Citrus Sinensis ID: 031104

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-----
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMTAYNKKQESTEDEDEEESEKSKSEVHDDDDDEELEEEDEEEDDD
cccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHcHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccccccccHHHHHHHHHcccc
cccccccccccccHHHccccHHHHHccHHHHHHHHHHccccccccccccccccccccccccEEEEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHccHcccccccc
mkvtrgkgavkkdknevvkpvedraAGKRKAVLKASrssnkrtknvksakkdpnkpkrppsaFFVFLEEFRKVYKqehpnvkavsavgkaggekwksLTDAEKAPFEAKAAKRKLDYEKLMTAYNkkqestededeeeseksksevhdddddeeleeedeeeddd
mkvtrgkgavkkdknevvkpvedraagkrkavlkasrssnkrtknvksakkdpnkpkrppSAFFVFLEEFRKVYKqehpnvkavsavgkaggekwksltdaekapfeakaakrkldyEKLMTaynkkqestededeeeseksksevhdddddeeleeedeeeddd
MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDaekapfeakaakrkLDYEKLMTAYNkkqestededeeeseksksevhdddddeeleeedeeeddd
*************************************************************AFFVFLEEFRKVYKQEHPNVKAV*********************************************************************************
**********************************************************PPSAFFVFLEEFRK**********AVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKL*********************************************
**************NEVVKPVED**********************************RPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMTAYN****************************************
**************************************************KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMTAYNKK**************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMTAYNKKQESTEDEDEEESEKSKSEVHDDDDDEELEEEDEEEDDD
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 ?
Query165 2.2.26 [Sep-21-2011]
O49595178 High mobility group B pro yes no 0.872 0.808 0.615 7e-41
P40619144 HMG1/2-like protein OS=Ip N/A no 0.666 0.763 0.675 9e-34
P93047141 High mobility group B pro no no 0.654 0.765 0.669 6e-32
P26585152 HMG1/2-like protein OS=Gl no no 0.484 0.526 0.75 6e-29
O49596144 High mobility group B pro no no 0.715 0.819 0.571 4e-28
Q42344138 High mobility group B pro no no 0.684 0.818 0.542 3e-27
P40620149 HMG1/2-like protein OS=Vi N/A no 0.575 0.637 0.628 9e-27
P27347157 DNA-binding protein MNB1B N/A no 0.690 0.726 0.5 3e-23
P40621161 HMG1/2-like protein OS=Tr N/A no 0.454 0.465 0.64 2e-21
O49597125 High mobility group B pro no no 0.545 0.72 0.478 1e-18
>sp|O49595|HMGB1_ARATH High mobility group B protein 1 OS=Arabidopsis thaliana GN=HMGB1 PE=1 SV=1 Back     alignment and function desciption
 Score =  166 bits (419), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 93/151 (61%), Positives = 115/151 (76%), Gaps = 7/151 (4%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MK  +GK  VK  K E +KPV+DR  GKRKA   A + + + T+  K AKKDPNKPKR P
Sbjct: 1   MKTAKGKDKVKTTK-EALKPVDDRKVGKRKAP--AEKPTKRETRKEKKAKKDPNKPKRAP 57

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKL 120
           SAFFVFLE+FR  +K+E+PNVKAVSAVGKAGG+KWKS++ AEKAP+E KAAKRK +YEK 
Sbjct: 58  SAFFVFLEDFRVTFKKENPNVKAVSAVGKAGGQKWKSMSQAEKAPYEEKAAKRKAEYEKQ 117

Query: 121 MTAYNKKQESTEDEDEEESEKSKSEVHDDDD 151
           M AYNK  E    E  +ESEKS+SE++D+D+
Sbjct: 118 MDAYNKNLE----EGSDESEKSRSEINDEDE 144
Binds preferentially double-stranded DNA. Modulates general plant growth and stress tolerance. Confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses.
Arabidopsis thaliana (taxid: 3702)
>sp|P40619|HMGL_IPONI HMG1/2-like protein OS=Ipomoea nil PE=2 SV=1 Back     alignment and function description
>sp|P93047|HMGB3_ARATH High mobility group B protein 3 OS=Arabidopsis thaliana GN=HMGB3 PE=1 SV=1 Back     alignment and function description
>sp|P26585|HMGL_SOYBN HMG1/2-like protein OS=Glycine max PE=2 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|Q42344|HMGB4_ARATH High mobility group B protein 4 OS=Arabidopsis thaliana GN=HMGB4 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|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 ?
Query165
359386154165 group B HMG-box protein [Citrus sinensis 1.0 1.0 1.0 6e-86
225448398166 PREDICTED: high mobility group B protein 0.890 0.885 0.789 6e-55
224112525176 high mobility group family [Populus tric 0.909 0.852 0.707 3e-52
225448400156 PREDICTED: high mobility group B protein 0.818 0.865 0.792 4e-50
118484946171 unknown [Populus trichocarpa] 0.933 0.900 0.647 2e-48
224098541179 high mobility group family [Populus tric 0.933 0.860 0.647 3e-48
255571919190 DNA-binding protein MNB1B, putative [Ric 0.951 0.826 0.707 2e-46
449461783169 PREDICTED: high mobility group B protein 0.903 0.881 0.675 2e-45
255574381171 DNA-binding protein MNB1B, putative [Ric 0.915 0.883 0.651 2e-44
359486418151 PREDICTED: high mobility group B protein 0.8 0.874 0.700 2e-43
>gi|359386154|gb|AEV43366.1| group B HMG-box protein [Citrus sinensis] Back     alignment and taxonomy information
 Score =  321 bits (823), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 165/165 (100%), Positives = 165/165 (100%)

Query: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60
           MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP
Sbjct: 1   MKVTRGKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRTKNVKSAKKDPNKPKRPP 60

Query: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKL 120
           SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKL
Sbjct: 61  SAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKL 120

Query: 121 MTAYNKKQESTEDEDEEESEKSKSEVHDDDDDEELEEEDEEEDDD 165
           MTAYNKKQESTEDEDEEESEKSKSEVHDDDDDEELEEEDEEEDDD
Sbjct: 121 MTAYNKKQESTEDEDEEESEKSKSEVHDDDDDEELEEEDEEEDDD 165

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225448398|ref|XP_002269398.1| PREDICTED: high mobility group B protein 1 isoform 1 [Vitis vinifera] gi|147854340|emb|CAN83423.1| hypothetical protein VITISV_023376 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224112525|ref|XP_002316220.1| high mobility group family [Populus trichocarpa] gi|222865260|gb|EEF02391.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225448400|ref|XP_002270185.1| PREDICTED: high mobility group B protein 1 isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|118484946|gb|ABK94338.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224098541|ref|XP_002311212.1| high mobility group family [Populus trichocarpa] gi|222851032|gb|EEE88579.1| high mobility group family [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255571919|ref|XP_002526902.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223533801|gb|EEF35533.1| DNA-binding protein MNB1B, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|449461783|ref|XP_004148621.1| PREDICTED: high mobility group B protein 1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255574381|ref|XP_002528104.1| DNA-binding protein MNB1B, putative [Ricinus communis] gi|223532493|gb|EEF34283.1| DNA-binding protein MNB1B, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|359486418|ref|XP_003633441.1| PREDICTED: high mobility group B protein 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 ?
Query165
TAIR|locus:505006135144 HMGB2 "high mobility group B2" 0.587 0.673 0.463 1.2e-19
TAIR|locus:2053893138 HMGB4 "high mobility group B4" 0.593 0.710 0.438 2e-17
TAIR|locus:2128003125 HMGB5 "high mobility group B5" 0.545 0.72 0.404 1.4e-14
TAIR|locus:2154433241 HMGB6 "high-mobility group box 0.593 0.406 0.396 5.6e-13
UNIPROTKB|F1N927214 HMGB1 "High mobility group pro 0.678 0.523 0.347 2e-10
UNIPROTKB|Q9YH06215 HMG1 "High mobility group 1 pr 0.678 0.520 0.347 2e-10
UNIPROTKB|P40618202 HMGB3 "High mobility group pro 0.448 0.366 0.413 4.1e-10
UNIPROTKB|B6ZLK1706 SSRP1 "Structure-specific reco 0.618 0.144 0.339 4.1e-10
UNIPROTKB|Q04678706 SSRP1 "FACT complex subunit SS 0.618 0.144 0.339 4.1e-10
UNIPROTKB|Q08945709 SSRP1 "FACT complex subunit SS 0.606 0.141 0.358 4.1e-10
TAIR|locus:505006135 HMGB2 "high mobility group B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 45/97 (46%), Positives = 62/97 (63%)

Query:    29 RKAVLKASRSSNKRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVG 88
             R + L  ++   K     K+A KDPNKPKRP SAFFVF+E+FR+ +K+E+P  K+V+ VG
Sbjct:    11 RSSKLSVTKKPAKGAGRGKAAAKDPNKPKRPASAFFVFMEDFRETFKKENPKNKSVATVG 70

Query:    89 KAGGEKWKSLTDXXXXXXXXXXXXXXLDYEKLMTAYN 125
             KA G+KWKSL+D              ++YEK + AYN
Sbjct:    71 KAAGDKWKSLSDSEKAPYVAKAEKRKVEYEKNIKAYN 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: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
TAIR|locus:2154433 HMGB6 "high-mobility group box 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|F1N927 HMGB1 "High mobility group protein B1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q9YH06 HMG1 "High mobility group 1 protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|P40618 HMGB3 "High mobility group protein B3" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|B6ZLK1 SSRP1 "Structure-specific recognition protein 1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q04678 SSRP1 "FACT complex subunit SSRP1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q08945 SSRP1 "FACT complex subunit SSRP1" [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) ?
O49595HMGB1_ARATHNo assigned EC number0.61580.87270.8089yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query165
pfam0050569 pfam00505, HMG_box, HMG (high mobility group) box 1e-15
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 5e-14
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 3e-13
smart0039870 smart00398, HMG, high mobility group 9e-12
COG5648211 COG5648, NHP6B, Chromatin-associated proteins cont 5e-09
PTZ0019994 PTZ00199, PTZ00199, high mobility group protein; P 2e-08
cd0138872 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I 2e-07
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 5e-07
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 3e-04
cd0138977 cd01389, MATA_HMG-box, MATA_HMG-box, class I membe 4e-04
PTZ001081388 PTZ00108, PTZ00108, DNA topoisomerase 2-like prote 8e-04
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box Back     alignment and domain information 
 Score = 66.9 bits (164), Expect = 1e-15
 Identities = 35/70 (50%), Positives = 45/70 (64%), Gaps = 1/70 (1%)

Query: 56  PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKL 115
           PKRP SAFF+F +E R   K E+P +K  + + K  GEKWK+L++ EK P+E KA K K 
Sbjct: 1   PKRPLSAFFLFSQEQRAKLKAENPGLK-NAEISKILGEKWKNLSEEEKKPYEEKAEKEKA 59

Query: 116 DYEKLMTAYN 125
            YEK   AY 
Sbjct: 60  RYEKAYPAYK 69

Length = 69
>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|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|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|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins Back     alignment and domain information
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 165
PTZ0019994 high mobility group protein; Provisional 99.92
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.83
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.81
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.81
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.8
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.8
smart0039870 HMG high mobility group. 99.79
COG5648211 NHP6B Chromatin-associated proteins containing the 99.78
KOG038196 consensus HMG box-containing protein [General func 99.75
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.73
KOG0526615 consensus Nucleosome-binding factor SPN, POB3 subu 99.66
KOG0527 331 consensus HMG-box transcription factor [Transcript 99.61
KOG4715 410 consensus SWI/SNF-related matrix-associated actin- 99.33
KOG3248 421 consensus Transcription factor TCF-4 [Transcriptio 99.1
KOG0528511 consensus HMG-box transcription factor SOX5 [Trans 98.88
KOG2746 683 consensus HMG-box transcription factor Capicua and 98.29
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 98.22
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 97.06
PF06382183 DUF1074: Protein of unknown function (DUF1074); In 96.88
COG5648211 NHP6B Chromatin-associated proteins containing the 96.83
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.12
PF06244122 DUF1014: Protein of unknown function (DUF1014); In 91.83
PF04769201 MAT_Alpha1: Mating-type protein MAT alpha 1; Inter 90.37
KOG3223221 consensus Uncharacterized conserved protein [Funct 89.03
TIGR03481198 HpnM hopanoid biosynthesis associated membrane pro 87.17
PRK15117211 ABC transporter periplasmic binding protein MlaC; 82.99
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information 
Probab=99.92  E-value=1.4e-24  Score=155.16  Aligned_cols=85  Identities=44%  Similarity=0.674  Sum_probs=78.8

Q ss_pred             ccccccccCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCc-cHHHHHHHHHHhhcCCChhhhhHHHHHHHHHHHHHHH
Q 031104           41 KRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVK-AVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEK  119 (165)
Q Consensus        41 k~~kk~~k~~kdp~~PKRP~sAY~lF~~e~r~~ik~~~p~~~-~~~ei~k~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~  119 (165)
                      +.+++++++.+||++|+||+||||||++++|..|..+||++. ++.+|+++||++|+.||+++|.+|.++|..++.+|..
T Consensus         8 ~~~k~~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~   87 (94)
T PTZ00199          8 VLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEK   87 (94)
T ss_pred             ccccccCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence            444566677899999999999999999999999999999984 4899999999999999999999999999999999999


