Citrus Sinensis ID: 032798

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---
MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLVIFFGIIVVYNDNSDDRMIIY
ccccccccccccHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcccccccccccc
cccccccccHHHHHHHHHHccccccccccccccccccccccccccEEEEEHHHHHHHHHHcccccccHHHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcEEEEEcccccccEEEc
mkggrskadavgtdsklkskgaragkrtakpkaakdpnkpkrppsaFFVFMEEFRKQFkeahpnnksvaTVGKAAGEkwksmsedekapFVERAEKRKSDYNKNMQDYNKQLVIFFGIIVVyndnsddrmiiy
mkggrskadavgtdsklkskgaragkrtakpkaakdpnkpkrpPSAFFVFMEEFRKQFkeahpnnksvatvgkaagekwksmsedekapfveraekrksdynknMQDYNKQLVIFFGIIVVYndnsddrmiiy
MKGGRSKADAVGTDSKLKSKGARAGKRTakpkaakdpnkpkrppSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLVIFFGIIVVYNDNSDDRMIIY
**********************************************FFVFMEE*****************************************************DYNKQLVIFFGIIVVYND*********
*****************************************RPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQD**************************
*****************************************RPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLVIFFGIIVVYNDNSDDRMIIY
*******************KG****************NKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLVIFFGIIVVYNDNSDDRMIIY
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFxxxxxxxxxxxxxxxxxxxxxLVIFFGIIVVYNDNSDDRMIIY
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 ?
Query133 2.2.26 [Sep-21-2011]
Q42344138 High mobility group B pro yes no 0.812 0.782 0.619 3e-35
P40619144 HMG1/2-like protein OS=Ip N/A no 0.804 0.743 0.639 7e-32
P26585152 HMG1/2-like protein OS=Gl no no 0.834 0.730 0.617 3e-31
P93047141 High mobility group B pro no no 0.804 0.758 0.607 4e-30
P40620149 HMG1/2-like protein OS=Vi N/A no 0.842 0.751 0.598 1e-29
P27347157 DNA-binding protein MNB1B N/A no 0.819 0.694 0.633 4e-29
O49596144 High mobility group B pro no no 0.804 0.743 0.6 5e-29
O49597125 High mobility group B pro no no 0.804 0.856 0.486 3e-27
P40621161 HMG1/2-like protein OS=Tr N/A no 0.819 0.677 0.619 8e-26
O49595178 High mobility group B pro no no 0.609 0.455 0.654 7e-24
>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 =  147 bits (370), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 70/113 (61%), Positives = 93/113 (82%), Gaps = 5/113 (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  AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLV 113
           A+PNNKSVATVGKAAG +WK+M++++KAP+V +AE RK++Y KN+Q YN +L 
Sbjct: 56  ANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNLKLA 108
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|P26585|HMGL_SOYBN HMG1/2-like protein OS=Glycine max 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|P40620|HMGL_VICFA HMG1/2-like protein OS=Vicia faba PE=2 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|O49596|HMGB2_ARATH High mobility group B protein 2 OS=Arabidopsis thaliana GN=HMGB2 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
>sp|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 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 ?
Query133
118484838144 unknown [Populus trichocarpa] 0.842 0.777 0.716 5e-37
224081483144 high mobility group family [Populus tric 0.842 0.777 0.707 1e-36
296088654154 unnamed protein product [Vitis vinifera] 0.849 0.733 0.703 4e-34
351725757139 uncharacterized protein LOC100499992 [Gl 0.804 0.769 0.685 1e-33
297836478143 hypothetical protein ARALYDRAFT_480649 [ 0.812 0.755 0.628 2e-33
15227862138 high mobility group B4 protein [Arabidop 0.812 0.782 0.619 2e-33
2832355138 HMG protein [Arabidopsis thaliana] 0.812 0.782 0.628 2e-33
145328748134 high mobility group B4 protein [Arabidop 0.812 0.805 0.619 2e-33
21592453138 putative HMG protein [Arabidopsis thalia 0.812 0.782 0.619 3e-33
359476973156 PREDICTED: high mobility group B2 protei 0.849 0.724 0.666 7e-33
>gi|118484838|gb|ABK94286.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 81/113 (71%), Positives = 95/113 (84%), Gaps = 1/113 (0%)

Query: 1   MKGGRSKADAVGTDSKLKSKGARAGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKE 60
           MKGGRSK+D+   D+KLK KGA AG + +K KAAKDPNKPKRP SAFFVFME+FRKQ+KE
Sbjct: 1   MKGGRSKSDSRNNDAKLKRKGAGAGTKASK-KAAKDPNKPKRPASAFFVFMEDFRKQYKE 59

Query: 61  AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLV 113
           +HPNNKSVA VGKA G+KWKS+SE EKAPF  +AEKRK +YNK+M  YNK+L 
Sbjct: 60  SHPNNKSVAAVGKAGGDKWKSLSEAEKAPFAAKAEKRKFEYNKDMAAYNKRLA 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|296088654|emb|CBI37645.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|351725757|ref|NP_001235312.1| uncharacterized protein LOC100499992 [Glycine max] gi|255628371|gb|ACU14530.1| unknown [Glycine max] Back     alignment and taxonomy information
>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
>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|359476973|ref|XP_002280084.2| PREDICTED: high mobility group B2 protein-like isoform 1 [Vitis vinifera] 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 ?
Query133
TAIR|locus:2053893138 HMGB4 "high mobility group B4" 0.804 0.775 0.544 8.2e-28
TAIR|locus:505006135144 HMGB2 "high mobility group B2" 0.827 0.763 0.491 2.3e-23
TAIR|locus:2128003125 HMGB5 "high mobility group B5" 0.796 0.848 0.419 1e-20
TAIR|locus:2154433241 HMGB6 "high-mobility group box 0.458 0.253 0.435 1.7e-11
UNIPROTKB|Q32L31200 HMGB3 "High mobility group pro 0.744 0.495 0.345 2.2e-11
UNIPROTKB|E1BIU3186 LOC532409 "Uncharacterized pro 0.744 0.532 0.345 2.2e-11
MGI|MGI:1098219200 Hmgb3 "high mobility group box 0.744 0.495 0.345 4.5e-11
RGD|1564407200 Hmgb3 "high mobility group box 0.744 0.495 0.345 4.5e-11
UNIPROTKB|F1RQ19202 LOC100517745 "Uncharacterized 0.744 0.490 0.336 5.8e-11
UNIPROTKB|P40618202 HMGB3 "High mobility group pro 0.744 0.490 0.345 1.2e-10
TAIR|locus:2053893 HMGB4 "high mobility group B4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 61/112 (54%), Positives = 83/112 (74%)

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

Query:    61 AHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQL 112
             A+PNNKSVATVGKAAG +WK+M++++KAP+V +AE RK++Y KN+Q YN +L
Sbjct:    56 ANPNNKSVATVGKAAGARWKAMTDEDKAPYVAKAESRKTEYIKNVQQYNLKL 107
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
TAIR|locus:2154433 HMGB6 "high-mobility group box 6" [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|E1BIU3 LOC532409 "Uncharacterized protein" [Bos taurus (taxid:9913)] 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|F1RQ19 LOC100517745 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|P40618 HMGB3 "High mobility group protein B3" [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 number0.61940.81200.7826yesno

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

Your Input:
HMGB915
SubName- Full=Putative uncharacterized protein; (145 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query133
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 8e-20
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 4e-19
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 4e-18
smart0039870 smart00398, HMG, high mobility group 7e-17
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 2e-11
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 1e-10
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 1e-10
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 7e-10
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 0.001
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 0.004
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information 
 Score = 76.9 bits (190), Expect = 8e-20
 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|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional Back     alignment and domain information
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) 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|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
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 133
PTZ0019994 high mobility group protein; Provisional 99.93
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.87
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.86
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.85
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.84
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.84
smart0039870 HMG high mobility group. 99.84
COG5648211 NHP6B Chromatin-associated proteins containing the 99.82
KOG038196 consensus HMG box-containing protein [General func 99.78
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.78
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.76
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.73
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.34
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.26
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 99.16
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.73
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 98.5
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 97.56
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 97.55
COG5648211 NHP6B Chromatin-associated proteins containing the 97.25
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.41
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 94.69
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 93.99
TIGR03481198 HpnM hopanoid biosynthesis associated membrane pro 90.54
PRK15117211 ABC transporter periplasmic binding protein MlaC; 87.56
PF12881328 NUT_N: NUT protein N terminus; InterPro: IPR024309 87.25
KOG3223221 consensus Uncharacterized conserved protein [Funct 84.09
PF05494170 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: 82.6
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.93  E-value=1.6e-25  Score=149.30  Aligned_cols=80  Identities=40%  Similarity=0.726  Sum_probs=75.3

Q ss_pred             CCcccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhcCCChhhhHHHHHHHHHHHHHHHHHHH
Q 032798           29 AKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKS--VATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQ  106 (133)
Q Consensus        29 ~k~k~~~dp~~PKrP~say~lF~~~~r~~~k~~~p~~~~--~~ei~k~l~~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~  106 (133)
                      ++++..+||+.|+||+|||++|++++|..|..+||+ ++  +.+|+++||++|+.||+++|.+|+++|+.++.+|..+|.
T Consensus        12 ~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~-~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~   90 (94)
T PTZ00199         12 KNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPE-LAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKA   90 (94)
T ss_pred             ccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcC-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345668999999999999999999999999999999 64  899999999999999999999999999999999999999


Q ss_pred             HHH
Q 032798          107 DYN  109 (133)
Q Consensus       107 ~y~  109 (133)
                      +|+
T Consensus        91 ~Y~   93 (94)
T PTZ00199         91 EYA   93 (94)
T ss_pred             HHh
Confidence            995

>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
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information
>smart00398 HMG high mobility group Back     alignment and domain information
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0381 consensus HMG box-containing protein [General function prediction only] 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
>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
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics] Back     alignment and domain information
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] 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
>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
>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
>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
>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
>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
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM Back     alignment and domain information
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional Back     alignment and domain information
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins Back     alignment and domain information
>KOG3223 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation [] 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 ?
Query133
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 2e-08
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 3e-06
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 7e-06
1nhm_A81 The Structure Of The Hmg Box And Its Interaction Wi 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
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 2e-05
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 5e-05
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 5e-05
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 3e-04
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 3e-04
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 3e-04
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 3e-04
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 4e-04
2eqz_A86 Solution Structure Of The First Hmg-Box Domain From 7e-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 = 54.3 bits (129), Expect = 2e-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|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 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|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|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|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|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17 Length = 71 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|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|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93 Back     alignment and structure
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 Back     alignment and structure
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High Mobility Group Protein B3 Length = 86 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 ?
Query133
1hme_A77 High mobility group protein fragment-B; DNA-bindin 4e-27
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 1e-25
2lhj_A97 High mobility group protein homolog NHP1; structur 2e-25
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-25
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 2e-25
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 6e-25
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 1e-24
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 5e-23
1wgf_A90 Upstream binding factor 1; transcription factor, D 4e-22
1ckt_A71 High mobility group 1 protein; high-mobility group 3e-21
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 3e-21
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 1e-20
2yrq_A173 High mobility group protein B1; HMG box domain, DN 1e-20
2yrq_A173 High mobility group protein B1; HMG box domain, DN 9e-16
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 6e-20
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 2e-18
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 3e-18
3tq6_A214 Transcription factor A, mitochondrial; transcripti 6e-13
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-17
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 8e-17
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 7e-17
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 3e-16
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 8e-13
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 1e-15
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-14
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 4e-14
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 2e-13
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 9e-13
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 2e-12
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 4e-12
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 5e-12
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 7e-12
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 1e-11
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 2e-11
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 5e-11
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 2e-10
2cto_A93 Novel protein; high mobility group box domain, hel 5e-04
>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 = 95.0 bits (237), Expect = 4e-27
 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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 93 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query133
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.94
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.94
2lhj_A97 High mobility group protein homolog NHP1; structur 99.93
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.93
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.93
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.92
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.92
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.92
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.92
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.92
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.91
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.91
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.91
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.91
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.9
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.9
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.9
1ckt_A71 High mobility group 1 protein; high-mobility group 99.9
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.9
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.89
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.89
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.89
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.89
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.89
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.88
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.88
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.88
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.88
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.88
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.87
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.87
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.85
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 99.85
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.84
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.83
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 99.83
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.83
2cto_A93 Novel protein; high mobility group box domain, hel 99.82
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.75
>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=99.94  E-value=1.2e-26  Score=155.65  Aligned_cols=87  Identities=29%  Similarity=0.538  Sum_probs=81.7

Q ss_pred             cccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 032798           31 PKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNK  110 (133)
Q Consensus        31 ~k~~~dp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~ei~k~l~~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~  110 (133)
                      +++.+||++|+||+||||||++++|..|+.+||+ +++.+|+++||++|++|++++|++|.++|+.++++|..+|++|+.
T Consensus         9 kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A            9 KKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             CSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4667899999999999999999999999999999 999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhcc
Q 032798          111 QLVIFFGI  118 (133)
Q Consensus       111 k~~~~~~~  118 (133)
                      .+......
T Consensus        88 ~~~~~~~~   95 (102)
T 2co9_A           88 SLVSKSYT   95 (102)
T ss_dssp             HHTSSCCC
T ss_pred             hccccccc
Confidence            88765443
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Back     alignment and structure
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} 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
>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
>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
>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
>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 133
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 5e-18
d1ckta_71 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 1e-16
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 3e-16
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 3e-16
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 5e-16
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 8e-16
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 2e-15
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 7e-15
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-13
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 2e-13
>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 = 74.5 bits (183), Expect = 3e-19
 Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 1/87 (1%)

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

Query: 86  EKAPFVERAEKRKSDYNKNMQDYNKQL 112
           EK P+  +A+  K  Y    + YN  L
Sbjct: 66  EKQPYEAKAQADKKRYESEKELYNATL 92
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 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
>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
>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
>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
>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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 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 ?
Query133
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.94
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.91
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.9
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.9
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.89
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.89
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.89
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.88
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.87
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.86
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.86
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.84
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 97.41
>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=99.94  E-value=2.9e-26  Score=149.98  Aligned_cols=88  Identities=34%  Similarity=0.640  Sum_probs=81.7

Q ss_pred             CCCCCCCcccCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCChhhhHHHHHHHHHHHHHHHH
Q 032798           24 AGKRTAKPKAAKDPNKPKRPPSAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK  103 (133)
Q Consensus        24 ~~kk~~k~k~~~dp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~ei~k~l~~~Wk~ls~~eK~~y~~~A~~~k~~y~~  103 (133)
                      .+.+++..+..+||++||||+|||++|++++|..++.+||+ +++.+|++.||++|++||+++|.+|.+.|++++++|..
T Consensus         5 ~~~~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~   83 (93)
T d1lwma_           5 REPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYES   83 (93)
T ss_dssp             CCTTSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            33444556677899999999999999999999999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 032798          104 NMQDYNKQL  112 (133)
Q Consensus       104 e~~~y~~k~  112 (133)
                      +|.+|+.+|
T Consensus        84 e~~~y~~~l   92 (93)
T d1lwma_          84 EKELYNATL   92 (93)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHhcc
Confidence            999999886
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>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
>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
>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