Citrus Sinensis ID: 031973

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150
MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAEENESDKSKSEVNDEDDEEGSGEVFLQLLTY
cccccccHHHHcHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHcc
cccccccccHHHHHHHHHHccccccccccccccccccccccccccEEEEEHHHHcHHHHHcccccccHHHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEEcccc
mkggrskadavgtdsklkskgaragkrtakpkaakdpnkpkrppsaFFVFMEEFRKQFkeahpnnksvaTVGKAAGEkwksmsedekapFVERAEKRKSDYNKNMQDYNKQLADGVnaaeenesdksksevndeddeegsgEVFLQLLTY
mkggrskadavgtdsklkskgaragkrtakpkaakdpnkpkrpPSAFFVFMEEFRKQFkeahpnnksvatvgkaagekwksmsedekapfveraekrksdynkNMQDYNKQLADGVNAaeenesdksksevndeddeegsgevflqllty
MKGGRSKADAVGTDSKLKSKGARAGKRTakpkaakdpnkpkrppSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAEENESDKSKSEVNDEDDEEGSGEVFLQLLTY
**********************************************FFVFMEE*************************************************************************************************
*****************************************RPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM**************************************FLQLLTY
*****************************************RPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADG*************************GEVFLQLLTY
*****************KSKGARA*************NKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQ****************************SGEVFLQLLTY
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFxxxxxxxxxxxxxxxxxxxxxLADGVxxxxxxxxxxxxxxxxxxxxxEGSGEVFLQLLTY
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query150 2.2.26 [Sep-21-2011]
Q42344138 High mobility group B pro yes no 0.88 0.956 0.615 2e-41
P40619144 HMG1/2-like protein OS=Ip N/A no 0.88 0.916 0.623 8e-36
P93047141 High mobility group B pro no no 0.833 0.886 0.598 4e-34
O49596144 High mobility group B pro no no 0.846 0.881 0.593 6e-33
P26585152 HMG1/2-like protein OS=Gl no no 0.766 0.756 0.613 2e-32
P40620149 HMG1/2-like protein OS=Vi N/A no 0.86 0.865 0.591 3e-32
O49595178 High mobility group B pro no no 0.686 0.578 0.601 2e-29
P27347157 DNA-binding protein MNB1B N/A no 0.726 0.694 0.633 3e-29
O49597125 High mobility group B pro no no 0.726 0.872 0.495 5e-29
P40621161 HMG1/2-like protein OS=Tr N/A no 0.726 0.677 0.619 5e-26
>sp|Q42344|HMGB4_ARATH High mobility group B protein 4 OS=Arabidopsis thaliana GN=HMGB4 PE=1 SV=1 Back     alignment and function desciption
 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 85/138 (61%), Positives = 112/138 (81%), Gaps = 6/138 (4%)

Query: 1   MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKE 60
           MKGG SKA+A  TD +LK++G +AGK+T K     DPN+PKRPPSAFFVF+E+FRK+F  
Sbjct: 1   MKGGESKAEATSTDQRLKTRGRKAGKKTKK-----DPNQPKRPPSAFFVFLEDFRKEFNL 55

Query: 61  AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAE 120
           A+PNNKSVATVGKAAG +WK+M++++KAP+V +AE RK++Y KN+Q YN +LA G N  E
Sbjct: 56  ANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNLKLASGTN-RE 114