Q ss_pred             HHHHHh
Q 031104          120 LMTAYN  125 (165)
Q Consensus       120 em~~Y~  125 (165)
                      +|.+|+
T Consensus        88 e~~~Y~   93 (94)
T PTZ00199         88 EKAEYA   93 (94)
T ss_pred             HHHHHh
Confidence            999995

>cd01389 MATA_HMG-box MATA_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
>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
>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
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics] Back     alignment and domain information
>KOG0527 consensus HMG-box transcription factor [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
>KOG3248 consensus Transcription factor TCF-4 [Transcription] Back     alignment and domain information
>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription] Back     alignment and domain information
>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
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function Back     alignment and domain information
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT) Back     alignment and domain information
>KOG3223 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM Back     alignment and domain information
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional 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 ?
Query165
1j3c_A79 Solution Structure Of The C-Terminal Domain Of The 9e-09
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 1e-08
2gzk_A159 Structure Of A Complex Of Tandem Hmg Boxes And Dna 2e-08
1hme_A77 Structure Of The Hmg Box Motif In The B-Domain Of H 2e-08
1j3d_A78 Solution Structure Of The C-Terminal Domain Of The 3e-08
1nhm_A81 The Structure Of The Hmg Box And Its Interaction Wi 1e-06
2yqi_A81 Solution Structure Of The Second Hmg-Box Domain Fro 2e-06
1hsm_A79 The Structure Of The Hmg Box And Its Interaction Wi 4e-06
1j5n_A93 Solution Structure Of The Non-Sequence-Specific Hmg 7e-06
1cg7_A93 Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len 7e-06
1e7j_A74 Hmg-D Complexed To A Bulge Dna Length = 74 9e-06
1hma_A73 The Solution Structure And Dynamics Of The Dna Bind 1e-05
1qrv_A73 Crystal Structure Of The Complex Of Hmg-D And Dna L 1e-05
2lhj_A97 Nmr Structure Of The High Mobility Group Protein-Li 1e-05
3nm9_A73 Hmgd(M13a)-Dna Complex Length = 73 2e-05
1wxl_A73 Solution Structure Of The Hmg-Box Domain In The Ssr 4e-05
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79 Back     alignment and structure 
Iteration: 1

 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 50  KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXX 109
           KKDPN PKRPPSAFF+F  E+R   K EHP + ++    K  GE W   +          
Sbjct: 3   KKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQK 61
Query: 110 XXXXXLDYEKLMTAY 124
                  YEK + AY
Sbjct: 62  AAKLKEKYEKDIAAY 76
>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|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159 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|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|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|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|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|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna Length = 73 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|3NM9|A Chain A, Hmgd(M13a)-Dna Complex Length = 73 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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query165
1hme_A77 High mobility group protein fragment-B; DNA-bindin 8e-23
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 1e-21
2lhj_A97 High mobility group protein homolog NHP1; structur 3e-21
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 6e-21
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 8e-21
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 3e-20
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-19
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 1e-18
1wgf_A90 Upstream binding factor 1; transcription factor, D 4e-18
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 5e-18
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 1e-17
2yrq_A173 High mobility group protein B1; HMG box domain, DN 2e-17
2yrq_A173 High mobility group protein B1; HMG box domain, DN 1e-10
1ckt_A71 High mobility group 1 protein; high-mobility group 4e-16
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-16
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 6e-14
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 3e-15
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 9e-14
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 7e-12
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 2e-11
3tq6_A214 Transcription factor A, mitochondrial; transcripti 3e-11
3tq6_A214 Transcription factor A, mitochondrial; transcripti 7e-09
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 2e-10
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 5e-09
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 1e-09
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 2e-09
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 1e-08
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 2e-08
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 4e-08
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 6e-08
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 2e-07
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 2e-07
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 3e-07
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 1e-06
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 6e-06
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 2e-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 = 85.0 bits (211), Expect = 8e-23
 Identities = 39/77 (50%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 51  KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKA 110
           KDPN PKRPPSAFF+F  E+R   K EHP +  +  V K  GE W +    +K P+E KA
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKA 60

