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Conserved domains on  [gi|5901892|ref|NP_009017|]
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WD repeat and HMG-box DNA-binding protein 1 isoform 1 [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 4.28e-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: 4.28e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 5901892     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 3.76e-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: 3.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200    6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200   85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200  165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 5901892   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 ...
 1014-1076 1.57e-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: 1.57e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5901892  1014 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1076
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 4.28e-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: 4.28e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 5901892     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 3.76e-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: 3.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200    6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200   85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200  165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 5901892   242 GQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRI 288
Cdd:cd00200  231 GYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 2.80e-35

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 139.66  E-value: 2.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWedlDDDDPKFINV----GEKAYSCAL-KSGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319  118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    85 VPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQ 164
Cdd:COG2319  195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   165 ISDQTCaisWPLLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQ 243
Cdd:COG2319  275 LATGEL---LRTLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 5901892   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 ...
 1014-1076 1.57e-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: 1.57e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5901892  1014 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1076
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
HMG smart00398
high mobility group;
1017-1074 8.82e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 55.78  E-value: 8.82e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 5901892     1017 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 1074
Cdd:smart00398    4 RPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKE 60
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 125-163 5.43e-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: 5.43e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 5901892      125 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
126-163 6.07e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 6.07e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 5901892     126 SSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:pfam00400    1 GKLLKTLEGHTGSVTSLAFSPDGKLLASGSDDGTVKVW 38
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1016-1111 1.20e-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: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892  1016 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 1095
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 5901892  1096 QEEKAKENLNLSKKQK 1111
Cdd:COG5648  147 PIGPFIENEPKIRPKV 162
HMG_box pfam00505
HMG (high mobility group) box;
1017-1070 9.01e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 9.01e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 5901892    1017 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAK 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 4.28e-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: 4.28e-122
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     431 KPFQSGSTPLHLT-HRFMVWNSIGIIRCY-NDEQDNAIDVEFHDTSIHHATHLSNTLNYTIADLSHEAILLACESTDELA 508
Cdd:pfam12341    1 KPFQPGSTPWHLGdRRYLCWNLIGYVWTVkQDTDSNSITVEFHDTSRHREYHFTDYFGYDLASLNEEGALLASPAKQSKP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     509 SKLHCLHFSSWDSSKEWIIDLPQNEDIEAICLGQGWAAAATSALLLRLFTIGGVQKEVFSLAGPVVSMAGHGEQLFIVYH 588
Cdd:pfam12341   81 STLYYRPHESWGSNSEWSVTLPLGEEITAVALGSSWVAVATSLGYLRIFSLGGVQRRVFSLPGPVVTMAASEDYLFVVYH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     589 RGTGFDGDQCLGVQLLELGKKKKQilHGDPLPLTRKSYLAWIGFSAEGTPCYVDSEGIVRMLNRG---LGNTWTPICNTR 665
Cdd:pfam12341  161 NGGPLDGDQNLSYSLLDVSRDELQ--REGPLPLSPGSTLKWLGFSEEGDPCIYDSDGVLRVLSKWrspGQARWVPVLDTK 238

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 5901892     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 3.76e-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: 3.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    10 YGHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEK----AYSCALKSGKLVTAVSNNTIQVHTFPEGV 85
Cdd:cd00200    6 KGHTGGVTCVAFSPDGKLLATGSGDGTIKVW-DLETGELLRTLKGHTgpvrDVAASADGTYLASGSSDKTIRLWDLETGE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    86 PDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI 165
Cdd:cd00200   85 CVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   166 SDqtcaiswpllQKCNDVINA--KSICRLAWQPKSGKLLAIPVEKSVKLY--RRESWSHQFDLSDNFISQtlniVTWSPC 241
Cdd:cd00200  165 RT----------GKCVATLTGhtGEVNSVAFSPDGEKLLSSSSDGTIKLWdlSTGKCLGTLRGHENGVNS----VAFSPD 230

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 5901892   242 GQYLAAGSINGLIIVWNVETKDCMERVK-HEKGyaICGLAWHPTCGRI 288
Cdd:cd00200  231 GYLLASGSEDGTIRVWDLRTGECVQTLSgHTNS--VTSLAWSPDGKRL 276
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 2.80e-35

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 139.66  E-value: 2.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWedlDDDDPKFINV----GEKAYSCAL-KSGK-LVTAVSNNTIQVHTFPEG 84
Cdd:COG2319  118 GHTGAVRSVAFSPDGKTLASGSADGTVRLW---DLATGKLLRTltghSGAVTSVAFsPDGKlLASGSDDGTVRLWDLATG 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    85 VPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQ 164
Cdd:COG2319  195 KLLRTLTGHTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWD 274

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   165 ISDQTCaisWPLLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQ 243
Cdd:COG2319  275 LATGEL---LRTLTGHSGGVNS-----VAFSP-DGKLLASGSDdGTVRLWDLATGKLLRTLTGH--TGAVRSVAFSPDGK 343

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 5901892   244 YLAAGSINGLIIVWNVETKDCMERVK-HEKgyAICGLAWHP 283
Cdd:COG2319  344 TLASGSDDGTVRLWDLATGELLRTLTgHTG--AVTSVAFSP 382
WD40 COG2319
WD40 repeat [General function prediction only];
11-283 6.47e-30

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 123.48  E-value: 6.47e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWEDLDDDDPKFINVGEK---AYSCALKSGKLVTAVSNNTIQVHTFPEGVPD 87
Cdd:COG2319   34 GLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAavlSVAFSPDGRLLASASADGTVRLWDLATGLLL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    88 GILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQISD 167
Cdd:COG2319  114 RTLTGHTGAVRSVAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTGHSGAVTSVAFSPDGKLLASGSDDGTVRLWDLAT 193

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   168 QTCAISwplLQKCNDVINAksicrLAWQPkSGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYLA 246
Cdd:COG2319  194 GKLLRT---LTGHTGAVRS-----VAFSP-DGKLLASGSAdGTVRLWDLATGKLLRTLTGH--SGSVRSVAFSPDGRLLA 262

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 5901892   247 AGSINGLIIVWNVETKDCMERVKHEKGyAICGLAWHP 283
Cdd:COG2319  263 SGSADGTVRLWDLATGELLRTLTGHSG-GVNSVAFSP 298
WD40 COG2319
WD40 repeat [General function prediction only];
14-261 6.69e-29

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 120.79  E-value: 6.69e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    14 EGHTE----VCFDDSGSFIVTCGSDGDVRIWEDLDDDDPKFINVGEKA-YSCAL-KSGK-LVTAVSNNTIQVHTFPEGVP 86
Cdd:COG2319  159 TGHSGavtsVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAvRSVAFsPDGKlLASGSADGTVRLWDLATGKL 238

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    87 DGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQIS 166
Cdd:COG2319  239 LRTLTGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAFSPDGKLLASGSDDGTVRLWDLA 318

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   167 DQTCAISWPllqkcndvINAKSICRLAWQPKsGKLLAIPVE-KSVKLYRRESWSHQFDLSDNfiSQTLNIVTWSPCGQYL 245
Cdd:COG2319  319 TGKLLRTLT--------GHTGAVRSVAFSPD-GKTLASGSDdGTVRLWDLATGELLRTLTGH--TGAVTSVAFSPDGRTL 387

                        250
                 ....*....|....*.
gi 5901892   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 ...
 1014-1076 1.57e-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: 1.57e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 5901892  1014 ENQRPKTGFQMWLEENRSNILSDNPDFsDEADIIKEGMIRFRVLSTEERKVWANKAKGETASE 1076
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPEL-SEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDEE 62
WD40 COG2319
WD40 repeat [General function prediction only];
11-167 2.89e-23

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 103.84  E-value: 2.89e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWeDLDDDDPKFINVGEKAYSCAL---KSGK-LVTAVSNNTIQVHTFPEGVP 86
Cdd:COG2319  244 GHSGSVRSVAFSPDGRLLASGSADGTVRLW-DLATGELLRTLTGHSGGVNSVafsPDGKlLASGSDDGTVRLWDLATGKL 322

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    87 DGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQIS 166
Cdd:COG2319  323 LRTLTGHTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHTGAVTSVAFSPDGRTLASGSADGTVRLWDLA 402


                 .
gi 5901892   167 D 167
Cdd:COG2319  403 T 403
WD40 COG2319
WD40 repeat [General function prediction only];
67-283 3.62e-17

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 85.35  E-value: 3.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892    67 LVTAVSNNTIQVHTFPEGVPDGILTRFTTNANHVVFNGDGTKIAAGSSDFLVKIVDVMDSSQQKTFRGHDAPVLSLSFDP 146
Cdd:COG2319    9 LAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   147 KDIFLASASCDGSVRVWQISDQTCAiswPLLQKCNDVINAksicrLAWQPKSGKLLAIPVEKSVKLYRRESWSHQFDLSD 226
Cdd:COG2319   89 DGRLLASASADGTVRLWDLATGLLL---RTLTGHTGAVRS-----VAFSPDGKTLASGSADGTVRLWDLATGKLLRTLTG 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 5901892   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 4.23e-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: 4.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   130 KTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVWQI--------------------------------SDQTCAIsWPL- 176
Cdd:cd00200    3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLetgellrtlkghtgpvrdvaasadgtylasgsSDKTIRL-WDLe 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892   177 LQKCNDVIN--AKSICRLAWQPKSGKLLAIPVEKSVKLYRRESWSHQFDLSDnfISQTLNIVTWSPCGQYLAAGSINGLI 254
Cdd:cd00200   82 TGECVRTLTghTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRG--HTDWVNSVAFSPDGTFVASSSQDGTI 159

