Psyllid ID: psy10825

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
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNNQVPDSEEQSNDTGPGDSNTIKM
cccccccEEEEEEEcccEEEcccccccccccccHHcccccccccccccHHHHHHHHHHHHHccccccccEEEEEccccEEEEEEEEEEEEEcccccccEEEEEEEEEccccccccccccccccccccccccccccccccc
cEEcccccEEEEEcccccEcccccccEEccccHHHccccHHHHccHHHHHHHHHHHHHHHHccccccccEEEEEccccEEEEEEEEEEEEcccccccEEEEEcEEEEEcccccccccccccccccccHcccHHccccccc
mvgfkpvtfcmsdlmnstiydlvappiigylpfevlgtsgydyyhvddldsvVTCHEALmqkgegtsCYYRFLTKGQQWIWLQTRFYITYhqwnskpefivCTHRVVSYVNVlrrdnnqvpdseeqsndtgpgdsntikm
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRdnnqvpdseeqsndtgpgdsntikm
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNNQVPDSEEQSNDTGPGDSNTIKM
***FKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLR**************************
**GFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVS********************************
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNN**********************
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVL***************************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MVGFKPVTFCMSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNNQVPDSEEQSNDTGPGDSNTIKM
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 ?
Query140 2.2.26 [Sep-21-2011]
Q91YB0 865 Circadian locomoter outpu N/A N/A 0.857 0.138 0.656 3e-44
Q91YB2 865 Circadian locomoter outpu N/A N/A 0.857 0.138 0.656 3e-44
Q9WVS9 862 Circadian locomoter outpu yes N/A 0.857 0.139 0.656 4e-44
Q8QGQ6 875 Circadian locomoter outpu no N/A 0.857 0.137 0.656 4e-44
Q6YGZ4 851 Circadian locomoter outpu N/A N/A 0.857 0.141 0.656 5e-44
Q5RAK8 846 Circadian locomoter outpu yes N/A 0.857 0.141 0.648 7e-44
O15516 846 Circadian locomoter outpu yes N/A 0.857 0.141 0.648 7e-44
O08785 855 Circadian locomoter outpu yes N/A 0.857 0.140 0.648 8e-44
O61735 1027 Circadian locomoter outpu yes N/A 0.842 0.114 0.652 9e-44
Q91YA8 865 Circadian locomoter outpu N/A N/A 0.857 0.138 0.648 1e-43
>sp|Q91YB0|CLOCK_NANGA Circadian locomoter output cycles protein kaput OS=Nannospalax galili GN=Clock PE=1 SV=1 Back     alignment and function desciption
 Score =  176 bits (447), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 84/128 (65%), Positives = 99/128 (77%), Gaps = 8/128 (6%)

Query: 21  DLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWI 80
           D  APPIIGYLPFEVLGTSGYDYYHVDDL+++  CHE LMQ G+G SCYYRFLTKGQQWI
Sbjct: 290 DHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWI 349

Query: 81  WLQTRFYITYHQWNSKPEFIVCTHRVVSYVNV---LRRD---NNQVPD-SEEQSNDTGPG 133
           WLQT +YITYHQWNS+PEFIVCTH VVSY  V    RR+      +PD + ++S D+G  
Sbjct: 350 WLQTHYYITYHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPDAAADKSQDSGSD 409

Query: 134 DS-NTIKM 140
           +  NT+ +
Sbjct: 410 NRINTVSL 417
ARNTL/2-CLOCK heterodimers activate E-box element (3'-CACGTG-5') transcription of a number of proteins of the circadian clock. Activates transcription of PER1 and PER2. This transcription is inhibited in a feedback loop by PER and CRY proteins. Has intrinsic histone acetyltransferase activity and this enzymatic function contributes to chromatin-remodeling events implicated in circadian control of gene expression. Acetylates primarily histones H3 and H4. Acetylates also a non-histone substrate: ARNTL. Plays a role in DNA damage response (DDR) signaling during the S phase.
Nannospalax galili (taxid: 1026970)
EC: 2EC: .EC: 3EC: .EC: 1EC: .EC: 4EC: 8
>sp|Q91YB2|CLOCK_SPACA Circadian locomoter output cycles protein kaput OS=Spalax carmeli GN=Clock PE=2 SV=1 Back     alignment and function description
>sp|Q9WVS9|CLOCK_RAT Circadian locomoter output cycles protein kaput OS=Rattus norvegicus GN=Clock PE=2 SV=1 Back     alignment and function description
>sp|Q8QGQ6|CLOCK_CHICK Circadian locomoter output cycles protein kaput OS=Gallus gallus GN=CLOCK PE=1 SV=2 Back     alignment and function description
>sp|Q6YGZ4|CLOCK_TYTAL Circadian locomoter output cycles protein kaput OS=Tyto alba GN=CLOCK PE=2 SV=1 Back     alignment and function description
>sp|Q5RAK8|CLOCK_PONAB Circadian locomoter output cycles protein kaput OS=Pongo abelii GN=CLOCK PE=2 SV=1 Back     alignment and function description
>sp|O15516|CLOCK_HUMAN Circadian locomoter output cycles protein kaput OS=Homo sapiens GN=CLOCK PE=1 SV=1 Back     alignment and function description
>sp|O08785|CLOCK_MOUSE Circadian locomoter output cycles protein kaput OS=Mus musculus GN=Clock PE=1 SV=1 Back     alignment and function description
>sp|O61735|CLOCK_DROME Circadian locomoter output cycles protein kaput OS=Drosophila melanogaster GN=Clk PE=2 SV=3 Back     alignment and function description
>sp|Q91YA8|CLOCK_SPAJD Circadian locomoter output cycles protein kaput OS=Spalax judaei GN=Clock PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query140
305682538 522 CLOCK [Thermobia domestica] 0.835 0.224 0.764 4e-50
443497931 594 CLOCK [Gryllus bimaculatus] 0.835 0.196 0.752 2e-49
158294626 1030 AGAP005711-PA [Anopheles gambiae str. PE 0.785 0.106 0.790 2e-48
157132927 900 circadian locomoter output cycles kaput 0.785 0.122 0.790 2e-48
332021701 699 Circadian locomoter output cycles protei 0.771 0.154 0.796 3e-47
350423284 733 PREDICTED: neuronal PAS domain-containin 0.778 0.148 0.8 3e-47
340719080 733 PREDICTED: hypothetical protein LOC10065 0.778 0.148 0.8 4e-47
444245669 673 clock, partial [Solenopsis invicta] 0.671 0.139 0.904 4e-47
307168572 702 Circadian locomoter output cycles protei 0.678 0.135 0.894 6e-47
38176144 602 clock [Danaus plexippus] 0.778 0.181 0.770 6e-47
>gi|305682538|dbj|BAJ16353.1| CLOCK [Thermobia domestica] Back     alignment and taxonomy information
 Score =  202 bits (514), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 94/123 (76%), Positives = 105/123 (85%), Gaps = 6/123 (4%)