Query: 111 AKRKLDYEKLMTAYNKK 127
           AK K  YEK + AY  K
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
>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
>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
>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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92 Back     alignment and structure
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67 Back     alignment and structure
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens} Length = 87 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Length = 101 Back     alignment and structure
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108 Back     alignment and structure
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 81 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query165
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.92
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.92
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.91
2lhj_A97 High mobility group protein homolog NHP1; structur 99.91
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.9
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.9
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.9
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.89
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.89
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.89
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.89
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.89
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.88
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.88
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.87
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.87
1ckt_A71 High mobility group 1 protein; high-mobility group 99.87
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.86
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.86
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.86
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.86
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.86
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.86
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.85
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.85
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.85
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.85
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.84
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.84
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.83
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.83
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.81
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.79
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.78
2cto_A93 Novel protein; high mobility group box domain, hel 99.77
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.76
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.75
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.74
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.69
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
Probab=99.92  E-value=2.9e-25  Score=159.37  Aligned_cols=89  Identities=29%  Similarity=0.506  Sum_probs=82.4

Q ss_pred             cccccCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhhcCCChhhhhHHHHHHHHHHHHHHHHHHH
Q 031104           44 KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMTA  123 (165)
Q Consensus        44 kk~~k~~kdp~~PKRP~sAY~lF~~e~r~~ik~~~p~~~~~~ei~k~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~em~~  123 (165)
                      .+++++.+||++|+||+||||||++++|..|+.+||++ ++.+|+++||++|++|++++|.+|.++|..++.+|..+|..
T Consensus         6 ~~~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   84 (102)
T 2co9_A            6 SGKKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAA   84 (102)
T ss_dssp             CCSCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556778999999999999999999999999999999 79999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCcc
Q 031104          124 YNKKQESTED  133 (165)
Q Consensus       124 Y~~k~~~~~~  133 (165)
                      |+.++.....
T Consensus        85 Y~~~~~~~~~   94 (102)
T 2co9_A           85 YRASLVSKSY   94 (102)
T ss_dssp             HHHHHTSSCC
T ss_pred             HHhhcccccc
Confidence            9988776543
>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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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 165
d1lwma_93 a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces 2e-14
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 1e-13
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 1e-12
d1k99a_91 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 2e-12
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 3e-12
d1gt0d_80 a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 4e-12
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 1e-11
d1i11a_70 a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 3e-11
d1j46a_85 a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96 4e-11
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 6e-11
d2lefa_86 a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE 4e-09
d1v64a_108 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 9e-08
>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 = 63.0 bits (153), Expect = 2e-14
 Identities = 38/84 (45%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 44  KNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEK 103
           K     KKDPN PKR  SA+  F  E R + + E+P++     VGK  GEKWK+LT  EK
Sbjct: 9   KRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEK 67

Query: 104 APFEAKAAKRKLDYEKLMTAYNKK 127
            P+EAKA   K  YE     YN  
Sbjct: 68  QPYEAKAQADKKRYESEKELYNAT 91
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70 Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85 Back     information, alignment and structure
>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101 Back     information, alignment and structure
>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86 Back     information, alignment and structure
>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query165
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.91
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.9
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.88
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.86
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.86
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.86
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.85
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.84
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.82
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.82
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.81
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.8
d1l8ya_84 Nucleolar transcription factor 1 (Upstream binding 96.6
>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=99.91  E-value=2.3e-24  Score=150.65  Aligned_cols=86  Identities=44%  Similarity=0.692  Sum_probs=80.0

Q ss_pred             ccccccCCCCCCCCCCCCChHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhhcCCChhhhhHHHHHHHHHHHHHHHHHH
Q 031104           43 TKNVKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAEKAPFEAKAAKRKLDYEKLMT  122 (165)
Q Consensus        43 ~kk~~k~~kdp~~PKRP~sAY~lF~~e~r~~ik~~~p~~~~~~ei~k~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~em~  122 (165)
                      +++..++.++|++|+||+||||||++++|..|+.+||++ ++.+|++.||.+|++||+++|.+|..+|..++.+|..+|.
T Consensus         8 ~k~~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~   86 (93)
T d1lwma_           8 KKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE   86 (93)
T ss_dssp             TSCCCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566778999999999999999999999999999999 7999999999999999999999999999999999999999


Q ss_pred             HHhhcCC
Q 031104          123 AYNKKQE  129 (165)
Q Consensus       123 ~Y~~k~~  129 (165)
                      .|+.+++
T Consensus        87 ~y~~~l~   93 (93)
T d1lwma_          87 LYNATLA   93 (93)
T ss_dssp             HHHHHHC
T ss_pred             HHHhccC
Confidence            9998753
>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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} 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
>d1i11a_ a.21.1.1 (A:) Sox-5 {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
>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
>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