Citrus Sinensis ID: 032803

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---
MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPEEEEESEKSMSEEDDDE
cccccccccHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHcccccccccc
ccccccccccHHHHHccccccccccccccccccccccccccccHEEEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccc
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpasAFFVFMEEFREQykkdhpknksVAAVGKAggekwksmseadkapyvaKAEKRKVEYEKDMKNYnrrqaegtkpeeeeeseksmseeddde
mkggksksdtrnaklsvnkkpakagrksgkaakdpnkpkrpASAFFVFMEEFREqykkdhpknksvAAVGkaggekwksmseadkapyvakaekrkveyekdmknynrrqaegtkpeeeeeseksmseeddde
MKGGKSKSDTRNAKLSVNkkpakagrksgkaakDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPeeeeeseksmseeddde
********************************************FFVFME***********************************************************************************
****************************************PASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKD*******************************
***************************************RPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR*************************
***********************************NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ***********************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYxxxxxxxxxxxxxxxxxxxxxQAEGTKPEEEEESEKSMSEEDDDE
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]
P93047141 High mobility group B pro yes no 0.924 0.872 0.718 5e-44
O49596144 High mobility group B pro no no 0.947 0.875 0.703 6e-44
P26585152 HMG1/2-like protein OS=Gl yes no 0.849 0.743 0.689 7e-37
P40619144 HMG1/2-like protein OS=Ip N/A no 0.969 0.895 0.631 4e-34
P40620149 HMG1/2-like protein OS=Vi N/A no 0.939 0.838 0.614 9e-32
Q42344138 High mobility group B pro no no 0.947 0.913 0.537 9e-31
P27347157 DNA-binding protein MNB1B N/A no 0.849 0.719 0.625 6e-30
O49595178 High mobility group B pro no no 0.774 0.578 0.611 1e-27
P40621161 HMG1/2-like protein OS=Tr N/A no 0.812 0.670 0.633 3e-25
O49597125 High mobility group B pro no no 0.744 0.792 0.474 1e-22
>sp|P93047|HMGB3_ARATH High mobility group B protein 3 OS=Arabidopsis thaliana GN=HMGB3 PE=1 SV=1 Back     alignment and function desciption
 Score =  176 bits (445), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 92/128 (71%), Positives = 112/128 (87%), Gaps = 5/128 (3%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKG KSK++TR+ KLSV KKPAK  +    AAKDPNKPKRP+SAFFVFME+FR  YK++H
Sbjct: 1   MKGAKSKAETRSTKLSVTKKPAKGAKG---AAKDPNKPKRPSSAFFVFMEDFRVTYKEEH 57

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPEEEE 120
           PKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN++  EG  P+E+E
Sbjct: 58  PKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNKKLEEG--PKEDE 115

Query: 121 ESEKSMSE 128
           ES+KS+SE
Sbjct: 116 ESDKSVSE 123
Binds preferentially double-stranded DNA.
Arabidopsis thaliana (taxid: 3702)
>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|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil 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|Q42344|HMGB4_ARATH High mobility group B protein 4 OS=Arabidopsis thaliana GN=HMGB4 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|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 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|O49597|HMGB5_ARATH High mobility group B protein 5 OS=Arabidopsis thaliana GN=HMGB5 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 ?
Query133
297845042141 hypothetical protein ARALYDRAFT_472304 [ 0.962 0.907 0.744 1e-46
308569654146 high mobility group box 2 protein [Gossy 0.849 0.773 0.859 2e-46
312281681144 unnamed protein product [Thellungiella h 0.947 0.875 0.742 4e-45
312282031141 unnamed protein product [Thellungiella h 0.924 0.872 0.742 1e-44
224083306160 high mobility group family [Populus tric 0.849 0.706 0.789 1e-44
308569660142 high mobility group box 1 protein [Gossy 0.932 0.873 0.835 1e-43
8886929 662 F2D10.18 [Arabidopsis thaliana] 0.984 0.197 0.684 3e-43
145323962140 high mobility group B3 protein [Arabidop 0.962 0.914 0.699 8e-43
79318286142 high mobility group B2 protein [Arabidop 0.984 0.922 0.684 1e-42
18394900141 high mobility group B3 protein [Arabidop 0.924 0.872 0.718 3e-42
>gi|297845042|ref|XP_002890402.1| hypothetical protein ARALYDRAFT_472304 [Arabidopsis lyrata subsp. lyrata] gi|297336244|gb|EFH66661.1| hypothetical protein ARALYDRAFT_472304 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
 Score =  190 bits (483), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 99/133 (74%), Positives = 120/133 (90%), Gaps = 5/133 (3%)

Query: 1   MKGGKSKSDTRNAKLSVNKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDH 60
           MKGGKSK++TRNAKLSV KKPAK G+    AAKDPNKPKRP+SAFFVFME+FRE YKK+H
Sbjct: 3   MKGGKSKTETRNAKLSVTKKPAKGGKG---AAKDPNKPKRPSSAFFVFMEDFRETYKKEH 59

Query: 61  PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTKPEEEE 120
           PKNKSVAAVGKAGGEKWKS+S+++KAPYVAKA+KRKVEYEK+MK YN++  EG  P+E+E
Sbjct: 60  PKNKSVAAVGKAGGEKWKSLSDSEKAPYVAKADKRKVEYEKNMKAYNKKLEEG--PKEDE 117

Query: 121 ESEKSMSEEDDDE 133
           ES+KS+SE +D++
Sbjct: 118 ESDKSVSEVNDED 130

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|308569654|gb|ADO34793.1| high mobility group box 2 protein [Gossypium hirsutum] Back     alignment and taxonomy information
>gi|312281681|dbj|BAJ33706.1| unnamed protein product [Thellungiella halophila] Back     alignment and taxonomy information
>gi|312282031|dbj|BAJ33881.1| unnamed protein product [Thellungiella halophila] Back     alignment and taxonomy information
>gi|224083306|ref|XP_002306980.1| high mobility group family [Populus trichocarpa] gi|222856429|gb|EEE93976.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|308569660|gb|ADO34795.1| high mobility group box 1 protein [Gossypium hirsutum] Back     alignment and taxonomy information
>gi|8886929|gb|AAF80615.1|AC069251_8 F2D10.18 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|145323962|ref|NP_001077570.1| high mobility group B3 protein [Arabidopsis thaliana] gi|332191890|gb|AEE30011.1| high mobility group B3 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|79318286|ref|NP_001031074.1| high mobility group B2 protein [Arabidopsis thaliana] gi|297845040|ref|XP_002890401.1| hypothetical protein ARALYDRAFT_472301 [Arabidopsis lyrata subsp. lyrata] gi|297336243|gb|EFH66660.1| hypothetical protein ARALYDRAFT_472301 [Arabidopsis lyrata subsp. lyrata] gi|332191886|gb|AEE30007.1| high mobility group B2 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|18394900|ref|NP_564124.1| high mobility group B3 protein [Arabidopsis thaliana] gi|75220405|sp|P93047.1|HMGB3_ARATH RecName: Full=High mobility group B protein 3; AltName: Full=High mobility group protein B 2; Short=AtHMGbeta2; Short=HMG beta 2; AltName: Full=Nucleosome/chromatin assembly factor group D 03; Short=Nucleosome/chromatin assembly factor group D 3 gi|15724174|gb|AAL06479.1|AF411789_1 At1g20690/F2D10_15 [Arabidopsis thaliana] gi|1694976|emb|CAA70691.1| HMG1 [Arabidopsis thaliana] gi|2832361|emb|CAA74402.1| HMG protein [Arabidopsis thaliana] gi|20453325|gb|AAM19901.1| At1g20690/F2D10_15 [Arabidopsis thaliana] gi|21537072|gb|AAM61413.1| unknown [Arabidopsis thaliana] gi|22530942|gb|AAM96975.1| expressed protein [Arabidopsis thaliana] gi|23198424|gb|AAN15739.1| expressed protein [Arabidopsis thaliana] gi|332191888|gb|AEE30009.1| high mobility group B3 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 ?
Query133
TAIR|locus:505006135144 HMGB2 "high mobility group B2" 0.864 0.798 0.643 1.3e-36
TAIR|locus:2053893138 HMGB4 "high mobility group B4" 0.834 0.804 0.491 1.4e-25
TAIR|locus:2128003125 HMGB5 "high mobility group B5" 0.616 0.656 0.5 1e-20
MGI|MGI:1098219200 Hmgb3 "high mobility group box 0.609 0.405 0.457 4.8e-17
UNIPROTKB|F1RQ19202 LOC100517745 "Uncharacterized 0.609 0.400 0.445 4.8e-17
RGD|1564407200 Hmgb3 "high mobility group box 0.609 0.405 0.445 6e-17
UNIPROTKB|Q32L31200 HMGB3 "High mobility group pro 0.609 0.405 0.445 6e-17
UNIPROTKB|E7EQU1193 HMGB3 "High mobility group pro 0.609 0.419 0.433 6e-17
UNIPROTKB|E7ES08188 HMGB3 "High mobility group pro 0.609 0.430 0.433 6e-17
UNIPROTKB|O15347200 HMGB3 "High mobility group pro 0.609 0.405 0.433 6e-17
TAIR|locus:505006135 HMGB2 "high mobility group B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 394 (143.8 bits), Expect = 1.3e-36, P = 1.3e-36
 Identities = 74/115 (64%), Positives = 91/115 (79%)

