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Conserved domains on  [gi|578825436|ref|XP_006720075|]
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WD repeat and HMG-box DNA-binding protein 1 isoform X1 [Homo sapiens]

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 4.13e-122

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: 376.53  E-value: 4.13e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578825436   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 ...
 10-288 3.83e-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: 150.56  E-value: 3.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200     6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200    85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200   165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 578825436  242 GQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRI 288
Cdd:cd00200   231 GYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRL 276
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1012-1074 1.69e-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: 100.41  E-value: 1.69e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578825436 1012 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1074
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
 
Name Accession Description Interval E-value
Mcl1_mid pfam12341
Minichromosome loss protein, Mcl1, middle region; Mcl1_mid, or the middle domain of ...
 431-714 4.13e-122

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: 376.53  E-value: 4.13e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578825436   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 ...
 10-288 3.83e-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: 150.56  E-value: 3.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200     6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200    85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200   165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 578825436  242 GQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRI 288
Cdd:cd00200   231 GYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 2.79e-35

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 139.66  E-value: 2.79e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWedlDDDDPKFINV----GEKAYSCAL-KSGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319   118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   85 VPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQ 164
Cdd:COG2319   195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  165 ISDQTCaisWPLLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQ 243
Cdd:COG2319   275 LATGEL---LRTLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 578825436  244 YLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHP 283
Cdd:COG2319   344 TLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSP 382
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1012-1074 1.69e-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: 100.41  E-value: 1.69e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578825436 1012 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1074
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
HMG smart00398
high mobility group;
1015-1072 9.06e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 55.78  E-value: 9.06e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 578825436   1015 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 1072
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 125-163 5.47e-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: 50.00  E-value: 5.47e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 578825436    125 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
126-163 6.12e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 6.12e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 578825436   126 SSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:pfam00400    1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1014-1109 1.25e-04

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 44.47  E-value: 1.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436 1014 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 1093
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                          90
                  ....*....|....*.
gi 578825436 1094 QEEKAKENLNLSKKQK 1109
Cdd:COG5648   147 PIGPFIENEPKIRPKV 162
HMG_box pfam00505
HMG (high mobility group) box;
1015-1068 8.99e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 8.99e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 578825436  1015 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAK 1068
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 4.13e-122

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: 376.53  E-value: 4.13e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578825436   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 ...
 10-288 3.83e-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: 150.56  E-value: 3.83e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200     6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200    85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200   165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 578825436  242 GQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRI 288
Cdd:cd00200   231 GYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 2.79e-35

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 139.66  E-value: 2.79e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWedlDDDDPKFINV----GEKAYSCAL-KSGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319   118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   85 VPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQ 164
Cdd:COG2319   195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  165 ISDQTCaisWPLLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQ 243
Cdd:COG2319   275 LATGEL---LRTLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 578825436  244 YLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHP 283
Cdd:COG2319   344 TLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSP 382
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 6.45e-30

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 123.48  E-value: 6.45e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWEDLDDDDPKFINVGEK---AYSCALKSGKLVTAVSNNTIQVHTFPEGVPD 87
Cdd:COG2319    34 GLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAavlSVAFSPDGRLLASASADGTVRLWDLATGLLL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   88 GILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISD 167
Cdd:COG2319   114 RTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLAT 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  168 QTCAISwplLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLA 246
Cdd:COG2319   194 GKLLRT---LTGHTGAVRS-----VAFSP-DGKLLASGSAdGTVRLWDLATGKLLRTLTGH--SGSVRSVAFSPDGRLLA 262

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 578825436  247 AGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 283
Cdd:COG2319   263 SGSADGTVRLWDLATGELLRTLTGHSG-GVNSVAFSP 298
WD40 COG2319
WD40 repeat [General function prediction only];
14-261 6.68e-29

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 120.79  E-value: 6.68e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   14 EGHTE----VCFDDSGSFIVTCGSDGDVRIWEDLDDDDPKFINVGEKA-YSCAL-KSGK-LVTAVSNNTIQVHTFPEGVP 86
Cdd:COG2319   159 TGHSGavtsVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAvRSVAFsPDGKlLASGSADGTVRLWDLATGKL 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   87 DGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQIS 166
Cdd:COG2319   239 LRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLA 318

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  167 DQTCAISWPllqkcndvINAKSICRLAWQPKsGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYL 245
Cdd:COG2319   319 TGKLLRTLT--------GHTGAVRSVAFSPD-GKTLASGSDdGTVRLWDLATGELLRTLTGH--TGAVTSVAFSPDGRTL 387

                         250
                  ....*....|....*.
gi 578825436  246 AAGSINGLIIVWNVET 261
Cdd:COG2319   388 ASGSADGTVRLWDLAT 403
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1012-1074 1.69e-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: 100.41  E-value: 1.69e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578825436 1012 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1074
Cdd:cd21993     1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 COG2319
WD40 repeat [General function prediction only];
11-167 2.88e-23

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 103.84  E-value: 2.88e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEKAYSCAL---KSGK-LVTAVSNNTIQVHTFPEGVP 86
Cdd:COG2319   244 GHSGSVRSVAFSPDGRLLASGSADGTVRLW-DLATGELLRTLTGHSGGVNSVafsPDGKlLASGSDDGTVRLWDLATGKL 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   87 DGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQIS 166
Cdd:COG2319   323 LRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLA 402


                  .
gi 578825436  167 D 167
Cdd:COG2319   403 T 403
WD40 COG2319
WD40 repeat [General function prediction only];
67-283 3.61e-17

