Psyllid ID: psy3267

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-----
MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
ccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHccccccccccccHHHcccccHHHHcccccc
ccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccEccHHHHcHHHHHHHHHHHccccEEEEccHHHHHHHHHHHHHHHHHHHHHHHHcc
mqnklnmqGIAYAFFVQVCREehkkkhpeenVVFAEFSKKCAERWkssrivnpfvgrkfAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDyfglrala
mqnklnmqgiAYAFFVQVCREEHkkkhpeenvvfAEFSKKCAERWKssrivnpfvgrKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
******MQGIAYAFFVQVCREEH******ENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLR***
********GIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAE*W*****************FLTFLSRMKDSI*********************LDYFGLRALA
MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
*******QGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFGLRALA
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 ?
Query105 2.2.26 [Sep-21-2011]
Q24537 393 High mobility group prote yes N/A 0.352 0.094 0.810 5e-14
P26583209 High mobility group prote yes N/A 0.428 0.215 0.688 2e-12
P40673209 High mobility group prote yes N/A 0.428 0.215 0.688 2e-12
P30681 210 High mobility group prote no N/A 0.428 0.214 0.688 2e-12
P52925 210 High mobility group prote no N/A 0.428 0.214 0.688 3e-12
P17741 210 High mobility group prote yes N/A 0.428 0.214 0.688 3e-12
P26584207 High mobility group prote yes N/A 0.428 0.217 0.644 8e-12
P63159 215 High mobility group prote no N/A 0.352 0.172 0.756 2e-11
A9RA84 215 High mobility group prote N/A N/A 0.352 0.172 0.756 2e-11
P63158 215 High mobility group prote no N/A 0.352 0.172 0.756 2e-11
>sp|Q24537|HMG2_DROME High mobility group protein DSP1 OS=Drosophila melanogaster GN=Dsp1 PE=2 SV=1 Back     alignment and function desciption
 Score = 76.3 bits (186), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 30/37 (81%), Positives = 35/37 (94%)

Query: 11  AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
           AYA+FVQ CREEHKKKHP+E V+FAEFS+KCAERWK+
Sbjct: 185 AYAYFVQTCREEHKKKHPDETVIFAEFSRKCAERWKT 221
Binds preferentially single-stranded DNA and unwinds double stranded DNA.
Drosophila melanogaster (taxid: 7227)
>sp|P26583|HMGB2_HUMAN High mobility group protein B2 OS=Homo sapiens GN=HMGB2 PE=1 SV=2 Back     alignment and function description
>sp|P40673|HMGB2_BOVIN High mobility group protein B2 OS=Bos taurus GN=HMGB2 PE=1 SV=3 Back     alignment and function description
>sp|P30681|HMGB2_MOUSE High mobility group protein B2 OS=Mus musculus GN=Hmgb2 PE=1 SV=3 Back     alignment and function description
>sp|P52925|HMGB2_RAT High mobility group protein B2 OS=Rattus norvegicus GN=Hmgb2 PE=2 SV=2 Back     alignment and function description
>sp|P17741|HMGB2_PIG High mobility group protein B2 OS=Sus scrofa GN=HMGB2 PE=1 SV=2 Back     alignment and function description
>sp|P26584|HMGB2_CHICK High mobility group protein B2 OS=Gallus gallus GN=HMGB2 PE=2 SV=2 Back     alignment and function description
>sp|P63159|HMGB1_RAT High mobility group protein B1 OS=Rattus norvegicus GN=Hmgb1 PE=1 SV=2 Back     alignment and function description
>sp|A9RA84|HMGB1_PAPAN High mobility group protein B1 OS=Papio anubis GN=HMGB1 PE=3 SV=1 Back     alignment and function description
>sp|P63158|HMGB1_MOUSE High mobility group protein B1 OS=Mus musculus GN=Hmgb1 PE=1 SV=2 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 ?
Query105
270005614 557 hypothetical protein TcasGA2_TC007692 [T 0.438 0.082 0.795 1e-14
189236107 505 PREDICTED: similar to High mobility grou 0.352 0.073 0.945 2e-14
347962987 457 AGAP000005-PA [Anopheles gambiae str. PE 0.428 0.098 0.755 5e-14
312378819 527 hypothetical protein AND_09522 [Anophele 0.428 0.085 0.755 6e-14
193664382 410 PREDICTED: hypothetical protein LOC10016 0.352 0.090 0.891 8e-14
332375054 306 unknown [Dendroctonus ponderosae] 0.361 0.124 0.921 1e-13
170056683 372 conserved hypothetical protein [Culex qu 0.428 0.120 0.755 1e-13
242003301187 High mobility group protein B2, putative 0.438 0.245 0.782 2e-13
321478856190 hypothetical protein DAPPUDRAFT_232871 [ 0.428 0.236 0.777 5e-13
241122588 207 DNA-binding protein, putative [Ixodes sc 0.352 0.178 0.918 1e-12
>gi|270005614|gb|EFA02062.1| hypothetical protein TcasGA2_TC007692 [Tribolium castaneum] Back     alignment and taxonomy information
 Score = 83.6 bits (205), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/49 (79%), Positives = 40/49 (81%), Gaps = 3/49 (6%)

