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Conserved domains on  [gi|41055925|ref|NP_957297|]
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upstream binding transcription factor, like [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 297-379 1.24e-42

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


:

Pssm-ID: 438816 [Multi-domain]  Cd Length: 83  Bit Score: 148.76  E-value: 1.24e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 297 PTKPPPNGYSLYCAELMVNMKDVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRFLESLPDEERERVMGE 376
Cdd:cd22000   1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                ...
gi 41055925 377 EKL 379
Cdd:cd22000  81 EKA 83
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 523-608 3.88e-36

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


:

Pssm-ID: 438819 [Multi-domain]  Cd Length: 86  Bit Score: 130.88  E-value: 3.88e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 523 GEPKKPPVSGYQMFSQELLTNGELNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSPQERAV 602
Cdd:cd22003   1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                ....*.
gi 41055925 603 YKEFSS 608
Cdd:cd22003  81 YEEYST 86
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 111-187 5.86e-30

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


:

Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 112.80  E-value: 5.86e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 111 PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFKEDHPD 187
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 433-508 3.74e-27

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


:

Pssm-ID: 438818 [Multi-domain]  Cd Length: 72  Bit Score: 104.97  E-value: 3.74e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41055925 433 RLPETPKTPEEMWQQSVIGDYLAKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYEvqyrtvRELLEMR 508
Cdd:cd22002   1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYE------RELSEMR 70
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 198-271 6.46e-24

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


:

Pssm-ID: 438815 [Multi-domain]  Cd Length: 73  Bit Score: 95.40  E-value: 6.46e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 198 PEKPKTPQQLWYNHEKKTYMKIHPEvsQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAYIEAHPD 271
Cdd:cd21999   1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPD 72
 
Name Accession Description Interval E-value
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 297-379 1.24e-42

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


Pssm-ID: 438816 [Multi-domain]  Cd Length: 83  Bit Score: 148.76  E-value: 1.24e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 297 PTKPPPNGYSLYCAELMVNMKDVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRFLESLPDEERERVMGE 376
Cdd:cd22000   1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                ...
gi 41055925 377 EKL 379
Cdd:cd22000  81 EKA 83
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 523-608 3.88e-36

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


Pssm-ID: 438819 [Multi-domain]  Cd Length: 86  Bit Score: 130.88  E-value: 3.88e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 523 GEPKKPPVSGYQMFSQELLTNGELNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSPQERAV 602
Cdd:cd22003   1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                ....*.
gi 41055925 603 YKEFSS 608
Cdd:cd22003  81 YEEYST 86
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 111-187 5.86e-30

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


Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 112.80  E-value: 5.86e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 111 PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFKEDHPD 187
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 433-508 3.74e-27

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


Pssm-ID: 438818 [Multi-domain]  Cd Length: 72  Bit Score: 104.97  E-value: 3.74e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41055925 433 RLPETPKTPEEMWQQSVIGDYLAKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYEvqyrtvRELLEMR 508
Cdd:cd22002   1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYE------RELSEMR 70
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 432-509 6.52e-27

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.


Pssm-ID: 434287 [Multi-domain]  Cd Length: 84  Bit Score: 104.47  E-value: 6.52e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925   432 TRLPETPKTPEEMWQQSVIGDYLAKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYEvqyrtvRELLEMRT 509
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYE------RELSEMRA 72
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 198-271 6.46e-24

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


Pssm-ID: 438815 [Multi-domain]  Cd Length: 73  Bit Score: 95.40  E-value: 6.46e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 198 PEKPKTPQQLWYNHEKKTYMKIHPEvsQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAYIEAHPD 271
Cdd:cd21999   1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPD 72
HMG_box pfam00505
HMG (high mobility group) box;
114-181 6.40e-11

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 58.39  E-value: 6.40e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925   114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARF 181
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
85-262 2.81e-08

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 54.87  E-value: 2.81e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925  85 RTMTELIVDAIEYVKNPYKGKKLKTH------PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEK 158
Cdd:COG5648  36 TTLVELEKPLQQLLTKPRKKTKSKRLvrkkkdPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDE 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 159 KKLKYIQEFQREKESFEKnmarfkedhpdLIEERKKSDLPEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQ 238
Cdd:COG5648 116 EKEPYYKEANSDRERYQR-----------EKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSE 184

                       170       180
                ....*....|....*....|....
gi 41055925 239 LSDKKRLKWISKALELQKHYEDTM 262
Cdd:COG5648 185 LDESKKKKYIDKYKKLKEEYDSFY 208
HMG smart00398
high mobility group;
198-265 3.28e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.78  E-value: 3.28e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925    198 PEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAY 265
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG smart00398
high mobility group;
114-182 5.40e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 47.31  E-value: 5.40e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG smart00398
high mobility group;
525-591 1.21e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.54  E-value: 1.21e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    525 PKKPPVSGYQMFSQELLTNGELNH--FSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAW 591
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG smart00398
high mobility group;
297-361 2.01e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 2.01e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    297 PTKPPPNGYSLYCAELMVNMK----DVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRF 361
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKaenpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 195-259 2.68e-05

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.