Query: 121 ENESDKSKSEVNDEDDEE 138
           E++SDKSKSEV++   EE
Sbjct: 115 EDDSDKSKSEVDEAVSEE 132
Binds preferentially double-stranded DNA.
Arabidopsis thaliana (taxid: 3702)
>sp|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil PE=2 SV=1 Back     alignment and function description
>sp|P93047|HMGB3_ARATH High mobility group B protein 3 OS=Arabidopsis thaliana GN=HMGB3 PE=1 SV=1 Back     alignment and function description
>sp|O49596|HMGB2_ARATH High mobility group B protein 2 OS=Arabidopsis thaliana GN=HMGB2 PE=1 SV=1 Back     alignment and function description
>sp|P26585|HMGL_SOYBN HMG1/2-like protein OS=Glycine max PE=2 SV=1 Back     alignment and function description
>sp|P40620|HMGL_VICFA HMG1/2-like protein OS=Vicia faba PE=2 SV=1 Back     alignment and function description
>sp|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 SV=1 Back     alignment and function description
>sp|P27347|MNB1B_MAIZE DNA-binding protein MNB1B OS=Zea mays GN=MNB1B PE=1 SV=1 Back     alignment and function description
>sp|O49597|HMGB5_ARATH High mobility group B protein 5 OS=Arabidopsis thaliana GN=HMGB5 PE=2 SV=1 Back     alignment and function description
>sp|P40621|HMGL_WHEAT HMG1/2-like protein OS=Triticum aestivum PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query150
297836478143 hypothetical protein ARALYDRAFT_480649 [ 0.913 0.958 0.630 1e-43
296088654154 unnamed protein product [Vitis vinifera] 0.88 0.857 0.715 3e-42
118484838144 unknown [Populus trichocarpa] 0.846 0.881 0.704 9e-42
224081483144 high mobility group family [Populus tric 0.846 0.881 0.696 2e-41
359476973156 PREDICTED: high mobility group B2 protei 0.88 0.846 0.683 5e-41
15227862138 high mobility group B4 protein [Arabidop 0.88 0.956 0.615 1e-39
2832355138 HMG protein [Arabidopsis thaliana] 0.88 0.956 0.623 1e-39
145328748134 high mobility group B4 protein [Arabidop 0.873 0.977 0.614 1e-39
21592453138 putative HMG protein [Arabidopsis thalia 0.88 0.956 0.615 2e-39
13877775138 putative HMG protein [Arabidopsis thalia 0.88 0.956 0.608 1e-38
>gi|297836478|ref|XP_002886121.1| hypothetical protein ARALYDRAFT_480649 [Arabidopsis lyrata subsp. lyrata] gi|297331961|gb|EFH62380.1| hypothetical protein ARALYDRAFT_480649 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
 Score =  181 bits (458), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 92/146 (63%), Positives = 115/146 (78%), Gaps = 9/146 (6%)

Query: 1   MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKE 60
           MKGG SKA+A  TD +LK++G + GK+T K     DPN+PKRPPSAFFVF+E+FRK+F  
Sbjct: 1   MKGGESKAEATSTDQRLKTRGRKPGKKTKK-----DPNQPKRPPSAFFVFLEDFRKEFNL 55

Query: 61  AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAE 120
           A+PNNKSVATVGKAAG +WKSM+E++KAP+V +AE RK++Y K MQ YN +LA G N  E
Sbjct: 56  ANPNNKSVATVGKAAGARWKSMTEEDKAPYVAKAESRKTEYLKTMQQYNMKLASGTNRGE 115

Query: 121 ENESDKSKSEVNDEDDEEGSGEVFLQ 146
           E++SDKSKSEV    DE GS EVF+Q
Sbjct: 116 EDDSDKSKSEV----DEAGSEEVFMQ 137

