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Conserved domains on  [gi|1911157573|ref|XP_036195471|]
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nucleolar transcription factor 1 isoform X5 [Myotis myotis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 321-404 9.58e-45

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: 154.93  E-value: 9.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 321 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAANSS 400
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80


                  ....
gi 1911157573 401 KKMK 404
Cdd:pfam14887  81 KKMK 84
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 139-221 1.74e-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: 148.37  E-value: 1.74e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 139 PTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGE 218
Cdd:cd22000     1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                  ...
gi 1911157573 219 EKM 221
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 ...
 407-492 8.38e-39

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: 138.20  E-value: 8.38e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 407 GEPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLWVKSLSPQDRAA 486
Cdd:cd22003     1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                  ....*.
gi 1911157573 487 YKEYIS 492
Cdd:cd22003    81 YEEYST 86
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 38-112 5.44e-25

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: 98.48  E-value: 5.44e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDatTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDYIQKHPEL 112
Cdd:cd21999     1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPDF 73
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 247-312 1.57e-22

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: 91.59  E-value: 1.57e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22001     1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1-27 3.82e-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.


The actual alignment was detected with superfamily member cd21998:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 77  Bit Score: 48.09  E-value: 3.82e-07
                          10        20
                  ....*....|....*....|....*..
gi 1911157573   1 MKYIQDFQREKQEFERNLARFREDHPD 27
Cdd:cd21998    51 QKYIQDYEKEKEEYEQKMARFREEHPD 77
 
Name Accession Description Interval E-value
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 321-404 9.58e-45

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: 154.93  E-value: 9.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 321 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAANSS 400
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80


                  ....
gi 1911157573 401 KKMK 404
Cdd:pfam14887  81 KKMK 84
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 139-221 1.74e-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: 148.37  E-value: 1.74e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 139 PTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGE 218
Cdd:cd22000     1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                  ...
gi 1911157573 219 EKM 221
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 ...
 407-492 8.38e-39

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: 138.20  E-value: 8.38e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 407 GEPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLWVKSLSPQDRAA 486
Cdd:cd22003     1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                  ....*.
gi 1911157573 487 YKEYIS 492
Cdd:cd22003    81 YEEYST 86
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 322-393 2.45e-33

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: 122.30  E-value: 2.45e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1911157573 322 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP 393
Cdd:cd22002     1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEMRKP 72
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 38-112 5.44e-25

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: 98.48  E-value: 5.44e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDatTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDYIQKHPEL 112
Cdd:cd21999     1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPDF 73
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 247-312 1.57e-22

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: 91.59  E-value: 1.57e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22001     1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66
HMG_box pfam00505
HMG (high mobility group) box;
249-311 7.14e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 61.09  E-value: 7.14e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEK 63
HMG smart00398
high mobility group;
248-311 8.04e-12

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 61.18  E-value: 8.04e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573  248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEE 64
HMG smart00398
high mobility group;
38-105 8.23e-11

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 58.10  E-value: 8.23e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573   38 PEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
190-389 3.21e-10

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 60.65  E-value: 3.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 190 DQKKKDYEVELLRF---LESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQEGGKGSSEKPKRPVSAMFIFSEEKRRQ 266
Cdd:COG5648     9 PYLTLQAPLSLIIFhkmVFMSGIRQLHTTLVELEKPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDE 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 267 LQEERPELSESELTRLLARMWNDLSEKKKAKY--KAREAALKAQSERKPAGEREERGKLPESPKRAEEIWQQSVIGDYLa 344
Cdd:COG5648    89 IRKENPKLTFGEVGKLLSEKWKELTDEEKEPYykEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSP- 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1911157573 345 rfKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSE 389
Cdd:COG5648   168 --DKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210
HMG smart00398
high mobility group;
409-475 2.58e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 51.16  E-value: 2.58e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573  409 PKKPPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLW 475
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG smart00398
high mobility group;
139-200 1.05e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 49.24  E-value: 1.05e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573  139 PTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL 200
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKaenpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM 66
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1-27 3.82e-07

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: 48.09  E-value: 3.82e-07
                          10        20
                  ....*....|....*....|....*..
gi 1911157573   1 MKYIQDFQREKQEFERNLARFREDHPD 27
Cdd:cd21998    51 QKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG smart00398
high mobility group;
324-391 5.82e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 47.31  E-value: 5.82e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573  324 PESPKRAEEIWQQSVIGDYLARFKNDRVKAL-KAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR 391
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEIsKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
PTZ00121 PTZ00121
MAEBL; Provisional
 81-402 4.21e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 50.52  E-value: 4.21e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573   81 DKKRLKWIHKALEQRKEYEEIMRDYIQKHPELNISEEGITKSTLTKAERQLKDKFDGRptkpppnsyslycAELMANMKD 160
Cdd:PTZ00121  1222 DAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARK-------------ADELKKAEE 1288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  161 VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQE 240
Cdd:PTZ00121  1289 KKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEA 1368

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  241 GGKGSSEKPKRpvsamfifSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPagerEER 320
Cdd:PTZ00121  1369 AEKKKEEAKKK--------ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKA----DEA 1436

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  321 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTwNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAANSS 400
Cdd:PTZ00121  1437 KKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAK-KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515


                   ..
gi 1911157573  401 KK 402
Cdd:PTZ00121  1516 KK 1517
HMG_box pfam00505
HMG (high mobility group) box;
38-105 2.83e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 42.60  E-value: 2.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 139-203 1.07e-04

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


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 40.85  E-value: 1.07e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573 139 PTKP--PPNSYSLYCAELMANMKD----VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF 203
Cdd:pfam09011   1 PNKPkrARNAYAFFVQEMIPEHKRqnpvIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
PTZ00199 PTZ00199
high mobility group protein; Provisional
 249-314 2.73e-04

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 40.61  E-value: 2.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSE--SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPA 314
Cdd:PTZ00199   23 PKRALSAYMFFAKEKRAEIIAENPELAKdvAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKA 90
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
386-509 1.52e-03

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 40.62  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 386 ELSEMRAPPAAANSSKKMKFQGEPKKPpMNGYQKFSQ----ELLSNGelNHLPLKERMVEIGSRWQRISQSQKEHYKKLA 461
Cdd:COG5648    48 LLTKPRKKTKSKRLVRKKKDPNGPKRP-LSAYFLYSAenrdEIRKEN--PKLTFGEVGKLLSEKWKELTDEEKEPYYKEA 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1911157573 462 EEQQKQYKVHLDLWVKSLSPQDRAAykEYISNKRKSMTKLRGPNPKSS 509
Cdd:COG5648   125 NSDRERYQREKEEYNKKLPNKAPIG--PFIENEPKIRPKVEGPSPDKA 170
 
Name Accession Description Interval E-value
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 321-404 9.58e-45

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: 154.93  E-value: 9.58e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 321 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAANSS 400
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSS 80


                  ....
gi 1911157573 401 KKMK 404
Cdd:pfam14887  81 KKMK 84
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 139-221 1.74e-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: 148.37  E-value: 1.74e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 139 PTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGE 218
Cdd:cd22000     1 PTKPPPNGYSLFCAELMKNMKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVLGE 80


                  ...
gi 1911157573 219 EKM 221
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 ...
 407-492 8.38e-39

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: 138.20  E-value: 8.38e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 407 GEPKKPPMNGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLWVKSLSPQDRAA 486
Cdd:cd22003     1 GEPKKPPMSGYQLFSQEMLKNGELVHLSLKERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                  ....*.
gi 1911157573 487 YKEYIS 492
Cdd:cd22003    81 YEEYST 86
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 322-393 2.45e-33

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: 122.30  E-value: 2.45e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1911157573 322 KLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP 393
Cdd:cd22002     1 KLPELPKTAEEIWQQSVIEDYLARFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEMRKP 72
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 38-112 5.44e-25

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: 98.48  E-value: 5.44e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDatTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDYIQKHPEL 112
Cdd:cd21999     1 PKKPKTPFQLFYNKELKKLEPGTPD--KKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKKEHPDF 73
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 247-312 1.57e-22

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: 91.59  E-value: 1.57e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22001     1 EKPKRPISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEKK 66
HMG-box_UBF1_rpt3 cd22000
third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 409-488 7.25e-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: 70.18  E-value: 7.25e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 409 PKKPPMNGYQKFSQELLSNgeLNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLWVKSLSPQDRAAYK 488
Cdd:cd22000     1 PTKPPPNGYSLFCAELMKN--MKDVPSTERMVECSKQWKLLSQKEKDAYHKRCEQKKKQYEIELERFLESLPEEERERVL 78
HMG-box_UBF1_rpt6-like cd22003
sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 137-215 4.34e-14

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: 68.09  E-value: 4.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 137 GRPTKPPPNSYSLYCAELMANMKDVPST--ERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQR 214
Cdd:cd22003     1 GEPKKPPMSGYQLFSQEMLKNGELVHLSlkERMVEIAKRWKRLSESEKDKYKKKAEELQKQYKKKLDKYLKSLSPEERAA 80


                  .
gi 1911157573 215 V 215
Cdd:cd22003    81 Y 81
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 251-308 3.03e-12

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: 61.77  E-value: 3.03e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 251 RPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKER 58
HMG_box pfam00505
HMG (high mobility group) box;
249-311 7.14e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 61.09  E-value: 7.14e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEK 63
HMG smart00398
high mobility group;
248-311 8.04e-12

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 61.18  E-value: 8.04e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573  248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEE 64
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 249-317 4.27e-11

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


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 58.96  E-value: 4.27e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPAGER 317
Cdd:cd21979     3 PKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71
HMG smart00398
high mobility group;
38-105 8.23e-11

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 58.10  E-value: 8.23e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573   38 PEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
190-389 3.21e-10

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 60.65  E-value: 3.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 190 DQKKKDYEVELLRF---LESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQEGGKGSSEKPKRPVSAMFIFSEEKRRQ 266
Cdd:COG5648     9 PYLTLQAPLSLIIFhkmVFMSGIRQLHTTLVELEKPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDE 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 267 LQEERPELSESELTRLLARMWNDLSEKKKAKY--KAREAALKAQSERKPAGEREERGKLPESPKRAEEIWQQSVIGDYLa 344
Cdd:COG5648    89 IRKENPKLTFGEVGKLLSEKWKELTDEEKEPYykEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSP- 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1911157573 345 rfKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSE 389
Cdd:COG5648   168 --DKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYPE 210
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 248-308 3.91e-10

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: 56.50  E-value: 3.91e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573 248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22008     9 KPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEK 69
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 247-319 3.04e-09

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: 53.87  E-value: 3.04e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPAGEREE 319
Cdd:cd21998     2 DFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREE 74
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 249-314 1.78e-08

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: 51.98  E-value: 1.78e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPA 314
Cdd:cd01390    14 PKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAKDKKRYEEEKA 79
HMG-box_NHP10-like cd22016
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) ...
 249-298 2.04e-08

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: 51.57  E-value: 2.04e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEER----PELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22016     8 PKRPANAFFLFCQEQREKVREEYkeehQEIDHHDLTKALAQAWRNLDAEDKKPY 61
HMG smart00398
high mobility group;
409-475 2.58e-08

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 51.16  E-value: 2.58e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573  409 PKKPPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLW 475
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKAENpdLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY 69
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 249-298 3.19e-08

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


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 51.39  E-value: 3.19e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd21980     2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKY 51
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 142-196 3.29e-08

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: 50.59  E-value: 3.29e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 142 PPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDY 196
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKkenpDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 249-312 4.41e-08

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


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 50.66  E-value: 4.41e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd01389     1 IPRPPNAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEEHKLK 64
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 249-312 6.34e-08

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


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 49.95  E-value: 6.34e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22007     1 PKRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQE 64
HMG smart00398
high mobility group;
139-200 1.05e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 49.24  E-value: 1.05e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573  139 PTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL 200
Cdd:smart00398   1 KPKRPMSAFMLFSQENRAKIKaenpDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM 66
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 248-312 2.46e-07

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: 48.70  E-value: 2.46e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573 248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22004     1 HIKRPMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKE 65
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 249-301 2.54e-07

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: 48.05  E-value: 2.54e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAR 301
Cdd:cd22012     2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE 54
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 36-111 2.82e-07

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: 48.47  E-value: 2.82e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573  36 DIPEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDYIQKHPE 111
Cdd:cd21998     2 DFPKKPLTPYFRFFMEKRAKYAKKHPEMSNLELTKILSKKYKELPEKKKQKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 250-307 2.85e-07

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: 47.69  E-value: 2.85e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKA 307
Cdd:cd22005     1 KRPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKA 58
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 412-468 3.42e-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: 3.42e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 412 PPMNGYQKFSQELLSN--GELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQKQY 468
Cdd:cd00084     1 RPLSAYLLFSKEKRPKlkKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_UBF1_rpt1-like cd21998
first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1-27 3.82e-07

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: 48.09  E-value: 3.82e-07
                          10        20
                  ....*....|....*....|....*..
gi 1911157573   1 MKYIQDFQREKQEFERNLARFREDHPD 27
Cdd:cd21998    51 QKYIQDYEKEKEEYEQKMARFREEHPD 77
HMG smart00398
high mobility group;
324-391 5.82e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 47.31  E-value: 5.82e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573  324 PESPKRAEEIWQQSVIGDYLARFKNDRVKAL-KAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR 391
Cdd:smart00398   2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEIsKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 251-312 6.96e-07

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: 46.91  E-value: 6.96e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1911157573 251 RPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd21994     1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKA 62
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 249-311 7.51e-07

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


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 47.15  E-value: 7.51e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:cd22010     1 PKRPLSAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQRELSEYQK 63
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 250-308 9.96e-07

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


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 46.63  E-value: 9.96e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKA-----REAALKAQ 308
Cdd:cd21989     1 RRPMNAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDlakqyKEAFMKAN 64
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 250-308 1.51e-06

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


Pssm-ID: 438837 [Multi-domain]  Cd Length: 76  Bit Score: 46.19  E-value: 1.51e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22028     3 KRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQ 61
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 250-308 2.56e-06

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


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 45.31  E-value: 2.56e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd21984     1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQAEQ 59
PTZ00121 PTZ00121
MAEBL; Provisional
 81-402 4.21e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 50.52  E-value: 4.21e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573   81 DKKRLKWIHKALEQRKEYEEIMRDYIQKHPELNISEEGITKSTLTKAERQLKDKFDGRptkpppnsyslycAELMANMKD 160
Cdd:PTZ00121  1222 DAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARK-------------ADELKKAEE 1288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  161 VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQE 240
Cdd:PTZ00121  1289 KKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEA 1368

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  241 GGKGSSEKPKRpvsamfifSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPagerEER 320
Cdd:PTZ00121  1369 AEKKKEEAKKK--------ADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKA----DEA 1436

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  321 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTwNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAAANSS 400
Cdd:PTZ00121  1437 KKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAK-KKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515


                   ..
gi 1911157573  401 KK 402
Cdd:PTZ00121  1516 KK 1517
HMG-box_NSD2 cd21991
high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and ...
 248-301 5.50e-06

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


Pssm-ID: 438807 [Multi-domain]  Cd Length: 62  Bit Score: 44.23  E-value: 5.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAR 301
Cdd:cd21991     1 KKKVKKGQFEVFCQKHREEVAQEHPDLSEEEIEEYLKKQWNNMSEKQRARYKSK 54
HMG-box_UBF1_rpt2 cd21999
second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 324-392 6.89e-06

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: 44.55  E-value: 6.89e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 324 PESPKRAEEIWQQSVIGDYLaRFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA 392
Cdd:cd21999     1 PKKPKTPFQLFYNKELKKLE-PGTPDKKELKEKLREKWKQMSDKKKLKWINKALEDEKRYEEELKEYKK 68
PTZ00121 PTZ00121
MAEBL; Provisional
 30-387 9.04e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 49.37  E-value: 9.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573   30 QNAKKSDIPEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQwsqLSDKKRLKWIHKALEQRKEYEEIMRdyiqKH 109
Cdd:PTZ00121  1394 DEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKK---AEEAKKADEAKKKAEEAKKAEEAKK----KA 1466

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  110 PELNISEEGITKSTLTKAERQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERmvlcSQQWKLLSQKEKDAYHKKC 189
Cdd:PTZ00121  1467 EEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKK----ADEAKKAEEAKKADEAKKA 1542

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  190 DQKKKDYEV---ELLRFLESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQEGGKGSSEKPKRPVSAMFIfSEEKRRQ 266
Cdd:PTZ00121  1543 EEKKKADELkkaEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK-AEEAKIK 1621

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  267 LQEERPElsESELTRLLARMWNDLSEKKKA----------KYKAREAALKAQSERKPAGE----REERGKLPESPKRAEE 332
Cdd:PTZ00121  1622 AEELKKA--EEEKKKVEQLKKKEAEEKKKAeelkkaeeenKIKAAEEAKKAEEDKKKAEEakkaEEDEKKAAEALKKEAE 1699

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  333 IWQQSvigDYLARFKNDRVKalKAMEMTWNNMEKKEKLMWIKKAAEDQKRYEREL 387
Cdd:PTZ00121  1700 EAKKA---EELKKKEAEEKK--KAEELKKAEEENKIKAEEAKKEAEEDKKKAEEA 1749
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 249-301 1.22e-05

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: 43.40  E-value: 1.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAR 301
Cdd:cd21993     2 NKKKKSGFQLWLEENRSSIEEENPELSEAEIIKLAMQRFRALPKEEKQKWNEK 54
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 40-98 1.47e-05

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: 42.89  E-value: 1.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573  40 KPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEY 98
Cdd:cd00084     1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 249-312 1.62e-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: 43.30  E-value: 1.62e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEE-RPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22011     1 PKRPSSAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVE 65
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 139-198 2.60e-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: 42.27  E-value: 2.60e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 139 PTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEV 198
Cdd:cd22012     1 PPKRPASAYFLFAKEVRPKLKeenpNEKYTDITKLISEKWRSLDESEKEPYQEEYEKALEEYEE 64
HMG_box pfam00505
HMG (high mobility group) box;
38-105 2.83e-05

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 42.60  E-value: 2.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68
PTZ00121 PTZ00121
MAEBL; Provisional
 33-466 3.42e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.44  E-value: 3.42e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573   33 KKSDIPEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQ-WSQLSDKKRLKWIHKALEQRKeYEEIMRDYIQKHPE 111
Cdd:PTZ00121  1077 KDFDFDAKEDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEaKKKAEDARKAEEARKAEDARK-AEEARKAEDAKRVE 1155

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  112 LNISEEGITKSTLTKAERQLKDKFDGRPTKPPPNSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQ 191
Cdd:PTZ00121  1156 IARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEA 1235

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  192 KKKDYEVellRFLESLPEEEQQRVLGEEKMLNINKKQTTSPASKKPSQEGGKGSSEKPK----------RPVSAMFIFSE 261
Cdd:PTZ00121  1236 KKDAEEA---KKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKadeakkaeekKKADEAKKKAE 1312

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  262 EKRR--QLQEERPELSE-SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPAGER---EERGKLPESPKRAEEIWq 335
Cdd:PTZ00121  1313 EAKKadEAKKKAEEAKKkADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKkkeEAKKKADAAKKKAEEKK- 1391

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  336 qsvigdylarfKNDRVKAlKAMEMTWNNMEKKEKLMWIKKAAEDQKRYE--RELSEMRAPPAAANSSKKMKFQGEPKKPP 413
Cdd:PTZ00121  1392 -----------KADEAKK-KAEEDKKKADELKKAAAAKKKADEAKKKAEekKKADEAKKKAEEAKKADEAKKKAEEAKKA 1459

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1911157573  414 MNGYQKfSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQK 466
Cdd:PTZ00121  1460 EEAKKK-AEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKK 1511
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 250-306 3.99e-05

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


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 42.05  E-value: 3.99e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALK 306
Cdd:cd22006     1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEKYKEEK 57
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 246-298 4.49e-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: 43.01  E-value: 4.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 246 SEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22017    18 SNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRY 70
HMG-box_SoxF_SOX7 cd22046
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar ...
 241-308 5.03e-05

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


Pssm-ID: 438849 [Multi-domain]  Cd Length: 88  Bit Score: 42.37  E-value: 5.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 241 GGKGSSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22046     4 GEKGSEPRIRRPMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERLRVQ 71
HMG-box_SoxG_SOX15 cd22035
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and ...
 247-311 5.80e-05

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


Pssm-ID: 438844 [Multi-domain]  Cd Length: 84  Bit Score: 41.99  E-value: 5.80e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 311
Cdd:cd22035     6 EKVKRPMNAFMVWSSAQRRQMAQEHPKMHNSEISKRLGAAWKLLPEAEKRPFVEEAKRLRARHMR 70
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 248-312 6.97e-05

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: 41.51  E-value: 6.97e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573 248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd21983     4 PPEKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQ 68
HMG-box_UBF1_rpt5 cd22002
fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 38-105 7.89e-05

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: 41.41  E-value: 7.89e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKvRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:cd22002     3 PELPKTAEEIWQQSVIEDYLA-RFKNDRGKALKAMEATWNNMEKKEKLPWIKKAAEDQKRYERELSEM 69
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 139-203 1.07e-04

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


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 40.85  E-value: 1.07e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573 139 PTKP--PPNSYSLYCAELMANMKD----VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF 203
Cdd:pfam09011   1 PNKPkrARNAYAFFVQEMIPEHKRqnpvIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTY 71
HMG-box_HMO1-like cd22015
high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 ...
 249-301 1.35e-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: 40.55  E-value: 1.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAR 301
Cdd:cd22015     1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEKQLWEDK 53
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 39-100 1.53e-04

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: 40.36  E-value: 1.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  39 EKPKTPQQ--LWYTHEK-KVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEE 100
Cdd:cd22001     1 EKPKRPISamFIYSKEKrSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEALAKAEYEK 65
HMG-box_SoxE cd22031
high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) ...
 250-312 2.23e-04

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


Pssm-ID: 438840 [Multi-domain]  Cd Length: 75  Bit Score: 40.07  E-value: 2.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22031     3 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLSESEKRPFIEEAERLRVQHKKD 65
PTZ00199 PTZ00199
high mobility group protein; Provisional
 249-314 2.73e-04

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 40.61  E-value: 2.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSE--SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPA 314
Cdd:PTZ00199   23 PKRALSAYMFFAKEKRAEIIAENPELAKdvAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKA 90
HMG-box_SoxD cd22030
high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) ...
 250-322 3.18e-04

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


Pssm-ID: 438839 [Multi-domain]  Cd Length: 77  Bit Score: 39.99  E-value: 3.18e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQS-ERKPAGEREERGK 322
Cdd:cd22030     3 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKSMSNQEKQPYYEEQARLSKQHlEKYPDYKYKPRPK 76
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 141-209 3.55e-04

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: 39.44  E-value: 3.55e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 141 KPPPNSYSLYCAELMANMKDVPSTERMV-----LCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE 209
Cdd:cd22011     2 KRPSSAYFLFSQEIRKNLKSQGSPEEKVpelskRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKELPP 75
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 248-313 3.62e-04

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


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 39.31  E-value: 3.62e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 248 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKP 313
Cdd:pfam09011   3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREM 68
HMG-box_SoxC cd22029
high mobility group (HMG)-box found in group C SRY-related high-mobility group (HMG) box (Sox) ...
 250-298 7.76e-04

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


Pssm-ID: 438838 [Multi-domain]  Cd Length: 76  Bit Score: 38.57  E-value: 7.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22029     3 KRPMNAFMVWSQIERRKIMEQQPDMHNAEISKRLGKRWKLLSDSEKIPF 51
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 242-308 8.84e-04

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


Pssm-ID: 438850 [Multi-domain]  Cd Length: 81  Bit Score: 38.91  E-value: 8.84e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 242 GKGSSeKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22047     1 GKGES-RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
HMG-box_TOX-like cd21995
high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family ...
 250-317 1.05e-03

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.


Pssm-ID: 438811 [Multi-domain]  Cd Length: 70  Bit Score: 38.23  E-value: 1.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKPAGER 317
Cdd:cd21995     1 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKTEAAKKEYLKALAAYR 68
HMG-box_SoxB cd01388
high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) ...
 250-307 1.17e-03

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


Pssm-ID: 438790 [Multi-domain]  Cd Length: 80  Bit Score: 38.35  E-value: 1.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKA 307
Cdd:cd01388     4 KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSEAEKRPFIDEAKRLRA 61
HMG-box_SoxF cd22032
high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) ...
 250-298 1.21e-03

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


Pssm-ID: 438841 [Multi-domain]  Cd Length: 76  Bit Score: 38.17  E-value: 1.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22032     3 RRPMNAFMVWAKDERKRLADENPDLHNAELSKMLGKKWKSLSLAEKRPF 51
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 250-318 1.24e-03

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


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 37.91  E-value: 1.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY--KAREAALKAQSERKPAGERE 318
Cdd:cd21985     3 RKPMSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYeeKAAKDLERYNSQKKRAAEQP 73
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
386-509 1.52e-03

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 40.62  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 386 ELSEMRAPPAAANSSKKMKFQGEPKKPpMNGYQKFSQ----ELLSNGelNHLPLKERMVEIGSRWQRISQSQKEHYKKLA 461
Cdd:COG5648    48 LLTKPRKKTKSKRLVRKKKDPNGPKRP-LSAYFLYSAenrdEIRKEN--PKLTFGEVGKLLSEKWKELTDEEKEPYYKEA 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1911157573 462 EEQQKQYKVHLDLWVKSLSPQDRAAykEYISNKRKSMTKLRGPNPKSS 509
Cdd:COG5648   125 NSDRERYQREKEEYNKKLPNKAPIG--PFIENEPKIRPKVEGPSPDKA 170
HMG_box_5 pfam14887
HMG (high mobility group) box 5; Nucleolar transcription factor/upstream binding factor ...
 35-99 2.28e-03

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: 37.83  E-value: 2.28e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1911157573  35 SDIPEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKdSLGKQWSQLSDKKRLKWIHKALEQRKEYE 99
Cdd:pfam14887   1 GKLPESPKRAEEIWQQSVIGDYLARFKNDRVKALK-AMEMTWNNMEKKEKLMWIKKAAEDQKRYE 64
HMG_box pfam00505
HMG (high mobility group) box;
140-197 2.62e-03

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 36.82  E-value: 2.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1911157573 140 TKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE 197
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKaenpGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 409-481 2.85e-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: 37.13  E-value: 2.85e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 409 PKKPPmNGYQKFSQELLSNGELNHLPlKERMVEI----GSRWQRISQSQKEHYKKLAEEQQKQYKVHLDLWVKSLSP 481
Cdd:cd22011     1 PKRPS-SAYFLFSQEIRKNLKSQGSP-EEKVPELskraAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKELPP 75
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
83-310 2.93e-03

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


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 39.85  E-value: 2.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573  83 KRLKWIHKALEQRKEYEEIMRDYIQKHPEL-----NISEEGITKSTLTKAERQLKDKFDGRPTKPPPNSYSLYCA----E 153
Cdd:COG5648     9 PYLTLQAPLSLIIFHKMVFMSGIRQLHTTLvelekPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAenrdE 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 154 LMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPeeeqqrvlgeekmlninkkqttspa 233
Cdd:COG5648    89 IRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLP------------------------- 143

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 234 skkpsqeggkgssekPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSE 310
Cdd:COG5648   144 ---------------NKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYD 205
HMG-box_EGL13-like cd22042
high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 ...
 250-322 3.38e-03

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


Pssm-ID: 438848 [Multi-domain]  Cd Length: 78  Bit Score: 36.80  E-value: 3.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAAL-KAQSERKPAGEREERGK 322
Cdd:cd22042     4 KRPMNAFMVWAKDERRKILKACPDMHNSNISKILGAKWKAMSNAEKQPYYEEQSRLsKLHMEKHPDYRYRPRPK 77
HMG-box_SoxA_SRY cd22034
high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar ...
 247-312 3.40e-03

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


Pssm-ID: 438843 [Multi-domain]  Cd Length: 85  Bit Score: 37.31  E-value: 3.40e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1911157573 247 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd22034     3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 250-306 4.39e-03

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


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 36.67  E-value: 4.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALK 306
Cdd:cd21990     3 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVK 59
HMG-box_SoxH_SOX30 cd22033
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and ...
 250-308 4.77e-03

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


Pssm-ID: 438842 [Multi-domain]  Cd Length: 75  Bit Score: 36.24  E-value: 4.77e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22033     3 KRPMNAFMVWARIHRPALAKANPNANNADISVQLGEEWNKLTEEQKKPYYDEAQKLKEQ 61
HMG-box_HMO1-like cd22015
high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 ...
 38-105 5.03e-03

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: 36.32  E-value: 5.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1911157573  38 PEKPKTPQQLWYTHEKKVYLKVRPDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:cd22015     1 PKKPLTPYFAFSNHVRPQLKAERPKASPTEIAEEISERWANLSDEEKQLWEDKYEEEMKEYQKALEAY 68
HMG-box_HMGXB4 cd21982
high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar ...
 250-306 5.63e-03

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


Pssm-ID: 438798 [Multi-domain]  Cd Length: 61  Bit Score: 35.72  E-value: 5.63e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALK 306
Cdd:cd21982     2 KKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKLVWKQKAQYLQ 58
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 249-298 5.66e-03

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


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 36.49  E-value: 5.66e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22018     2 PKAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRY 51
HMG-box_SoxC_SOX12 cd22038
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and ...
 250-298 5.88e-03

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


Pssm-ID: 438847 [Multi-domain]  Cd Length: 88  Bit Score: 36.58  E-value: 5.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd22038    13 KRPMNAFMVWSQIERRKIMEQWPDMHNAEISKRLGRRWKLLQDYEKIPF 61
HMG-box_SoxF_SOX18 cd22048
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and ...
 250-308 6.71e-03

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


Pssm-ID: 438851 [Multi-domain]  Cd Length: 80  Bit Score: 36.20  E-value: 6.71e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1911157573 250 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQ 308
Cdd:cd22048     5 RRPMNAFMVWAKDERKRLAQQNPDLHNAVLSKMLGQSWKSLSAAEKRPFVEEAERLRVQ 63
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 249-312 7.63e-03

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


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 35.76  E-value: 7.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1911157573 249 PKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 312
Cdd:cd21977     1 KKKWVNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRARELSQLHNRK 64
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 139-203 8.06e-03

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: 36.08  E-value: 8.06e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573 139 PTKP--PPNSYSLYCAE----LMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRF 203
Cdd:cd22008     7 PNKPkkPASSYLLFGKEyrkkLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAVLMEKYKKEVEEY 77
HMG-box_HMGXB3 cd21981
high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar ...
 219-298 8.92e-03

high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar proteins; HMGXB3, also called HMG box-containing protein 3, or protein SMF, is involved in DNA-damage repair and cell-cycle regulation.


Pssm-ID: 438797 [Multi-domain]  Cd Length: 105  Bit Score: 36.39  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1911157573 219 EKMLNINKKQTTSPASKKPSQEGGKGSSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 298
Cdd:cd21981    10 EEIEGCYTYTSPVPPKKKKKSKEQAEQGEKAKKPRSAYLLYYYDIHLKVQQEFPHLPQSEINKKISESWKLLSVAEKSYY 89
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 38-105 9.65e-03

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: 35.35  E-value: 9.65e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1911157573  38 PEKPKTPqqlWYTHEKKVYLKVR---PDATTKEVKDSLGKQWSQLSDKKRLKWIHKALEQRKEYEEIMRDY 105
Cdd:cd21983     5 PEKPLMP---YMRYSRKVWDQVKasnPDLKLWEIGKIIGQMWRELSDEEKQEYIEEYEAEKVEYEEQMKAY 72
 
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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