Pssm-ID: 434287 [Multi-domain]  Cd Length: 84  Bit Score: 43.22  E-value: 2.68e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055925   195 SDLPEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKeALRRQWSQLSDKKRLKWISKALELQKHYE 259
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALK-AMEMTWNNMEKKEKLMWIKKAAEDQKRYE 64
 
Name Accession Description Interval E-value
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 297-379 1.24e-42

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


Pssm-ID: 438816 [Multi-domain]  Cd Length: 83  Bit Score: 148.76  E-value: 1.24e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 297 PTKPPPNGYSLYCAELMVNMKDVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRFLESLPDEERERVMGE 376
Cdd:cd22000   1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                ...
gi 41055925 377 EKL 379
Cdd:cd22000  81 EKA 83
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 523-608 3.88e-36

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


Pssm-ID: 438819 [Multi-domain]  Cd Length: 86  Bit Score: 130.88  E-value: 3.88e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 523 GEPKKPPVSGYQMFSQELLTNGELNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSPQERAV 602
Cdd:cd22003   1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                ....*.
gi 41055925 603 YKEFSS 608
Cdd:cd22003  81 YEEYST 86
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 111-187 5.86e-30

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


Pssm-ID: 438814 [Multi-domain]  Cd Length: 77  Bit Score: 112.80  E-value: 5.86e-30
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 111 PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFKEDHPD 187
Cdd:cd21998   1 PDFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 433-508 3.74e-27

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


Pssm-ID: 438818 [Multi-domain]  Cd Length: 72  Bit Score: 104.97  E-value: 3.74e-27
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41055925 433 RLPETPKTPEEMWQQSVIGDYLAKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYEvqyrtvRELLEMR 508
Cdd:cd22002   1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYE------RELSEMR 70
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 432-509 6.52e-27

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.


Pssm-ID: 434287 [Multi-domain]  Cd Length: 84  Bit Score: 104.47  E-value: 6.52e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925   432 TRLPETPKTPEEMWQQSVIGDYLAKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYEvqyrtvRELLEMRT 509
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYE------RELSEMRA 72
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 198-271 6.46e-24

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


Pssm-ID: 438815 [Multi-domain]  Cd Length: 73  Bit Score: 95.40  E-value: 6.46e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 198 PEKPKTPQQLWYNHEKKTYMKIHPEvsQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAYIEAHPD 271
Cdd:cd21999   1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPD 72
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 295-373 3.48e-17

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


Pssm-ID: 438819 [Multi-domain]  Cd Length: 86  Bit Score: 76.95  E-value: 3.48e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 295 GRPTKPPPNGYSLYCAELMVNMKDVPST--ERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRFLESLPDEERER 372
Cdd:cd22003   1 GEPKKPPMSGYQLFSQEMLKNGELVHLSlkERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                .
gi 41055925 373 V 373
Cdd:cd22003  81 Y 81
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 525-604 4.22e-15

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


Pssm-ID: 438816 [Multi-domain]  Cd Length: 83  Bit Score: 70.95  E-value: 4.22e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 525 PKKPPVSGYQMFSQELLTNgeLNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSPQERAVYK 604
Cdd:cd22000   1 PTKPPPNGYSLFCAELMKN--MKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVL 78
HMG_box pfam00505
HMG (high mobility group) box;
114-181 6.40e-11

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 58.39  E-value: 6.40e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925   114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARF 181
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 114-181 1.31e-09

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: 54.85  E-value: 1.31e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARF 181
Cdd:cd22010   1 PKRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQKAKAEF 68
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 111-182 2.21e-08

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


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 51.53  E-value: 2.21e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41055925 111 PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd21983   2 PKPPEKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQMKAYH 73
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
85-262 2.81e-08

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 54.87  E-value: 2.81e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925  85 RTMTELIVDAIEYVKNPYKGKKLKTH------PDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEK 158
Cdd:COG5648  36 TTLVELEKPLQQLLTKPRKKTKSKRLvrkkkdPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDE 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 159 KKLKYIQEFQREKESFEKnmarfkedhpdLIEERKKSDLPEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQ 238
Cdd:COG5648 116 EKEPYYKEANSDRERYQR-----------EKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSE 184

                       170       180
                ....*....|....*....|....
gi 41055925 239 LSDKKRLKWISKALELQKHYEDTM 262
Cdd:COG5648 185 LDESKKKKYIDKYKKLKEEYDSFY 208
HMG smart00398
high mobility group;
198-265 3.28e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 50.78  E-value: 3.28e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925    198 PEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAY 265
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 300-354 1.95e-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: 48.28  E-value: 1.95e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 300 PPPNGYSLYCAELMVNMK----DVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQY 354
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKkenpDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 112-176 2.44e-07

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


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 48.06  E-value: 2.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055925 112 DFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEK 176
Cdd:cd22001   1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEK 65
HMG smart00398
high mobility group;
114-182 5.40e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 47.31  E-value: 5.40e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 435-495 9.19e-07

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


Pssm-ID: 438815 [Multi-domain]  Cd Length: 73  Bit Score: 46.86  E-value: 9.19e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41055925 435 PETPKTPEEMWQQSVIGDYLaKYRSDRKKAQNAMDAAWKAMEKKEKIPWIKKAAEDQKRYE 495
Cdd:cd21999   1 PKKPKTPFQLFYNKELKKLE-PGTPDKKELKEKLREKWKQMSDKKKLKWINKALEDEKRYE 60
HMG smart00398
high mobility group;
525-591 1.21e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 46.54  E-value: 1.21e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    525 PKKPPVSGYQMFSQELLTNGELNH--FSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAW 591
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 528-584 1.54e-06

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: 45.59  E-value: 1.54e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 528 PPVSGYQMFSQELLTN--GELNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEY 584
Cdd:cd00084   1 RPLSAYLLFSKEKRPKlkKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 108-178 1.72e-06

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


Pssm-ID: 438832 [Multi-domain]  Cd Length: 79  Bit Score: 46.17  E-value: 1.72e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055925 108 KTHPDFPKKPLTPYFRFFMEKR----AKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNM 178
Cdd:cd22016   2 EKDPNAPKRPANAFFLFCQEQRekvrEEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEM 76
HMG smart00398
high mobility group;
297-361 2.01e-06

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 45.77  E-value: 2.01e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925    297 PTKPPPNGYSLYCAELMVNMK----DVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRF 361
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKaenpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 299-366 7.42e-06

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 44.45  E-value: 7.42e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055925 299 KPPPNGYSLYCAELMVNMKDVPSTERMV-----LCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDLQRFLESLP 366
Cdd:cd22011   2 KRPSSAYFLFSQEIRKNLKSQGSPEEKVpelskRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKELP 74
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 200-258 8.42e-06

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: 43.66  E-value: 8.42e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 200 KPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHY 258
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 116-174 9.66e-06

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: 43.66  E-value: 9.66e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 116 KPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESF 174
Cdd:cd00084   1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 114-182 1.36e-05

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


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 43.69  E-value: 1.36e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd21980   2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQ 70
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 114-176 2.44e-05

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


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 42.66  E-value: 2.44e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEK 176
Cdd:cd22012   2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYEE 64
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 195-259 2.68e-05

HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.


Pssm-ID: 434287 [Multi-domain]  Cd Length: 84  Bit Score: 43.22  E-value: 2.68e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41055925   195 SDLPEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKeALRRQWSQLSDKKRLKWISKALELQKHYE 259
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALK-AMEMTWNNMEKKEKLMWIKKAAEDQKRYE 64
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 114-183 3.86e-05

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


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 42.65  E-value: 3.86e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFKE 183
Cdd:cd22018   2 PKAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAERDKQQYMKELREYQQ 71
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 103-196 6.91e-05

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B.


Pssm-ID: 438833 [Multi-domain]  Cd Length: 104  Bit Score: 42.63  E-value: 6.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055925 103 KGKKLKTHPDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd22017  10 KRKKPLRDSNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEKDKERYMKELEQYQ 89

                        90
                ....*....|....
gi 41055925 183 EDHPDLIEERKKSD 196
Cdd:cd22017  90 KTEAYKLFSRKAQD 103
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 105-182 7.08e-05

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


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 41.86  E-value: 7.08e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925 105 KKLKTHPDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd22008   1 KNKNVDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEYN 78
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 196-259 7.20e-05

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


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 41.13  E-value: 7.20e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 196 DLPEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYE 259
Cdd:cd22001   1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYE 64
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 525-597 7.21e-05

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 41.75  E-value: 7.21e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 525 PKKPPvSGYQMFSQELLTNgELNHFSLKERMVEIGKR----WHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSP 597
Cdd:cd22011   1 PKRPS-SAYFLFSQEIRKN-LKSQGSPEEKVPELSKRaaeqWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKELPP 75
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 197-259 1.54e-04

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


Pssm-ID: 438818 [Multi-domain]  Cd Length: 72  Bit Score: 40.64  E-value: 1.54e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055925 197 LPEKPKTPQQLWYNHEKKTYMKIHpEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYE 259
Cdd:cd22002   2 LPELPKTAEEIWQQSVIEDYLARF-KNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYE 63
HMG-box_HMO1-like cd22015
high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 ...
 114-181 2.13e-04

high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 (HMO1) and similar proteins; HMO1, also called high spontaneous mutagenesis protein 2 (HSM2), is a DNA-binding protein that is probably part of the rDNA transcription apparatus. It acts synergetically with the RPA49 subunit of RNA polymerase I during rDNA transcription. It may participate in mutagenesis control.


Pssm-ID: 438831 [Multi-domain]  Cd Length: 68  Bit Score: 40.17  E-value: 2.13e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARF 181
Cdd:cd22015   1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEKQLWEDKYEEEMKEYQKALEAY 68
HMG_box pfam00505
HMG (high mobility group) box;
198-265 2.41e-04

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 39.90  E-value: 2.41e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925   198 PEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAY 265
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG-box_HMO1-like cd22015
high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 ...
 198-265 3.99e-04

high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 (HMO1) and similar proteins; HMO1, also called high spontaneous mutagenesis protein 2 (HSM2), is a DNA-binding protein that is probably part of the rDNA transcription apparatus. It acts synergetically with the RPA49 subunit of RNA polymerase I during rDNA transcription. It may participate in mutagenesis control.


Pssm-ID: 438831 [Multi-domain]  Cd Length: 68  Bit Score: 39.40  E-value: 3.99e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925 198 PEKPKTPQQLWYNHEKKTYMKIHPEVSQKELKEALRRQWSQLSDKKRLKWISKALELQKHYEDTMRAY 265
Cdd:cd22015   1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEKQLWEDKYEEEMKEYQKALEAY 68
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 297-355 7.45e-04

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


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 38.42  E-value: 7.45e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055925 297 PTKPPPNGYSLYCAE----LMVNMKDVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYE 355
Cdd:cd22012   1 PPKRPASAYFLFAKEvrpkLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYE 63
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 525-586 1.27e-03

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


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 37.65  E-value: 1.27e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 525 PKKPpVSGYQMFSQELLTN--GELNHFSLKERMVEIGKRWHKLSQSQKDKYKKQVEEQQLEYKA 586
Cdd:cd22012   2 PKRP-ASAYFLFAKEVRPKlkEENPNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYEE 64
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 116-182 1.55e-03

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: 37.66  E-value: 1.55e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 116 KPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd21994   1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 114-186 2.15e-03

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 37.52  E-value: 2.15e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055925 114 PKKPLTPYFRFFMEKRAKYAKI-HPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFKEDHP 186
Cdd:cd22011   1 PKRPSSAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKELP 74
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 106-182 3.14e-03

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


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 37.15  E-value: 3.14e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41055925 106 KLKTHPDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARFK 182
Cdd:cd22013   1 KKKKDPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYK 77
HMG-box_CMB1-like cd22014
high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 ...
 299-358 3.82e-03

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


Pssm-ID: 438830 [Multi-domain]  Cd Length: 62  Bit Score: 36.19  E-value: 3.82e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41055925 299 KPPPNGYSLYCAELMVN-MKDVPSTERMVLCSKQWKMMTQKEKDAFQKRCEQKKKQYEIDL 358
Cdd:cd22014   2 KRPPSPFLLFMEEFRRNeDNGKNLVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 198-251 5.71e-03

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: 35.70  E-value: 5.71e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 41055925 198 PEKPKTPQQLWYNHEKKTYMKIHPEVSQKEL-KEALrRQWSQLSDKKRLKWISKA 251
Cdd:cd21993   2 NKKKKSGFQLWLEENRSSIEEENPELSEAEIiKLAM-QRFRALPKEEKQKWNEKA 55
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 527-599 7.07e-03

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


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 35.99  E-value: 7.07e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41055925 527 KPPVSGYQMFSQE-----LLTNGELNhFSLKERMveIGKRWHKLSQSQKDKYKKQVEEQQLEYKAELEAWVKSLSPQE 599
Cdd:cd21980   3 KAPLTGYVRFLNErreklRAENPDLS-FPEITKI--LGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQQTEAYKA 77
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 103-181 7.24e-03

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


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 36.19  E-value: 7.24e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055925 103 KGKKLKTHPDFPKKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKESFEKNMARF 181
Cdd:cd01390   3 KKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKAAY 81
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 115-187 7.85e-03

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


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 35.60  E-value: 7.85e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055925 115 KKPLTPYFRFFMEKRAKYAKIHPEMSNLDLTKILSKKYKELPEKKKLKYIQEFQREKEsfeknmaRFKEDHPD 187
Cdd:cd22004   3 KRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLRE-------EHKKEYPD 68
 
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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