Query: 21  DLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWI 80
           D  A PIIGYLPFEVLGTSGYDYYH+DDL+ VVTCHEALMQKGEGTSCYYRFLTKGQQWI
Sbjct: 277 DHRASPIIGYLPFEVLGTSGYDYYHIDDLEKVVTCHEALMQKGEGTSCYYRFLTKGQQWI 336

Query: 81  WLQTRFYITYHQWNSKPEFIVCTHRVVSYVNVLR--RDNNQVPDSEEQSNDTGP----GD 134
           WLQTR+YITYHQWNSKPEFIVCTHRVVSY +V++  R NNQ  +++  S+D  P    GD
Sbjct: 337 WLQTRYYITYHQWNSKPEFIVCTHRVVSYADVMKQLRKNNQDSNNKLLSSDNDPVLGNGD 396

Query: 135 SNT 137
           SN+
Sbjct: 397 SNS 399

Source: Thermobia domestica

Species: Thermobia domestica

Genus: Thermobia

Family: Lepismatidae

Order:

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|443497931|dbj|BAM76759.1| CLOCK [Gryllus bimaculatus] Back     alignment and taxonomy information
>gi|158294626|ref|XP_315720.4| AGAP005711-PA [Anopheles gambiae str. PEST] gi|157015652|gb|EAA11642.4| AGAP005711-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|157132927|ref|XP_001662706.1| circadian locomoter output cycles kaput protein (dclock) (dpas1) [Aedes aegypti] gi|108871039|gb|EAT35264.1| AAEL012562-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|332021701|gb|EGI62057.1| Circadian locomoter output cycles protein kaput [Acromyrmex echinatior] Back     alignment and taxonomy information
>gi|350423284|ref|XP_003493431.1| PREDICTED: neuronal PAS domain-containing protein 2-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|340719080|ref|XP_003397985.1| PREDICTED: hypothetical protein LOC100650446 [Bombus terrestris] Back     alignment and taxonomy information
>gi|444245669|gb|AGD94516.1| clock, partial [Solenopsis invicta] Back     alignment and taxonomy information
>gi|307168572|gb|EFN61630.1| Circadian locomoter output cycles protein kaput [Camponotus floridanus] Back     alignment and taxonomy information
>gi|38176144|gb|AAR13011.1| clock [Danaus plexippus] 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 ?
Query140
FB|FBgn0023076 1027 Clk "Clock" [Drosophila melano 0.821 0.111 0.660 9.4e-42
UNIPROTKB|F1NGR0 675 F1NGR0 "Uncharacterized protei 0.735 0.152 0.75 2.8e-41
UNIPROTKB|Q91YB0 865 Clock "Circadian locomoter out 0.835 0.135 0.664 3.1e-41
UNIPROTKB|Q91YB2 865 Clock "Circadian locomoter out 0.835 0.135 0.664 3.1e-41
UNIPROTKB|D4A4R8 833 Clock "Circadian locomoter out 0.835 0.140 0.664 3.5e-41
UNIPROTKB|F1NKI9 854 CLOCK "Circadian locomoter out 0.835 0.137 0.664 3.9e-41
UNIPROTKB|F1M012 857 Clock "Circadian locomoter out 0.835 0.136 0.664 3.9e-41
UNIPROTKB|F1NKI8 859 CLOCK "Circadian locomoter out 0.835 0.136 0.664 3.9e-41
RGD|620271 862 Clock "clock circadian regulat 0.835 0.135 0.664 4e-41
UNIPROTKB|Q9WVS9 862 Clock "Circadian locomoter out 0.835 0.135 0.664 4e-41
FB|FBgn0023076 Clk "Clock" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 440 (159.9 bits), Expect = 9.4e-42, Sum P(2) = 9.4e-42
 Identities = 76/115 (66%), Positives = 90/115 (78%)

Query:    24 APPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQ 83
             APPIIGY+PFEVLGTSGYDYYH DDLDS+V CHE L Q GEG SCYYRFLTKGQQWIWLQ
Sbjct:   284 APPIIGYMPFEVLGTSGYDYYHFDDLDSIVACHEELRQTGEGKSCYYRFLTKGQQWIWLQ 343