Query: 11  AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWK---SSRIVNPFVG 56
           AYAFFVQ CREEHKKKHPEENVVFAEFSKKCAERWK    S I   F+G
Sbjct: 313 AYAFFVQTCREEHKKKHPEENVVFAEFSKKCAERWKPPEESYITISFLG 361

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|189236107|ref|XP_973934.2| PREDICTED: similar to High mobility group protein DSP1 (Protein dorsal switch 1) [Tribolium castaneum] Back     alignment and taxonomy information
>gi|347962987|ref|XP_311155.4| AGAP000005-PA [Anopheles gambiae str. PEST] gi|333467412|gb|EAA06432.5| AGAP000005-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|312378819|gb|EFR25283.1| hypothetical protein AND_09522 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|193664382|ref|XP_001944154.1| PREDICTED: hypothetical protein LOC100167132 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|332375054|gb|AEE62668.1| unknown [Dendroctonus ponderosae] Back     alignment and taxonomy information
>gi|170056683|ref|XP_001864141.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167876428|gb|EDS39811.1| conserved hypothetical protein [Culex quinquefasciatus] Back     alignment and taxonomy information
>gi|242003301|ref|XP_002422686.1| High mobility group protein B2, putative [Pediculus humanus corporis] gi|212505508|gb|EEB09948.1| High mobility group protein B2, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
>gi|321478856|gb|EFX89813.1| hypothetical protein DAPPUDRAFT_232871 [Daphnia pulex] Back     alignment and taxonomy information
>gi|241122588|ref|XP_002403591.1| DNA-binding protein, putative [Ixodes scapularis] gi|215493481|gb|EEC03122.1| DNA-binding protein, putative [Ixodes scapularis] 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 ?
Query105
FB|FBgn0011764 393 Dsp1 "Dorsal switch protein 1" 0.352 0.094 0.810 2.1e-13
UNIPROTKB|P40673209 HMGB2 "High mobility group pro 0.428 0.215 0.688 4.4e-13
UNIPROTKB|E2QY30 210 HMGB2 "Uncharacterized protein 0.428 0.214 0.688 4.4e-13
UNIPROTKB|D6R9A6134 HMGB2 "High mobility group pro 0.428 0.335 0.688 4.4e-13
UNIPROTKB|P26583209 HMGB2 "High mobility group pro 0.428 0.215 0.688 4.4e-13
UNIPROTKB|P17741 210 HMGB2 "High mobility group pro 0.428 0.214 0.688 4.4e-13
MGI|MGI:96157 210 Hmgb2 "high mobility group box 0.428 0.214 0.688 4.4e-13
RGD|1564519 210 RGD1564519 "similar to High mo 0.428 0.214 0.688 4.4e-13
RGD|69291 210 Hmgb2 "high mobility group box 0.428 0.214 0.688 4.4e-13
RGD|1561694209 RGD1561694 "similar to High mo 0.342 0.172 0.805 7.1e-13
FB|FBgn0011764 Dsp1 "Dorsal switch protein 1" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 181 (68.8 bits), Expect = 2.1e-13, P = 2.1e-13
 Identities = 30/37 (81%), Positives = 35/37 (94%)