                        170       180       190
                 ....*....|....*....|....*....|....
gi 5901892   255 IVWNVETKDCMERVKHEKGYaICGLAWHPTCGRI 288
Cdd:cd00200  160 KLWDLRTGKCVATLTGHTGE-VNSVAFSPDGEKL 192
HMG smart00398
high mobility group;
1017-1074 8.82e-10

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 55.78  E-value: 8.82e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 5901892     1017 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKGETA 1074
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 ...
 1017-1083 2.79e-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: 2.79e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 5901892  1017 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetasegtEAKKR 1083
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 5.43e-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: 5.43e-08
                            10        20        30
                    ....*....|....*....|....*....|....*....
gi 5901892      125 DSSQQKTFRGHDAPVLSLSFDPKDIFLASASCDGSVRVW 163
Cdd:smart00320    1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
WD40 pfam00400
WD domain, G-beta repeat;
126-163 6.07e-08

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 49.65  E-value: 6.07e-08
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 5901892     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 ...
 1017-1070 5.71e-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: 5.71e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 5901892  1017 RPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAK 1070
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLS-FTEISKLLGERWKELSEEEKQPYEEKAK 53
WD40 smart00320
WD40 repeats; Note that these repeats are permuted with respect to the structural repeats ...
 11-41 3.19e-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: 3.19e-05
                            10        20        30
                    ....*....|....*....|....*....|.
gi 5901892       11 GHTEGHTEVCFDDSGSFIVTCGSDGDVRIWE 41
Cdd:smart00320   10 GHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1016-1111 1.20e-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: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892  1016 QRPKTGFQMWLEENRSNILSDNPDFSdEADIIKEGMIRFRVLSTEERKVWANKAKgetaSEGTEAKKRKRVVDESDETEN 1095
Cdd:COG5648   72 KRPLSAYFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEAN----SDRERYQREKEEYNKKLPNKA 146

                         90
                 ....*....|....*.
gi 5901892  1096 QEEKAKENLNLSKKQK 1111
Cdd:COG5648  147 PIGPFIENEPKIRPKV 162
WD40 pfam00400
WD domain, G-beta repeat;
11-41 3.13e-04

WD domain, G-beta repeat;


Pssm-ID: 459801 [Multi-domain]  Cd Length: 39  Bit Score: 39.25  E-value: 3.13e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 5901892      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 ...
 1016-1089 4.81e-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: 39.74  E-value: 4.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5901892  1016 QRPKTGFQMWLEENRSNILSDNP--DFSDEADIIKEgmiRFRVLSTEERKVWANKAKgetasegTEAKKRKRVVDE 1089
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 1.40e-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: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     192 LAWQPKSgKLLAIPVEK-SVKLYRReSWSHQFDLSDNFISQTLNIVTWSPCGQYLAAGSINGLIIVWNVETKDCMERVKH 270
Cdd:pfam12894    1 MSWCPTM-DLIALATEDgELLLHRL-NWQRVWTLSPDKEDLEVTSLAWRPDGKLLAVGYSDGTVRLLDAENGKIVHHFSA 78

                           90
                   ....*....|.
gi 5901892     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 1.92e-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: 1.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5901892     193 AWQPKSGKLLAI--PVEKSVKLYrreswSHQFDLSDNFISQTLNIVTWSPCGQYLAA---GSINGLIIVWNVETKDCMER 267
Cdd:pfam08662   66 AWSPNGKEFAVIygYMPAKVSFF-----DLKGNVIHSFGEQPRNTIFWSPFGRLVLLagfGNLAGDIEFWDVVNKKKIAT 140

                           90
                   ....*....|....*..
gi 5901892     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 ...
 1016-1083 8.34e-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: 8.34e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 5901892  1016 QRPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAKGETaSEGTEAKKR 1083
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 ...
 1017-1074 8.98e-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: 8.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 5901892  1017 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAKGETA 1074
Cdd:cd22005    2 RPPTAFFLFLADFRKTYKKKNPDKSV-KAVGKAAGEKWKSMSDEEKAPYVEKAEKEKA 58
HMG_box pfam00505
HMG (high mobility group) box;
1017-1070 9.01e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.05  E-value: 9.01e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 5901892    1017 RPKTGFQMWLEENRSNILSDNPDFSDeADIIKEGMIRFRVLSTEERKVWANKAK 1070
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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