Psyllid ID: psy3429

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-------170-------180-------190--
TVDLPQLFLNEILILSSPLLSDSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMPQNSPPGGSDMKASPPRPSPSPTMT
ccccccHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHcHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
TVDLPQLFLNEILilsspllsdsnkgdppklnvnlrkhkpnrkprtpfttQQLLSLEKKFREKQYLSIAEraefssslhlteTQVKIWFQNRRAKAKRLQEAEIEKIKMSAIaaarphplygpgpsphlhqyfqhaspeallhhphpfsallgrhpamahfmpaapmpqnsppggsdmkaspprpspsptmt
TVDLPQLFLNEILIlsspllsdsnkgdPPKLNVnlrkhkpnrkprtpfttqqllslEKKFREKQYLSIAeraefssslhltetqvkiwFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMPQNSPPGGSDMkaspprpspsptmt
TVDLPQLFLNEililsspllsdsNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRhpamahfmpaapmpQNSPPGGSDMKAspprpspspTMT
*****QLFLNEILILS***********************************************QYLSIAERAEFSSSLHLTETQVKIWFQNRRA*************************************YF********L********L*****************************************
***********************************************FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKA************************************************************************************************
TVDLPQLFLNEILILSSPLLSDSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQN********QEAEIEKIKMSAIAAARPHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMP************************
********************************************RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE**************************HLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMPQNSPPGGSDMKASP**********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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TVDLPQLFLNEILILSSPLLSDSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGPGPSPHLHQYFQHASPEALLHHPHPFSALLGRHPAMAHFMPAAPMPQNSPPGGSDMKASPPRPSPSPTMT
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 ?
Query192 2.2.26 [Sep-21-2011]
Q03372515 Muscle segmentation homeo yes N/A 0.494 0.184 0.835 1e-40
P1585779 Homeobox protein H17 (Fra no N/A 0.411 1.0 0.924 1e-36
Q03357257 Homeobox protein MSH-A OS yes N/A 0.765 0.571 0.527 1e-34
P35993291 Homeobox protein XHOX-7.1 N/A N/A 0.416 0.274 0.862 3e-34
P50223288 Homeobox protein GHOX-7 O yes N/A 0.411 0.274 0.860 4e-34
Q2VL80297 Homeobox protein MSX-1 OS N/A N/A 0.411 0.265 0.860 7e-34
P23410259 Homeobox protein MSX-2 OS N/A N/A 0.421 0.312 0.851 8e-34
Q9GK08267 Homeobox protein MSX-2 OS yes N/A 0.416 0.299 0.85 8e-34
Q2VL86297 Homeobox protein MSX-1 OS N/A N/A 0.411 0.265 0.860 9e-34
Q2VL82297 Homeobox protein MSX-1 OS N/A N/A 0.411 0.265 0.860 9e-34
>sp|Q03372|HMSH_DROME Muscle segmentation homeobox OS=Drosophila melanogaster GN=Dr PE=2 SV=2 Back     alignment and function desciption
 Score =  166 bits (419), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 81/97 (83%), Positives = 87/97 (89%), Gaps = 2/97 (2%)

Query: 21  SDSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHL 80
            D+N  +PP++  NLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSL L
Sbjct: 403 GDAN--EPPRIKCNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLRL 460