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 85.35  E-value: 3.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   67 LVTAVSNNTIQVHTFPEGVPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDP 146
Cdd:COG2319     9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSP 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  147 KDIFLASASCDGSVRVWQISDQTCAiswPLLQKCNDVINAksicrLAWQPKSGKLLAIPVEKSVKLYRRESWSHQFDLSD 226
Cdd:COG2319    89 DGRLLASASADGTVRLWDLATGLLL---RTLTGHTGAVRS-----VAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 578825436  227 NfiSQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 283
Cdd:COG2319   161 H--SGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTG-AVRSVAFSP 214
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 130-288 4.26e-12

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: 68.13  E-value: 4.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  130 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI--------------------------------SDQTCAIsWPL- 176
Cdd:cd00200     3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLetgellrtlkghtgpvrdvaasadgtylasgsSDKTIRL-WDLe 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436  177 LQKCNDVIN--AKSICRLAWQPKSGKLLAIPVEKSVKLYRRESWSHQFDLSDnfISQTLNIVTWSPCGQYLAAGSINGLI 254
Cdd:cd00200    82 TGECVRTLTghTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRG--HTDWVNSVAFSPDGTFVASSSQDGTI 159

                         170       180       190
                  ....*....|....*....|....*....|....
gi 578825436  255 IVWNVETKDCMERVKHEKGYaICGLAWHPTCGRI 288
Cdd:cd00200   160 KLWDLRTGKCVATLTGHTGE-VNSVAFSPDGEKL 192
HMG smart00398
high mobility group;
1015-1072 9.06e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 55.78  E-value: 9.06e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 578825436   1015 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 1072
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1015-1081 2.81e-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: 51.53  E-value: 2.81e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 578825436 1015 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetasegtEAKKR 1081
Cdd:cd21994     1 RPMSAYMLWLNENREKIKKENPGIS-VTEISKKAGEIWKELDEEDKEKWEQKAE--------KAKER 58
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 125-163 5.47e-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: 50.00  E-value: 5.47e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 578825436    125 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
126-163 6.12e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 6.12e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 578825436   126 SSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:pfam00400    1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1015-1068 5.87e-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: 47.51  E-value: 5.87e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 578825436 1015 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAK 1068
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLS-FTEISKLLGERWKELSEEEKQPYEEKAK 53
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 11-41 3.21e-05

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: 41.91  E-value: 3.21e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 578825436     11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWE 41
Cdd:smart00320   10 GHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1014-1109 1.25e-04

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 44.47  E-value: 1.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436 1014 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 1093
Cdd:COG5648    72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                          90
                  ....*....|....*.
gi 578825436 1094 QEEKAKENLNLSKKQK 1109
Cdd:COG5648   147 PIGPFIENEPKIRPKV 162
WD40 pfam00400
WD domain, G-beta repeat;
11-41 3.15e-04

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 39.25  E-value: 3.15e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 578825436    11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWE 41
Cdd:pfam00400    9 GHTGSVTSLAFSPDGKLLASGSDDGTVKVWD 39
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1014-1087 4.99e-04

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: 39.36  E-value: 4.99e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 578825436 1014 QRPKTGFQMWLEENRSNILSDNP--DFSDEADIIKEgmiRFRVLSTEERKVWANKAKgetasegTEAKKRKRVVDE 1087
Cdd:cd22006     1 KKPKTAYFLWCKDQREEVKKENPnaDFSEVSKILGA---KWKNLSEEEKKPYEEKYK-------EEKEKYLKVVGE 66
ANAPC4_WD40 pfam12894
Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped ...
 192-281 1.43e-03

Anaphase-promoting complex subunit 4 WD40 domain; Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,


Pssm-ID: 403945 [Multi-domain]  Cd Length: 91  Bit Score: 38.80  E-value: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   192 LAWQPKSgKLLAIPVEK-SVKLYRReSWSHQFDLSDNFISQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKH 270
Cdd:pfam12894    1 MSWCPTM-DLIALATEDgELLLHRL-NWQRVWTLSPDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSA 78

                           90
                   ....*....|.
gi 578825436   271 EKGYAICgLAW 281
Cdd:pfam12894   79 GSDLITC-LGW 88
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 193-284 1.90e-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: 1.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578825436   193 AWQPKSGKLLAI--PVEKSVKLYrreswSHQFDLSDNFISQTLNIVTWSPCGQYLAA---GSINGLIIVWNVETKDCMER 267
Cdd:pfam08662   66 AWSPNGKEFAVIygYMPAKVSFF-----DLKGNVIHSFGEQPRNTIFWSPFGRLVLLagfGNLAGDIEFWDVVNKKKIAT 140

                           90
                   ....*....|....*..
gi 578825436   268 VKHEKGyaiCGLAWHPT 284
Cdd:pfam08662  141 AEASNA---TLCEWSPD 154
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1014-1081 8.66e-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: 8.66e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578825436 1014 QRPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAKGETaSEGTEAKKR 1081
Cdd:cd22010     2 KRPLSAYFLYFQEHRSDFVKENPDAKM-TEISKIGGDKWKNLSADDKKKYEDDFQREL-SEYQKAKAE 67
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 1015-1072 8.96e-03

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: 35.75  E-value: 8.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 578825436 1015 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAKGETA 1072
Cdd:cd22005     2 RPPTAFFLFLADFRKTYKKKNPDKSV-KAVGKAAGEKWKSMSDEEKAPYVEKAEKEKA 58
HMG_box pfam00505
HMG (high mobility group) box;
1015-1068 8.99e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 8.99e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 578825436  1015 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAK 1068
Cdd:pfam00505    3 RPMSAFFLFSKEQRAKLKAENPGLKN-AEISKILGEKWKALSEEEKKPYEEKAE 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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