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|296088654|emb|CBI37645.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|118484838|gb|ABK94286.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224081483|ref|XP_002306429.1| high mobility group family [Populus trichocarpa] gi|222855878|gb|EEE93425.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359476973|ref|XP_002280084.2| PREDICTED: high mobility group B2 protein-like isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
>gi|15227862|ref|NP_179347.1| high mobility group B4 protein [Arabidopsis thaliana] gi|145323080|ref|NP_001031364.2| high mobility group B4 protein [Arabidopsis thaliana] gi|310947092|sp|Q42344.1|HMGB4_ARATH RecName: Full=High mobility group B protein 4; AltName: Full=High mobility group protein G; Short=AtHMGgamma; Short=HMG gamma; AltName: Full=Nucleosome/chromatin assembly factor group D 04; Short=Nucleosome/chromatin assembly factor group D 4 gi|13926177|gb|AAK49570.1|AF370562_1 putative HMG protein [Arabidopsis thaliana] gi|4914377|gb|AAD32913.1| putative HMG protein [Arabidopsis thaliana] gi|23297615|gb|AAN12992.1| putative HMG protein [Arabidopsis thaliana] gi|330251557|gb|AEC06651.1| high mobility group B4 protein [Arabidopsis thaliana] gi|330251558|gb|AEC06652.1| high mobility group B4 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|2832355|emb|CAA74403.1| HMG protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|145328748|ref|NP_001077909.1| high mobility group B4 protein [Arabidopsis thaliana] gi|222423535|dbj|BAH19737.1| AT2G17560 [Arabidopsis thaliana] gi|330251559|gb|AEC06653.1| high mobility group B4 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|21592453|gb|AAM64404.1| putative HMG protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|13877775|gb|AAK43965.1|AF370150_1 putative HMG protein [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query150
TAIR|locus:2053893138 HMGB4 "high mobility group B4" 0.88 0.956 0.550 1.1e-34
TAIR|locus:505006135144 HMGB2 "high mobility group B2" 0.92 0.958 0.517 2e-31
TAIR|locus:2128003125 HMGB5 "high mobility group B5" 0.826 0.992 0.384 1.6e-22
UNIPROTKB|Q32L31200 HMGB3 "High mobility group pro 0.853 0.64 0.352 1.8e-14
UNIPROTKB|P40618202 HMGB3 "High mobility group pro 0.86 0.638 0.352 6.2e-14
TAIR|locus:2154433241 HMGB6 "high-mobility group box 0.653 0.406 0.343 6.2e-14
UNIPROTKB|F1RQ19202 LOC100517745 "Uncharacterized 0.866 0.643 0.323 7.9e-14
MGI|MGI:1098219200 Hmgb3 "high mobility group box 0.866 0.65 0.330 1.3e-13
RGD|1564407200 Hmgb3 "high mobility group box 0.866 0.65 0.330 1.3e-13
UNIPROTKB|P36194201 HMGB1 "High mobility group pro 0.86 0.641 0.345 1.6e-13
TAIR|locus:2053893 HMGB4 "high mobility group B4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 76/138 (55%), Positives = 102/138 (73%)

Query:     1 MKGGRSKADAVGTDSKLKSKGARAGKRTXXXXXXXXXXXXXXXXSAFFVFMEEFRKQFKE 60
             MKGG SKA+A  TD +LK++G +AGK+T                SAFFVF+E+FRK+F  
Sbjct:     1 MKGGESKAEATSTDQRLKTRGRKAGKKTKKDPNQPKRPP-----SAFFVFLEDFRKEFNL 55

Query:    61 AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAE 120
             A+PNNKSVATVGKAAG +WK+M++++KAP+V +AE RK++Y KN+Q YN +LA G N  E
Sbjct:    56 ANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNLKLASGTNR-E 114

Query:   121 ENESDKSKSEVNDEDDEE 138
             E++SDKSKSEV++   EE
Sbjct:   115 EDDSDKSKSEVDEAVSEE 132
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0000785 "chromatin" evidence=TAS
GO:0003682 "chromatin binding" evidence=TAS
GO:0006333 "chromatin assembly or disassembly" evidence=RCA;TAS
GO:0030527 "structural constituent of chromatin" evidence=TAS
GO:0005737 "cytoplasm" evidence=IDA
GO:0006084 "acetyl-CoA metabolic process" evidence=RCA
GO:0006342 "chromatin silencing" evidence=RCA
GO:0006364 "rRNA processing" evidence=RCA
GO:0008283 "cell proliferation" evidence=RCA
GO:0016572 "histone phosphorylation" evidence=RCA
GO:0051567 "histone H3-K9 methylation" evidence=RCA
GO:0003677 "DNA binding" evidence=ISS;IDA
TAIR|locus:505006135 HMGB2 "high mobility group B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2128003 HMGB5 "high mobility group B5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q32L31 HMGB3 "High mobility group protein B3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|P40618 HMGB3 "High mobility group protein B3" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
TAIR|locus:2154433 HMGB6 "high-mobility group box 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1RQ19 LOC100517745 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1098219 Hmgb3 "high mobility group box 3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1564407 Hmgb3 "high mobility group box 3" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|P36194 HMGB1 "High mobility group protein B1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q42344HMGB4_ARATHNo assigned EC number0.61590.880.9565yesno
P40619HMGL_IPONINo assigned EC number0.62310.880.9166N/Ano
P40620HMGL_VICFANo assigned EC number0.59120.860.8657N/Ano

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query150
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 7e-19
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 2e-17
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 5e-17
smart0039870 smart00398, HMG, high mobility group 1e-15
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 6e-10
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 1e-09
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 3e-09
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 5e-09
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 8e-04
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information 
 Score = 75.0 bits (185), Expect = 7e-19
 Identities = 34/70 (48%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 40  PKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKS 99
           PKRP SAFF+F +E R + K  +P  K  A + K  GEKWK++SE+EK P+ E+AEK K+
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 100 DYNKNMQDYN 109
            Y K    Y 
Sbjct: 60  RYEKAYPAYK 69

Length = 69
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors Back     alignment and domain information
>gnl|CDD|197700 smart00398, HMG, high mobility group Back     alignment and domain information
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional Back     alignment and domain information
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 150
PTZ0019994 high mobility group protein; Provisional 99.9
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.84
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.83
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.82
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.8
smart0039870 HMG high mobility group. 99.8
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.78
COG5648211 NHP6B Chromatin-associated proteins containing the 99.75
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.73
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.72
KOG038196 consensus HMG box-containing protein [General func 99.71
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.59
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.45
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 99.21
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.2
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.68
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 98.04
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 97.43
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 97.19
COG5648211 NHP6B Chromatin-associated proteins containing the 96.94
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 95.69
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 94.05
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 93.45
KOG3223221 consensus Uncharacterized conserved protein [Funct 89.7
TIGR03481198 HpnM hopanoid biosynthesis associated membrane pro 84.45
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.90  E-value=2.2e-23  Score=144.82  Aligned_cols=84  Identities=38%  Similarity=0.662  Sum_probs=77.1

Q ss_pred             CccccCCccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHhhccCChhhhhhHHHHHHHHHHHHH
Q 031973           25 GKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKS--VATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYN  102 (150)
Q Consensus        25 ~k~kk~kk~~~dp~~PKrP~~aY~lF~~~~r~~~k~~~p~~~~--~~eisk~l~~~Wk~l~~eeK~~y~~~A~~~k~~y~  102 (150)
                      +.++++++..+||+.|+||+|||||||+++|..|..+||+ ++  +.+|+++||++|+.|++++|.+|+++|..++.+|.
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~-~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~   86 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPE-LAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYE   86 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcC-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            3444455668999999999999999999999999999999 75  89999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 031973          103 KNMQDYN  109 (150)
Q Consensus       103 ~~~~~y~  109 (150)
                      .+|..|.
T Consensus        87 ~e~~~Y~   93 (94)
T PTZ00199         87 KEKAEYA   93 (94)
T ss_pred             HHHHHHh
Confidence            9999995