Query:    84 TRFYITYHQWNSKPEFIVCTHRVVSYVNVLRRDNNQVPDSEEQSNDTGPGDSNTI 138
             T +Y++YHQ+NSKP+++VCTH+VVSY  VL+    +   S   ++ T  G S  I
Sbjct:   344 TDYYVSYHQFNSKPDYVVCTHKVVSYAEVLKDSRKEGQKSGNSNSITNNGSSKVI 398
GO:0003677 "DNA binding" evidence=IDA;NAS
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IGI;NAS;TAS
GO:0007623 "circadian rhythm" evidence=NAS;IMP;TAS
GO:0046982 "protein heterodimerization activity" evidence=NAS;IPI
GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IPI
GO:0008134 "transcription factor binding" evidence=IPI
GO:0005634 "nucleus" evidence=NAS
GO:0048148 "behavioral response to cocaine" evidence=NAS;TAS
GO:0045475 "locomotor rhythm" evidence=IMP;NAS;TAS
GO:0008062 "eclosion rhythm" evidence=NAS;TAS
GO:0045187 "regulation of circadian sleep/wake cycle, sleep" evidence=IMP
GO:0007622 "rhythmic behavior" evidence=TAS
GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA;NAS;TAS
GO:0007165 "signal transduction" evidence=IEA
GO:0005667 "transcription factor complex" evidence=IEA
GO:0005737 "cytoplasm" evidence=IEA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0004871 "signal transducer activity" evidence=IEA
GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=NAS
GO:0032922 "circadian regulation of gene expression" evidence=IMP
GO:0005515 "protein binding" evidence=IPI
UNIPROTKB|F1NGR0 F1NGR0 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q91YB0 Clock "Circadian locomoter output cycles protein kaput" [Nannospalax galili (taxid:1026970)] Back     alignment and assigned GO terms
UNIPROTKB|Q91YB2 Clock "Circadian locomoter output cycles protein kaput" [Spalax carmeli (taxid:164324)] Back     alignment and assigned GO terms
UNIPROTKB|D4A4R8 Clock "Circadian locomoter output cycles protein kaput" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1NKI9 CLOCK "Circadian locomoter output cycles protein kaput" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1M012 Clock "Circadian locomoter output cycles protein kaput" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1NKI8 CLOCK "Circadian locomoter output cycles protein kaput" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
RGD|620271 Clock "clock circadian regulator" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q9WVS9 Clock "Circadian locomoter output cycles protein kaput" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q5RAK8CLOCK_PONAB2, ., 3, ., 1, ., 4, 80.64840.85710.1418yesN/A
O08785CLOCK_MOUSE2, ., 3, ., 1, ., 4, 80.64840.85710.1403yesN/A
O61735CLOCK_DROMENo assigned EC number0.65250.84280.1148yesN/A
Q9WVS9CLOCK_RAT2, ., 3, ., 1, ., 4, 80.65620.85710.1392yesN/A
O15516CLOCK_HUMAN2, ., 3, ., 1, ., 4, 80.64840.85710.1418yesN/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 ?
Query140
pfam0844790 pfam08447, PAS_3, PAS fold 2e-13
cd00130103 cd00130, PAS, PAS domain; PAS motifs appear in arc 8e-13
smart0008643 smart00086, PAC, Motif C-terminal to PAS motifs (l 4e-06
>gnl|CDD|219844 pfam08447, PAS_3, PAS fold Back     alignment and domain information 
 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 27  IIGYLPFEVLGT--SGYDYYHVDDLDSVVTCH-EALMQKGEGTSCYYRFLTKGQQWIWLQ 83
           I+GY P E+  +     D  H +D + V     E  ++KGE  S  YR   K  ++ W++
Sbjct: 11  ILGYTPEELKSSYEGWLDLVHPEDRERVRRALQEFSLKKGEPYSGEYRIRRKDGEYRWVE 70

Query: 84  TRFYITYHQWNSKPEFIVCTH 104
            R        N KP  ++   
Sbjct: 71  ARGRPIR-DENGKPVRVIGVA 90

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 90
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya Back     alignment and domain information
>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 140
PF14598111 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W 99.91
PF0844791 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold 99.73
KOG3558|consensus 768 99.72
PF13426104 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_ 99.71
PF00989113 PAS: PAS fold; InterPro: IPR013767 PAS domains are 99.61
PF08448110 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold 99.53
KOG3559|consensus 598 99.44
PRK13557 540 histidine kinase; Provisional 99.3
PRK10060 663 RNase II stability modulator; Provisional 99.28
KOG3560|consensus 712 99.28
cd00130103 PAS PAS domain; PAS motifs appear in archaea, euba 99.24
PRK13559 361 hypothetical protein; Provisional 99.23
PRK09776 1092 putative diguanylate cyclase; Provisional 99.22
PRK11091 779 aerobic respiration control sensor protein ArcB; P 99.21
KOG3753|consensus 1114 99.21
PRK13558 665 bacterio-opsin activator; Provisional 99.15
TIGR00229124 sensory_box PAS domain S-box. The PAS domain was p 99.11
PRK13560 807 hypothetical protein; Provisional 99.11
TIGR02040 442 PpsR-CrtJ transcriptional regulator PpsR. This mod 99.11
TIGR02040442 PpsR-CrtJ transcriptional regulator PpsR. This mod 99.08
TIGR02938 494 nifL_nitrog nitrogen fixation negative regulator N 99.06
PRK11359 799 cyclic-di-GMP phosphodiesterase; Provisional 99.01
PRK09776 1092 putative diguanylate cyclase; Provisional 98.97
PRK11359 799 cyclic-di-GMP phosphodiesterase; Provisional 98.94
PRK13560 807 hypothetical protein; Provisional 98.82
PF13596106 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D. 98.7
KOG3561|consensus 803 98.52
PRK11360 607 sensory histidine kinase AtoS; Provisional 98.46
TIGR02966 333 phoR_proteo phosphate regulon sensor kinase PhoR. 98.38
PRK11073 348 glnL nitrogen regulation protein NR(II); Provision 98.37
PF12860115 PAS_7: PAS fold 98.3
KOG3561|consensus 803 97.75
KOG0501|consensus 971 97.71
COG2202232 AtoS FOG: PAS/PAC domain [Signal transduction mech 97.52
TIGR02938 494 nifL_nitrog nitrogen fixation negative regulator N 97.48
KOG3558|consensus 768 97.41
PRK11006 430 phoR phosphate regulon sensor protein; Provisional 97.2
PRK10820 520 DNA-binding transcriptional regulator TyrR; Provis 97.12
smart0009167 PAS PAS domain. PAS motifs appear in archaea, euba 97.11
PF07310137 PAS_5: PAS domain; InterPro: IPR009922 This family 97.05
COG5002 459 VicK Signal transduction histidine kinase [Signal 96.88
TIGR02373124 photo_yellow photoactive yellow protein. Members o 96.84
KOG1229|consensus 775 96.68
smart0008643 PAC Motif C-terminal to PAS motifs (likely to cont 96.62
KOG3559|consensus 598 96.6
PRK11086 542 sensory histidine kinase DcuS; Provisional 96.36
PF08670148 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK 96.19
PRK11388 638 DNA-binding transcriptional regulator DhaR; Provis 95.99
COG3829 560 RocR Transcriptional regulator containing PAS, AAA 95.94
COG5000 712 NtrY Signal transduction histidine kinase involved 95.88
PF1318864 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A. 95.77
KOG3560|consensus 712 95.57
COG3290 537 CitA Signal transduction histidine kinase regulati 94.74
PRK15053 545 dpiB sensor histidine kinase DpiB; Provisional 94.57
KOG3753|consensus 1114 93.83
COG3852 363 NtrB Signal transduction histidine kinase, nitroge 93.75
PRK09959 1197 hybrid sensory histidine kinase in two-component r 92.96
PF08446110 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold 92.76
PF08348118 PAS_6: YheO-like PAS domain; InterPro: IPR013559 T 91.05
COG5388209 Uncharacterized protein conserved in bacteria [Fun 90.52
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A Back     alignment and domain information 
Probab=99.91  E-value=8.2e-24  Score=136.83  Aligned_cols=105  Identities=41%  Similarity=0.721  Sum_probs=94.7

