.24e-59
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK 1187
Cdd:cd21990      1 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKAHPDWKWCSKDRKK 78
DUF4819 pfam16090
Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. ...
 254-350 1.04e-23

Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 82 and 99 amino acids in length.


:

Pssm-ID: 465014  Cd Length: 84  Bit Score: 96.98  E-value: 1.04e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  254 DVVLDATPPPGALVVGTAVCTCV----EPGVAAYREGVVVEVATKPAAYKVRLSPgpssqpgppgslpqppqplHREPEE 329
Cdd:pfam16090    1 DVILDASPSLSDVAVGTRVCVRLdpglEGGENVYREGVVVEVNNKPVRYVVKVSG-------------------GDEAKG 61

                           90       100
                   ....*....|....*....|.
gi 1864461801  330 AVWVARSSLRLLRPPWEPEAL 350
Cdd:pfam16090   62 GVWVKRADLRLLRPPWWDELE 82
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1767-2188 1.78e-12

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 73.82  E-value: 1.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1767 SGPAPTTSIRFTLPPGTSTNGKVLAATaptPGIPILQSVPSAPPPKAQSVSPvqaPPPGGSaqllpgkvlvplatPSMSV 1846
Cdd:PHA03247  2578 SEPAVTSRARRPDAPPQSARPRAPVDD---RGDPRGPAPPSPLPPDTHAPDP---PPPSPS--------------PAANE 2637

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1847 RGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLT--PVPVSTPSGLVPPLSPATL-----------PGPTSQPQKVLLPS 1913
Cdd:PHA03247  2638 PDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGraAQASSPPQRPRRRAARPTVgsltsladpppPPPTPEPAPHALVS 2717

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1914 STRITYVQSAGGH---ALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLLSAGQA---PLLAPGQVGVSP 1987
Cdd:PHA03247  2718 ATPLPPGPAAARQaspALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRltrPAVASLSESRES 2797

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1988 VPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATSTTPPAATILPKGPTAPATATPAPTSPFPS 2067
Cdd:PHA03247  2798 LPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAA 2877

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2068 ATGSMTYSLVAPKAQR-------PSPKAPQKVKAAIASIPVGSFEAGASGRPGPAPR---QPLEPGPVREPTAPESELEG 2137
Cdd:PHA03247  2878 PARPPVRRLARPAVSRstesfalPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPpppRPQPPLAPTTDPAGAGEPSG 2957

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 2138 QPTPPAPPPPPETWTPMARSSPPPPLPAEErTSAKGPETMASKFPSSSSDW 2188
Cdd:PHA03247  2958 AVPQPWLGALVPGRVAVPRFRVPQPAPSRE-APASSTPPLTGHSLSRVSSW 3007
dnaA super family cl42516
chromosomal replication initiator protein DnaA;
873-1049 7.48e-04

chromosomal replication initiator protein DnaA;


The actual alignment was detected with superfamily member PRK14086:

Pssm-ID: 455861 [Multi-domain]  Cd Length: 617  Bit Score: 44.82  E-value: 7.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  873 VPPAAPTAVAQPMPTFGLASSPFQPVAFHPSPAALLPVLVPSSY----TSHPAPKKEVIMGRPGTvWtnvePRSVAVFPW 948
Cdd:PRK14086    93 GEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQdqlpTARPAYPAYQQRPEPGA-W----PRAADDYGW 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  949 HSlvPFLAPSQPDPSVQPSEAQQPASH---PVASNQSKEPAESAAVAHERP----PGGTGSADPGRPPGA-----TCPES 1016
Cdd:PRK14086   168 QQ--QRLGFPPRAPYASPASYAPEQERdrePYDAGRPEYDQRRRDYDHPRPdwdrPRRDRTDRPEPPPGAghvhrGGPGP 245

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1864461801 1017 PGPGPPHPLGVVEPGKGLPPTTEEEAPGPPGES 1049
Cdd:PRK14086   246 PERDDAPVVPIRPSAPGPLAAQPAPAPGPGEPT 278
DUF5585 super family cl39316
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1506-1875 1.89e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


The actual alignment was detected with superfamily member pfam17823:

Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 43.41  E-value: 1.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1506 TDPATfRRKRPESVGGLEPAGPSviAAPPSGGGSILQTLVLPPNKEEQEGGGARVPSAPTPSlaygAPAAPLSRPAATMV 1585
Cdd:pfam17823   98 SEPAT-REGAADGAASRALAAAA--SSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANASA----APRAAIAAASAPHA 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1586 TnvvrpvSSTPVPIASKPFPTSGRAEASPNDTAGARTEMGTGSRVPGGSPLGVSLVYSDKKSATATSPAphlvAGPLLGT 1665
Cdd:pfam17823  171 A------SPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPARGISTAATATGHPAAGTALAAVGN----SSPAAGT 240

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1666 VGKAPATVTNLLVGTpgygapVPPAVQFIAQGAPGGGTSAGSGAGAGSGPNGPVPLGILQPGALSKA---GGITQVQYIL 1742
Cdd:pfam17823  241 VTAAVGTVTPAALAT------LAAAAGTVASAAGTINMGDPHARRLSPAKHMPSDTMARNPAAPMGAqaqGPIIQVSTDQ 314

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1743 PTMpqqlqvapapapapGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTPGIPILQSVPSAPP---PKAQSVSPV 1819
Cdd:pfam17823  315 PVH--------------NTAGEPTPSPSNTTLEPNTPKSVASTNLAVVTTTKAQAKEPSASPVPVLHTsmiPEVEATSPT 380

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1820 QAPPPGGSAQLL--PGKVLVPLATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSK 1875
Cdd:pfam17823  381 TQPSPLLPTQGAagPGILLAPEQVATEATAGTASAGPTPRSSGDPKTLAMASCQLSTQ 438
 
Name Accession Description Interval E-value
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 1110-1187 2.24e-59

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 198.45  E-value: 2.24e-59
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK 1187
Cdd:cd21990      1 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKAHPDWKWCSKDRKK 78
DUF4819 pfam16090
Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. ...
 254-350 1.04e-23

Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 82 and 99 amino acids in length.


Pssm-ID: 465014  Cd Length: 84  Bit Score: 96.98  E-value: 1.04e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  254 DVVLDATPPPGALVVGTAVCTCV----EPGVAAYREGVVVEVATKPAAYKVRLSPgpssqpgppgslpqppqplHREPEE 329
Cdd:pfam16090    1 DVILDASPSLSDVAVGTRVCVRLdpglEGGENVYREGVVVEVNNKPVRYVVKVSG-------------------GDEAKG 61

                           90       100
                   ....*....|....*....|.
gi 1864461801  330 AVWVARSSLRLLRPPWEPEAL 350
Cdd:pfam16090   62 GVWVKRADLRLLRPPWWDELE 82
HMG smart00398
high mobility group;
1110-1179 9.64e-19

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 82.36  E-value: 9.64e-19
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG_box pfam00505
HMG (high mobility group) box;
1111-1178 3.57e-17

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 77.65  E-value: 3.57e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDW 1178
Cdd:pfam00505    1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1767-2188 1.78e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 73.82  E-value: 1.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1767 SGPAPTTSIRFTLPPGTSTNGKVLAATaptPGIPILQSVPSAPPPKAQSVSPvqaPPPGGSaqllpgkvlvplatPSMSV 1846
Cdd:PHA03247  2578 SEPAVTSRARRPDAPPQSARPRAPVDD---RGDPRGPAPPSPLPPDTHAPDP---PPPSPS--------------PAANE 2637

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1847 RGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLT--PVPVSTPSGLVPPLSPATL-----------PGPTSQPQKVLLPS 1913
Cdd:PHA03247  2638 PDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGraAQASSPPQRPRRRAARPTVgsltsladpppPPPTPEPAPHALVS 2717

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1914 STRITYVQSAGGH---ALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLLSAGQA---PLLAPGQVGVSP 1987
Cdd:PHA03247  2718 ATPLPPGPAAARQaspALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRltrPAVASLSESRES 2797

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1988 VPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATSTTPPAATILPKGPTAPATATPAPTSPFPS 2067
Cdd:PHA03247  2798 LPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAA 2877

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2068 ATGSMTYSLVAPKAQR-------PSPKAPQKVKAAIASIPVGSFEAGASGRPGPAPR---QPLEPGPVREPTAPESELEG 2137
Cdd:PHA03247  2878 PARPPVRRLARPAVSRstesfalPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPpppRPQPPLAPTTDPAGAGEPSG 2957

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 2138 QPTPPAPPPPPETWTPMARSSPPPPLPAEErTSAKGPETMASKFPSSSSDW 2188
Cdd:PHA03247  2958 AVPQPWLGALVPGRVAVPRFRVPQPAPSRE-APASSTPPLTGHSLSRVSSW 3007
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1082-1226 1.43e-06

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 51.40  E-value: 1.43e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1082 TQSLSALPKERDSSSEKDGRSPnkrekdhiRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYH 1161
Cdd:COG5648     50 TKPRKKTKSKRLVRKKKDPNGP--------KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYY 121

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1162 DLAFQVKEAHFKA-HPDwkwcnkDRKKSSSEAKPTSLGLAGGHKETRERSMSETG----TAAAPGVSSEL 1226
Cdd:COG5648    122 KEANSDRERYQREkEEY------NKKLPNKAPIGPFIENEPKIRPKVEGPSPDKAlveeTKIISKAWSEL 185
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1094-1168 1.78e-06

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 48.31  E-value: 1.78e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1094 SSSEKDGRSPNKREKDHI--RRPMNAFMIFSKRHRALVHQRHPN--QDNRTVSKILGEWWYALGPKEKQKYHDLAFQVK 1168
Cdd:PTZ00199     4 KQGKVLVRKNKRKKKDPNapKRALSAYMFFAKEKRAEIIAENPElaKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK 82
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1840-2049 3.42e-05

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 48.98  E-value: 3.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1840 ATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVLLPSSTRITY 1919
Cdd:COG3469     14 GASATAVTLLGAAATAASVTLTAATATTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTS 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1920 VQSAGghALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLLSAGQAPLLAPGQVGVSPVPSPQLPSACAA 1999
Cdd:COG3469     94 ATLVA--TSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTT 171

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2000 PGGPVITAFYSGSPAPTSSAPLAQPSQAPPslvytvaTSTTPPAATILPK 2049
Cdd:COG3469    172 TTSASTTPSATTTATATTASGATTPSATTT-------ATTTGPPTPGLPK 214
dnaA PRK14086
chromosomal replication initiator protein DnaA;
873-1049 7.48e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.82  E-value: 7.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  873 VPPAAPTAVAQPMPTFGLASSPFQPVAFHPSPAALLPVLVPSSY----TSHPAPKKEVIMGRPGTvWtnvePRSVAVFPW 948
Cdd:PRK14086    93 GEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQdqlpTARPAYPAYQQRPEPGA-W----PRAADDYGW 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  949 HSlvPFLAPSQPDPSVQPSEAQQPASH---PVASNQSKEPAESAAVAHERP----PGGTGSADPGRPPGA-----TCPES 1016
Cdd:PRK14086   168 QQ--QRLGFPPRAPYASPASYAPEQERdrePYDAGRPEYDQRRRDYDHPRPdwdrPRRDRTDRPEPPPGAghvhrGGPGP 245

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1864461801 1017 PGPGPPHPLGVVEPGKGLPPTTEEEAPGPPGES 1049
Cdd:PRK14086   246 PERDDAPVVPIRPSAPGPLAAQPAPAPGPGEPT 278
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1506-1875 1.89e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 43.41  E-value: 1.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1506 TDPATfRRKRPESVGGLEPAGPSviAAPPSGGGSILQTLVLPPNKEEQEGGGARVPSAPTPSlaygAPAAPLSRPAATMV 1585
Cdd:pfam17823   98 SEPAT-REGAADGAASRALAAAA--SSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANASA----APRAAIAAASAPHA 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1586 TnvvrpvSSTPVPIASKPFPTSGRAEASPNDTAGARTEMGTGSRVPGGSPLGVSLVYSDKKSATATSPAphlvAGPLLGT 1665
Cdd:pfam17823  171 A------SPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPARGISTAATATGHPAAGTALAAVGN----SSPAAGT 240

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1666 VGKAPATVTNLLVGTpgygapVPPAVQFIAQGAPGGGTSAGSGAGAGSGPNGPVPLGILQPGALSKA---GGITQVQYIL 1742
Cdd:pfam17823  241 VTAAVGTVTPAALAT------LAAAAGTVASAAGTINMGDPHARRLSPAKHMPSDTMARNPAAPMGAqaqGPIIQVSTDQ 314

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1743 PTMpqqlqvapapapapGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTPGIPILQSVPSAPP---PKAQSVSPV 1819
Cdd:pfam17823  315 PVH--------------NTAGEPTPSPSNTTLEPNTPKSVASTNLAVVTTTKAQAKEPSASPVPVLHTsmiPEVEATSPT 380

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1820 QAPPPGGSAQLL--PGKVLVPLATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSK 1875
Cdd:pfam17823  381 TQPSPLLPTQGAagPGILLAPEQVATEATAGTASAGPTPRSSGDPKTLAMASCQLSTQ 438
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1791-2206 2.85e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.22  E-value: 2.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1791 AATAPTPGIPILQSVPSA-PPPKAQSVSPVQAPPPGgsaqlLPGKVLVPLATPSMSVRGGGAGQPLPLVSPpfSVPVQNG 1869
Cdd:pfam03154  180 AASPPSPPPPGTTQAATAgPTPSAPSVPPQGSPATS-----QPPNQTQSTAAPHTLIQQTPTLHPQRLPSP--HPPLQPM 252

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1870 AQP-PSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVllPSSTRITYVQSAGGHALPLGTSPASSQAGTVTSYGPT 1948
Cdd:pfam03154  253 TQPpPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPV--PPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPS 330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1949 SSvalgftSLGPSGPAFVQPLLSAGQA--PLLAPGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQ-PS 2025
Cdd:pfam03154  331 QS------QLQSQQPPREQPLPPAPLSmpHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSlST 404

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2026 QAPPSlvytvatsTTPPAATILPKGPTapatatpaptspfpsatgsmtysLVAPKAQRPSPKAPQKVKAAIASIPvgsfe 2105
Cdd:pfam03154  405 HHPPS--------AHPPPLQLMPQSQQ-----------------------LPPPPAQPPVLTQSQSLPPPAASHP----- 448

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2106 agasgrpgpaPRQPLEPGPVREPTAPESELEGQPTPPAPPPPPETWTPMARSSPPPPLPAEERTSAKGPETMASKFPSSS 2185
Cdd:pfam03154  449 ----------PTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQ 518

                          410       420
                   ....*....|....*....|.
gi 1864461801 2186 SDWRVPGQGLESRGEPPTPPS 2206
Cdd:pfam03154  519 IKEEALDEAEEPESPPPPPRS 539
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1483-1904 2.97e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 2.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1483 PLRPPPPGAAGPATPSKATRFLPT--------DPATFRRKRPESVGGLE--------PAGPSVIAAPPSGGGSILQTLVL 1546
Cdd:PHA03247  2623 APDPPPPSPSPAANEPDPHPPPTVppperprdDPAPGRVSRPRRARRLGraaqasspPQRPRRRAARPTVGSLTSLADPP 2702

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1547 PPNKEEQEGGGARVPSAPTPSlaygAPAAPLSRPAATMVTNVVRPVSSTPVpiaskpFPTSGRAEASPNDTAGARTEMGT 1626
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPLPP----GPAAARQASPALPAAPAPPAVPAGPA------TPGGPARPARPPTTAGPPAPAPP 2772

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1627 GSRVPGGSPLGVSLVYSDKKSATATSPAPHLVAGPLLGTVGKAPATVTNllvGTPGYGAPVPPAVQFIAQGAPGGGTSAG 1706
Cdd:PHA03247  2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPA---ASPAGPLPPPTSAQPTAPPPPPGPPPPS 2849

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1707 SGAGAGSGPNGPVplgilqpgalsKAGGITQVQYILPTMPQQLQVapapapapgtkaAAPSGPAPTTSIR-FTLPPgtst 1785
Cdd:PHA03247  2850 LPLGGSVAPGGDV-----------RRRPPSRSPAAKPAAPARPPV------------RRLARPAVSRSTEsFALPP---- 2902

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1786 ngkvlaATAPTPGIPILQSVPSAPPPKAQSVSPVQAPPPGGsaqlLPGKVLVPLATPSmsvrggGAGQPLPLVSPPFSVP 1865
Cdd:PHA03247  2903 ------DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPP----RPQPPLAPTTDPA------GAGEPSGAVPQPWLGA 2966

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1864461801 1866 VQNGAQPPSKIIQLTPVP-VSTPSGLVPPLSPATLPGPTS 1904
Cdd:PHA03247  2967 LVPGRVAVPRFRVPQPAPsREAPASSTPPLTGHSLSRVSS 3006
 
Name Accession Description Interval E-value
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 1110-1187 2.24e-59

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 198.45  E-value: 2.24e-59
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK 1187
Cdd:cd21990      1 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKAHPDWKWCSKDRKK 78
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 1112-1180 4.49e-34

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 125.98  E-value: 4.49e-34
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKW 1180
Cdd:cd21989      1 RRPMNAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLAKQYKEAFMKANPNFKW 69
DUF4819 pfam16090
Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. ...
 254-350 1.04e-23

Domain of unknown function (DUF4819); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 82 and 99 amino acids in length.


Pssm-ID: 465014  Cd Length: 84  Bit Score: 96.98  E-value: 1.04e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  254 DVVLDATPPPGALVVGTAVCTCV----EPGVAAYREGVVVEVATKPAAYKVRLSPgpssqpgppgslpqppqplHREPEE 329
Cdd:pfam16090    1 DVILDASPSLSDVAVGTRVCVRLdpglEGGENVYREGVVVEVNNKPVRYVVKVSG-------------------GDEAKG 61

                           90       100
                   ....*....|....*....|.
gi 1864461801  330 AVWVARSSLRLLRPPWEPEAL 350
Cdd:pfam16090   62 GVWVKRADLRLLRPPWWDELE 82
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 1110-1183 2.75e-22

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 92.61  E-value: 2.75e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNK 1183
Cdd:cd22004      1 HIKRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYKYRPR 74
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 1111-1179 1.42e-21

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 90.34  E-value: 1.42e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:cd01389      1 IPRPPNAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLKYPDYK 69
HMG-box_SoxH_SOX30 cd22033
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and ...
 1110-1181 7.40e-20

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins; SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438842 [Multi-domain]  Cd Length: 75  Bit Score: 85.55  E-value: 7.40e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWC 1181
Cdd:cd22033      1 HIKRPMNAFMVWARIHRPALAKANPNANNADISVQLGEEWNKLTEEQKKPYYDEAQKLKEQHRKEHPGWVYQ 72
HMG smart00398
high mobility group;
1110-1179 9.64e-19

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 82.36  E-value: 9.64e-19
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG-box_HBP1 cd21988
high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar ...
 1112-1179 1.96e-18

high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar proteins; HBP1, also called HMG box transcription factor 1, or high mobility group box transcription factor 1, is a transcriptional repressor that binds to the promoter region of target genes. It plays a role in the regulation of the cell cycle and the Wnt pathway. HBP1 binds preferentially to the sequence 5'-TTCATTCATTCA-3'.


Pssm-ID: 438804 [Multi-domain]  Cd Length: 69  Bit Score: 81.35  E-value: 1.96e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPD-WK 1179
Cdd:cd21988      1 KRPMNAFMLFAKKYRVEYTQMHPGKDNRAISVILGDRWKKMKNEERRVYTLEAKALAEEHKRLHPDcWK 69
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 1110-1187 2.16e-18

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types.


Pssm-ID: 438837 [Multi-domain]  Cd Length: 76  Bit Score: 81.63  E-value: 2.16e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKK 1187
Cdd:cd22028      1 RVKRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQHMKEHPDYKY--RPRRK 76
HMG_box pfam00505
HMG (high mobility group) box;
1111-1178 3.57e-17

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 77.65  E-value: 3.57e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDW 1178
Cdd:pfam00505    1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG-box_EGL13-like cd22042
high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 ...
 1110-1180 8.26e-17

high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 (EGL-13) and similar proteins; EGL-13 may act as a transcription factor that is required for uterine cell fate decisions in Caenorhabditis elegans. It controls genes required for the specification and differentiation of O(2) and CO(2)-sensing neurons and for maintaining URX sensory neuronal cell fate.


Pssm-ID: 438848 [Multi-domain]  Cd Length: 78  Bit Score: 77.25  E-value: 8.26e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKW 1180
Cdd:cd22042      2 HIKRPMNAFMVWAKDERRKILKACPDMHNSNISKILGAKWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRY 72
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1113-1171 2.77e-16

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 74.86  E-value: 2.77e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAH 1171
Cdd:cd00084      1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_SoxB cd01388
high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) ...
 1109-1190 1.21e-15

high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis.


Pssm-ID: 438790 [Multi-domain]  Cd Length: 80  Bit Score: 73.79  E-value: 1.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1109 DHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKKS 1188
Cdd:cd01388      1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSEAEKRPFIDEAKRLRALHMKEHPDYKY--RPRRKT 78


                   ..
gi 1864461801 1189 SS 1190
Cdd:cd01388     79 KT 80
HMG-box_SoxD cd22030
high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) ...
 1110-1187 4.26e-15

high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxD transcription factors includes three members, Sox5, Sox6, and Sox13. They function as important transcriptional regulators of glial development in the central nervous system. SoxD proteins influence multiple stages of oligodendrocyte development and modulate SoxE protein function. This subfamily also contains SoxD transcription factor homolog EGL-13, which specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans. SOX-5 plays important roles in various cancer types. It binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-6 plays a key role in cell proliferation, differentiation, and cell fate determination, as well as neurogenesis and skeleton formation. It is a tumor suppressor and downregulated in various cancers. SOX-6 binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-13, also called Islet cell antigen 12 (ICA12), or type 1 diabetes auto-antigen ICA12, modulates T cell specification and is an autoimmune antigen. It binds to the sequence 5'-AACAAT-3'.


Pssm-ID: 438839 [Multi-domain]  Cd Length: 77  Bit Score: 72.35  E-value: 4.26e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKK 1187
Cdd:cd22030      1 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKSMSNQEKQPYYEEQARLSKQHLEKYPDYKY--KPRPK 76
HMG-box_SoxE cd22031
high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) ...
 1110-1180 8.35e-15

high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxE transcription factors includes three members: Sox8, Sox9, and Sox10. They function as important transcriptional regulators of neural differentiation and nervous system development. They regulate mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. SOX-8 is specifically expressed by M cells in the intestinal epithelium. It acts as a transcription factor necessary for the maintenance of spermatogenesis. It may play a role in central nervous system, limb and facial development. SOX-9 is involved in cell differentiation, sex determination, and tumorigenesis. It plays a role in chondrocyte differentiation and skeletal development. SOX-10 plays a central role in the development of melanocytes and glial cells from neural crest precursors.


Pssm-ID: 438840 [Multi-domain]  Cd Length: 75  Bit Score: 71.27  E-value: 8.35e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKW 1180
Cdd:cd22031      1 HVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLSESEKRPFIEEAERLRVQHKKDHPDYKY 71
HMG-box_TCF7-like cd21996
high mobility group (HMG)-box found in the transcription factor 7 (TCF-7)-like family; The ...
 1110-1187 2.35e-14

high mobility group (HMG)-box found in the transcription factor 7 (TCF-7)-like family; The TCF7-like family includes TCF-7, TCF7-like 1 (TF7L1), lymphoid enhancer-binding factor 1 (LEF-1), and similar proteins. TCF-7, also called T-cell-specific transcription factor 1, or T-cell factor 1 (TCF-1), is a T lymphocyte-specific transcriptional activator involved in T-cell lymphocyte differentiation. It is necessary for the survival of CD4(+) CD8(+) immature thymocytes. It binds to the T-lymphocyte-specific enhancer element (5'-WWCAAAG-3') found in the promoter of the CD3E gene. TF7L1, also called HMG box transcription factor 3 (TCF-3), participates in the Wnt signaling pathway. It binds to DNA and acts as a repressor in the absence of CTNNB1, and as an activator in its presence. TF7L2, also called HMG box transcription factor 4, or T-cell-specific transcription factor 4, or T-cell factor 4, or TCF-4, participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner. It acts as a repressor in the absence of CTNNB1, and it activates transcription from promoters with several copies of the TCF motif 5'-CCTTTGATC-3' in the presence of CTNNB1. LEF-1, also called T cell-specific transcription factor 1-alpha (TCF1-alpha), is a transcription factor that binds DNA in a sequence-specific manner. It may participate in the Wnt signaling pathway. All family members contain one HMG-box domain.


Pssm-ID: 438812 [Multi-domain]  Cd Length: 85  Bit Score: 70.44  E-value: 2.35e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK-----WCNKD 1184
Cdd:cd21996      1 HIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSardnyGKKKK 80


                   ...
gi 1864461801 1185 RKK 1187
Cdd:cd21996     81 RKR 83
HMG-box_SoxF cd22032
high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) ...
 1110-1180 2.97e-14

high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxF transcription factors includes three members: Sox7, Sox17, and Sox18. They regulate endothelial cell fate as well as development and differentiation of the developing heart, blood cells, and lymphatic vessels.


Pssm-ID: 438841 [Multi-domain]  Cd Length: 76  Bit Score: 69.75  E-value: 2.97e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKW 1180
Cdd:cd22032      1 RIRRPMNAFMVWAKDERKRLADENPDLHNAELSKMLGKKWKSLSLAEKRPFVEEAERLRVQHMQDYPNYKY 71
HMG-box_SoxC cd22029
high mobility group (HMG)-box found in group C SRY-related high-mobility group (HMG) box (Sox) ...
 1110-1187 6.64e-14

high mobility group (HMG)-box found in group C SRY-related high-mobility group (HMG) box (Sox) transcription factors; SoxC transcription factors includes three members: SOX4, SOX11 and SOX12. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. SOX-4 is a transcriptional activator that promotes neuronal differentiation both in the adult and embryonic neural progenitors. It binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif. SOX-4 is abnormally expressed in various cancers. SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'.


Pssm-ID: 438838 [Multi-domain]  Cd Length: 76  Bit Score: 68.62  E-value: 6.64e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKK 1187
Cdd:cd22029      1 HIKRPMNAFMVWSQIERRKIMEQQPDMHNAEISKRLGKRWKLLSDSEKIPFIEEAERLRLLHMQEYPDYKY--RPRKK 76
HMG-box_SoxF_SOX7 cd22046
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar ...
 1101-1187 1.28e-13

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438849 [Multi-domain]  Cd Length: 88  Bit Score: 68.56  E-value: 1.28e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1101 RSP-NKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:cd22046      1 RSPgEKGSEPRIRRPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERLRVQHMQDYPNYK 80


                   ....*...
gi 1864461801 1180 WCNKDRKK 1187
Cdd:cd22046     81 YRPRRKKQ 88
HMG-box_SoxF_SOX18 cd22048
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and ...
 1111-1187 1.60e-13

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and similar proteins; SOX-18 is a transcription factor involved in the development of cardiovascular and lymphatic vessels during embryonic development. It binds to the consensus sequence 5'-AACAAAG-3' and is able to trans-activate transcription via this site. SOX-18 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438851 [Multi-domain]  Cd Length: 80  Bit Score: 67.79  E-value: 1.60e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK 1187
Cdd:cd22048      4 IRRPMNAFMVWAKDERKRLAQQNPDLHNAVLSKMLGQSWKSLSAAEKRPFVEEAERLRVQHLQDHPNYKYRPRRKKQ 80
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 1111-1180 1.11e-12

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438850 [Multi-domain]  Cd Length: 81  Bit Score: 65.49  E-value: 1.11e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKW 1180
Cdd:cd22047      7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKY 76
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1767-2188 1.78e-12

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 73.82  E-value: 1.78e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1767 SGPAPTTSIRFTLPPGTSTNGKVLAATaptPGIPILQSVPSAPPPKAQSVSPvqaPPPGGSaqllpgkvlvplatPSMSV 1846
Cdd:PHA03247  2578 SEPAVTSRARRPDAPPQSARPRAPVDD---RGDPRGPAPPSPLPPDTHAPDP---PPPSPS--------------PAANE 2637

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1847 RGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLT--PVPVSTPSGLVPPLSPATL-----------PGPTSQPQKVLLPS 1913
Cdd:PHA03247  2638 PDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGraAQASSPPQRPRRRAARPTVgsltsladpppPPPTPEPAPHALVS 2717

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1914 STRITYVQSAGGH---ALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLLSAGQA---PLLAPGQVGVSP 1987
Cdd:PHA03247  2718 ATPLPPGPAAARQaspALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRltrPAVASLSESRES 2797

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1988 VPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATSTTPPAATILPKGPTAPATATPAPTSPFPS 2067
Cdd:PHA03247  2798 LPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAA 2877

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2068 ATGSMTYSLVAPKAQR-------PSPKAPQKVKAAIASIPVGSFEAGASGRPGPAPR---QPLEPGPVREPTAPESELEG 2137
Cdd:PHA03247  2878 PARPPVRRLARPAVSRstesfalPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPpppRPQPPLAPTTDPAGAGEPSG 2957

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 2138 QPTPPAPPPPPETWTPMARSSPPPPLPAEErTSAKGPETMASKFPSSSSDW 2188
Cdd:PHA03247  2958 AVPQPWLGALVPGRVAVPRFRVPQPAPSRE-APASSTPPLTGHSLSRVSSW 3007
HMG-box_SoxG_SOX15 cd22035
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and ...
 1109-1188 2.32e-12

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and similar proteins; SOX-15, also called SOX-12, SOX-20, SOX-26, or SOX-27, is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. SOX-5 is the only member of group G SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438844 [Multi-domain]  Cd Length: 84  Bit Score: 64.72  E-value: 2.32e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1109 DHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKKS 1188
Cdd:cd22035      6 EKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMRDYPDYKY--RPRRKG 83
HMG-box_SoxC_SOX12 cd22038
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and ...
 1105-1188 1.01e-10

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and similar proteins; SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'. SOX-12 belongs to the group C of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438847 [Multi-domain]  Cd Length: 88  Bit Score: 60.08  E-value: 1.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1105 KREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKD 1184
Cdd:cd22038      6 KTPSGHIKRPMNAFMVWSQIERRKIMEQWPDMHNAEISKRLGRRWKLLQDYEKIPFIKEAERLRLKHMADYPDYKY--RP 83


                   ....
gi 1864461801 1185 RKKS 1188
Cdd:cd22038     84 RKKS 87
HMG-box_SoxA_SRY cd22034
high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar ...
 1108-1187 7.14e-10

high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar proteins; SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438843 [Multi-domain]  Cd Length: 85  Bit Score: 57.72  E-value: 7.14e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1108 KDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKDRKK 1187
Cdd:cd22034      2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 1098-1171 8.12e-10

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 57.38  E-value: 8.12e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1864461801 1098 KDGRSPNKREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAH 1171
Cdd:cd01390      1 KKKKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRY 74
HMG-box_SoxC_SOX4 cd22036
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 4 (SOX4) and similar ...
 1110-1187 1.48e-09

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 4 (SOX4) and similar proteins; SOX-4 is a transcriptional activator that promotes neuronal differentiation both in the adult and embryonic neural progenitors. It binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif. SOX-4 is abnormally expressed in various cancers. SOX-4 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438845 [Multi-domain]  Cd Length: 79  Bit Score: 56.68  E-value: 1.48e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1110 HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWcnKDRKK 1187
Cdd:cd22036      2 HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIREAERLRLKHMADYPDYKY--RPRKK 77
HMG-box_SoxC_SOX11 cd22037
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 11 (SOX11) and ...
 1105-1190 1.56e-09

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 11 (SOX11) and similar proteins; SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-11 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438846 [Multi-domain]  Cd Length: 92  Bit Score: 57.03  E-value: 1.56e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1105 KREKDHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWKWCNKD 1184
Cdd:cd22037      6 KTATGHIKRPMNAFMVWSKIERRKIMEQSPDMHNAEISKRLGKRWKMLKDSEKIPFIREAERLRLKHMADYPDYKYRPRK 85


                   ....*.
gi 1864461801 1185 RKKSSS 1190
Cdd:cd22037     86 KPKVDP 91
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1113-1179 1.38e-08

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 53.46  E-value: 1.38e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:cd21994      1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 1112-1169 1.81e-08

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 53.32  E-value: 1.81e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKE 1169
Cdd:cd21980      3 KAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKE 60
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1113-1162 7.25e-08

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 51.13  E-value: 7.25e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHD 1162
Cdd:cd22012      4 RPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQE 53
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1112-1173 1.46e-07

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 50.53  E-value: 1.46e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFK 1173
Cdd:cd22006      1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLK 62
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1103-1174 5.84e-07

third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 49.18  E-value: 5.84e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1103 PNKREKdhirrPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKA 1174
Cdd:cd22008      7 PNKPKK-----PASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKE 73
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1112-1173 5.86e-07

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 48.95  E-value: 5.86e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFK 1173
Cdd:cd21979      4 KRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEK 65
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1112-1178 1.31e-06

first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 47.92  E-value: 1.31e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDW 1178
Cdd:cd22010      2 KRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAEF 68
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1082-1226 1.43e-06

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 51.40  E-value: 1.43e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1082 TQSLSALPKERDSSSEKDGRSPnkrekdhiRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYH 1161
Cdd:COG5648     50 TKPRKKTKSKRLVRKKKDPNGP--------KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYY 121

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1162 DLAFQVKEAHFKA-HPDwkwcnkDRKKSSSEAKPTSLGLAGGHKETRERSMSETG----TAAAPGVSSEL 1226
Cdd:COG5648    122 KEANSDRERYQREkEEY------NKKLPNKAPIGPFIENEPKIRPKVEGPSPDKAlveeTKIISKAWSEL 185
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1094-1168 1.78e-06

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 48.31  E-value: 1.78e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1864461801 1094 SSSEKDGRSPNKREKDHI--RRPMNAFMIFSKRHRALVHQRHPN--QDNRTVSKILGEWWYALGPKEKQKYHDLAFQVK 1168
Cdd:PTZ00199     4 KQGKVLVRKNKRKKKDPNapKRALSAYMFFAKEKRAEIIAENPElaKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK 82
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1573-2043 4.06e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.63  E-value: 4.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1573 PAAPLSRPAATmvTNVVRPVSSTPVPIASKPFPTSGRAEASPNDTAGartemgtgsRVPGGSPlgvslvySDKKSATATS 1652
Cdd:PHA03247  2554 PLPPAAPPAAP--DRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARP---------RAPVDDR-------GDPRGPAPPS 2615

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1653 PAPHLVAGPLLGTVGKAPATvtNLLVGTPGYGAPVPPAVQFIAQGAPGGGTSAGSGAGAGSGPNGPvPLGILQPGALSKA 1732
Cdd:PHA03247  2616 PLPPDTHAPDPPPPSPSPAA--NEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-PQRPRRRAARPTV 2692

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1733 GGITQVQYILPTMPQQLQVAPAPAPAPGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTPGIPILQSVPSAPPPK 1812
Cdd:PHA03247  2693 GSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPP 2772

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1813 AqsvSPVQAPPPggsaqllpgkVLVPLATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLTPVPVSTPSGLVP 1892
Cdd:PHA03247  2773 A---APAAGPPR----------RLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1893 PLSPATLPGPTSQPQKVllpsstrityvqSAGGHALPLGTSPASSQAGTVTSYGPTSSVALgfTSLGPSGPAFVQPLLS- 1971
Cdd:PHA03247  2840 PPPPGPPPPSLPLGGSV------------APGGDVRRRPPSRSPAAKPAAPARPPVRRLAR--PAVSRSTESFALPPDQp 2905

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1972 ------AGQAPLLAPGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATSTTPPA 2043
Cdd:PHA03247  2906 erppqpQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPA 2983
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 1103-1178 8.51e-06

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 45.47  E-value: 8.51e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1864461801 1103 PNKRekdhiRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDW 1178
Cdd:pfam09011    1 PNKP-----KRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1112-1174 1.21e-05

second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 44.94  E-value: 1.21e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKA 1174
Cdd:cd22007      2 KRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQE 64
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1109-1169 1.24e-05

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 44.98  E-value: 1.24e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1109 DHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKE 1169
Cdd:cd22001      1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKA 61
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 1097-1169 1.94e-05

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins; NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex.


Pssm-ID: 438832 [Multi-domain]  Cd Length: 79  Bit Score: 45.02  E-value: 1.94e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1097 EKDGRSPnkrekdhiRRPMNAFMIFSKRHRALVHQR----HPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKE 1169
Cdd:cd22016      2 EKDPNAP--------KRPANAFFLFCQEQREKVREEykeeHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKE 70
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1791-2178 2.15e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.98  E-value: 2.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1791 AATAPTPGIPILQSVPSAPPPKAQSvsPVQAPPPGGSAqllPGKVLVPLATPSMSVRGGGAGQPLPLVSPPFSVPVQNGA 1870
Cdd:PRK07764   406 PAAAPAPAAAAPAAAAAPAPAAAPQ--PAPAPAPAPAP---PSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAP 480

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1871 QPPSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVL--LPSSTRIT------YVQSAG--GHALPLG-TSPAS--- 1936
Cdd:PRK07764   481 APAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILaaVPKRSRKTwaillpEATVLGvrGDTLVLGfSTGGLarr 560

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1937 -SQAGTVTSY------------GPTSSVALGFTSLGPSGPAFVQPLLSAGQAPllAPGQVGVSPVPSPQLPSACAAPGGP 2003
Cdd:PRK07764   561 fASPGNAEVLvtalaeelggdwQVEAVVGPAPGAAGGEGPPAPASSGPPEEAA--RPAAPAAPAAPAAPAPAGAAAAPAE 638

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2004 VITAFYSGSPAPTSSAPlAQPSQAPPSLVYTVATSTTPPAATILPKGPTAPATATPAPTSPFPSATGSMTyslVAPKAQR 2083
Cdd:PRK07764   639 ASAAPAPGVAAPEHHPK-HVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAA---TPPAGQA 714

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2084 PSPKAPQKVKAAIASIPVGSfeAGASGRPGPAPRQPLEPGPVREPTAPESELEGQPTPPAPPPPPETWTpmARSSPPPPL 2163
Cdd:PRK07764   715 DDPAAQPPQAAQGASAPSPA--ADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSE--EEEMAEDDA 790

                          410
                   ....*....|....*
gi 1864461801 2164 PAEERTSAKGPETMA 2178
Cdd:PRK07764   791 PSMDDEDRRDAEEVA 805
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1840-2049 3.42e-05

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 48.98  E-value: 3.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1840 ATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVLLPSSTRITY 1919
Cdd:COG3469     14 GASATAVTLLGAAATAASVTLTAATATTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTS 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1920 VQSAGghALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLLSAGQAPLLAPGQVGVSPVPSPQLPSACAA 1999
Cdd:COG3469     94 ATLVA--TSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTT 171

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2000 PGGPVITAFYSGSPAPTSSAPLAQPSQAPPslvytvaTSTTPPAATILPK 2049
Cdd:COG3469    172 TTSASTTPSATTTATATTASGATTPSATTT-------ATTTGPPTPGLPK 214
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 1111-1171 3.45e-05

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 44.07  E-value: 3.45e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAH 1171
Cdd:cd21985      2 IRKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAKDLERY 62
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 1113-1168 4.36e-05

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 43.07  E-value: 4.36e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVK 1168
Cdd:cd22005      2 RPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEK 57
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1112-1169 1.15e-04

first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438794 [Multi-domain]  Cd Length: 69  Bit Score: 42.29  E-value: 1.15e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQ--DNRTVSKILGEWWYALGPKEKQKYHDLAFQVKE 1169
Cdd:cd21978      3 RGKMSSYAFFVQTCREEHKKKHPNEsvNFSEFSKKCSERWKTMSAKEKKKFEDMAKKDKA 62
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1115-1171 3.12e-04

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 41.15  E-value: 3.12e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1115 MNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAH 1171
Cdd:cd21977      5 VNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRARELSQLH 61
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1879-2092 3.49e-04

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 45.90  E-value: 3.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1879 LTPVPVSTPSGLVPPLSPATLPGPTSQPQKVLLPSSTriTYVQSAGGHALPLGTSPASSQAGTVTSYGPTSSVALGFTSL 1958
Cdd:COG3469      2 SSVSTAASPTAGGASATAVTLLGAAATAASVTLTAAT--ATTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTT 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1959 GP---SGPAFVQPLLSAGQAPLLAPGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTV 2035
Cdd:COG3469     80 ATataAAAAATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSGTETA 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 2036 ATSTTPPAATILPKGPTAPATATPAPTSPFPSATGSMTYSLVAPKAQRPSPKAPQKV 2092
Cdd:COG3469    160 TGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLPKHV 216
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1781-2173 4.97e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 4.97e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1781 PGTSTNGKVLAATAPTPGIPILQSVPSAPPPKA---------QSVSPVQAPPPGGSAQLLPgkvlvPLATPSMSVRGGGA 1851
Cdd:PHA03247  2496 PDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPvhprmltwiRGLEELASDDAGDPPPPLP-----PAAPPAAPDRSVPP 2570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1852 GQPLPLVSPPfsvPVQNGAQPPSKIIQLT--PVPVSTPSGLVPPLSPATLPGPTSQPQKVllPSSTRITYVQSAGGHALP 1929
Cdd:PHA03247  2571 PRPAPRPSEP---AVTSRARRPDAPPQSArpRAPVDDRGDPRGPAPPSPLPPDTHAPDPP--PPSPSPAANEPDPHPPPT 2645

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1930 LGTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPafvqpllSAGQAPLLAPGQVGvsPVPSPQLPSACAAPGGPVITAFY 2009
Cdd:PHA03247  2646 VPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------PQRPRRRAARPTVG--SLTSLADPPPPPPTPEPAPHALV 2716

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2010 SGSPAPTSSAPLAQPSQAPPSLVYTVAtsttPPAATILPKGPTAPATATPAPTSPFPsatgsmtyslvAPKAQRPSPKAP 2089
Cdd:PHA03247  2717 SATPLPPGPAAARQASPALPAAPAPPA----VPAGPATPGGPARPARPPTTAGPPAP-----------APPAAPAAGPPR 2781

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2090 QKVKAAIASIPVGSFEAGASGRPGPAPRQPLEPGPVREPTAPESELEGQPTPPAPPpppetwtpmarSSPPPPLPAEERT 2169
Cdd:PHA03247  2782 RLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPT-----------APPPPPGPPPPSL 2850


                   ....
gi 1864461801 2170 SAKG 2173
Cdd:PHA03247  2851 PLGG 2854
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 1113-1162 5.21e-04

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 40.74  E-value: 5.21e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHD 1162
Cdd:cd21983      7 KPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIE 56
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1112-1169 6.06e-04

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 39.92  E-value: 6.06e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKE 1169
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQAE 58
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 1767-2171 7.45e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 7.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1767 SGPAPTtsirftlppgtstngkvlAATAPTPGIPILQSVPSAPPPKAQsvSPVQAPPPGGSAqllPGKVLVPLATPSMSV 1846
Cdd:PRK07764   400 SAAAAA------------------PAAAPAPAAAAPAAAAAPAPAAAP--QPAPAPAPAPAP---PSPAGNAPAGGAPSP 456

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1847 RGGGAGQPLPLVSPPFSVPVQNGAQPPSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVL--LPSSTRIT------ 1918
Cdd:PRK07764   457 PPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRERWPEILaaVPKRSRKTwaillp 536

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1919 YVQSAG--GHALPLG-TSPAS----SQAGTVTSY------------GPTSSVALGFTSLGPSGPAFVQPLLSAGQAPllA 1979
Cdd:PRK07764   537 EATVLGvrGDTLVLGfSTGGLarrfASPGNAEVLvtalaeelggdwQVEAVVGPAPGAAGGEGPPAPASSGPPEEAA--R 614

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1980 PGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPlAQPSQAPPSLVYTVATSTTPPAATILPKGPTAPATATP 2059
Cdd:PRK07764   615 PAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPK-HVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAP 693

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2060 APTSPFPSATGSMTyslVAPKAQRPSPKAPQKVKAAIASIPVGSFEAGASGRPGPAPRQPLEPGPVREPTAPESELEGQP 2139
Cdd:PRK07764   694 AGAAPAQPAPAPAA---TPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAP 770

                          410       420       430
                   ....*....|....*....|....*....|..
gi 1864461801 2140 TPPAPPPPPETWTPMARSSPPPPLPAEERTSA 2171
Cdd:PRK07764   771 AAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802
dnaA PRK14086
chromosomal replication initiator protein DnaA;
873-1049 7.48e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.82  E-value: 7.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  873 VPPAAPTAVAQPMPTFGLASSPFQPVAFHPSPAALLPVLVPSSY----TSHPAPKKEVIMGRPGTvWtnvePRSVAVFPW 948
Cdd:PRK14086    93 GEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQdqlpTARPAYPAYQQRPEPGA-W----PRAADDYGW 167

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  949 HSlvPFLAPSQPDPSVQPSEAQQPASH---PVASNQSKEPAESAAVAHERP----PGGTGSADPGRPPGA-----TCPES 1016
Cdd:PRK14086   168 QQ--QRLGFPPRAPYASPASYAPEQERdrePYDAGRPEYDQRRRDYDHPRPdwdrPRRDRTDRPEPPPGAghvhrGGPGP 245

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1864461801 1017 PGPGPPHPLGVVEPGKGLPPTTEEEAPGPPGES 1049
Cdd:PRK14086   246 PERDDAPVVPIRPSAPGPLAAQPAPAPGPGEPT 278
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
1922-2162 1.00e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 44.46  E-value: 1.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1922 SAGGHALPLGTSPASsQAGTVTSYGPTSSVALGFTSLGPSGPAFVQPLL-----SAGQAPLLAPGQVGVSPVPSPQLPSA 1996
Cdd:PRK07003   361 AVTGGGAPGGGVPAR-VAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAalapkAAAAAAATRAEAPPAAPAPPATADRG 439

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1997 CAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVA-TSTTPPAATILPKGPTAPATATPAPTSPFPSATGSMTYS 2075
Cdd:PRK07003   440 DDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASApASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASRE 519

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2076 LVAPKAQRPSPKAPQKVKAAIASIPVGSFEAGA---------------SGRPGPAPRQPLEPGPVREPTAPESELEGQPT 2140
Cdd:PRK07003   520 DAPAAAAPPAPEARPPTPAAAAPAARAGGAAAAldvlrnagmrvssdrGARAAAAAKPAAAPAAAPKPAAPRVAVQVPTP 599

                          250       260
                   ....*....|....*....|....*....
gi 1864461801 2141 PPAPPPPPETWTPMARS-------SPPPP 2162
Cdd:PRK07003   600 RARAATGDAPPNGAARAeqaaesrGAPPP 628
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1805-2133 1.14e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 1.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1805 VPSAPPPKAQSVSPVQAPPPGGSAQLLPGKVLVPLATPSMSVRGGGAGQPLPLVSPPFSVP--VQNGAQPPSKIIQlTPV 1882
Cdd:PHA03307    67 PPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPpsPAPDLSEMLRPVG-SPG 145

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1883 PVSTPSGLVPPLSPATLPGPTSQPQK--VLLPSSTRITYVQSAGGHALPLGTSPASSQAGTVTSYGPTSSVALGFTSLGP 1960
Cdd:PHA03307   146 PPPAASPPAAGASPAAVASDAASSRQaaLPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPG 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1961 SGPAFVQP----LLSAGQAPLLAPGQVGVSPVPSPQ---LPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVY 2033
Cdd:PHA03307   226 RSAADDAGasssDSSSSESSGCGWGPENECPLPRPApitLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGS 305

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2034 TVATSTTPPAATILPKGPTAPATATPAPTSPFPSATGSMTYSLVAPKAQRPSPKA-PQKVKAAIASIPVGSFEAGASGRP 2112
Cdd:PHA03307   306 GPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPAdPSSPRKRPRPSRAPSSPAASAGRP 385

                          330       340
                   ....*....|....*....|.
gi 1864461801 2113 GPAPRQPLEPGPVREPTAPES 2133
Cdd:PHA03307   386 TRRRARAAVAGRARRRDATGR 406
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 1105-1179 1.49e-03

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 39.46  E-value: 1.49e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1864461801 1105 KREKD--HIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKAHPDWK 1179
Cdd:cd22013      1 KKKKDpnAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYK 77
HMG-box_NSD2 cd21991
high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and ...
 1111-1160 1.65e-03

high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2, also called multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), acts as a histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness.


Pssm-ID: 438807 [Multi-domain]  Cd Length: 62  Bit Score: 38.83  E-value: 1.65e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1111 IRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKY 1160
Cdd:cd21991      2 KKVKKGQFEVFCQKHREEVAQEHPDLSEEEIEEYLKKQWNNMSEKQRARY 51
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
798-1011 1.78e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 43.71  E-value: 1.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  798 GPSVRRVPAVQRDSPVIVRNPDVPLPSKFPGEVGTAGDVRAGGPGRgcrETPVPPGVASGKPGLPPPLPApvpitVPPAA 877
Cdd:PRK12323   380 APVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPAR---RSPAPEALAAARQASARGPGG-----APAPA 451

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  878 PTAVAQPMPTfglASSPFQPVAFHPSPAALLPVLVPSSYTSHPAPKkevimgrpgtvwtnveprsvAVFPWHSLVPFLA- 956
Cdd:PRK12323   452 PAPAAAPAAA---ARPAAAGPRPVAAAAAAAPARAAPAAAPAPADD--------------------DPPPWEELPPEFAs 508

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801  957 --PSQPDPSVQPSEAQ---QPASHPVASNQSKEPAESAAVAHERPPGGTGSADPGRPPGA 1011
Cdd:PRK12323   509 paPAQPDAAPAGWVAEsipDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRA 568
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1959-2199 1.80e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 43.71  E-value: 1.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1959 GPSGPAFVQPLLSAGQAPLLAPGQVgVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQPSQAPPSLVYTVATS 2038
Cdd:PRK12323   370 GGAGPATAAAAPVAQPAPAAAAPAA-AAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAP 448

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2039 TTPPAATILPKGPTApatatpaptspfPSATGSMTYSLVAPKAQRPSPKAPQKvKAAIASIPVGSFEAGASGRPGPAPRQ 2118
Cdd:PRK12323   449 APAPAPAAAPAAAAR------------PAAAGPRPVAAAAAAAPARAAPAAAP-APADDDPPPWEELPPEFASPAPAQPD 515

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2119 PLEPGPVREPTAPESELEGQPTPPAPPPPPETWTPMARSSPPPPLPAEERTSAKGPETMaskfPSSSSDWRVPGQGLESR 2198
Cdd:PRK12323   516 AAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLP----DMFDGDWPALAARLPVR 591


                   .
gi 1864461801 2199 G 2199
Cdd:PRK12323   592 G 592
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 1506-1875 1.89e-03

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 43.41  E-value: 1.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1506 TDPATfRRKRPESVGGLEPAGPSviAAPPSGGGSILQTLVLPPNKEEQEGGGARVPSAPTPSlaygAPAAPLSRPAATMV 1585
Cdd:pfam17823   98 SEPAT-REGAADGAASRALAAAA--SSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANASA----APRAAIAAASAPHA 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1586 TnvvrpvSSTPVPIASKPFPTSGRAEASPNDTAGARTEMGTGSRVPGGSPLGVSLVYSDKKSATATSPAphlvAGPLLGT 1665
Cdd:pfam17823  171 A------SPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPARGISTAATATGHPAAGTALAAVGN----SSPAAGT 240

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1666 VGKAPATVTNLLVGTpgygapVPPAVQFIAQGAPGGGTSAGSGAGAGSGPNGPVPLGILQPGALSKA---GGITQVQYIL 1742
Cdd:pfam17823  241 VTAAVGTVTPAALAT------LAAAAGTVASAAGTINMGDPHARRLSPAKHMPSDTMARNPAAPMGAqaqGPIIQVSTDQ 314

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1743 PTMpqqlqvapapapapGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAPTPGIPILQSVPSAPP---PKAQSVSPV 1819
Cdd:pfam17823  315 PVH--------------NTAGEPTPSPSNTTLEPNTPKSVASTNLAVVTTTKAQAKEPSASPVPVLHTsmiPEVEATSPT 380

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1864461801 1820 QAPPPGGSAQLL--PGKVLVPLATPSMSVRGGGAGQPLPLVSPPFSVPVQNGAQPPSK 1875
Cdd:pfam17823  381 TQPSPLLPTQGAagPGILLAPEQVATEATAGTASAGPTPRSSGDPKTLAMASCQLSTQ 438
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 1112-1173 1.89e-03

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex.


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 39.57  E-value: 1.89e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHDLAFQVKEAHFK 1173
Cdd:cd22018      3 KAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMK 64
HMG-box_HMGXB4 cd21982
high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar ...
 1112-1158 2.73e-03

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.


Pssm-ID: 438798 [Multi-domain]  Cd Length: 61  Bit Score: 38.41  E-value: 2.73e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1864461801 1112 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQ 1158
Cdd:cd21982      2 KKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKL 48
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1791-2206 2.85e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.22  E-value: 2.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1791 AATAPTPGIPILQSVPSA-PPPKAQSVSPVQAPPPGgsaqlLPGKVLVPLATPSMSVRGGGAGQPLPLVSPpfSVPVQNG 1869
Cdd:pfam03154  180 AASPPSPPPPGTTQAATAgPTPSAPSVPPQGSPATS-----QPPNQTQSTAAPHTLIQQTPTLHPQRLPSP--HPPLQPM 252

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1870 AQP-PSKIIQLTPVPVSTPSGLVPPLSPATLPGPTSQPQKVllPSSTRITYVQSAGGHALPLGTSPASSQAGTVTSYGPT 1948
Cdd:pfam03154  253 TQPpPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPV--PPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTPPS 330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1949 SSvalgftSLGPSGPAFVQPLLSAGQA--PLLAPGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPAPTSSAPLAQ-PS 2025
Cdd:pfam03154  331 QS------QLQSQQPPREQPLPPAPLSmpHIKPPPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSlST 404

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2026 QAPPSlvytvatsTTPPAATILPKGPTapatatpaptspfpsatgsmtysLVAPKAQRPSPKAPQKVKAAIASIPvgsfe 2105
Cdd:pfam03154  405 HHPPS--------AHPPPLQLMPQSQQ-----------------------LPPPPAQPPVLTQSQSLPPPAASHP----- 448

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2106 agasgrpgpaPRQPLEPGPVREPTAPESELEGQPTPPAPPPPPETWTPMARSSPPPPLPAEERTSAKGPETMASKFPSSS 2185
Cdd:pfam03154  449 ----------PTSGLHQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVSCPLPPVQ 518

                          410       420
                   ....*....|....*....|.
gi 1864461801 2186 SDWRVPGQGLESRGEPPTPPS 2206
Cdd:pfam03154  519 IKEEALDEAEEPESPPPPPRS 539
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1483-1904 2.97e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 2.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1483 PLRPPPPGAAGPATPSKATRFLPT--------DPATFRRKRPESVGGLE--------PAGPSVIAAPPSGGGSILQTLVL 1546
Cdd:PHA03247  2623 APDPPPPSPSPAANEPDPHPPPTVppperprdDPAPGRVSRPRRARRLGraaqasspPQRPRRRAARPTVGSLTSLADPP 2702

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1547 PPNKEEQEGGGARVPSAPTPSlaygAPAAPLSRPAATMVTNVVRPVSSTPVpiaskpFPTSGRAEASPNDTAGARTEMGT 1626
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPLPP----GPAAARQASPALPAAPAPPAVPAGPA------TPGGPARPARPPTTAGPPAPAPP 2772

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1627 GSRVPGGSPLGVSLVYSDKKSATATSPAPHLVAGPLLGTVGKAPATVTNllvGTPGYGAPVPPAVQFIAQGAPGGGTSAG 1706
Cdd:PHA03247  2773 AAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPA---ASPAGPLPPPTSAQPTAPPPPPGPPPPS 2849

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1707 SGAGAGSGPNGPVplgilqpgalsKAGGITQVQYILPTMPQQLQVapapapapgtkaAAPSGPAPTTSIR-FTLPPgtst 1785
Cdd:PHA03247  2850 LPLGGSVAPGGDV-----------RRRPPSRSPAAKPAAPARPPV------------RRLARPAVSRSTEsFALPP---- 2902

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1786 ngkvlaATAPTPGIPILQSVPSAPPPKAQSVSPVQAPPPGGsaqlLPGKVLVPLATPSmsvrggGAGQPLPLVSPPFSVP 1865
Cdd:PHA03247  2903 ------DQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPP----RPQPPLAPTTDPA------GAGEPSGAVPQPWLGA 2966

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1864461801 1866 VQNGAQPPSKIIQLTPVP-VSTPSGLVPPLSPATLPGPTS 1904
Cdd:PHA03247  2967 LVPGRVAVPRFRVPQPAPsREAPASSTPPLTGHSLSRVSS 3006
HMG-box_CMB1-like cd22014
high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 ...
 1113-1174 3.02e-03

high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins; Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain.


Pssm-ID: 438830 [Multi-domain]  Cd Length: 62  Bit Score: 38.12  E-value: 3.02e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1864461801 1113 RPMNAFMIFSKRHRALVHQRHPNQDNrtvSKILGEWWYALGPKEKQKYHDLAFQVKEAHFKA 1174
Cdd:cd22014      3 RPPSPFLLFMEEFRRNEDNGKNLVEL---SRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQ 61
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1109-1177 3.03e-03

first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains.


Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 38.46  E-value: 3.03e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1864461801 1109 DHIRRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPKEKQKYHD------LAFQVKEAHFKA-HPD 1177
Cdd:cd21998      2 DFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQdyekekEEYEQKMARFREeHPD 77
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 1910-2028 3.07e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 42.74  E-value: 3.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1910 LLPSSTRITYVQSAGGHALPLGTS----PASSQAGTVTSYGPTSSVALG-FTSLGPSGPAFVQPLLSAGQAPLL------ 1978
Cdd:PRK14959   361 MLPRLMPVESLRPSGGGASAPSGSaaegPASGGAATIPTPGTQGPQGTApAAGMTPSSAAPATPAPSAAPSPRVpwddap 440

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1864461801 1979 -APGQVGVSPVPSPQLPSACAAPGGPVITAFYSGSPaPTSSAPLAQPSQAP 2028
Cdd:PRK14959   441 pAPPRSGIPPRPAPRMPEASPVPGAPDSVASASDAP-PTLGDPSDTAEHTP 490
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
1931-2131 6.41e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 41.79  E-value: 6.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1931 GTSPASSQAGTVTSYGPTSSVALGFTSLGPSGPAFV-QPLLSAGQAPLLAPGQVGVSPVPSPQLPSACAAPGGPVitafy 2009
Cdd:PRK12323   371 GAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPaAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPG----- 445

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 2010 sGSPAPTSSAPLAQPSQAPPSlvytVATSTTPPAATILPKGPTAPATATPAPTSPFPSATgSMTYSLVAPKAQRPSPKAP 2089
Cdd:PRK12323   446 -GAPAPAPAPAAAPAAAARPA----AAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWE-ELPPEFASPAPAQPDAAPA 519

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1864461801 2090 QKVKAAI----ASIPVGSFEAGASGRP-GPAPRQPLEPGPVREPTAP 2131
Cdd:PRK12323   520 GWVAESIpdpaTADPDDAFETLAPAPAaAPAPRAAAATEPVVAPRPP 566
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1478-1828 8.19e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.85  E-value: 8.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1478 GSTAGPLRPPPPGAAGPATPSKATRFLPTDPAtfrrkrPESVGGLEPAGPSVIAAPPSGGGSILQTLVLPPNKEEQEGGg 1557
Cdd:PHA03247  2693 GSLTSLADPPPPPPTPEPAPHALVSATPLPPG------PAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG- 2765

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1558 arvPSAPTPSLAYGAPAAPLSRPAATMVTNVVRPVSSTPVPIASKPFPTSGRAEASPNDTAGARTEMGTGSRVPGGSPLG 1637
Cdd:PHA03247  2766 ---PPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPP 2842

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1638 VSLVYSDKKSATATSPaphlvAGPLL--GTVGKAPATVTnllvgtpgygAPVPPAVQFIAQGAPgggtsagsgagagSGP 1715
Cdd:PHA03247  2843 PGPPPPSLPLGGSVAP-----GGDVRrrPPSRSPAAKPA----------APARPPVRRLARPAV-------------SRS 2894

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1864461801 1716 NGPVPLGILQPGALSKAGGITQvqyilPTMPQQLQVAPAPAPAPGTKAAAPSGPAPTTSIRFTLPPGTSTNGKVLAATAP 1795
Cdd:PHA03247  2895 TESFALPPDQPERPPQPQAPPP-----PQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVP 2969

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 1864461801 1796 ----TPGIPILQSVPSAPPPKAQSVSPVQAPPPGGSA 1828
Cdd:PHA03247  2970 grvaVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSS 3006
 
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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