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin Back     alignment and domain information
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>smart00398 HMG high mobility group Back     alignment and domain information
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors Back     alignment and domain information
>KOG0527 consensus HMG-box transcription factor [Transcription] Back     alignment and domain information
>KOG0381 consensus HMG box-containing protein [General function prediction only] Back     alignment and domain information
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics] Back     alignment and domain information
>KOG3248 consensus Transcription factor TCF-4 [Transcription] Back     alignment and domain information
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] Back     alignment and domain information
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics] Back     alignment and domain information
>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription] Back     alignment and domain information
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A Back     alignment and domain information
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta Back     alignment and domain information
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ] Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [] Back     alignment and domain information
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function Back     alignment and domain information
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT) Back     alignment and domain information
>KOG3223 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query150
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 1e-08
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 4e-06
1nhm_A81 The Structure Of The Hmg Box And Its Interaction Wi 1e-05
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 1e-05
1hsm_A79 The Structure Of The Hmg Box And Its Interaction Wi 1e-05
1hme_A77 Structure Of The Hmg Box Motif In The B-Domain Of H 2e-05
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 4e-05
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 4e-05
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 5e-05
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 2e-04
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 2e-04
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 4e-04
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 5e-04
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81 Back     alignment and structure 
Iteration: 1

 Score = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 45  SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
           S FF+F  EFR + K  +P   S+  V K  GE W ++++ EK P++ +A K K  Y K+
Sbjct: 15  SGFFLFCSEFRPKIKSTNPG-ISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKD 73
Query: 105 MQDY 108
           + DY
Sbjct: 74  VADY 77
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 81 Back     alignment and structure
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 Back     alignment and structure
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 79 Back     alignment and structure
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1 Length = 77 Back     alignment and structure
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1 Length = 173 Back     alignment and structure
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS AT 2.77 A RESOLUTION Length = 106 Back     alignment and structure
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159 Back     alignment and structure
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93 Back     alignment and structure
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93 Back     alignment and structure
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription Factor Sox-17 Length = 82 Back     alignment and structure
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query150
1hme_A77 High mobility group protein fragment-B; DNA-bindin 8e-26
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 8e-25
2lhj_A97 High mobility group protein homolog NHP1; structur 6e-24
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 1e-23
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 2e-23
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 2e-23
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 4e-23
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 3e-22
1wgf_A90 Upstream binding factor 1; transcription factor, D 2e-20
1ckt_A71 High mobility group 1 protein; high-mobility group 6e-20
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 8e-20
2yrq_A173 High mobility group protein B1; HMG box domain, DN 2e-19
2yrq_A173 High mobility group protein B1; HMG box domain, DN 9e-15
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 2e-19
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 7e-18
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 3e-17
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 3e-16
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-16
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 5e-16
3tq6_A214 Transcription factor A, mitochondrial; transcripti 6e-16
3tq6_A214 Transcription factor A, mitochondrial; transcripti 3e-11
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 9e-16
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-14
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 3e-14
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 2e-11
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 5e-14
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 1e-13
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 7e-13
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 1e-12
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 2e-12
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 3e-12
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 4e-12
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 7e-12
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 2e-09
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 3e-09
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 2e-08
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77 Back     alignment and structure
 Score = 92.3 bits (230), Expect = 8e-26
 Identities = 34/77 (44%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 35  KDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERA 94
           KDPN PKRPPSAFF+F  E+R + K  HP   S+  V K  GE W + + D+K P+ ++A
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 95  EKRKSDYNKNMQDYNKQ 111
            K K  Y K++  Y  +
Sbjct: 61  AKLKEKYEKDIAAYRAK 77
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93 Back     alignment and structure
>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86 Back     alignment and structure
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102 Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92 Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 90 Back     alignment and structure
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Length = 71 Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67 Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87 Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159 Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159 Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214 Back     alignment and structure
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82 Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238 Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106 Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Length = 76 Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} PDB: 2yul_A Length = 83 Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79 Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Length = 81 Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Length = 86 Back     alignment and structure
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Length = 85 Back     alignment and structure
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80 Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query150
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.92
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.91
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.91
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.9
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.9
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.9
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.89
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.89
2lhj_A97 High mobility group protein homolog NHP1; structur 99.89
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.89
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.89
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.88
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.88
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.87
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.87
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.87
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.87
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.87
1ckt_A71 High mobility group 1 protein; high-mobility group 99.86
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.86
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.86
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.86
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.86
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.86
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.85
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.85
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.85
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.83
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.82
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.82
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.82
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.8
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.78
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.77
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.77
2cto_A93 Novel protein; high mobility group box domain, hel 99.75
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.75
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.73
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.7
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
Probab=99.92  E-value=7.3e-25  Score=153.02  Aligned_cols=88  Identities=28%  Similarity=0.570  Sum_probs=82.3