Query:    11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
             AYA+FVQ CREEHKKKHP+E V+FAEFS+KCAERWK+
Sbjct:   185 AYAYFVQTCREEHKKKHPDETVIFAEFSRKCAERWKT 221
GO:0005634 "nucleus" evidence=IC;IDA
GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA
GO:0043388 "positive regulation of DNA binding" evidence=IDA
GO:0003677 "DNA binding" evidence=IDA
GO:0017025 "TBP-class protein binding" evidence=IPI
GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IDA
GO:0032502 "developmental process" evidence=IMP
GO:0008134 "transcription factor binding" evidence=IPI
GO:0006338 "chromatin remodeling" evidence=IMP
GO:0007379 "segment specification" evidence=IMP
GO:0008301 "DNA binding, bending" evidence=IDA
GO:0035218 "leg disc development" evidence=IMP
GO:0008348 "negative regulation of antimicrobial humoral response" evidence=IGI;IMP
GO:0005700 "polytene chromosome" evidence=IDA
UNIPROTKB|P40673 HMGB2 "High mobility group protein B2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2QY30 HMGB2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|D6R9A6 HMGB2 "High mobility group protein B2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P26583 HMGB2 "High mobility group protein B2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P17741 HMGB2 "High mobility group protein B2" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:96157 Hmgb2 "high mobility group box 2" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1564519 RGD1564519 "similar to High mobility group protein 2 (HMG-2)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
RGD|69291 Hmgb2 "high mobility group box 2" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
RGD|1561694 RGD1561694 "similar to High mobility group protein 2 (HMG-2)" [Rattus norvegicus (taxid:10116)] 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) ?
P17741HMGB2_PIGNo assigned EC number0.68880.42850.2142yesN/A
P40673HMGB2_BOVINNo assigned EC number0.68880.42850.2153yesN/A
P26583HMGB2_HUMANNo assigned EC number0.68880.42850.2153yesN/A
P26584HMGB2_CHICKNo assigned EC number0.64440.42850.2173yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query105
pfam0901169 pfam09011, DUF1898, Domain of unknown function (DU 3e-08
cd0139066 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class 6e-07
cd0008466 cd00084, HMG-box, High Mobility Group (HMG)-box is 2e-05
smart0039870 smart00398, HMG, high mobility group 2e-04
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898) Back     alignment and domain information 
 Score = 46.3 bits (110), Expect = 3e-08
 Identities = 19/37 (51%), Positives = 25/37 (67%), Gaps = 1/37 (2%)

Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
          AY FFVQ  R E K++ P+     AEFSK C+E+WK+
Sbjct: 10 AYFFFVQTMRPELKREGPQVP-GVAEFSKLCSEKWKA 45

This domain is predominantly found in Maelstrom homolog proteins. It has no known function. 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 105
COG5648211 NHP6B Chromatin-associated proteins containing the 99.76
PTZ0019994 high mobility group protein; Provisional 99.73
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 99.55
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 99.54
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 99.52
smart0039870 HMG high mobility group. 99.46
KOG0526|consensus615 99.44
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 99.44
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 99.4
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 99.38
KOG0381|consensus96 99.35
KOG0527|consensus 331 99.04
PTZ0019994 high mobility group protein; Provisional 98.53
cd0138977 MATA_HMG-box MATA_HMG-box, class I member of the H 98.21
cd0138872 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of 98.19
COG5648211 NHP6B Chromatin-associated proteins containing the 98.12
cd0139066 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II 97.94
KOG0528|consensus511 97.85
KOG4715|consensus 410 97.82
PF0050569 HMG_box: HMG (high mobility group) box; InterPro: 97.79
cd0008466 HMG-box High Mobility Group (HMG)-box is found in 97.65
smart0039870 HMG high mobility group. 97.58
KOG0381|consensus96 97.49
KOG3248|consensus 421 97.14
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 96.12
PF0901173 HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi 95.97
KOG2746|consensus 683 95.37
KOG0526|consensus615 95.28
PF0807355 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 95.07
PF04690170 YABBY: YABBY protein; InterPro: IPR006780 YABBY pr 95.05
KOG0527|consensus 331 93.31
KOG2746|consensus 683 84.52
PF1488785 HMG_box_5: HMG (high mobility group) box 5; PDB: 1 81.14
PF0441875 DUF543: Domain of unknown function (DUF543); Inter 80.59
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] Back     alignment and domain information 
Probab=99.76  E-value=7.5e-19  Score=136.35  Aligned_cols=93  Identities=19%  Similarity=0.168  Sum_probs=82.3

Q ss_pred             CCCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCC--CCCC-----------------CC---
Q psy3267           1 MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVN--PFVG-----------------RK---   58 (105)
Q Consensus         1 ~PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~ee--ky~~-----------------e~---   58 (105)
                      +||+||||+||||+|++.+|+++.+.||++  +|+|++|.+||+||.++++|  +|..                 .+   
T Consensus        67 dpN~PKRp~sayf~y~~~~R~ei~~~~p~l--~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~  144 (211)
T COG5648          67 DPNGPKRPLSAYFLYSAENRDEIRKENPKL--TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPN  144 (211)
T ss_pred             CCCCCCCchhHHHHHHHHHHHHHHHhCCCC--ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCC
Confidence            699999999999999999999999999999  58999999999999999986  3441                 12   


Q ss_pred             -CCchHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267          59 -FAPVFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC   95 (105)
Q Consensus        59 -~APsa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~   95 (105)
                       +++..|.-+....|+.+.+.+|..   +.+++|++.|+|.
T Consensus       145 ~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el  185 (211)
T COG5648         145 KAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSEL  185 (211)
T ss_pred             CCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhh
Confidence             333888889999999999999987   8899999999984

>PTZ00199 high mobility group protein; Provisional 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
>cd01389 MATA_HMG-box MATA_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
>smart00398 HMG high mobility group Back     alignment and domain information
>KOG0526|consensus 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
>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
>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
>KOG0381|consensus Back     alignment and domain information
>KOG0527|consensus Back     alignment and domain information
>PTZ00199 high mobility group protein; Provisional Back     alignment and domain information
>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
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics] 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
>KOG0528|consensus Back     alignment and domain information
>KOG4715|consensus 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
>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
>smart00398 HMG high mobility group Back     alignment and domain information
>KOG0381|consensus Back     alignment and domain information
>KOG3248|consensus 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
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins Back     alignment and domain information
>KOG2746|consensus Back     alignment and domain information
>KOG0526|consensus 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
>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
>KOG0527|consensus Back     alignment and domain information
>KOG2746|consensus 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
>PF04418 DUF543: Domain of unknown function (DUF543); InterPro: IPR007512 This family of short eukaryotic proteins has no known function 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 ?
Query105
2yrq_A173 Solution Structure Of The Tandem Hmg Box Domain Fro 2e-12
1j3x_A77 Solution Structure Of The N-Terminal Domain Of The 2e-12
2ly4_A83 Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo 2e-12
1ckt_A71 Crystal Structure Of Hmg1 Domain A Bound To A Cispl 2e-12
2eqz_A86 Solution Structure Of The First Hmg-Box Domain From 4e-12
1aab_A83 Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 1e-11
>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 
Iteration: 1

 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
          +YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 22 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 58
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77 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|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A Cisplatin-modified Dna Duplex Length = 71 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
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83 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 ?
Query105
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 2e-13
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 2e-13
1ckt_A71 High mobility group 1 protein; high-mobility group 6e-13
2yrq_A173 High mobility group protein B1; HMG box domain, DN 6e-10
2yrq_A173 High mobility group protein B1; HMG box domain, DN 3e-05
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 3e-09
2lhj_A97 High mobility group protein homolog NHP1; structur 8e-09
3tq6_A 214 Transcription factor A, mitochondrial; transcripti 2e-07
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 5e-07
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 7e-07
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 5e-06
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 8e-06
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 1e-05
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 1e-05
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 2e-05
1hme_A77 High mobility group protein fragment-B; DNA-bindin 3e-05
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 8e-05
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 3e-04
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83 Back     alignment and structure
 Score = 59.2 bits (144), Expect = 2e-13
 Identities = 27/37 (72%), Positives = 33/37 (89%)

Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
          +YAFFVQ  REEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 14 SYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT 50
>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
>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
>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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73 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
>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
>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
>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
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92 Back     alignment and structure
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query105
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.94
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.9
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.9
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.88
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 99.8
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 99.79
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 99.77
1ckt_A71 High mobility group 1 protein; high-mobility group 99.77
1hme_A77 High mobility group protein fragment-B; DNA-bindin 99.73
1wgf_A90 Upstream binding factor 1; transcription factor, D 99.71
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 99.71
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 99.7
2lhj_A97 High mobility group protein homolog NHP1; structur 99.7
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 99.7
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 99.7
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 99.7
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 99.7
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 99.7
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 99.69
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 99.68
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 99.67
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 99.66
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 99.66
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 99.63
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 99.62
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 99.62
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 99.62
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 99.61
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 99.6
2cto_A93 Novel protein; high mobility group box domain, hel 99.6
2gzk_A159 Sex-determining region on Y / HMGB1; protein-DNA c 99.57
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 99.56
2yrq_A173 High mobility group protein B1; HMG box domain, DN 99.56
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 99.56
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 99.54
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 99.51
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 99.47
3tmm_A238 Transcription factor A, mitochondrial; HMG, high m 99.26
3tq6_A214 Transcription factor A, mitochondrial; transcripti 99.25
2yuk_A90 Myeloid/lymphoid or mixed-lineage leukemia protein 98.67
1wgf_A90 Upstream binding factor 1; transcription factor, D 98.45
2d7l_A81 WD repeat and HMG-box DNA binding protein 1; high 98.45
3nm9_A73 HMG-D, high mobility group protein D; DNA bending, 98.44
1k99_A99 Upstream binding factor 1; alpha-helix, L-shape, D 98.44
1aab_A83 High mobility group protein; HMG-BOX, DNA-binding; 98.42
1wxl_A73 Single-strand recognition protein; FACT, SSRP1, HM 98.41
1hry_A76 Human SRY; DNA, DNA-binding protein, DNA binding p 98.38
1hme_A77 High mobility group protein fragment-B; DNA-bindin 98.37
2crj_A92 SWI/SNF-related matrix-associated actin- dependent 98.35
2eqz_A86 High mobility group protein B3; HMG-box domain, mo 98.33
2e6o_A87 HMG box-containing protein 1; HMG-box domain, HMG- 98.3
3u2b_C79 Transcription factor SOX-4; HMG domain, transcript 98.29
2co9_A102 Thymus high mobility group box protein TOX; TOX pr 98.28
4a3n_A71 Transcription factor SOX-17; 2.40A {Homo sapiens} 98.27
2cs1_A92 PMS1 protein homolog 1; DNA mismatch repair protei 98.26
1cg7_A93 Protein (NON histone protein 6 A); HMG BOX, DNA be 98.26
1j46_A85 SRY, sex-determining region Y protein; MALE sex de 98.25
1ckt_A71 High mobility group 1 protein; high-mobility group 98.24
1wz6_A82 HMG-box transcription factor BBX; bobby SOX homolo 98.22
3f27_D83 Transcription factor SOX-17; protein-DNA complex, 98.21
1gt0_D80 Transcription factor SOX-2; POU factors, SOX prote 98.2
1i11_A81 Transcription factor SOX-5; HMG BOX, DNA bending, 98.2
2lhj_A97 High mobility group protein homolog NHP1; structur 98.19
2lef_A86 LEF-1 HMG, protein (lymphoid enhancer-binding fact 98.18
3fgh_A67 Transcription factor A, mitochondrial; HMG domain, 98.11
4euw_A106 Transcription factor SOX-9; protein-DNA complex, H 98.03
2cto_A93 Novel protein; high mobility group box domain, hel 97.48
1l8y_A91 Upstream binding factor 1; HUBF, HMG box 5, DNA bi 97.43
1v64_A108 Nucleolar transcription factor 1; DNA binding, str 97.3
1v63_A101 Nucleolar transcription factor 1; DNA binding, str 96.75
>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
Probab=99.94  E-value=2.8e-27  Score=171.70  Aligned_cols=95  Identities=38%  Similarity=0.584  Sum_probs=84.1

Q ss_pred             CCCCCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC--CC-----------------------
Q psy3267           1 MQNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP--FV-----------------------   55 (105)
Q Consensus         1 ~PnkPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek--y~-----------------------   55 (105)
                      +||+||||+|||++|++++|++++++||+.+++++||+|.||++|++|+++|+  |.                       
T Consensus        12 dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~~~   91 (173)
T 2yrq_A           12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE   91 (173)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCCCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Confidence            69999999999999999999999999999777899999999999999999852  22                       


Q ss_pred             -----CCCCCc----hHHHHhhhccchhhhhcCCcc---hhhhhhHhhHHHH
Q psy3267          56 -----GRKFAP----VFLTFLSRMKDSILFCVNPVL---AVGSRILEKFDEC   95 (105)
Q Consensus        56 -----~e~~AP----sa~~~f~~~~r~~l~~~nP~l---~v~~v~~~~~~~~   95 (105)
                           .++++|    +||++||++.|+.|+.+||++   .|+.+||+.|...
T Consensus        92 ~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~l  143 (173)
T 2yrq_A           92 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT  143 (173)
T ss_dssp             SSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHS
T ss_pred             hcccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence                 145666    999999999999999999998   5666799999764
>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
>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
>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
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, 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
>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
>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
>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
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} 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
>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
>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
>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
>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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A* Back     alignment and structure
>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
>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
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} 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
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Back     alignment and structure
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Back     alignment and structure
>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
>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
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0 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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Back     alignment and structure
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Back     alignment and structure
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Back     alignment and structure
>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; 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
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Back     alignment and structure
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A Back     alignment and structure
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Back     alignment and structure
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1 Back     alignment and structure
>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
>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
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} 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
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A Back     alignment and structure
>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
>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

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 105
d1ckta_71 a.21.1.1 (A:) High mobility group protein 1, HMG1 4e-08
d1qrva_73 a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI 1e-04
d1hsma_79 a.21.1.1 (A:) High mobility group protein 1, HMG1 3e-04
d1v63a_101 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 7e-04
d1wgfa_90 a.21.1.1 (A:) Nucleolar transcription factor 1 (Up 8e-04
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71 Back     information, alignment and structure

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 44.1 bits (104), Expect = 4e-08
 Identities = 28/37 (75%), Positives = 34/37 (91%)

Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
          +YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 8  SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 44
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73 Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query105
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 99.7
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 99.68
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 99.67
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 99.63
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 99.61
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 99.61
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 99.6
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 99.58
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 99.57
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 99.4
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 99.24
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 99.15
d1qrva_73 HMG-D {Drosophila melanogaster [TaxId: 7227]} 98.42
d1hsma_79 High mobility group protein 1, HMG1 {Hamster (Cric 98.37
d1i11a_70 Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} 98.34
d1j46a_85 SRY {Human (Homo sapiens) [TaxId: 9606]} 98.29
d1gt0d_80 Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 98.25
d2lefa_86 Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus 98.23
d1ckta_71 High mobility group protein 1, HMG1 {Rat (Rattus n 98.16
d1k99a_91 Nucleolar transcription factor 1 (Upstream binding 98.12
d1wgfa_90 Nucleolar transcription factor 1 (Upstream binding 98.07
d1lwma_93 NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T 97.93
d1v63a_101 Nucleolar transcription factor 1 (Upstream binding 97.64
d1v64a_108 Nucleolar transcription factor 1 (Upstream binding 97.01
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.70  E-value=1e-17  Score=104.87  Aligned_cols=50  Identities=58%  Similarity=0.973  Sum_probs=48.0

Q ss_pred             CCCCCCchHHHhHHHHHHHHHHhCCCCchhHHHHHHHHHHHhhhcccCCC
Q psy3267           4 KLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNP   53 (105)
Q Consensus         4 kPKr~~SAY~fF~q~~Ree~KkknPd~sv~faE~sKk~ge~WK~ms~eek   53 (105)
                      +||||+|||++|++++|++++.+||+.++++++|+|.+|++|+.|+++++
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK   50 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEK   50 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTS
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHH
Confidence            69999999999999999999999999888899999999999999999985
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} 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
>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} 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
>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
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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
>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
>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Back     information, alignment and structure
>d1i11a_ a.21.1.1 (A:) Sox-5 {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
>d1gt0d_ a.21.1.1 (D:) Sox-2 {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
>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>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
>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>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