Query:     1 MKGGKSKSDTRNAKLSVNXXXXXXXXXXXXXXXDPNKPKRPASAFFVFMEEFREQYKKDH 60
             MKG KSK++TR++KLSV                DPNKPKRPASAFFVFME+FRE +KK++
Sbjct:     1 MKGAKSKTETRSSKLSVTKKPAKGAGRGKAAAKDPNKPKRPASAFFVFMEDFRETFKKEN 60

Query:    61 PKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK 115
             PKNKSVA VGKA G+KWKS+S+++KAPYVAKAEKRKVEYEK++K YN++  EG K
Sbjct:    61 PKNKSVATVGKAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYNKKLEEGPK 115
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:0006096 "glycolysis" evidence=RCA
GO:0006833 "water transport" evidence=RCA
GO:0006972 "hyperosmotic response" evidence=RCA
GO:0007030 "Golgi organization" evidence=RCA
GO:0009266 "response to temperature stimulus" evidence=RCA
GO:0009651 "response to salt stress" evidence=RCA
GO:0046686 "response to cadmium ion" evidence=RCA
GO:0003677 "DNA binding" evidence=ISS;IDA
TAIR|locus:2053893 HMGB4 "high mobility group B4" [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
MGI|MGI:1098219 Hmgb3 "high mobility group box 3" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1RQ19 LOC100517745 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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|Q32L31 HMGB3 "High mobility group protein B3" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E7EQU1 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E7ES08 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|O15347 HMGB3 "High mobility group protein B3" [Homo sapiens (taxid:9606)] 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) ?
O49596HMGB2_ARATHNo assigned EC number0.70310.94730.875nono
P40619HMGL_IPONINo assigned EC number0.63150.96990.8958N/Ano
P40620HMGL_VICFANo assigned EC number0.61480.93980.8389N/Ano
P93047HMGB3_ARATHNo assigned EC number0.71870.92480.8723yesno
P26585HMGL_SOYBNNo assigned EC number0.68900.84960.7434yesno

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:
fgenesh2_kg.1__2258__AT1G20696.3
annotation not avaliable (141 aa)
(Arabidopsis lyrata)
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 3e-16
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 2e-14
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 6e-14
smart0039870 smart00398, HMG, high mobility group 8e-12
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 5e-08
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 9e-08
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 3e-07
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 1e-06
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information 
 Score = 67.6 bits (166), Expect = 3e-16
 Identities = 35/70 (50%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 38  PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
           PKRP SAFF+F +E R + K ++P  K  A + K  GEKWK++SE +K PY  KAEK K 
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 98  EYEKDMKNYN 107
            YEK    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

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 99.94
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
smart0039870 HMG high mobility group. 99.84
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.84
COG5648211 NHP6B Chromatin-associated proteins containing the 99.83
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.78
KOG038196 consensus HMG box-containing protein [General func 99.78
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.75
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.67
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.42
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.34
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 99.16
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.82
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 98.4
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 97.48
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 97.38
COG5648211 NHP6B Chromatin-associated proteins containing the 97.18
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.56
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 94.99
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 94.73
TIGR03481198 HpnM hopanoid biosynthesis associated membrane pro 91.54
PRK15117211 ABC transporter periplasmic binding protein MlaC; 90.04
PF05494170 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: 83.14
KOG3223221 consensus Uncharacterized conserved protein [Funct 81.86
PF12881328 NUT_N: NUT protein N terminus; InterPro: IPR024309 81.36
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.94  E-value=2.4e-26  Score=154.55  Aligned_cols=89  Identities=44%  Similarity=0.696  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhhCCChHHhHHHHHHHHHH
Q 032803           18 NKKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKS--VAAVGKAGGEKWKSMSEADKAPYVAKAEKR   95 (133)
Q Consensus        18 ~k~~~~~~kk~~k~~~dp~~PKrP~say~lF~~e~r~~~k~~~p~~~~--~~eisk~l~~~Wk~ls~eeK~~Y~~~a~~~   95 (133)
                      ++.+.+.+++++++.+||+.|+||+|||+|||.++|..|..+||+ +.  +++|+++||++|+.||+++|++|.++|..+
T Consensus         3 ~~~~~~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~-~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~d   81 (94)
T PTZ00199          3 KKQGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPE-LAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQED   81 (94)
T ss_pred             ccccCccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcC-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            355677777888889999999999999999999999999999999 64  899999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 032803           96 KVEYEKDMKNYN  107 (133)
Q Consensus        96 k~~y~~e~~~y~  107 (133)
                      +.+|..+|..|+
T Consensus        82 k~rY~~e~~~Y~   93 (94)
T PTZ00199         82 KVRYEKEKAEYA   93 (94)
T ss_pred             HHHHHHHHHHHh
Confidence            999999999996

>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
>KOG0381 consensus HMG box-containing protein [General function prediction only] 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
>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
>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
>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
>KOG3223 consensus Uncharacterized conserved protein [Function unknown] 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query133
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 1e-12
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 3e-12
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 4e-12
1hme_A77 Structure Of The Hmg Box Motif In The B-Domain Of H 4e-11
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 5e-11
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 5e-11
1nhm_A81 The Structure Of The Hmg Box And Its Interaction Wi 7e-10
1hsm_A79 The Structure Of The Hmg Box And Its Interaction Wi 3e-09
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 5e-09
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 5e-09
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 5e-08
1qrv_A73 Crystal Structure Of The Complex Of Hmg-D And Dna L 1e-07
1e7j_A74 Hmg-D Complexed To A Bulge Dna Length = 74 1e-07
1hma_A73 The Solution Structure And Dynamics Of The Dna Bind 2e-07
1j3x_A77 Solution Structure Of The N-Terminal Domain Of The 2e-07
3nm9_A73 Hmgd(M13a)-Dna Complex Length = 73 3e-07
2ly4_A83 Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo 2e-06
1wxl_A73 Solution Structure Of The Hmg-Box Domain In The Ssr 3e-06
1aab_A83 Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 4e-06
4euw_A106 Crystal Structure Of A Hmg Domain Of Transcription 4e-06
2yul_A82 Solution Structure Of The Hmg Box Of Human Transcri 5e-06
4a3n_A71 Crystal Structure Of Hmg-Box Of Human Sox17 Length 6e-06
3f27_D83 Structure Of Sox17 Bound To Dna Length = 83 6e-06
2crj_A92 Solution Structure Of The Hmg Domain Of Mouse Hmg D 1e-05
1ckt_A71 Crystal Structure Of Hmg1 Domain A Bound To A Cispl 6e-05
1o4x_B88 Ternary Complex Of The Dna Binding Domains Of The O 6e-05
3tq6_A214 Crystal Structure Of Human Mitochondrial Transcript 7e-05
3u2b_C79 Structure Of The Sox4 Hmg Domain Bound To Dna Lengt 9e-05
3fgh_A67 Human Mitochondrial Transcription Factor A Box B Le 1e-04
2e6o_A87 Solution Structure Of The Hmg Box Domain From Human 2e-04
1wgf_A90 Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1 2e-04
1hrz_A76 The 3d Structure Of The Human Sry-Dna Complex Solve 3e-04
1j47_A85 3d Solution Nmr Structure Of The M9i Mutant Of The 3e-04
1k99_A99 Solution Structure Of The First Hmg Box In Human Up 4e-04
1j46_A85 3d Solution Nmr Structure Of The Wild Type Hmg-Box 4e-04
3tmm_A238 Tfam Imposes A U-Turn On Mitochondrial Dna Length = 4e-04
2le4_A81 Solution Structure Of The Hmg Box Dna-Binding Domai 5e-04
1gt0_D80 Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Le 5e-04
2eqz_A86 Solution Structure Of The First Hmg-Box Domain From 6e-04
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure 
Iteration: 1

 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
           DPN PKRP SAFF+F  E+R + K +HP   S+    K  GE W   S  DK PY  KA 
Sbjct: 5   DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 63
Query: 94  KRKVEYEKDMKNY 106
           K K +YEKD+  Y
Sbjct: 64  KLKEKYEKDIAAY 76
>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
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78 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|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|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|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|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A) Length = 97 Back     alignment and structure
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73 Back     alignment and structure
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna Length = 74 Back     alignment and structure
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding Domain Of Hmg-D From Drosophila Melanogaster Length = 73 Back     alignment and structure
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77 Back     alignment and structure
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73 Back     alignment and structure
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53 Transactivation Domain Interaction And Is Regulated By The Acidic Tail Length = 83 Back     alignment and structure
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73 Back     alignment and structure
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 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|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
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna Length = 83 Back     alignment and structure
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92 Back     alignment and structure
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A Cisplatin-modified Dna Duplex Length = 71 Back     alignment and structure
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 88 Back     alignment and structure
>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription Factor A, Tfam Or Mttfa, Bound To The Light Strand Promoter Lsp Length = 214 Back     alignment and structure
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna Length = 79 Back     alignment and structure
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B Length = 67 Back     alignment and structure
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1 Length = 87 Back     alignment and structure
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1 Length = 90 Back     alignment and structure
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr Length = 76 Back     alignment and structure
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream Binding Factor Length = 99 Back     alignment and structure
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain Of The Human Male Sex Determining Factor Sry Complexed To Dna Length = 85 Back     alignment and structure
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna Length = 238 Back     alignment and structure
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of Human Stem Cell Transcription Factor Sox2 Length = 81 Back     alignment and structure
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX Length = 80 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-22
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 1e-20
2lhj_A97 High mobility group protein homolog NHP1; structur 1e-20
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 2e-20
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 3e-20
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 6e-20
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 1e-19
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 3e-18
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 6e-17
1ckt_A71 High mobility group 1 protein; high-mobility group 6e-17
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 7e-17
1wgf_A90 Upstream binding factor 1; transcription factor, D 1e-16
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 1e-15
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 2e-15
2yrq_A173 High mobility group protein B1; HMG box domain, DN 4e-15
2yrq_A173 High mobility group protein B1; HMG box domain, DN 2e-10
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-13
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 2e-12
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 2e-12
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 4e-12
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 8e-11
3tq6_A214 Transcription factor A, mitochondrial; transcripti 1e-08
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 2e-10
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 5e-10
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 3e-09
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 6e-09
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 4e-08
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 2e-08
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 2e-08
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 5e-08
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 6e-08
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 9e-08
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 2e-07
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 3e-06
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 2e-05
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 5e-05
>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 = 82.3 bits (204), Expect = 4e-22
 Identities = 37/77 (48%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 33  KDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
           KDPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +  DK PY  KA
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 93  EKRKVEYEKDMKNYNRR 109
            K K +YEKD+  Y  +
Sbjct: 61  AKLKEKYEKDIAAYRAK 77
>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
>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
>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
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

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 99.95
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 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 99.92
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
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.92
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.92
2lhj_A97 High mobility group protein homolog NHP1; structur 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
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
1ckt_A71 High mobility group 1 protein; high-mobility group 99.9
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.9
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.9
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.89
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 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
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.89
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.89
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.89
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
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.88
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.88
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.87
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.86
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.85
3tmm_A 238 Transcription factor A, mitochondrial; HMG, high m 99.84
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 99.84
2cto_A93 Novel protein; high mobility group box domain, hel 99.82
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.82
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.81
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.8
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.76
>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=99.95  E-value=6.1e-27  Score=158.30  Aligned_cols=90  Identities=28%  Similarity=0.493  Sum_probs=83.6

Q ss_pred             CCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhCCChHHhHHHHHHHHHHHHHHHHHHH
Q 032803           25 GRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMK  104 (133)
Q Consensus        25 ~kk~~k~~~dp~~PKrP~say~lF~~e~r~~~k~~~p~~~~~~eisk~l~~~Wk~ls~eeK~~Y~~~a~~~k~~y~~e~~  104 (133)
                      ..+++++.+||++|+||+|||||||+++|..|+.+||+ +++.+|+++||++|+.|++++|++|+++|..++++|..+|.
T Consensus         5 ~~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   83 (102)
T 2co9_A            5 SSGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLA   83 (102)
T ss_dssp             CCCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445667899999999999999999999999999999 89999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCC
Q 032803          105 NYNRRQAEGTK  115 (133)
Q Consensus       105 ~y~~~~~~~~~  115 (133)
                      .|+..+.....
T Consensus        84 ~Y~~~~~~~~~   94 (102)
T 2co9_A           84 AYRASLVSKSY   94 (102)
T ss_dssp             HHHHHHTSSCC
T ss_pred             HHHhhcccccc
Confidence            99998877655
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; 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
>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
>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
>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
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>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
>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
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {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
>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
>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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {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
>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 133
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 1e-13
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-12
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 5e-12
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 9e-12
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 2e-11
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 5e-11
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 1e-10
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-10
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 4e-10
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 3e-09
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-08
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-06
>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 = 59.9 bits (145), Expect = 1e-13
 Identities = 34/93 (36%), Positives = 53/93 (56%), Gaps = 1/93 (1%)

Query: 19  KKPAKAGRKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWK 78
             P +  +++ +  KDPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK
Sbjct: 2   VTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWK 60

Query: 79  SMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQA 111
           +++  +K PY AKA+  K  YE + + YN   A
Sbjct: 61  ALTPEEKQPYEAKAQADKKRYESEKELYNATLA 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
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 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
>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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 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

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 99.93
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.92
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.91
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 99.88
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.88
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.87
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.86
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.86
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.85
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 97.07
>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=99.93  E-value=8.1e-26  Score=148.90  Aligned_cols=85  Identities=39%  Similarity=0.691  Sum_probs=79.5

Q ss_pred             CCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhCCChHHhHHHHHHHHHHHHHHHHHHHH
Q 032803           26 RKSGKAAKDPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKN  105 (133)
Q Consensus        26 kk~~k~~~dp~~PKrP~say~lF~~e~r~~~k~~~p~~~~~~eisk~l~~~Wk~ls~eeK~~Y~~~a~~~k~~y~~e~~~  105 (133)
                      ++.++..++|++||||+|||+|||.++|..|+.+||+ +++.+|++.||.+|+.||+++|++|.++|..++.+|..+|..
T Consensus         9 k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~   87 (93)
T d1lwma_           9 KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKEL   87 (93)
T ss_dssp             SCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444566799999999999999999999999999999 999999999999999999999999999999999999999999


Q ss_pred             HHHhCC
Q 032803          106 YNRRQA  111 (133)
Q Consensus       106 y~~~~~  111 (133)
                      |+.+|+
T Consensus        88 y~~~l~   93 (93)
T d1lwma_          88 YNATLA   93 (93)
T ss_dssp             HHHHHC
T ss_pred             HHhccC
Confidence            998864
>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
>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
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {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