Q ss_pred             cCCccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 031973           29 AKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDY  108 (150)
Q Consensus        29 k~kk~~~dp~~PKrP~~aY~lF~~~~r~~~k~~~p~~~~~~eisk~l~~~Wk~l~~eeK~~y~~~A~~~k~~y~~~~~~y  108 (150)
                      ++++..+||++|+||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|.++|..++++|..+|+.|
T Consensus         7 ~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y   85 (102)
T 2co9_A            7 GKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAY   85 (102)
T ss_dssp             CSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345667899999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             HhhccCCcc
Q 031973          109 NKQLADGVN  117 (150)
Q Consensus       109 ~~~~~~~~~  117 (150)
                      ...+.....
T Consensus        86 ~~~~~~~~~   94 (102)
T 2co9_A           86 RASLVSKSY   94 (102)
T ss_dssp             HHHHTSSCC
T ss_pred             Hhhcccccc
Confidence            998876543
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Back     alignment and structure
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Back     alignment and structure
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Back     alignment and structure
>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Back     alignment and structure
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A* Back     alignment and structure
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A* Back     alignment and structure
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Back     alignment and structure
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 Back     alignment and structure
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A Back     alignment and structure
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A Back     alignment and structure
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 150
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 3e-19
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 9e-17
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-16
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 4e-16
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 7e-16
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 2e-15
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 4e-15
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 4e-15
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 3e-14
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-14
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 3e-13
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-12
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93 Back     information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 74.9 bits (184), Expect = 3e-19
 Identities = 31/88 (35%), Positives = 46/88 (52%), Gaps = 1/88 (1%)

Query: 26  KRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSED 85
            +    +  KDPN PKR  SA+  F  E R   +  +P+  +   VGK  GEKWK+++ +
Sbjct: 7   PKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPE 65

Query: 86  EKAPFVERAEKRKSDYNKNMQDYNKQLA 113
           EK P+  +A+  K  Y    + YN  LA
Sbjct: 66  EKQPYEAKAQADKKRYESEKELYNATLA 93
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 Back     information, alignment and structure
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91 Back     information, alignment and structure
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80 Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90 Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101 Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query150
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.9
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.89
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.88
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.87
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.87
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.86
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.85
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.85
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.85
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.82
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.81
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.8
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 95.91
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.90  E-value=8e-24  Score=143.87  Aligned_cols=83  Identities=36%  Similarity=0.675  Sum_probs=78.4

Q ss_pred             cCCccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhhccCChhhhhhHHHHHHHHHHHHHHHHHHH
Q 031973           29 AKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDY  108 (150)
Q Consensus        29 k~kk~~~dp~~PKrP~~aY~lF~~~~r~~~k~~~p~~~~~~eisk~l~~~Wk~l~~eeK~~y~~~A~~~k~~y~~~~~~y  108 (150)
                      +..+..++|++|+||+|||+|||+++|..|+.+||+ +++.+|++.||.+|++|++++|.+|.++|..++.+|..+|..|
T Consensus        10 ~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y   88 (93)
T d1lwma_          10 RTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY   88 (93)
T ss_dssp             CCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344456789999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             Hhhc
Q 031973          109 NKQL  112 (150)
Q Consensus       109 ~~~~  112 (150)
                      +..+
T Consensus        89 ~~~l   92 (93)
T d1lwma_          89 NATL   92 (93)
T ss_dssp             HHHH
T ss_pred             Hhcc
Confidence            9876
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Back     information, alignment and structure
>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure