Psyllid ID: psy10745

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-------
PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDLEME
cccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccEEEcccHHHHHHHHHHccccccccccccEEccccccc
cccHHHHHEEcccHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHccEEEcccccEEEccccccHHHHHHHHHHHHccEEcccccEEEccccccHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHccccEEEEEccccEEccccccc
ptpqlltpflcprryyetgsfkagviggskpkvatapVVDAIAsykrenptmFAWEIRDRLLAEGicsqdnvpsvssinRYITyvpighggvnqlggvfvngrplpdVVRQRIVAsrshggvnqlggvfvngrplpdVVRQRIVELAhngvrpcdisrqlrvshgcvskilsresnlhnYRLVREEgcfelsdleme
ptpqlltpflcPRRYYETGSfkagviggskpkvatAPVVDAIasykrenpTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASrshggvnqlggvfvngrpLPDVVRQRIVELAhngvrpcdisrqlRVSHGCVSKilsresnlhnyrlvreegcfelsdleme
PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDLEME
****LLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFE*******
***QLLTPFLCPRRYYETG***************TAPVVDAIASYKRENPTMFAWEIRDRLLA********VPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCF********
PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDLEME
PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELS*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDLEME
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 ?
Query197 2.2.26 [Sep-21-2011]
O57682 494 Paired box protein Pax-2- N/A N/A 0.350 0.139 0.840 4e-27
O57685 497 Paired box protein Pax-2- N/A N/A 0.350 0.138 0.840 5e-27
P32114 414 Paired box protein Pax-2 no N/A 0.350 0.166 0.840 6e-27
Q02962 417 Paired box protein Pax-2 no N/A 0.350 0.165 0.840 7e-27
Q90268 410 Paired box protein Pax-2a no N/A 0.350 0.168 0.811 3e-26
Q9YH95 388 Paired box protein Pax-5 N/A N/A 0.350 0.177 0.811 8e-26
Q06710 450 Paired box protein Pax-8 no N/A 0.350 0.153 0.782 2e-25
A0JMA6 458 Paired box protein Pax-8 no N/A 0.350 0.150 0.782 2e-25
P47240 459 Paired box protein Pax-8 no N/A 0.350 0.150 0.782 2e-25
Q00288 457 Paired box protein Pax-8 no N/A 0.350 0.150 0.782 2e-25
>sp|O57682|PAX2B_XENLA Paired box protein Pax-2-B OS=Xenopus laevis GN=pax2-b PE=2 SV=2 Back     alignment and function desciption
 Score =  120 bits (302), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 59/69 (85%)

Query: 14  RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
           RYYETGS K GVIGGSKPKVAT  VVD IA YKR+NPTMFAWEIRDRLLAEGIC  D VP
Sbjct: 70  RYYETGSIKPGVIGGSKPKVATPKVVDKIADYKRQNPTMFAWEIRDRLLAEGICDNDTVP 129

Query: 74  SVSSINRYI 82
           SVSSINR I
Sbjct: 130 SVSSINRII 138
Probable transcription factor. Involved in kidney development, acting synergistically with lhx1/lim-1 in pronephric morphogenesis during the tailbud stages.
Xenopus laevis (taxid: 8355)
>sp|O57685|PAX2A_XENLA Paired box protein Pax-2-A OS=Xenopus laevis GN=pax2-a PE=2 SV=2 Back     alignment and function description
>sp|P32114|PAX2_MOUSE Paired box protein Pax-2 OS=Mus musculus GN=Pax2 PE=1 SV=2 Back     alignment and function description
>sp|Q02962|PAX2_HUMAN Paired box protein Pax-2 OS=Homo sapiens GN=PAX2 PE=1 SV=4 Back     alignment and function description
>sp|Q90268|PAX2A_DANRE Paired box protein Pax-2a OS=Danio rerio GN=pax2a PE=2 SV=2 Back     alignment and function description
>sp|Q9YH95|PAX5_XENLA Paired box protein Pax-5 OS=Xenopus laevis GN=pax5 PE=2 SV=1 Back     alignment and function description
>sp|Q06710|PAX8_HUMAN Paired box protein Pax-8 OS=Homo sapiens GN=PAX8 PE=1 SV=2 Back     alignment and function description
>sp|A0JMA6|PAX8_XENTR Paired box protein Pax-8 (Fragment) OS=Xenopus tropicalis GN=pax8 PE=2 SV=2 Back     alignment and function description
>sp|P47240|PAX8_CANFA Paired box protein Pax-8 OS=Canis familiaris GN=PAX8 PE=2 SV=1 Back     alignment and function description
>sp|Q00288|PAX8_MOUSE Paired box protein Pax-8 OS=Mus musculus GN=Pax8 PE=2 SV=3 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 ?
Query197
195173607 871 GL18401 [Drosophila persimilis] gi|19411 0.350 0.079 0.942 4e-31
195064058 862 GH23966 [Drosophila grimshawi] gi|193892 0.350 0.080 0.942 5e-31
195402209 863 GJ13730 [Drosophila virilis] gi|19415591 0.350 0.079 0.942 5e-31
345494898 536 PREDICTED: hypothetical protein LOC10012 0.355 0.130 0.928 7e-31
195134006 965 GI14046 [Drosophila mojavensis] gi|19391 0.350 0.071 0.942 8e-31
322791121173 hypothetical protein SINV_00870 [Solenop 0.360 0.410 0.929 9e-31
328712072 651 PREDICTED: hypothetical protein LOC10015 0.350 0.105 0.913 1e-30
254733070233 shaven [Nasonia vitripennis] 0.355 0.300 0.928 1e-30
270004886 472 shaven [Tribolium castaneum] 0.350 0.146 0.942 1e-30
194913410 842 GG16406 [Drosophila erecta] gi|190647905 0.350 0.081 0.927 2e-30
>gi|195173607|ref|XP_002027579.1| GL18401 [Drosophila persimilis] gi|194114491|gb|EDW36534.1| GL18401 [Drosophila persimilis] Back     alignment and taxonomy information
 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 65/69 (94%), Positives = 67/69 (97%)

Query: 14  RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
           RYYETGSFKAGVIGGSKPKVAT PVVDAIA+YKRENPTMFAWEIRDRLLAEGICSQDNVP
Sbjct: 238 RYYETGSFKAGVIGGSKPKVATPPVVDAIANYKRENPTMFAWEIRDRLLAEGICSQDNVP 297

Query: 74  SVSSINRYI 82
           SVSSINR +
Sbjct: 298 SVSSINRIV 306

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|195064058|ref|XP_001996488.1| GH23966 [Drosophila grimshawi] gi|193892034|gb|EDV90900.1| GH23966 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|195402209|ref|XP_002059699.1| GJ13730 [Drosophila virilis] gi|194155913|gb|EDW71097.1| GJ13730 [Drosophila virilis] Back     alignment and taxonomy information
>gi|345494898|ref|XP_001604502.2| PREDICTED: hypothetical protein LOC100120909 [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|195134006|ref|XP_002011429.1| GI14046 [Drosophila mojavensis] gi|193912052|gb|EDW10919.1| GI14046 [Drosophila mojavensis] Back     alignment and taxonomy information
>gi|322791121|gb|EFZ15683.1| hypothetical protein SINV_00870 [Solenopsis invicta] Back     alignment and taxonomy information
>gi|328712072|ref|XP_003244722.1| PREDICTED: hypothetical protein LOC100159241 isoform 2 [Acyrthosiphon pisum] Back     alignment and taxonomy information
>gi|254733070|gb|ACT79980.1| shaven [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|270004886|gb|EFA01334.1| shaven [Tribolium castaneum] Back     alignment and taxonomy information
>gi|194913410|ref|XP_001982689.1| GG16406 [Drosophila erecta] gi|190647905|gb|EDV45208.1| GG16406 [Drosophila erecta] 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 ?
Query197
FB|FBgn0005561 844 sv "shaven" [Drosophila melano 0.350 0.081 0.927 4.5e-29
UNIPROTKB|F1PDS6346 PAX2 "Uncharacterized protein" 0.583 0.332 0.593 1.2e-26
UNIPROTKB|G3V5S4303 PAX2 "Paired box protein Pax-2 0.583 0.379 0.593 1.2e-26
UNIPROTKB|F1MNR2 417 PAX2 "Uncharacterized protein" 0.583 0.275 0.593 1.2e-26
UNIPROTKB|F1PJT0 418 PAX2 "Uncharacterized protein" 0.583 0.275 0.593 1.2e-26
UNIPROTKB|Q02962 417 PAX2 "Paired box protein Pax-2 0.583 0.275 0.593 1.2e-26
UNIPROTKB|Q5SZP1214 PAX2 "Paired box protein Pax-2 0.583 0.537 0.593 1.2e-26
UNIPROTKB|F1S8U8 417 PAX2 "Uncharacterized protein" 0.583 0.275 0.593 1.2e-26
UNIPROTKB|G3V5U4 393 PAX2 "Paired box protein Pax-2 0.583 0.292 0.593 1.2e-26
UNIPROTKB|D5GSQ9 393 pax2 "Paired box 2" [Ovis arie 0.583 0.292 0.593 1.2e-26
FB|FBgn0005561 sv "shaven" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 333 (122.3 bits), Expect = 4.5e-29, P = 4.5e-29
 Identities = 64/69 (92%), Positives = 66/69 (95%)

Query:    14 RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
             RYYETGSFKAGVIGGSKPKVAT PVVDAIA+YKRENPTMFAWEIRDRLLAE ICSQDNVP
Sbjct:   230 RYYETGSFKAGVIGGSKPKVATPPVVDAIANYKRENPTMFAWEIRDRLLAEAICSQDNVP 289

Query:    74 SVSSINRYI 82
             SVSSINR +
Sbjct:   290 SVSSINRIV 298
GO:0005634 "nucleus" evidence=NAS;IDA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=NAS
GO:0042676 "compound eye cone cell fate commitment" evidence=TAS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS
GO:0003677 "DNA binding" evidence=IEA
GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA
GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IDA
GO:0048666 "neuron development" evidence=IMP
GO:0007517 "muscle organ development" evidence=IMP
GO:0048813 "dendrite morphogenesis" evidence=IMP
GO:0042673 "regulation of retinal cone cell fate specification" evidence=IGI;IMP
GO:0045676 "regulation of R7 cell differentiation" evidence=IGI;IMP
UNIPROTKB|F1PDS6 PAX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|G3V5S4 PAX2 "Paired box protein Pax-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1MNR2 PAX2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1PJT0 PAX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q02962 PAX2 "Paired box protein Pax-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q5SZP1 PAX2 "Paired box protein Pax-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1S8U8 PAX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|G3V5U4 PAX2 "Paired box protein Pax-2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|D5GSQ9 pax2 "Paired box 2" [Ovis aries (taxid:9940)] 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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 ?
Query197
smart00351125 smart00351, PAX, Paired Box domain 2e-35
smart00351125 smart00351, PAX, Paired Box domain 2e-34
cd00131128 cd00131, PAX, Paired Box domain 2e-34
pfam00292125 pfam00292, PAX, 'Paired box' domain 8e-33
cd00131128 cd00131, PAX, Paired Box domain 2e-32
pfam00292125 pfam00292, PAX, 'Paired box' domain 7e-32
cd0009078 cd00090, HTH_ARSR, Arsenical Resistance Operon Rep 0.004
>gnl|CDD|128645 smart00351, PAX, Paired Box domain Back     alignment and domain information 
 Score =  120 bits (303), Expect = 2e-35
 Identities = 50/56 (89%), Positives = 50/56 (89%)

Query: 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
            HGGVNQLGGVFVNGRPLPD  RQRIVELA NGVRPCDISRQL VSHGCVSKIL R
Sbjct: 1   GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGR 56

Length = 125
>gnl|CDD|128645 smart00351, PAX, Paired Box domain Back     alignment and domain information
>gnl|CDD|238076 cd00131, PAX, Paired Box domain Back     alignment and domain information
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain Back     alignment and domain information
>gnl|CDD|238076 cd00131, PAX, Paired Box domain Back     alignment and domain information
>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain Back     alignment and domain information
>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 197
KOG3517|consensus334 100.0
PF00292125 PAX: 'Paired box' domain; InterPro: IPR001523 The 99.98
PF00292125 PAX: 'Paired box' domain; InterPro: IPR001523 The 99.96
KOG3517|consensus 334 99.95
KOG3862|consensus327 99.94
KOG3862|consensus 327 99.94
KOG0849|consensus354 99.83
KOG0849|consensus 354 99.71
cd00131128 PAX Paired Box domain 99.65
smart00351125 PAX Paired Box domain. 99.59
cd00131128 PAX Paired Box domain 99.58
smart00351125 PAX Paired Box domain. 99.49
PF1356577 HTH_32: Homeodomain-like domain 97.87
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 97.84
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 97.41
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 97.05
PF1351852 HTH_28: Helix-turn-helix domain 97.0
PF13551112 HTH_29: Winged helix-turn helix 96.68
PF13551112 HTH_29: Winged helix-turn helix 96.66
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 96.61
COG3415138 Transposase and inactivated derivatives [DNA repli 96.41
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 96.38
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 96.1
PF1142750 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C 96.1
PF1275946 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR 95.85
PF0605658 Terminase_5: Putative ATPase subunit of terminase 95.4
PF01710119 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr 95.32
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 95.02
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 94.69
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 94.53
PF1301185 LZ_Tnp_IS481: leucine-zipper of insertion element 93.6
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR- 92.99
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 92.91
TIGR0253188 yecD_yerC TrpR-related protein YerC/YecD. This mod 92.29
smart0055068 Zalpha Z-DNA-binding domain in adenosine deaminase 92.2
PF01710119 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr 91.89
PF0132560 Fe_dep_repress: Iron dependent repressor, N-termin 91.84
PF0035646 LacI: Bacterial regulatory proteins, lacI family; 90.93
KOG0400|consensus151 90.69
TIGR00721137 tfx DNA-binding protein, Tfx family. Tfx from Meth 90.14
PF1280262 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP 89.85
cd0009078 HTH_ARSR Arsenical Resistance Operon Repressor and 89.81
PRK03975141 tfx putative transcriptional regulator; Provisiona 89.78
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 89.54
PF1356577 HTH_32: Homeodomain-like domain 89.1
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 88.85
PRK06759154 RNA polymerase factor sigma-70; Validated 88.73
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 88.69
COG3415138 Transposase and inactivated derivatives [DNA repli 88.66
PRK04217110 hypothetical protein; Provisional 88.38
PRK13413200 mpi multiple promoter invertase; Provisional 88.1
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 87.98
PRK00118104 putative DNA-binding protein; Validated 87.55
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 87.5
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 87.36
cd0139252 HTH_LacI Helix-turn-helix (HTH) DNA binding domain 86.57
PRK13919186 putative RNA polymerase sigma E protein; Provision 86.28
PRK11924179 RNA polymerase sigma factor; Provisional 86.26
PRK09639166 RNA polymerase sigma factor SigX; Provisional 85.98
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 85.74
PRK15418 318 transcriptional regulator LsrR; Provisional 85.63
PRK12534187 RNA polymerase sigma factor; Provisional 85.61
PHA0259183 hypothetical protein; Provisional 85.58
TIGR02859198 spore_sigH RNA polymerase sigma-H factor. Members 85.58
PRK12514179 RNA polymerase sigma factor; Provisional 85.5
PRK09047161 RNA polymerase factor sigma-70; Validated 85.28
TIGR01529146 argR_whole arginine repressor. This model includes 85.14
PHA00738108 putative HTH transcription regulator 85.05
PF1284061 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_ 84.71
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 84.23
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 84.09
PRK12536181 RNA polymerase sigma factor; Provisional 83.98
PRK12537182 RNA polymerase sigma factor; Provisional 83.56
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 83.47
PRK10141117 DNA-binding transcriptional repressor ArsR; Provis 83.45
PF0806960 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal doma 83.33
PF1344363 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3 83.22
PRK06986236 fliA flagellar biosynthesis sigma factor; Validate 82.85
TIGR02479224 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f 82.82
PRK09645173 RNA polymerase sigma factor SigL; Provisional 82.75
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 81.92
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 81.27
PRK12532195 RNA polymerase sigma factor; Provisional 81.16
PRK10840216 transcriptional regulator RcsB; Provisional 81.15
PRK12542185 RNA polymerase sigma factor; Provisional 80.56
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 80.56
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 80.41
PRK12515189 RNA polymerase sigma factor; Provisional 80.32
TIGR0387973 near_KaiC_dom probable regulatory domain. This mod 80.18
TIGR02984189 Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl 80.17
PRK02277 200 orotate phosphoribosyltransferase-like protein; Pr 80.1
>KOG3517|consensus Back     alignment and domain information 
Probab=100.00  E-value=2.3e-34  Score=253.76  Aligned_cols=84  Identities=55%  Similarity=0.871  Sum_probs=82.7

Q ss_pred             CCCcccccccc----cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccc
Q psy10745          2 TPQLLTPFLCP----RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSS   77 (197)
Q Consensus         2 ~~~~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSS   77 (197)
                      ||||.|+|+||    .||.|||||.||+|||||||++||.|++.|.+||+..|+||||||||||+.+||||+.|||||||
T Consensus        43 SRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSS  122 (334)
T KOG3517|consen   43 SRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSS  122 (334)
T ss_pred             hhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHH
Confidence            79999999999    89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccc
Q psy10745         78 INRYITYV   85 (197)
Q Consensus        78 I~Rilr~~   85 (197)
                      |+|||||+
T Consensus       123 ISRILRNK  130 (334)
T KOG3517|consen  123 ISRILRNK  130 (334)
T ss_pred             HHHHHHhh
Confidence            99999985

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ] Back     alignment and domain information
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ] Back     alignment and domain information
>KOG3517|consensus Back     alignment and domain information
>KOG3862|consensus Back     alignment and domain information
>KOG3862|consensus Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>cd00131 PAX Paired Box domain Back     alignment and domain information
>smart00351 PAX Paired Box domain Back     alignment and domain information
>cd00131 PAX Paired Box domain Back     alignment and domain information
>smart00351 PAX Paired Box domain Back     alignment and domain information
>PF13565 HTH_32: Homeodomain-like domain Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A 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
>PF13518 HTH_28: Helix-turn-helix domain Back     alignment and domain information
>PF13551 HTH_29: Winged helix-turn helix Back     alignment and domain information
>PF13551 HTH_29: Winged helix-turn helix Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] 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
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C Back     alignment and domain information
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA Back     alignment and domain information
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after [] Back     alignment and domain information
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition 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
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 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
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481 Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities Back     alignment and domain information
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD Back     alignment and domain information
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases Back     alignment and domain information
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family Back     alignment and domain information
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>KOG0400|consensus Back     alignment and domain information
>TIGR00721 tfx DNA-binding protein, Tfx family Back     alignment and domain information
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B Back     alignment and domain information
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional 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
>PF13565 HTH_32: Homeodomain-like domain 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
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>PRK13413 mpi multiple promoter invertase; Provisional 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
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed Back     alignment and domain information
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A Back     alignment and domain information
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>PRK15418 transcriptional regulator LsrR; Provisional Back     alignment and domain information
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PHA02591 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR01529 argR_whole arginine repressor Back     alignment and domain information
>PHA00738 putative HTH transcription regulator Back     alignment and domain information
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B Back     alignment and domain information
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional Back     alignment and domain information
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>PRK12532 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK10840 transcriptional regulator RcsB; Provisional Back     alignment and domain information
>PRK12542 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR03879 near_KaiC_dom probable regulatory domain Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 Back     alignment and domain information
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query197
1k78_A149 Pax5(1-149)+ets-1(331-440)+dna Length = 149 2e-26
1k78_A149 Pax5(1-149)+ets-1(331-440)+dna Length = 149 3e-25
2k27_A159 Solution Structure Of Human Pax8 Paired Box Domain 2e-26
2k27_A159 Solution Structure Of Human Pax8 Paired Box Domain 2e-23
6pax_A133 Crystal Structure Of The Human Pax-6 Paired Domain- 2e-22
6pax_A133 Crystal Structure Of The Human Pax-6 Paired Domain- 5e-21
1pdn_C128 Crystal Structure Of A Paired Domain-Dna Complex At 2e-18
>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149 Back     alignment and structure 
Iteration: 1

 Score =  115 bits (287), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 55/69 (79%), Positives = 58/69 (84%)
Query: 14  RYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP 73
           RYYETGS K GVIGGSKPKVAT  VV+ IA YKR+NPTMFAWEIRDRLLAE +C  D VP
Sbjct: 71  RYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVP 130
Query: 74  SVSSINRYI 82
           SVSSINR I
Sbjct: 131 SVSSINRII 139
>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149 Back     alignment and structure
>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159 Back     alignment and structure
>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159 Back     alignment and structure
>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133 Back     alignment and structure
>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133 Back     alignment and structure
>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128 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 ?
Query197
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 7e-27
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 4e-22
2k27_A159 Paired box protein PAX-8; paired domain, solution 7e-27
2k27_A159 Paired box protein PAX-8; paired domain, solution 9e-21
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 4e-26
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 2e-21
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 3e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 3e-05
1u78_A141 TC3 transposase, transposable element TC3 transpos 6e-04
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128 Back     alignment and structure
 Score = 98.2 bits (244), Expect = 7e-27
 Identities = 41/55 (74%), Positives = 49/55 (89%)

Query: 119 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
            G VNQLGGVF+NGRPLP+ +R +IVE+A +G+RPC ISRQLRVSHGCVSKIL+R
Sbjct: 2   QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNR 56
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Length = 128 Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159 Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159 Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149 Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Length = 149 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
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 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
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Length = 141 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query197
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 99.06
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 98.86
2k27_A159 Paired box protein PAX-8; paired domain, solution 98.35
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 98.35
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 98.32
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 98.22
2k27_A159 Paired box protein PAX-8; paired domain, solution 98.18
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 97.42
1u78_A141 TC3 transposase, transposable element TC3 transpos 97.39
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 97.24
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 96.79
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 96.01
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 95.98
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 95.91
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 94.76
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 94.59
2jpc_A61 SSRB; DNA binding protein, structural genomics, PS 94.39
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 94.12
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 94.11
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 93.88
1u78_A141 TC3 transposase, transposable element TC3 transpos 93.81
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 93.77
3hot_A 345 Transposable element mariner, complete CDS; protei 93.66
1y0u_A96 Arsenical resistance operon repressor, putative; s 93.54
3uj3_X193 DNA-invertase; helix-turn-helix, site-specific rec 93.21
3pqk_A102 Biofilm growth-associated repressor; helix-turn-he 92.89
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 92.78
3cuo_A99 Uncharacterized HTH-type transcriptional regulato; 92.63
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 92.51
2jsc_A118 Transcriptional regulator RV1994C/MT2050; cadmium, 92.34
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 92.18
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type dom 92.11
2zkz_A99 Transcriptional repressor PAGR; protein-DNA, HTH m 92.1
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 92.06
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 92.02
1r1u_A106 CZRA, repressor protein; zinc, DNA binding, transc 91.68
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 91.33
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 91.29
3c57_A95 Two component transcriptional regulatory protein; 91.2
2oqg_A114 Possible transcriptional regulator, ARSR family P; 91.17
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP 91.15
3jth_A98 Transcription activator HLYU; transcription factor 90.84
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 90.69
1gdt_A183 GD resolvase, protein (gamma delta resolvase); pro 90.63
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 90.54
1ub9_A100 Hypothetical protein PH1061; helix-turn-helix moti 90.31
3plo_X193 DNA-invertase; resolvase, helix-turn-helix, serine 90.1
2lkp_A119 Transcriptional regulator, ARSR family; symmetric 90.1
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 90.02
3f6o_A118 Probable transcriptional regulator, ARSR family pr 90.0
3hot_A 345 Transposable element mariner, complete CDS; protei 89.93
2kko_A108 Possible transcriptional regulatory protein (possi 89.8
1r1t_A122 Transcriptional repressor SMTB; zinc, transcriptio 89.8
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 89.76
1u2w_A122 CADC repressor, cadmium efflux system accessory pr 89.62
2d1h_A109 ST1889, 109AA long hypothetical transcriptional re 89.57
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 89.21
2w7n_A101 TRFB transcriptional repressor protein; INCP, plas 89.06
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-h 88.74
3f6v_A151 Possible transcriptional regulator, ARSR family pr 88.52
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 88.49
1iuf_A144 Centromere ABP1 protein; riken structural genomics 87.14
2q0o_A236 Probable transcriptional activator protein TRAR; h 86.82
1l3l_A234 Transcriptional activator protein TRAR; helix-turn 86.54
1jhg_A101 Trp operon repressor; complex (regulatory protein- 86.41
3tgn_A146 ADC operon repressor ADCR; helix-turn-helix, trans 86.04
1zx4_A 192 P1 PARB, plasmid partition PAR B protein, PARB; tr 85.38
1z7u_A112 Hypothetical protein EF0647; winged-helix-turn-hel 85.33
1qgp_A77 Protein (double stranded RNA adenosine deaminase); 84.99
2pn6_A150 ST1022, 150AA long hypothetical transcriptional re 84.6
2r0q_C209 Putative transposon TN552 DNA-invertase BIN3; site 83.84
3t72_q99 RNA polymerase sigma factor RPOD, DNA-directed RN 83.46
1neq_A74 DNA-binding protein NER; NMR {Enterobacteria phage 83.37
1b4a_A149 Arginine repressor; helix turn helix; 2.50A {Geoba 83.36
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 83.29
1oyi_A82 Double-stranded RNA-binding protein; (alpha+beta) 83.1
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial 82.85
1l0o_C243 Sigma factor; bergerat fold, helix-turn-helix, pro 82.77
1qbj_A81 Protein (double-stranded RNA specific adenosine D 82.74
1q1h_A110 TFE, transcription factor E, TFE; TFIIE, transcrip 82.64
2pg4_A95 Uncharacterized protein; structural genomics, join 81.95
2l0k_A93 Stage III sporulation protein D; SPOIIID, solution 81.73
2hzt_A107 Putative HTH-type transcriptional regulator YTCD; 81.03
1sfx_A109 Conserved hypothetical protein AF2008; structural 80.8
2qlz_A 232 Transcription factor PF0095; 2.50A {Pyrococcus fur 80.56
3szt_A237 QCSR, quorum-sensing control repressor; quorum sen 80.13
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Back     alignment and structure
Probab=99.06  E-value=1e-10  Score=85.10  Aligned_cols=64  Identities=66%  Similarity=1.114  Sum_probs=59.5

Q ss_pred             CCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcc
Q psy10745        118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR  181 (197)
Q Consensus       118 ~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~  181 (197)
                      |+|.+|++||+|..+++++++.|.+|++|+..|....+||+.|+||+.+|++.+.||.+++.+.
T Consensus         1 ~~~~~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~   64 (128)
T 1pdn_C            1 GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIR   64 (128)
T ss_dssp             -CEEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCchHhhhcccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcc
Confidence            5789999999999999999999999999999999999999999999999999999998877543
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} 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
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} 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
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 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
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} 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
>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
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} 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
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19 Back     alignment and structure
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} 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
>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
>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
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 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
>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A* Back     alignment and structure
>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5 Back     alignment and structure
>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X Back     alignment and structure
>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12} 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
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Back     alignment and structure
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Back     alignment and structure
>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis} 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
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Back     alignment and structure
>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A Back     alignment and structure
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 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
>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP} Back     alignment and structure
>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3 Back     alignment and structure
>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus} Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Back     alignment and structure
>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28 Back     alignment and structure
>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis} Back     alignment and structure
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A Back     alignment and structure
>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP} Back     alignment and structure
>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A* Back     alignment and structure
>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A Back     alignment and structure
>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Back     alignment and structure
>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A Back     alignment and structure
>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50 Back     alignment and structure
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A Back     alignment and structure
>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli} Back     alignment and structure
>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3 Back     alignment and structure
>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP} Back     alignment and structure
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7 Back     alignment and structure
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Back     alignment and structure
>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A* Back     alignment and structure
>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A* Back     alignment and structure
>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae} Back     alignment and structure
>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A Back     alignment and structure
>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69 Back     alignment and structure
>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19 Back     alignment and structure
>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A* Back     alignment and structure
>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus} Back     alignment and structure
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Back     alignment and structure
>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A Back     alignment and structure
>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A Back     alignment and structure
>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP} Back     alignment and structure
>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19 Back     alignment and structure
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Back     alignment and structure
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Back     alignment and structure
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A Back     alignment and structure
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Back     alignment and structure
>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48 Back     alignment and structure
>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis} Back     alignment and structure
>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69 Back     alignment and structure
>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50 Back     alignment and structure
>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A Back     alignment and structure
>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa} 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 197
d1k78a261 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta 2e-33
d6paxa265 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta 4e-31
d1k78a163 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax 1e-24
d1pdnc_123 a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros 1e-24
d1pdnc_123 a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros 3e-20
>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 61 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  111 bits (280), Expect = 2e-33
 Identities = 46/58 (79%), Positives = 49/58 (84%)

Query: 25 VIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYI 82
          VIGGSKPKVAT  VV+ IA YKR+NPTMFAWEIRDRLLAE +C  D VPSVSSINR I
Sbjct: 1  VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRII 58
>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Length = 65 Back     information, alignment and structure
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 63 Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123 Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123 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 ?
Query197
d1k78a261 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 99.97
d6paxa265 Pax-6 {Human (Homo sapiens) [TaxId: 9606]} 99.96
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 99.9
d1pdnc_123 Paired protein (prd) {Fruit fly (Drosophila melano 99.84
d1pdnc_123 Paired protein (prd) {Fruit fly (Drosophila melano 99.8
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 97.95
d1hlva166 DNA-binding domain of centromere binding protein B 96.73
d1gdta143 gamma,delta resolvase (C-terminal domain) {Escheri 96.56
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 94.07
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 93.68
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 93.64
d2isya163 Iron-dependent regulator IdeR {Mycobacterium tuber 92.47
d1a04a167 Nitrate/nitrite response regulator (NarL) {Escheri 92.13
d1s7oa_106 Hypothetical protein SPy1201 {Streptococcus pyogen 91.81
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 91.57
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 91.08
d2ev0a161 Manganese transport regulator MntR {Bacillus subti 90.83
d1xsva_106 Hypothetical protein SAV1236 {Staphylococcus aureu 90.24
d1z05a171 Transcriptional regulator VC2007 N-terminal domain 89.82
d1l3la165 Quorum-sensing transcription factor TraR, C-termin 88.65
d1yioa170 Response regulatory protein StyR, C-terminal domai 87.68
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Esch 86.94
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Esch 86.5
d1r1ua_94 Metal-sensing transcriptional repressor CzrA {Stap 86.21
d1u2wa1108 Cadmium efflux system accessory protein CadC {Stap 86.1
d1qpza157 Purine repressor (PurR), N-terminal domain {Escher 85.62
d1z6ra170 Mlc protein N-terminal domain {Escherichia coli [T 84.8
d2hsga157 Glucose-resistance amylase regulator CcpA, N-termi 84.75
d1qpza157 Purine repressor (PurR), N-terminal domain {Escher 84.71
d3ctaa185 Ta1064 (RFK), N-terminal domain {Thermoplasma acid 84.64
d1p4wa_87 Transcriptional regulator RcsB {Erwinia amylovora 84.02
d1r1ta_98 SmtB repressor {Cyanobacteria (Synechococcus), pcc 82.92
>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {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: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.1e-32  Score=190.09  Aligned_cols=61  Identities=75%  Similarity=1.137  Sum_probs=59.3

Q ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccccc
Q psy10745         25 VIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYV   85 (197)
Q Consensus        25 ~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~   85 (197)
                      +|||||||++||+|+++|++||++||+||||||||+|+++|+|+++||||+|||||+||+.
T Consensus         1 vIGGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~egiC~~~nvPSvSsInRilR~k   61 (61)
T d1k78a2           1 VIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK   61 (61)
T ss_dssp             CCCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCcccHHHHHHHHHHcCCCCCCCCCchHHHHHHhhcC
Confidence            5899999999999999999999999999999999999999999999999999999999963
>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {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
>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {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
>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} 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
>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]} Back     information, alignment and structure
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} 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
>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]} Back     information, alignment and structure
>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]} Back     information, alignment and structure
>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]} Back     information, alignment and structure
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]} Back     information, alignment and structure
>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]} Back     information, alignment and structure