Q ss_pred             EEEEEe--cCCEEEEcCC-cccccCcCcchhcCCCcceeeCccCHHH-HHHHHHHHHHcCCcccEEeeeEecCCcEEEEE
Q psy10825          8 TFCMSD--LMNSTIYDLV-APPIIGYLPFEVLGTSGYDYYHVDDLDS-VVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQ   83 (140)
Q Consensus         8 ~~v~~~--d~~i~~~n~a-~~~~lGy~~~el~g~~~~~~vhpdd~~~-~~~~~~~~~~~g~~~~~e~r~~~~~G~~~wv~   83 (140)
                      +|+.++  ||+|++++++ +..++||.++||+|+++++++||+|.+. +.+.+..++..|+.....||++.++|+|+|++
T Consensus         3 ~F~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq   82 (111)
T PF14598_consen    3 EFTTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ   82 (111)
T ss_dssp             EEEEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred             eEEEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence            567666  5579999999 6999999999999999999999999997 88899999999998887899999999999999


Q ss_pred             EEEEEEEecCCCCceEEEEEeEEccchhh
Q psy10825         84 TRFYITYHQWNSKPEFIVCTHRVVSYVNV  112 (140)
Q Consensus        84 ~~~~~~~~~~~~~~~~iv~~~~~it~~~~  112 (140)
                      +.+.++.+|+++++++|+|++.++++.|+
T Consensus        83 t~~~~~~n~~~~~~~~Iv~~n~vlse~e~  111 (111)
T PF14598_consen   83 TKATLFYNPWTSKPEFIVCTNTVLSEEEA  111 (111)
T ss_dssp             EEEEEEEETTTTCEEEEEEEEEEESCEB-
T ss_pred             EEEEEEECCCCCCccEEEEEEEEeccCCC
Confidence            99999999999999999999999998764

...
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [] Back     alignment and domain information
>KOG3558|consensus Back     alignment and domain information
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A Back     alignment and domain information
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [] Back     alignment and domain information
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [] Back     alignment and domain information
>KOG3559|consensus Back     alignment and domain information
>PRK13557 histidine kinase; Provisional Back     alignment and domain information
>PRK10060 RNase II stability modulator; Provisional Back     alignment and domain information
>KOG3560|consensus Back     alignment and domain information
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya Back     alignment and domain information
>PRK13559 hypothetical protein; Provisional Back     alignment and domain information
>PRK09776 putative diguanylate cyclase; Provisional Back     alignment and domain information
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional Back     alignment and domain information
>KOG3753|consensus Back     alignment and domain information
>PRK13558 bacterio-opsin activator; Provisional Back     alignment and domain information
>TIGR00229 sensory_box PAS domain S-box Back     alignment and domain information
>PRK13560 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR Back     alignment and domain information
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR Back     alignment and domain information
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL Back     alignment and domain information
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional Back     alignment and domain information
>PRK09776 putative diguanylate cyclase; Provisional Back     alignment and domain information
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional Back     alignment and domain information
>PRK13560 hypothetical protein; Provisional Back     alignment and domain information
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D Back     alignment and domain information
>KOG3561|consensus Back     alignment and domain information
>PRK11360 sensory histidine kinase AtoS; Provisional Back     alignment and domain information
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR Back     alignment and domain information
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional Back     alignment and domain information
>PF12860 PAS_7: PAS fold Back     alignment and domain information
>KOG3561|consensus Back     alignment and domain information
>KOG0501|consensus Back     alignment and domain information
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms] Back     alignment and domain information
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL Back     alignment and domain information
>KOG3558|consensus Back     alignment and domain information
>PRK11006 phoR phosphate regulon sensor protein; Provisional Back     alignment and domain information
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional Back     alignment and domain information
>smart00091 PAS PAS domain Back     alignment and domain information
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long Back     alignment and domain information
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms] Back     alignment and domain information
>TIGR02373 photo_yellow photoactive yellow protein Back     alignment and domain information
>KOG1229|consensus Back     alignment and domain information
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) Back     alignment and domain information
>KOG3559|consensus Back     alignment and domain information
>PRK11086 sensory histidine kinase DcuS; Provisional Back     alignment and domain information
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins Back     alignment and domain information
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional Back     alignment and domain information
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms] Back     alignment and domain information
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms] Back     alignment and domain information
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A Back     alignment and domain information
>KOG3560|consensus Back     alignment and domain information
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms] Back     alignment and domain information
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional Back     alignment and domain information
>KOG3753|consensus Back     alignment and domain information
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms] Back     alignment and domain information
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional Back     alignment and domain information
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [] Back     alignment and domain information
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT) Back     alignment and domain information
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown] 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 ?
Query140
4f3l_A361 Crystal Structure Of The Heterodimeric Clock:bmal1 1e-43
4h6j_A113 Identification Of Cys 255 In Hif-1 As A Novel Site 8e-13
4f3l_B387 Crystal Structure Of The Heterodimeric Clock:bmal1 1e-12
1p97_A114 Nmr Structure Of The C-Terminal Pas Domain Of Hif2a 2e-12
3f1n_A117 Crystal Structure Of A High Affinity Heterodimer Of 2e-12
2a24_A107 Haddock Structure Of Hif-2aARNT PAS-B Heterodimer L 4e-12
1wa9_A368 Crystal Structure Of The Pas Repeat Region Of The D 1e-09
3rty_A339 Structure Of An Enclosed Dimer Formed By The Drosop 1e-09
3gec_A312 Crystal Structure Of A Tandem Pas Domain Fragment O 2e-09
2kdk_A121 Structure Of Human Circadian Clock Protein Bmal2 C- 9e-09
2hv1_A119 Haddock Structure Of Arnt Pas-B Homodimer Length = 2e-07
4h6j_B116 Identification Of Cys 255 In Hif-1 As A Novel Site 2e-07
3f1n_B121 Crystal Structure Of A High Affinity Heterodimer Of 3e-07
2a24_B108 Haddock Structure Of Hif-2aARNT PAS-B Heterodimer L 4e-07
2b02_A119 Crystal Structure Of Arnt Pas-B Domain Length = 119 7e-07
2k7s_A119 Human Arnt C-Terminal Pas Domain, 3 Residue Ib Slip 8e-07
4dj3_A317 Unwinding The Differences Of The Mammalian Period C 1e-05
3gdi_A309 Mammalian Clock Protein Mper2 - Crystal Struture Of 4e-05
4dj2_A320 Unwinding The Differences Of The Mammalian Period C 7e-05
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 361 Back     alignment and structure 
Iteration: 1

 Score =  171 bits (433), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 75/92 (81%), Positives = 81/92 (88%)
Query: 21  DLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWI 80
           D  APPIIGYLPFEVLGTSGYDYYHVDDL+++  CHE LMQ G+G SCYYRFLTKGQQWI
Sbjct: 267 DHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWI 326
Query: 81  WLQTRFYITYHQWNSKPEFIVCTHRVVSYVNV 112
           WLQT +YITYHQWNS+PEFIVCTH VVSY  V
Sbjct: 327 WLQTHYYITYHQWNSRPEFIVCTHTVVSYAEV 358
>pdb|4H6J|A Chain A, Identification Of Cys 255 In Hif-1 As A Novel Site For Development Of Covalent Inhibitors Of Hif-1 ARNT PASB DOMAIN PROTEIN-Protein Interaction Length = 113 Back     alignment and structure
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 387 Back     alignment and structure
>pdb|1P97|A Chain A, Nmr Structure Of The C-Terminal Pas Domain Of Hif2a Length = 114 Back     alignment and structure
>pdb|3F1N|A Chain A, Crystal Structure Of A High Affinity Heterodimer Of Hif2 Alpha And Arnt C-Terminal Pas Domains, With Internally Bound Ethylene Glycol. Length = 117 Back     alignment and structure
>pdb|2A24|A Chain A, Haddock Structure Of Hif-2aARNT PAS-B Heterodimer Length = 107 Back     alignment and structure
>pdb|1WA9|A Chain A, Crystal Structure Of The Pas Repeat Region Of The Drosophila Clock Protein Period Length = 368 Back     alignment and structure
>pdb|3RTY|A Chain A, Structure Of An Enclosed Dimer Formed By The Drosophila Period Protein Length = 339 Back     alignment and structure
>pdb|3GEC|A Chain A, Crystal Structure Of A Tandem Pas Domain Fragment Of Drosophila Period Length = 312 Back     alignment and structure
>pdb|2KDK|A Chain A, Structure Of Human Circadian Clock Protein Bmal2 C-Terminal Pas Domain Length = 121 Back     alignment and structure
>pdb|2HV1|A Chain A, Haddock Structure Of Arnt Pas-B Homodimer Length = 119 Back     alignment and structure
>pdb|4H6J|B Chain B, Identification Of Cys 255 In Hif-1 As A Novel Site For Development Of Covalent Inhibitors Of Hif-1 ARNT PASB DOMAIN PROTEIN-Protein Interaction Length = 116 Back     alignment and structure
>pdb|3F1N|B Chain B, Crystal Structure Of A High Affinity Heterodimer Of Hif2 Alpha And Arnt C-Terminal Pas Domains, With Internally Bound Ethylene Glycol. Length = 121 Back     alignment and structure
>pdb|2A24|B Chain B, Haddock Structure Of Hif-2aARNT PAS-B Heterodimer Length = 108 Back     alignment and structure
>pdb|2B02|A Chain A, Crystal Structure Of Arnt Pas-B Domain Length = 119 Back     alignment and structure
>pdb|2K7S|A Chain A, Human Arnt C-Terminal Pas Domain, 3 Residue Ib Slip Length = 119 Back     alignment and structure
>pdb|4DJ3|A Chain A, Unwinding The Differences Of The Mammalian Period Clock Proteins From Crystal Structure To Cellular Function Length = 317 Back     alignment and structure
>pdb|3GDI|A Chain A, Mammalian Clock Protein Mper2 - Crystal Struture Of A Pas Domain Fragment Length = 309 Back     alignment and structure
>pdb|4DJ2|A Chain A, Unwinding The Differences Of The Mammalian Period Clock Proteins From Crystal Structure To Cellular Function Length = 320 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 ?
Query140
3f1p_A117 Endothelial PAS domain-containing protein 1; PAS d 3e-41
4f3l_A361 Mclock, circadian locomoter output cycles protein 1e-37
3f1p_B121 ARYL hydrocarbon receptor nuclear translocator; PA 8e-37
4f3l_B387 BMAL1B; BHLH, PAS, circadian rhythm proteins, tran 8e-36
2kdk_A121 ARYL hydrocarbon receptor nuclear translocator-LI 2e-35
3gdi_A309 Period circadian protein homolog 2; tandem PAS dom 6e-34
4dj3_A317 Period circadian protein homolog 3; PAS domain, ci 6e-33
4dj2_A320 Period circadian protein homolog 1; PAS domains, c 1e-31
3rty_A339 Period circadian protein; PAS domain, signalling, 2e-31
1oj5_A132 Steroid receptor coactivator 1A; transcriptional c 7e-24
2vlg_A111 Sporulation kinase A; histidine kinase, two-compon 2e-13
3h9w_A115 Diguanylate cyclase with PAS/PAC sensor; alpha-bet 6e-05
3icy_A118 Sensor protein; sensory box histidine kinase/respo 6e-04
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A Length = 117 Back     alignment and structure
 Score =  132 bits (334), Expect = 3e-41
 Identities = 31/85 (36%), Positives = 51/85 (60%)

Query: 24  APPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIWLQ 83
              +IGY P E+LG S Y++YH  D +++   H+ L  KG+  S  YR L K   ++WL+
Sbjct: 28  ITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLE 87

Query: 84  TRFYITYHQWNSKPEFIVCTHRVVS 108
           T+  + Y+  N +P+ I+C + V+S
Sbjct: 88  TQGTVIYNPRNLQPQCIMCVNYVLS 112
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361 Back     alignment and structure
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A* 2k7s_A 2a24_B Length = 121 Back     alignment and structure
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387 Back     alignment and structure
>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens} Length = 121 Back     alignment and structure
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Length = 309 Back     alignment and structure
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus} Length = 317 Back     alignment and structure
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus} Length = 320 Back     alignment and structure
>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A Length = 339 Back     alignment and structure
>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8 Length = 132 Back     alignment and structure
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis} Length = 111 Back     alignment and structure
>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei} Length = 115 Back     alignment and structure
>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum} Length = 118 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query140
3f1p_A117 Endothelial PAS domain-containing protein 1; PAS d 99.89
3f1p_B121 ARYL hydrocarbon receptor nuclear translocator; PA 99.89
4f3l_A361 Mclock, circadian locomoter output cycles protein 99.89
4dj3_A317 Period circadian protein homolog 3; PAS domain, ci 99.87
4dj2_A320 Period circadian protein homolog 1; PAS domains, c 99.87
3rty_A339 Period circadian protein; PAS domain, signalling, 99.87
4f3l_B387 BMAL1B; BHLH, PAS, circadian rhythm proteins, tran 99.87
3gdi_A309 Period circadian protein homolog 2; tandem PAS dom 99.85
2kdk_A121 ARYL hydrocarbon receptor nuclear translocator-LI 99.83
1oj5_A132 Steroid receptor coactivator 1A; transcriptional c 99.83
3h9w_A115 Diguanylate cyclase with PAS/PAC sensor; alpha-bet 99.81
3mr0_A142 Sensory box histidine kinase/response regulator; P 99.78
2vlg_A111 Sporulation kinase A; histidine kinase, two-compon 99.77
2gj3_A120 Nitrogen fixation regulatory protein; PAS domain, 99.73
1n9l_A109 PHOT-LOV1, putative blue light receptor; phototrop 99.72
3icy_A118 Sensor protein; sensory box histidine kinase/respo 99.72
3nja_A125 Probable ggdef family protein; structural genomics 99.7
2vv6_A119 FIXL, sensor protein FIXL; signaling protein, tran 99.68
4hia_A176 LOV protein; PAS, HTH, signaling protein; HET: FMN 99.67
2pr5_A132 Blue-light photoreceptor; light-oxygen-voltage, LO 99.67
3t50_A128 Blue-light-activated histidine kinase; PAS superfa 99.67
4eet_B115 Phototropin-2; LOV, blue light photoreceptor, sign 99.66
3ewk_A227 Sensor protein; PAS domain, alpha/beta fold, kinas 99.66
3mqq_A120 Transcriptional regulator, LUXR family; PAS domain 99.63
3p7n_A258 Sensor histidine kinase; LOV domain, light-activat 99.62
3ue6_A166 Aureochrome1; PAS/LOV domain, FMN-binding blue-lig 99.62
2wkq_A 332 NPH1-1, RAS-related C3 botulinum toxin substrate 1 99.6
3eeh_A125 Putative light and redox sensing histidine kinase; 99.58
1d06_A130 Nitrogen fixation regulatory protein FIXL; oxygen 99.58
3mjq_A126 Uncharacterized protein; NESG, structural genomics 99.57
3luq_A114 Sensor protein; PAS, histidine, kinase, PSI, MCSG, 99.57
3lyx_A124 Sensory BOX/ggdef domain protein; structural genom 99.56
3sw1_A162 Sensory box protein; light-oxygen-voltage, LOV, PA 99.55
3d72_A149 Vivid PAS protein VVD; circadian, photoreceptor, b 99.54
2z6d_A130 Phototropin-2; PAS-fold, LOV-fold, alternative spl 99.53
2r78_A117 Sensor protein; sensory box sensor histidine kinas 99.51
2v0u_A146 NPH1-1, LOV2; kinase, transferase, ATP-binding, se 99.51
1byw_A110 Protein (human ERG potassium channel); PAS domain, 99.5
3ewk_A227 Sensor protein; PAS domain, alpha/beta fold, kinas 99.48
2l0w_A138 Potassium voltage-gated channel, subfamily H (EAG 99.44
4eho_A635 Bacteriophytochrome, PAS/PAC sensor; photoreceptor 99.44
3mfx_A129 Sensory BOX/ggdef family protein; alpha-beta prote 99.43
3olo_A118 Two-component sensor histidine kinase; structural 99.4
3mxq_A152 Sensor protein; PSI2, MCSG, structural genomics, p 99.39
3k3c_A158 Protein RV1364C/MT1410; sensor, PAS, signal transd 99.38
1v9y_A167 Heme PAS sensor protein; signaling protein; HET: H 99.38
1ll8_A114 PAS kinase; PAS domain, ligand binding, ligand scr 99.37
3kx0_X185 Uncharacterized protein RV1364C/MT1410; PAS domain 99.37
3bwl_A126 Sensor protein; structural genomics, APC87707.1, P 99.34
3fc7_A125 HTR-like protein, sensor protein; APC87712.1, HTR- 99.22
3fg8_A118 Uncharacterized protein RHA05790; PAS domain, stru 99.22
3b33_A115 Sensor protein; structural genomics, PAS domain, n 99.17
3a0s_A96 Sensor protein; PAS-fold, kinase, phosphoprotein, 99.04
2qkp_A151 Uncharacterized protein; structural genomics, unkn 99.03
4f3l_A 361 Mclock, circadian locomoter output cycles protein 99.01
4f3l_B 387 BMAL1B; BHLH, PAS, circadian rhythm proteins, tran 98.99
3cax_A369 Uncharacterized protein PF0695; structural genomic 98.81
3vol_A233 Aerotaxis transducer AER2; heme, oxygen sensor pro 98.78
4hi4_A121 Aerotaxis transducer AER2; PAS domain, diatomic GA 98.77
4dj3_A 317 Period circadian protein homolog 3; PAS domain, ci 98.72
3rty_A 339 Period circadian protein; PAS domain, signalling, 98.71
3a0r_A 349 Sensor protein; four helix bundle, PAS fold, kinas 98.7
3gdi_A 309 Period circadian protein homolog 2; tandem PAS dom 98.65
1mzu_A129 PPR; photoactive yellow protein, PAS, PYP, signali 98.65
1nwz_A125 PYP, photoactive yellow protein; PAS, LOV, GAF, do 98.63
2w0n_A118 Sensor protein DCUS; signal transduction, two-comp 98.44
4dj2_A 320 Period circadian protein homolog 1; PAS domains, c 98.33
2jhe_A190 Transcription regulator TYRR; aromatic hydrocarbon 98.17
2ykf_A305 Pdtas, probable sensor histidine kinase pdtas; tra 96.77
2ool_A 337 Sensor protein; bacteriophytochrome, photoconversi 96.47
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial 92.54
4e04_A 327 Bacteriophytochrome (light-regulated signal trans 87.1
3s7o_A 343 Bacteriophytochrome; biliverdin, PAS, GAF, photore 84.43
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A Back     alignment and structure
Probab=99.89  E-value=3.7e-23  Score=131.43  Aligned_cols=109  Identities=34%  Similarity=0.563  Sum_probs=96.8