Query: 81  TETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARP 117
           TETQVKIWFQNRRAKAKRLQEAEIEKIKM+A+    P
Sbjct: 461 TETQVKIWFQNRRAKAKRLQEAEIEKIKMAALGRGAP 497
Plays a key role in the specification of proneural and promuscular cluster formation. Required for the specification of dorsal and lateral muscle progenitor cells.
Drosophila melanogaster (taxid: 7227)
>sp|P15857|HM17_APIME Homeobox protein H17 (Fragment) OS=Apis mellifera PE=3 SV=1 Back     alignment and function description
>sp|Q03357|MSXA_DANRE Homeobox protein MSH-A OS=Danio rerio GN=msxa PE=2 SV=2 Back     alignment and function description
>sp|P35993|HOX7P_XENLA Homeobox protein XHOX-7.1' (Fragment) OS=Xenopus laevis PE=2 SV=1 Back     alignment and function description
>sp|P50223|HMGX7_CHICK Homeobox protein GHOX-7 OS=Gallus gallus GN=GHOX-7 PE=2 SV=1 Back     alignment and function description
>sp|Q2VL80|MSX1_PERPO Homeobox protein MSX-1 OS=Perodicticus potto edwarsi GN=MSX1 PE=3 SV=1 Back     alignment and function description
>sp|P23410|MSX2_COTJA Homeobox protein MSX-2 OS=Coturnix coturnix japonica GN=MSX2 PE=2 SV=1 Back     alignment and function description
>sp|Q9GK08|MSX2_CANFA Homeobox protein MSX-2 OS=Canis familiaris GN=MSX2 PE=2 SV=1 Back     alignment and function description
>sp|Q2VL86|MSX1_SAIBB Homeobox protein MSX-1 OS=Saimiri boliviensis boliviensis GN=MSX1 PE=3 SV=1 Back     alignment and function description
>sp|Q2VL82|MSX1_SAGOE Homeobox protein MSX-1 OS=Saguinus oedipus GN=MSX1 PE=3 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 ?
Query192
328714228 518 PREDICTED: hypothetical protein LOC10057 0.708 0.262 0.767 4e-53
242018184200 Homeobox protein MSX-1, putative [Pedicu 0.729 0.7 0.744 1e-50
91091014292 PREDICTED: similar to Drop CG1897-PA [Tr 0.729 0.479 0.645 8e-42
198449864 533 GA15116 [Drosophila pseudoobscura pseudo 0.489 0.176 0.840 3e-39
194765260 530 GF23351 [Drosophila ananassae] gi|190615 0.494 0.179 0.835 3e-39
195445065 515 GK11900 [Drosophila willistoni] gi|19416 0.489 0.182 0.840 3e-39
195036336 545 GH18901 [Drosophila grimshawi] gi|193893 0.489 0.172 0.843 4e-39
157113786121 hypothetical protein AaeL_AAEL006593 [Ae 0.520 0.826 0.81 5e-39
345497030 389 PREDICTED: hypothetical protein LOC10011 0.520 0.257 0.780 6e-39
195574761 514 GD21441 [Drosophila simulans] gi|1942012 0.494 0.184 0.835 6e-39
>gi|328714228|ref|XP_003245303.1| PREDICTED: hypothetical protein LOC100575011 [Acyrthosiphon pisum] Back     alignment and taxonomy information
 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 109/142 (76%), Positives = 118/142 (83%), Gaps = 6/142 (4%)

Query: 22  DSNKGDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLT 81
           DSN G+PPKL  NLRKHKPNRKPRTPFTTQQLL+LEKKFREKQYLSIAERAEFS+SLHLT
Sbjct: 311 DSNNGEPPKLKCNLRKHKPNRKPRTPFTTQQLLNLEKKFREKQYLSIAERAEFSNSLHLT 370

Query: 82  ETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARP-HPLYGPGPSPHLHQYFQHASPEA 140
           ETQVKIWFQNRRAKAKRLQEAEIEK+KM+A+AAARP HPLYG   +PHL  YFQH  P  
Sbjct: 371 ETQVKIWFQNRRAKAKRLQEAEIEKLKMAAVAAARPHHPLYG---NPHLPHYFQH--PSE 425

Query: 141 LLHHPHPFSALLGRHPAMAHFM 162
           L  H H   +LL   P MAH +
Sbjct: 426 LFGHQHQLQSLLSHRPTMAHLI 447

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|242018184|ref|XP_002429560.1| Homeobox protein MSX-1, putative [Pediculus humanus corporis] gi|212514514|gb|EEB16822.1| Homeobox protein MSX-1, putative [Pediculus humanus corporis] Back     alignment and taxonomy information
>gi|91091014|ref|XP_975059.1| PREDICTED: similar to Drop CG1897-PA [Tribolium castaneum] gi|270013175|gb|EFA09623.1| hypothetical protein TcasGA2_TC011744 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|198449864|ref|XP_001357750.2| GA15116 [Drosophila pseudoobscura pseudoobscura] gi|198130789|gb|EAL26884.2| GA15116 [Drosophila pseudoobscura pseudoobscura] Back     alignment and taxonomy information
>gi|194765260|ref|XP_001964745.1| GF23351 [Drosophila ananassae] gi|190615017|gb|EDV30541.1| GF23351 [Drosophila ananassae] Back     alignment and taxonomy information
>gi|195445065|ref|XP_002070156.1| GK11900 [Drosophila willistoni] gi|194166241|gb|EDW81142.1| GK11900 [Drosophila willistoni] Back     alignment and taxonomy information
>gi|195036336|ref|XP_001989626.1| GH18901 [Drosophila grimshawi] gi|193893822|gb|EDV92688.1| GH18901 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|157113786|ref|XP_001657901.1| hypothetical protein AaeL_AAEL006593 [Aedes aegypti] gi|108877576|gb|EAT41801.1| AAEL006593-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|345497030|ref|XP_001601013.2| PREDICTED: hypothetical protein LOC100116547 [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|195574761|ref|XP_002105352.1| GD21441 [Drosophila simulans] gi|194201279|gb|EDX14855.1| GD21441 [Drosophila simulans] 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 ?
Query192
FB|FBgn0000492515 Dr "Drop" [Drosophila melanoga 0.473 0.176 0.868 5.5e-38
ZFIN|ZDB-GENE-980526-312233 msxe "muscle segment homeobox 0.567 0.467 0.644 1.8e-32
UNIPROTKB|P28361249 MSX1 "Homeobox protein MSX-1" 0.442 0.341 0.804 3.7e-32
ZFIN|ZDB-GENE-980526-492251 msxd "muscle segment homeobox 0.437 0.334 0.821 4.7e-32
UNIPROTKB|P28362259 MSX2 "Homeobox protein MSX-2" 0.401 0.297 0.883 6e-32
UNIPROTKB|Q0P5C3267 MSX2 "Homeobox protein MSX-2" 0.401 0.288 0.883 6e-32
UNIPROTKB|Q9GK08267 MSX2 "Homeobox protein MSX-2" 0.401 0.288 0.883 6e-32
UNIPROTKB|P35548267 MSX2 "Homeobox protein MSX-2" 0.401 0.288 0.883 6e-32
UNIPROTKB|A1YF16267 MSX2 "Homeobox protein MSX-2" 0.401 0.288 0.883 6e-32
UNIPROTKB|A1YG93267 MSX2 "Homeobox protein MSX-2" 0.401 0.288 0.883 6e-32
FB|FBgn0000492 Dr "Drop" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 79/91 (86%), Positives = 84/91 (92%)

Query:    27 DPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86
             +PP++  NLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSL LTETQVK
Sbjct:   407 EPPRIKCNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLRLTETQVK 466

Query:    87 IWFQNRRAKAKRLQEAEIEKIKMSAIAAARP 117
             IWFQNRRAKAKRLQEAEIEKIKM+A+    P
Sbjct:   467 IWFQNRRAKAKRLQEAEIEKIKMAALGRGAP 497
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0003677 "DNA binding" evidence=ISS
GO:0005634 "nucleus" evidence=ISS;IDA
GO:0007450 "dorsal/ventral pattern formation, imaginal disc" evidence=IMP
GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP
GO:0042659 "regulation of cell fate specification" evidence=IMP
GO:0007419 "ventral cord development" evidence=NAS;TAS
GO:0007517 "muscle organ development" evidence=TAS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;NAS
GO:0009953 "dorsal/ventral pattern formation" evidence=TAS
GO:0007400 "neuroblast fate determination" evidence=TAS
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0007420 "brain development" evidence=IMP;TAS
GO:0007398 "ectoderm development" evidence=TAS
GO:0007417 "central nervous system development" evidence=NAS
GO:0007389 "pattern specification process" evidence=NAS
GO:0035309 "wing and notum subfield formation" evidence=IMP
GO:0035222 "wing disc pattern formation" evidence=IMP
GO:0021782 "glial cell development" evidence=IMP
GO:0010629 "negative regulation of gene expression" evidence=IMP
GO:0007485 "imaginal disc-derived male genitalia development" evidence=IMP
ZFIN|ZDB-GENE-980526-312 msxe "muscle segment homeobox E" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|P28361 MSX1 "Homeobox protein MSX-1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-980526-492 msxd "muscle segment homeobox D" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|P28362 MSX2 "Homeobox protein MSX-2" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q0P5C3 MSX2 "Homeobox protein MSX-2" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|Q9GK08 MSX2 "Homeobox protein MSX-2" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P35548 MSX2 "Homeobox protein MSX-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|A1YF16 MSX2 "Homeobox protein MSX-2" [Gorilla gorilla gorilla (taxid:9595)] Back     alignment and assigned GO terms
UNIPROTKB|A1YG93 MSX2 "Homeobox protein MSX-2" [Pan paniscus (taxid:9597)] 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) ?
P15857HM17_APIMENo assigned EC number0.92400.41141.0noN/A
Q03372HMSH_DROMENo assigned EC number0.83500.49470.1844yesN/A
Q03357MSXA_DANRENo assigned EC number0.52720.76560.5719yesN/A
P50223HMGX7_CHICKNo assigned EC number0.86070.41140.2743yesN/A
Q9GK08MSX2_CANFANo assigned EC number0.850.41660.2996yesN/A
Q09604VAB15_CAEELNo assigned EC number0.72040.45830.3911yesN/A
O02786MSX1_BOVINNo assigned EC number0.86070.41140.2659yesN/A
Q2VL84MSX1_CALJANo assigned EC number0.86070.41140.2659yesN/A
Q2VL88MSX1_PANTRNo assigned EC number0.86070.41140.2659yesN/A
P13297MSX1_MOUSENo assigned EC number0.86070.41140.2659yesN/A
P28360MSX1_HUMANNo assigned EC number0.86070.41140.2659yesN/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 ?
Query192
pfam0004657 pfam00046, Homeobox, Homeobox domain 2e-27
smart0038957 smart00389, HOX, Homeodomain 3e-22
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 4e-22
COG5576156 COG5576, COG5576, Homeodomain-containing transcrip 7e-11
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 97.9 bits (245), Expect = 2e-27
 Identities = 33/57 (57%), Positives = 40/57 (70%)

Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
          R+ RT FT +QL  LEK+F + +Y S  ER E +  L LTE QVK+WFQNRRAK KR
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 192
KOG0492|consensus246 99.87
KOG0488|consensus309 99.87
KOG0484|consensus125 99.85
KOG0489|consensus261 99.85
KOG0485|consensus268 99.84
KOG0494|consensus332 99.83
KOG0842|consensus307 99.83
KOG0487|consensus308 99.81
KOG0850|consensus245 99.81
KOG0843|consensus197 99.8
KOG2251|consensus228 99.78
KOG0848|consensus317 99.77
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.76
KOG0491|consensus194 99.76
KOG0493|consensus342 99.71
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.68
KOG0844|consensus408 99.67
KOG0486|consensus351 99.66
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.65
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.65
KOG3802|consensus398 99.59
KOG0483|consensus198 99.58
KOG4577|consensus383 99.55
COG5576156 Homeodomain-containing transcription factor [Trans 99.55
KOG0847|consensus288 99.51
KOG0490|consensus235 99.42
KOG0849|consensus354 99.36
KOG1168|consensus385 99.21
KOG0775|consensus304 99.12
KOG0774|consensus334 99.03
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.78
KOG2252|consensus558 98.68
KOG0490|consensus235 98.38
KOG1146|consensus 1406 98.02
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 97.51
KOG0773|consensus342 97.28
KOG3623|consensus 1007 96.28
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 96.05
KOG1924|consensus 1102 95.92
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 92.66
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 87.85
PRK03975141 tfx putative transcriptional regulator; Provisiona 87.57
KOG3755|consensus769 87.3
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 86.34
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 85.33
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 83.71
PRK04217110 hypothetical protein; Provisional 81.84
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 80.98
>KOG0492|consensus Back     alignment and domain information 
Probab=99.87  E-value=4.3e-22  Score=160.29  Aligned_cols=84  Identities=85%  Similarity=1.163  Sum_probs=79.4

Q ss_pred             CCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHHHHh
Q psy3429          30 KLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKM  109 (192)
Q Consensus        30 ~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~~~~  109 (192)
                      ...|.++|++.+|+.||-||.+||..||+.|++.+|.++.||.|++..|.|+++||||||||||+|.||.++.+.++.++
T Consensus       133 p~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~km  212 (246)
T KOG0492|consen  133 PTTCTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKM  212 (246)
T ss_pred             cccchhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhh
Confidence            34588899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhhh
Q psy3429         110 SAIA  113 (192)
Q Consensus       110 ~~~~  113 (192)
                      +...
T Consensus       213 aa~~  216 (246)
T KOG0492|consen  213 AAKS  216 (246)
T ss_pred             hhcc
Confidence            7654

>KOG0488|consensus Back     alignment and domain information
>KOG0484|consensus Back     alignment and domain information
>KOG0489|consensus Back     alignment and domain information
>KOG0485|consensus Back     alignment and domain information
>KOG0494|consensus Back     alignment and domain information
>KOG0842|consensus Back     alignment and domain information
>KOG0487|consensus Back     alignment and domain information
>KOG0850|consensus Back     alignment and domain information
>KOG0843|consensus Back     alignment and domain information
>KOG2251|consensus Back     alignment and domain information
>KOG0848|consensus Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0491|consensus Back     alignment and domain information
>KOG0493|consensus Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0844|consensus Back     alignment and domain information
>KOG0486|consensus Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>KOG3802|consensus Back     alignment and domain information
>KOG0483|consensus Back     alignment and domain information
>KOG4577|consensus Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0847|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>KOG1168|consensus Back     alignment and domain information
>KOG0775|consensus Back     alignment and domain information
>KOG0774|consensus Back     alignment and domain information
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [] Back     alignment and domain information
>KOG2252|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>KOG1146|consensus Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>KOG0773|consensus Back     alignment and domain information
>KOG3623|consensus Back     alignment and domain information
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere Back     alignment and domain information
>KOG1924|consensus Back     alignment and domain information
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs) Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>KOG3755|consensus Back     alignment and domain information
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella 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 ?
Query192
1ig7_A58 Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 9e-25
2m34_A71 Nmr Structure Of The Homeodomain Transcription Fact 4e-15
2djn_A70 The Solution Structure Of The Homeobox Domain Of Hu 5e-14
1b72_A97 Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le 5e-12
3rkq_A58 Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt 9e-12
3a01_A93 Crystal Structure Of Aristaless And Clawless Homeod 2e-11
2dmt_A80 Solution Structure Of The Homeobox Domain Of Homeob 3e-11
1hdd_C61 Crystal Structure Of An Engrailed Homeodomain-Dna C 1e-10
1qry_A80 Homeobox Protein Vnd (Ventral Nervous System Defect 1e-10
3hdd_A60 Engrailed Homeodomain Dna Complex Length = 60 2e-10
1ftt_A68 Thyroid Transcription Factor 1 Homeodomain (Rattus 2e-10
1nk2_P77 VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES 2e-10
1puf_A77 Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo 2e-10
2l9r_A69 Solution Nmr Structure Of Homeobox Domain Of Homeob 3e-10
1p7j_A59 Crystal Structure Of Engrailed Homeodomain Mutant K 3e-10
1ztr_A61 Solution Structure Of Engrailed Homeodomain L16a Mu 4e-10
2hdd_A61 Engrailed Homeodomain Q50k Variant Dna Complex Leng 4e-10
1p7i_A59 Crystal Structure Of Engrailed Homeodomain Mutant K 4e-10
1enh_A54 Structural Studies Of The Engrailed Homeodomain Len 5e-10
1du0_A57 Engrailed Homeodomain Q50a Variant Dna Complex Leng 9e-10
2lp0_A60 The Solution Structure Of Homeodomain-Protein Compl 1e-09
2h1k_A63 Crystal Structure Of The Pdx1 Homeodomain In Comple 1e-09
3a03_A56 Crystal Structure Of Hox11l1 Homeodomain Length = 5 1e-09
2kt0_A84 Solution Structure Of Human Stem Cell Transcription 4e-09
2hos_A63 Phage-selected Homeodomain Bound To Unmodified Dna 5e-09
2r5y_A88 Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO 6e-09
1b8i_A81 Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX 7e-09
2vi6_A62 Crystal Structure Of The Nanog Homeodomain Length = 9e-09
2dmu_A70 Solution Structure Of The Homeobox Domain Of Homeob 1e-08
1jgg_A60 Even-Skipped Homeodomain Complexed To At-Rich Dna L 1e-08
2e1o_A70 Solution Structure Of Rsgi Ruh-028, A Homeobox Doma 2e-08
2l7f_P68 Solution Structure Of The Pitx2 Homeodomain Length 3e-08
1fjl_A81 Homeodomain From The Drosophila Paired Protein Boun 4e-08
2l7m_P68 Solution Structure Of The Pitx2 Homeodomain R24h Mu 4e-08
1hom_A68 Determination Of The Three-Dimensional Structure Of 5e-08
2l7z_A73 Nmr Structure Of A13 Homedomain Length = 73 6e-08
1ahd_P68 Determination Of The Nmr Solution Structure Of An A 6e-08
2ld5_A67 Solution Nmr-Derived Complex Structure Of Hoxa13 Dn 6e-08
9ant_A62 Antennapedia Homeodomain-Dna Complex Length = 62 7e-08
1ftz_A70 Nuclear Magnetic Resonance Solution Structure Of Th 8e-08
1san_A62 The Des(1-6)antennapedia Homeodomain: Comparison Of 2e-07
2m0c_A75 Solution Nmr Structure Of Homeobox Domain Of Human 2e-07
2k40_A67 Nmr Structure Of Hesx-1 Homeodomain Double Mutant R 2e-07
3a01_B67 Crystal Structure Of Aristaless And Clawless Homeod 3e-07
1zq3_P68 Nmr Solution Structure Of The Bicoid Homeodomain Bo 3e-07
2cra_A70 Solution Structure Of The Homeobox Domain Of Human 3e-07
3cmy_A61 Structure Of A Homeodomain In Complex With Dna Leng 7e-07
3lnq_A58 Structure Of Aristaless Homeodomain In Complex With 9e-07
2dms_A80 Solution Structure Of The Homeobox Domain Of Homeob 1e-06
2cue_A80 Solution Structure Of The Homeobox Domain Of The Hu 3e-06
2p81_A44 Engrailed Homeodomain Helix-Turn-Helix Motif Length 8e-06
3a02_A60 Crystal Structure Of Aristaless Homeodomain Length 8e-06
1o4x_A167 Ternary Complex Of The Dna Binding Domains Of The O 3e-04
1pog_A67 Solution Structure Of The Oct-1 Pou-Homeo Domain De 3e-04
1hf0_A159 Crystal Structure Of The Dna-Binding Domain Of Oct- 4e-04
1cqt_A163 Crystal Structure Of A Ternary Complex Containing A 5e-04
1oct_C156 Crystal Structure Of The Oct-1 Pou Domain Bound To 5e-04
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 Back     alignment and structure 
Iteration: 1

 Score =  109 bits (273), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
          RKPRTPFTT QLL+LE+KFR+KQYLSIAERAEFSSSL LTETQVKIWFQNRRAKAKRL
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1 From Homo Sapiens Length = 71 Back     alignment and structure
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5 Length = 70 Back     alignment and structure
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 97 Back     alignment and structure
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Length = 58 Back     alignment and structure
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 93 Back     alignment and structure
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80 Back     alignment and structure
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61 Back     alignment and structure
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective Protein) Length = 80 Back     alignment and structure
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60 Back     alignment and structure
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus Norvegicus) Length = 68 Back     alignment and structure
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES Length = 77 Back     alignment and structure
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 77 Back     alignment and structure
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69 Back     alignment and structure
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e Length = 59 Back     alignment and structure
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant Length = 61 Back     alignment and structure
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex Length = 61 Back     alignment and structure
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a Length = 59 Back     alignment and structure
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain Length = 54 Back     alignment and structure
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex Length = 57 Back     alignment and structure
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex Length = 60 Back     alignment and structure
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With Dna Length = 63 Back     alignment and structure
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain Length = 56 Back     alignment and structure
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor Nanog Homeodomain Fragment Length = 84 Back     alignment and structure
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna Length = 63 Back     alignment and structure
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd Site Length = 88 Back     alignment and structure
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 81 Back     alignment and structure
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain Length = 62 Back     alignment and structure
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70 Back     alignment and structure
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna Length = 60 Back     alignment and structure
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna Length = 70 Back     alignment and structure
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain Length = 68 Back     alignment and structure
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81 Back     alignment and structure
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant Length = 68 Back     alignment and structure
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The Antennapedia Homeodomain From Drosophila In Solution By 1h Nuclear Magnetic Resonance Spectroscopy Length = 68 Back     alignment and structure
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain Length = 73 Back     alignment and structure
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An Antennapedia Homeodomain-Dna Complex Length = 68 Back     alignment and structure
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna Binding Domain Bound To Dna Length = 67 Back     alignment and structure
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex Length = 62 Back     alignment and structure
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi Tarazu Homeodomain From Drosophila And Comparison With The Antennapedia Homeodomain Length = 70 Back     alignment and structure
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The Nmr Solution Structure And The Dna Binding Affinity With The Intact Antennapedia Homeodomain Length = 62 Back     alignment and structure
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75 Back     alignment and structure
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L Length = 67 Back     alignment and structure
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67 Back     alignment and structure
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To The Consensus Dna Binding Site Taatcc Length = 68 Back     alignment and structure
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo Box B13 Length = 70 Back     alignment and structure
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna Length = 61 Back     alignment and structure
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58 Back     alignment and structure
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Otx2 Length = 80 Back     alignment and structure
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human Paired Box Protein Pax-6 Length = 80 Back     alignment and structure
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif Length = 44 Back     alignment and structure
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60 Back     alignment and structure
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And Sox2 Transcription Factors With A 19mer Oligonucleotide From The Hoxb1 Regulatory Element Length = 167 Back     alignment and structure
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain Determined By Nmr And Restrained Molecular Dynamics Length = 67 Back     alignment and structure
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound To Dna As A Dimer Length = 159 Back     alignment and structure
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B Peptide, The Oct-1 Pou Domain, And An Octamer Element Length = 163 Back     alignment and structure
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An Octamer Site: Dna Recognition With Tethered Dna-Binding Modules Length = 156 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 ?
Query192
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 7e-36
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 3e-34
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 4e-34
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 9e-34
3a01_A93 Homeodomain-containing protein; homeodomain, prote 1e-33
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 2e-33
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 2e-33
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 5e-32
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 1e-31
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 1e-28
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 1e-27
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 6e-27
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 6e-26
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 3e-24
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 4e-24
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 2e-23
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 4e-22
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 3e-21
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 6e-21
2xsd_C164 POU domain, class 3, transcription factor 1; trans 1e-20
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 1e-20
1e3o_C160 Octamer-binding transcription factor 1; transcript 1e-20
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 2e-20
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 3e-20
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 3e-20
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 8e-20
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 1e-19
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 2e-19
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 1e-17
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 1e-17
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 3e-17
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 3e-17
3d1n_I151 POU domain, class 6, transcription factor 1; prote 2e-16
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-16
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 2e-16
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 2e-16
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 3e-16
3a02_A60 Homeobox protein aristaless; homeodomain, developm 4e-16
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 5e-16
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 2e-15
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 4e-15
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 5e-15
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 7e-15
1uhs_A72 HOP, homeodomain only protein; structural genomics 1e-14
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 1e-13
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 2e-13
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 4e-13
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 1e-12
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 4e-12
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 7e-12
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 3e-10
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 2e-08
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 2e-07
1lfb_A99 Liver transcription factor (LFB1); transcription r 2e-07
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 4e-07
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 5e-07
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 4e-06
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 4e-05
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58 Back     alignment and structure
 Score =  118 bits (299), Expect = 7e-36
 Identities = 53/58 (91%), Positives = 56/58 (96%)

Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
          RKPRTPFTT QLL+LE+KFR+KQYLSIAERAEFSSSL LTETQVKIWFQNRRAKAKRL
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62 Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93 Back     alignment and structure
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69 Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84 Back     alignment and structure
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77 Back     alignment and structure
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56 Back     alignment and structure
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61 Back     alignment and structure
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61 Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60 Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63 Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68 Back     alignment and structure
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97 Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 Back     alignment and structure
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81 Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160 Back     alignment and structure
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73 Back     alignment and structure
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77 Back     alignment and structure
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88 Back     alignment and structure
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146 Back     alignment and structure
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67 Back     alignment and structure
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155 Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76 Back     alignment and structure
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151 Back     alignment and structure
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 Back     alignment and structure
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68 Back     alignment and structure
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60 Back     alignment and structure
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81 Back     alignment and structure
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80 Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80 Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66 Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66 Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71 Back     alignment and structure
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89 Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75 Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89 Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194 Back     alignment and structure
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96 Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99 Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221 Back     alignment and structure
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76 Back     alignment and structure
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query192
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.87
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.87
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.87
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.87
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.86
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.86
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.86
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.86
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.86
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.86
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.86
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.86
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.86
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.85
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.85
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.85
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.85
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.85
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.85
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.85
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.85
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.85
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.85
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.85
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.85
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.84
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.84
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.84
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.84
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.84
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.84
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.84
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.84
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.84
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.83
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.83
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.83
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.83
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.83
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.83
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.83
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.82
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.82
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.82
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.82
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.82
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.8
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.8
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.8
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.8
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.8
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.8
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.8
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.79
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.79
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.79
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.79
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.79
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.78
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.78
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.78
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.78
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.78
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.77
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.77
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.77
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.75
2e19_A64 Transcription factor 8; homeobox domain, structura 99.74
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.74
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.73
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.73
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.68
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.67
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.6
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.6
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.57
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.45
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.69
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 96.7
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 91.6
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 91.37
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 90.98
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 90.91
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 86.05
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 85.35
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 85.32
3c57_A95 Two component transcriptional regulatory protein; 84.27
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 84.2
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 82.49
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 81.93
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 81.13
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 80.66
1fi6_A92 EH domain protein REPS1; EPS15 homology domain, EF 80.56
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
Probab=99.87  E-value=2.7e-22  Score=140.07  Aligned_cols=63  Identities=48%  Similarity=0.767  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429          37 KHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL   99 (192)
Q Consensus        37 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~   99 (192)
                      ..++.||.||.|+.+|+.+||.+|+.++||+..++++||..|||++.||++||||||+|+||.
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            356778899999999999999999999999999999999999999999999999999999974
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Back     alignment and structure
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Back     alignment and structure
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Back     alignment and structure
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Back     alignment and structure
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Back     alignment and structure
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Back     alignment and structure
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Back     alignment and structure
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Back     alignment and structure
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Back     alignment and structure
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Back     alignment and structure
>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Back     alignment and structure
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Back     alignment and structure
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Back     alignment and structure
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P Back     alignment and structure
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B* Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens} Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Back     alignment and structure
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Back     alignment and structure
>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Back     alignment and structure
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} Back     alignment and structure
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis} Back     alignment and structure
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Back     alignment and structure
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Back     alignment and structure
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis} Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Back     alignment and structure
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Back     alignment and structure
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2 Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Back     alignment and structure
>1fi6_A EH domain protein REPS1; EPS15 homology domain, EF hand, calcium, RAS signal transduction, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: a.39.1.6 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 192
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 2e-26
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 4e-25
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 1e-24
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 3e-24
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 6e-24
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 4e-23
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 5e-22
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 6e-22
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 6e-22
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 1e-21
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 4e-21
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 5e-21
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 6e-21
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 8e-21
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 1e-20
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 3e-20
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 8e-20
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 2e-19
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 5e-19
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 4e-18
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 7e-18
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 1e-17
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 1e-16
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 2e-16
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 2e-16
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 7e-16
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 2e-15
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 1e-14
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 1e-14
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 4e-13
d2ecca176 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H 3e-12
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 6e-12
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 94.1 bits (234), Expect = 2e-26
 Identities = 32/68 (47%), Positives = 41/68 (60%)

Query: 34  NLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93
           N    +  RK R P+T  Q L LEK+F    YL+   R E +  L+LTE QVKIWFQNRR
Sbjct: 6   NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRR 65

Query: 94  AKAKRLQE 101
            K K++ +
Sbjct: 66  MKMKKINK 73
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58 Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 Back     information, alignment and structure
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53 Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82 Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67 Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72 Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52 Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71 Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59 Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78 Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80 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 ?
Query192
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.89
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.89
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.88
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.88
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.88
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.88
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.88
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.87
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.87
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.87
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.86
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.86
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.86
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.86
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.86
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.84
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.84
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.84
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.83
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.82
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.82
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.81
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.8
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.78
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.77
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.76
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.76
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.72
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.72
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.71
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.71
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.7
d1hlva166 DNA-binding domain of centromere binding protein B 93.88
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 86.27
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 85.52
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 84.91
d1f54a_77 Calmodulin {Baker's yeast (Saccharomyces cerevisia 80.85
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=5.9e-24  Score=138.50  Aligned_cols=57  Identities=39%  Similarity=0.761  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429          42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR   98 (192)
Q Consensus        42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr   98 (192)
                      ||.||.||.+|+.+||+.|..++||+..+|++||..|||++.||++||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            677999999999999999999999999999999999999999999999999999875
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
>d1f54a_ a.39.1.5 (A:) Calmodulin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure