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Conserved domains on  [gi|585168923|ref|XP_006736518|]
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WD repeat and HMG-box DNA-binding protein 1 isoform X1 [Leptonychotes weddellii]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
431-714 2.24e-128

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


:

Pssm-ID: 463539  Cd Length: 288  Bit Score: 393.09  E-value: 2.24e-128
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   431 KPFQSGSTPMHLT-HRFMVWNSVGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNSLNYTVADLSYEAVLLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   509 SKLHCLHFSSWDSSKEWIVDMPQNEDIEAICLGLGWAAAATSAMLLRLFTIGGVQKELFSLPGPVVSMAGHGEQLFIAYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   589 RGAGFDGDQCLGVQLLELGKKKKQilHGEPLPLTRKSYLVWVGFSAEGTPCYTDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 585168923   666 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 714
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
11-289 4.47e-40

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


:

Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 150.18  E-value: 4.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWeDLDDDDPKSINVGEK----AYSCALKNGKLVTAVSNNTIQVHTFPEGVP 86
Cdd:cd00200     7 GHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGEC 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   87 DGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQIS 166
Cdd:cd00200    86 VRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLR 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  167 DqtctvswpllQKCNDVINA--KSICRLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQY 244
Cdd:cd00200   166 T----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGH--ENGVNSVAFSPDGYL 233
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 585168923  245 LAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRIA 289
Cdd:cd00200   234 LASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRLA 277
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
1014-1076 9.29e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


:

Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.10  E-value: 9.29e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 585168923 1014 ENQRPKTGFQMWLEENRSSILSDNPDFsDEADIIKEGMIRFRVLSAEERKAWASKAKGGTTSD 1076
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
PTZ00121 super family cl31754
MAEBL; Provisional
797-1111 2.12e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  797 IKYASRSRRLILAQRLSElaVEKAAELATTQVEEEEEEDFRKELNAGYSNTATEwsQPRLRNQVEEDAEDTREADDKEEK 876
Cdd:PTZ00121 1217 ARKAEDAKKAEAVKKAEE--AKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR--QAAIKAEEARKADELKKAEEKKKA 1292
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  877 PELHK-----HGQNLFSKSTNPSDVPAVKSGAvtSSNQGRVNPFKVSSNSKEPATSMNSARSSNILDSMNKSSKKSTALN 951
Cdd:PTZ00121 1293 DEAKKaeekkKADEAKKKAEEAKKADEAKKKA--EEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAE 1370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  952 RATNNEKSpviKPLVPKPKSKQASAASYFQKRTSQTDKTED--VKEEHPKNSSSETPamcpQNTENQRPKTGFQMWLEEN 1029
Cdd:PTZ00121 1371 KKKEEAKK---KADAAKKKAEEKKKADEAKKKAEEDKKKADelKKAAAAKKKADEAK----KKAEEKKKADEAKKKAEEA 1443
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923 1030 RSSilSDNPDFSDEADIIKEGMIRfrvlSAEERKAWASKAKGGTTSDGAEAKKR----KHVVDESHETENEKEKAKENLN 1105
Cdd:PTZ00121 1444 KKA--DEAKKKAEEAKKAEEAKKK----AEEAKKADEAKKKAEEAKKADEAKKKaeeaKKKADEAKKAAEAKKKADEAKK 1517

                  ....*.
gi 585168923 1106 LPKKQK 1111
Cdd:PTZ00121 1518 AEEAKK 1523
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
431-714 2.24e-128

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 393.09  E-value: 2.24e-128
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   431 KPFQSGSTPMHLT-HRFMVWNSVGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNSLNYTVADLSYEAVLLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   509 SKLHCLHFSSWDSSKEWIVDMPQNEDIEAICLGLGWAAAATSAMLLRLFTIGGVQKELFSLPGPVVSMAGHGEQLFIAYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   589 RGAGFDGDQCLGVQLLELGKKKKQilHGEPLPLTRKSYLVWVGFSAEGTPCYTDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 585168923   666 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 714
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
11-289 4.47e-40

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 150.18  E-value: 4.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWeDLDDDDPKSINVGEK----AYSCALKNGKLVTAVSNNTIQVHTFPEGVP 86
Cdd:cd00200     7 GHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGEC 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   87 DGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQIS 166
Cdd:cd00200    86 VRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLR 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  167 DqtctvswpllQKCNDVINA--KSICRLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQY 244
Cdd:cd00200   166 T----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGH--ENGVNSVAFSPDGYL 233
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 585168923  245 LAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRIA 289
Cdd:cd00200   234 LASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRLA 277
WD40 COG2319
WD40 repeat [General function prediction only];
11-295 4.97e-37

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 144.67  E-value: 4.97e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWedlDDDDPKSINV----GEKAYSCAL-KNGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319   118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   85 VPDGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQ 164
Cdd:COG2319   195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  165 ISDQTCTVswpLLQKCNDVINAksicrLAWQPkSGKLLAVPVE-KSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQ 243
Cdd:COG2319   275 LATGELLR---TLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 585168923  244 YLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHPTCGRIAYTDAEG 295
Cdd:COG2319   344 TLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSPDGRTLASGSADG 394
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
1014-1076 9.29e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.10  E-value: 9.29e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 585168923 1014 ENQRPKTGFQMWLEENRSSILSDNPDFsDEADIIKEGMIRFRVLSAEERKAWASKAKGGTTSD 1076
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
HMG smart00398
high mobility group;
1017-1070 4.34e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.86  E-value: 4.34e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 585168923   1017 RPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAK 56
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
130-163 2.25e-08

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 50.77  E-value: 2.25e-08
                            10        20        30
                    ....*....|....*....|....*....|....
gi 585168923    130 KTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVW 163
Cdd:smart00320    6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
127-163 2.49e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.81  E-value: 2.49e-08
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 585168923   127 SQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVW 163
Cdd:pfam00400    2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1016-1103 8.13e-06

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.93  E-value: 8.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923 1016 QRPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAKggttSDGAEAKKRKHVVDESHETEN 1095
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                  ....*...
gi 585168923 1096 EKEKAKEN 1103
Cdd:COG5648   147 PIGPFIEN 154
PTZ00121 PTZ00121
MAEBL; Provisional
797-1111 2.12e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  797 IKYASRSRRLILAQRLSElaVEKAAELATTQVEEEEEEDFRKELNAGYSNTATEwsQPRLRNQVEEDAEDTREADDKEEK 876
Cdd:PTZ00121 1217 ARKAEDAKKAEAVKKAEE--AKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR--QAAIKAEEARKADELKKAEEKKKA 1292
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  877 PELHK-----HGQNLFSKSTNPSDVPAVKSGAvtSSNQGRVNPFKVSSNSKEPATSMNSARSSNILDSMNKSSKKSTALN 951
Cdd:PTZ00121 1293 DEAKKaeekkKADEAKKKAEEAKKADEAKKKA--EEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAE 1370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  952 RATNNEKSpviKPLVPKPKSKQASAASYFQKRTSQTDKTED--VKEEHPKNSSSETPamcpQNTENQRPKTGFQMWLEEN 1029
Cdd:PTZ00121 1371 KKKEEAKK---KADAAKKKAEEKKKADEAKKKAEEDKKKADelKKAAAAKKKADEAK----KKAEEKKKADEAKKKAEEA 1443
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923 1030 RSSilSDNPDFSDEADIIKEGMIRfrvlSAEERKAWASKAKGGTTSDGAEAKKR----KHVVDESHETENEKEKAKENLN 1105
Cdd:PTZ00121 1444 KKA--DEAKKKAEEAKKAEEAKKK----AEEAKKADEAKKKAEEAKKADEAKKKaeeaKKKADEAKKAAEAKKKADEAKK 1517

                  ....*.
gi 585168923 1106 LPKKQK 1111
Cdd:PTZ00121 1518 AEEAKK 1523
HMG_box pfam00505
HMG (high mobility group) box;
1017-1070 7.54e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 7.54e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 585168923  1017 RPKTGFQMWLEENRSSILSDNPDFSDeADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:pfam00505    3 RPMSAFFLFSKEQRAKLKAENPGLKN-AEISKILGEKWKALSEEEKKPYEEKAE 55
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
431-714 2.24e-128

Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.


Pssm-ID: 463539  Cd Length: 288  Bit Score: 393.09  E-value: 2.24e-128
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   431 KPFQSGSTPMHLT-HRFMVWNSVGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNSLNYTVADLSYEAVLLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   509 SKLHCLHFSSWDSSKEWIVDMPQNEDIEAICLGLGWAAAATSAMLLRLFTIGGVQKELFSLPGPVVSMAGHGEQLFIAYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   589 RGAGFDGDQCLGVQLLELGKKKKQilHGEPLPLTRKSYLVWVGFSAEGTPCYTDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 585168923   666 EHCK--GKSDHYWVVGIHEnpQQLRCIPCKGS-RFPPTLPRPAVAILSFKLP 714
Cdd:pfam12341  239 LLLRkgGKSDTYWPVGVSE--DKLRCIICKGGeKYPGFLPRPLLSELPLKLP 288
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
11-289 4.47e-40

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 150.18  E-value: 4.47e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWeDLDDDDPKSINVGEK----AYSCALKNGKLVTAVSNNTIQVHTFPEGVP 86
Cdd:cd00200     7 GHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGEC 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   87 DGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQIS 166
Cdd:cd00200    86 VRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLR 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  167 DqtctvswpllQKCNDVINA--KSICRLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQY 244
Cdd:cd00200   166 T----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGH--ENGVNSVAFSPDGYL 233
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 585168923  245 LAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRIA 289
Cdd:cd00200   234 LASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRLA 277
WD40 COG2319
WD40 repeat [General function prediction only];
11-295 4.97e-37

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 144.67  E-value: 4.97e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWedlDDDDPKSINV----GEKAYSCAL-KNGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319   118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   85 VPDGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQ 164
Cdd:COG2319   195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  165 ISDQTCTVswpLLQKCNDVINAksicrLAWQPkSGKLLAVPVE-KSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQ 243
Cdd:COG2319   275 LATGELLR---TLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 585168923  244 YLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHPTCGRIAYTDAEG 295
Cdd:COG2319   344 TLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSPDGRTLASGSADG 394
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
11-258 1.32e-32

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 128.61  E-value: 1.32e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWeDLDDDDPKSINVGEKAY--SCA-LKNGKLVTAVS-NNTIQVHTFPEGVP 86
Cdd:cd00200    49 GHTGPVRDVAASADGTYLASGSSDKTIRLW-DLETGECVRTLTGHTSYvsSVAfSPDGRILSSSSrDKTIKVWDVETGKC 127
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   87 DGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQIS 166
Cdd:cd00200   128 LTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLS 207
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  167 DQTCTVSwplLQKCNDVINAksicrLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLS--DNFISQalnvVTWSPCGQY 244
Cdd:cd00200   208 TGKCLGT---LRGHENGVNS-----VAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSghTNSVTS----LAWSPDGKR 275
                         250
                  ....*....|....
gi 585168923  245 LAAGSINGLIIVWN 258
Cdd:cd00200   276 LASGSADGTIRIWD 289
WD40 COG2319
WD40 repeat [General function prediction only];
11-261 5.19e-32

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 130.03  E-value: 5.19e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWEDLDDDDPKSINVGEKA-YSCAL-KNGK-LVTAVSNNTIQVHTFPEGVPD 87
Cdd:COG2319   160 GHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAvRSVAFsPDGKlLASGSADGTVRLWDLATGKLL 239
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   88 GILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQISD 167
Cdd:COG2319   240 RTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLAT 319
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  168 QTCTVSWPllqkcndvINAKSICRLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQYLAA 247
Cdd:COG2319   320 GKLLRTLT--------GHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGH--TGAVTSVAFSPDGRTLAS 389
                         250
                  ....*....|....
gi 585168923  248 GSINGLIIVWNVET 261
Cdd:COG2319   390 GSADGTVRLWDLAT 403
WD40 COG2319
WD40 repeat [General function prediction only];
9-283 1.12e-31

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 128.88  E-value: 1.12e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923    9 RFGHTEGHTDVCFDDLGSYIVTCGSDGDVRIWEDLDDDDPKSINVGEK---AYSCALKNGKLVTAVSNNTIQVHTFPEGV 85
Cdd:COG2319    32 LLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAavlSVAFSPDGRLLASASADGTVRLWDLATGL 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   86 PDGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQI 165
Cdd:COG2319   112 LLRTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDL 191
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  166 SDQTCTVSwplLQKCNDVINAksicrLAWQPkSGKLLAVPVE-KSVKLYRRETWNNQHDLSDNfiSQALNVVTWSPCGQY 244
Cdd:COG2319   192 ATGKLLRT---LTGHTGAVRS-----VAFSP-DGKLLASGSAdGTVRLWDLATGKLLRTLTGH--SGSVRSVAFSPDGRL 260
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 585168923  245 LAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 283
Cdd:COG2319   261 LASGSADGTVRLWDLATGELLRTLTGHSG-GVNSVAFSP 298
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
1014-1076 9.29e-25

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 98.10  E-value: 9.29e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 585168923 1014 ENQRPKTGFQMWLEENRSSILSDNPDFsDEADIIKEGMIRFRVLSAEERKAWASKAKGGTTSD 1076
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 COG2319
WD40 repeat [General function prediction only];
67-299 1.17e-19

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 92.67  E-value: 1.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   67 LVTAVSNNTIQVHTFPEGVPDGILTRFTTNANHVVFNGDGAKIAAGSSDFLVKVVDVMDCSQQKTFRGHDAPVLSLSFDP 146
Cdd:COG2319     9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSP 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  147 KDIFLASASCDGTVKVWQISDQTCTVswpLLQKCNDVINAksicrLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSD 226
Cdd:COG2319    89 DGRLLASASADGTVRLWDLATGLLLR---TLTGHTGAVRS-----VAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 585168923  227 NfiSQALNVVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHPTCGRIAYTDAEGNLGL 299
Cdd:COG2319   161 H--SGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG-AVRSVAFSPDGKLLASGSADGTVRL 230
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
130-289 9.92e-15

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 76.22  E-value: 9.92e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  130 KTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVWQI--------------------------------SDQTCTVsWPL- 176
Cdd:cd00200     3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLetgellrtlkghtgpvrdvaasadgtylasgsSDKTIRL-WDLe 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  177 LQKCNDVIN--AKSICRLAWQPKSGKLLAVPVEKSVKLYRRETWNNQHDLSDnfISQALNVVTWSPCGQYLAAGSINGLI 254
Cdd:cd00200    82 TGECVRTLTghTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRG--HTDWVNSVAFSPDGTFVASSSQDGTI 159
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 585168923  255 IVWNVETKDCMERVKHEKGYaICGLAWHPTCGRIA 289
Cdd:cd00200   160 KLWDLRTGKCVATLTGHTGE-VNSVAFSPDGEKLL 193
HMG smart00398
high mobility group;
1017-1070 4.34e-09

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 53.86  E-value: 4.34e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 585168923   1017 RPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAK 56
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
1017-1083 1.52e-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: 52.30  E-value: 1.52e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 585168923 1017 RPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAKggttsdgaEAKKR 1083
Cdd:cd21994     1 RPMSAYMLWLNENREKIKKENPGIS-VTEISKKAGEIWKELDEEDKEKWEQKAE--------KAKER 58
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
130-163 2.25e-08

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 50.77  E-value: 2.25e-08
                            10        20        30
                    ....*....|....*....|....*....|....
gi 585168923    130 KTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVW 163
Cdd:smart00320    6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
127-163 2.49e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 50.81  E-value: 2.49e-08
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 585168923   127 SQQKTFRGHDAPVLSLSFDPKDIFLASASCDGTVKVW 163
Cdd:pfam00400    2 KLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
1017-1070 9.50e-07

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: 46.74  E-value: 9.50e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 585168923 1017 RPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLS-FTEISKLLGERWKELSEEEKQPYEEKAK 53
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1016-1103 8.13e-06

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 47.93  E-value: 8.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923 1016 QRPKTGFQMWLEENRSSILSDNPDFSdEADIIKEGMIRFRVLSAEERKAWASKAKggttSDGAEAKKRKHVVDESHETEN 1095
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                  ....*...
gi 585168923 1096 EKEKAKEN 1103
Cdd:COG5648   147 PIGPFIEN 154
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
11-41 8.80e-06

WD40 repeats; Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain.


Pssm-ID: 197651 [Multi-domain]  Cd Length: 40  Bit Score: 43.46  E-value: 8.80e-06
                            10        20        30
                    ....*....|....*....|....*....|.
gi 585168923     11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWE 41
Cdd:smart00320   10 GHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
1016-1089 8.28e-05

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: 41.67  E-value: 8.28e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 585168923 1016 QRPKTGFQMWLEENRSSILSDNP--DFSDEADIIKEgmiRFRVLSAEERKAWASKAKggttsdgAEAKKRKHVVDE 1089
Cdd:cd22006     1 KKPKTAYFLWCKDQREEVKKENPnaDFSEVSKILGA---KWKNLSEEEKKPYEEKYK-------EEKEKYLKVVGE 66
WD40 pfam00400
WD domain, G-beta repeat;
11-41 2.35e-04

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 39.64  E-value: 2.35e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 585168923    11 GHTEGHTDVCFDDLGSYIVTCGSDGDVRIWE 41
Cdd:pfam00400    9 GHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
193-284 1.77e-03

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 40.72  E-value: 1.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923   193 AWQPKSGKLLAV--PVEKSVKLYrretwNNQHDLSDNFISQALNVVTWSPCGQYLAA---GSINGLIIVWNVETKDCMER 267
Cdd:pfam08662   66 AWSPNGKEFAVIygYMPAKVSFF-----DLKGNVIHSFGEQPRNTIFWSPFGRLVLLagfGNLAGDIEFWDVVNKKKIAT 140
                           90
                   ....*....|....*..
gi 585168923   268 VKHEKGyaiCGLAWHPT 284
Cdd:pfam08662  141 AEASNA---TLCEWSPD 154
PTZ00121 PTZ00121
MAEBL; Provisional
797-1111 2.12e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  797 IKYASRSRRLILAQRLSElaVEKAAELATTQVEEEEEEDFRKELNAGYSNTATEwsQPRLRNQVEEDAEDTREADDKEEK 876
Cdd:PTZ00121 1217 ARKAEDAKKAEAVKKAEE--AKKDAEEAKKAEEERNNEEIRKFEEARMAHFARR--QAAIKAEEARKADELKKAEEKKKA 1292
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  877 PELHK-----HGQNLFSKSTNPSDVPAVKSGAvtSSNQGRVNPFKVSSNSKEPATSMNSARSSNILDSMNKSSKKSTALN 951
Cdd:PTZ00121 1293 DEAKKaeekkKADEAKKKAEEAKKADEAKKKA--EEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAE 1370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923  952 RATNNEKSpviKPLVPKPKSKQASAASYFQKRTSQTDKTED--VKEEHPKNSSSETPamcpQNTENQRPKTGFQMWLEEN 1029
Cdd:PTZ00121 1371 KKKEEAKK---KADAAKKKAEEKKKADEAKKKAEEDKKKADelKKAAAAKKKADEAK----KKAEEKKKADEAKKKAEEA 1443
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 585168923 1030 RSSilSDNPDFSDEADIIKEGMIRfrvlSAEERKAWASKAKGGTTSDGAEAKKR----KHVVDESHETENEKEKAKENLN 1105
Cdd:PTZ00121 1444 KKA--DEAKKKAEEAKKAEEAKKK----AEEAKKADEAKKKAEEAKKADEAKKKaeeaKKKADEAKKAAEAKKKADEAKK 1517

                  ....*.
gi 585168923 1106 LPKKQK 1111
Cdd:PTZ00121 1518 AEEAKK 1523
HMG_box pfam00505
HMG (high mobility group) box;
1017-1070 7.54e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 7.54e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 585168923  1017 RPKTGFQMWLEENRSSILSDNPDFSDeADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:pfam00505    3 RPMSAFFLFSKEQRAKLKAENPGLKN-AEISKILGEKWKALSEEEKKPYEEKAE 55
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
1016-1070 9.02e-03

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: 35.97  E-value: 9.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 585168923 1016 QRPKTGFQMWLEENRSSILSDNPDFSDeADIIKEGMIRFRVLSAEERKAWASKAK 1070
Cdd:cd22010     2 KRPLSAYFLYFQEHRSDFVKENPDAKM-TEISKIGGDKWKNLSADDKKKYEDDFQ 55
 
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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