Q ss_pred             ccceEEE--EEecCCEEEEcCCcccccCcCcchhcCCCcceeeCccCHHHHHHHHHHHHHcCCcccEEeeeEecCCcEEE
Q psy10825          4 FKPVTFC--MSDLMNSTIYDLVAPPIIGYLPFEVLGTSGYDYYHVDDLDSVVTCHEALMQKGEGTSCYYRFLTKGQQWIW   81 (140)
Q Consensus         4 ~~~~~~v--~~~d~~i~~~n~a~~~~lGy~~~el~g~~~~~~vhpdd~~~~~~~~~~~~~~g~~~~~e~r~~~~~G~~~w   81 (140)
                      ++...++  .+.+|+++|+|++++.++||+++|++|+++.+++||+|.+.+...+..++..+.....++|+++++|+++|
T Consensus         6 l~~~~~i~~~d~~g~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~~w   85 (117)
T 3f1p_A            6 LDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW   85 (117)
T ss_dssp             TGGGEEEEEECTTCBEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSEEE
T ss_pred             cCCccEEEEECCCceEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHHHHHhCCCeeeeEEEEEecCCCEEE
Confidence            3444555  55677899999999999999999999999999999999999999999988888877779999999999999


Q ss_pred             EEEEEEEEEecCCCCceEEEEEeEEccchhh
Q psy10825         82 LQTRFYITYHQWNSKPEFIVCTHRVVSYVNV  112 (140)
Q Consensus        82 v~~~~~~~~~~~~~~~~~iv~~~~~it~~~~  112 (140)
                      ++.++.++.++.++.+.+++|+.+|||+++.
T Consensus        86 ~~~~~~~~~d~~~g~~~~iv~~~~DITer~~  116 (117)
T 3f1p_A           86 LETQGTVIYNPRNLQPQCIMCVNYVLSEIEK  116 (117)
T ss_dssp             EEEEEEEEEETTTTEEEEEEEEEEECSCCBC
T ss_pred             EEEeeEEEECCCCCCceEEEEEeeecccccc
Confidence            9999999998767888999999999998653
>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B Back     alignment and structure
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus} Back     alignment and structure
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus} Back     alignment and structure
>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A Back     alignment and structure
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Back     alignment and structure
>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens} Back     alignment and structure
>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8 Back     alignment and structure
>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei} Back     alignment and structure
>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis} Back     alignment and structure
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis} Back     alignment and structure
>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii} Back     alignment and structure
>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A* Back     alignment and structure
>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum} Back     alignment and structure
>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum} Back     alignment and structure
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen FIX PER-ARNT-SIM, metal-binding, PAS, iron, heme; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A* Back     alignment and structure
>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A* Back     alignment and structure
>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A* Back     alignment and structure
>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis} Back     alignment and structure
>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A* Back     alignment and structure
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Back     alignment and structure
>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A Back     alignment and structure
>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis} Back     alignment and structure
>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A* Back     alignment and structure
>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A* Back     alignment and structure
>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui} Back     alignment and structure
>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two-C system, signaling protein; HET: HEM; 1.40A {Sinorhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A* Back     alignment and structure
>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense} Back     alignment and structure
>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens} Back     alignment and structure
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea} Back     alignment and structure
>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida} Back     alignment and structure
>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B* Back     alignment and structure
>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A* Back     alignment and structure
>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca} Back     alignment and structure
>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal trans phototropin1, nucleotide-binding; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A* Back     alignment and structure
>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6 Back     alignment and structure
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Back     alignment and structure
>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2, isoform CRA_B; HERG, PAS domain, voltage-gated potassium channel, membrane; NMR {Homo sapiens} PDB: 2l1m_A 2l4r_A Back     alignment and structure
>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis} Back     alignment and structure
>3olo_A Two-component sensor histidine kinase; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, TRA; 2.09A {Nostoc SP} Back     alignment and structure
>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor} Back     alignment and structure
>3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A Back     alignment and structure
>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L* Back     alignment and structure
>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5 Back     alignment and structure
>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis} Back     alignment and structure
>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protei protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049} Back     alignment and structure
>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui} Back     alignment and structure
>3fg8_A Uncharacterized protein RHA05790; PAS domain, structural genomics, PS protein structure initiative, midwest center for structural genomics, MCSG; HET: 3PB; 1.80A {Rhodococcus SP} Back     alignment and structure
>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633} Back     alignment and structure
>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A* Back     alignment and structure
>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans} Back     alignment and structure
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Back     alignment and structure
>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638} Back     alignment and structure
>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa} Back     alignment and structure
>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa} Back     alignment and structure
>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus} Back     alignment and structure
>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A Back     alignment and structure
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima} Back     alignment and structure
>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Back     alignment and structure
>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1 Back     alignment and structure
>1nwz_A PYP, photoactive yellow protein; PAS, LOV, GAF, domains fold, signaling protein; HET: HC4; 0.82A {Halorhodospira halophila} SCOP: d.110.3.1 PDB: 1kou_A* 1ot9_A* 1otb_A* 1s4r_A* 1s4s_A* 1ts0_A* 1ts6_A* 1ts7_A* 1ts8_A* 1uwn_X* 1uwp_X* 2d01_A* 2phy_A* 2pyp_A* 2pyr_A* 2qj5_A* 2qj7_A* 2qws_A* 2zoh_A* 2zoi_A* ... Back     alignment and structure
>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli} Back     alignment and structure
>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus} Back     alignment and structure
>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli} Back     alignment and structure
>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A Back     alignment and structure
>2ool_A Sensor protein; bacteriophytochrome, photoconversion, photoreceptor, biliver signaling protein; HET: LBV; 2.20A {Rhodopseudomonas palustris} SCOP: d.110.2.1 d.110.3.9 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
>4e04_A Bacteriophytochrome (light-regulated signal trans histidine kinase), PHYB1; bacteriophytochrome chromophore binding domain; HET: LBV; 1.79A {Rhodopseudomonas palustris} Back     alignment and structure
>3s7o_A Bacteriophytochrome; biliverdin, PAS, GAF, photoreceptor, fluorescent protein; HET: LBV GOL; 1.24A {Deinococcus radiodurans} PDB: 3s7n_A* 3s7p_A* 3s7q_A* 2o9c_A* 2o9b_A* 1ztu_A* 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 140
d1oj5a_109 d.110.3.8 (A:) PAS domain of steroid receptor coac 4e-20
d1p97a_114 d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-t 0.001
>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 109 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 77.4 bits (190), Expect = 4e-20
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 3/91 (3%)

Query: 21  DLVAPPIIGYLPFE-VLGTSGYDYYHVDDLDSVVTC--HEALMQKGEGTSCYYRFLTKGQ 77
           D  +    G   +E ++    Y ++     +        + +M +G  +S  YRF+    
Sbjct: 18  DTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDG 77

Query: 78  QWIWLQTRFYITYHQWNSKPEFIVCTHRVVS 108
             +   TR  + Y Q      FI+  H +  
Sbjct: 78  TMLSAHTRCKLCYPQSPDMQPFIMGIHIIDR 108
>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 114 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 ?
Query140
d1oj5a_109 PAS domain of steroid receptor coactivator 1A, NCo 99.91
d1p97a_114 Hypoxia-inducible factor Hif2a, C-terminal domain 99.91
d1n9la_109 Putative blue light receptor, phot-lov1 domain {Gr 99.85
d1jnua_104 Photoreceptor phy3 flavin-binding domain, lov2 {Ma 99.78
d1bywa_110 Erg potassium channel, N-terminal domain {Human (H 99.77
d1xj3a1106 Histidine kinase FixL heme domain {Bradyrhizobium 99.67
d1ew0a_130 Histidine kinase FixL heme domain {Rhizobium melil 99.6
d1ll8a_114 N-terminal PAS domain of Pas kinase {Human (Homo s 99.51
d1v9ya_113 Direct oxygen sensor protein, DOS {Escherichia col 99.49
d1mzua_110 PYP domain of sensor histidine kinase Ppr {Rhodosp 99.32
d1nwza_125 Photoactive yellow protein, PYP {Ectothiorhodospir 99.31
d2oola2114 Sensor protein PhyB2 {Rhodopseudomonas palustris [ 98.39
d2veaa3127 Phytochrome-like protein Cph1 {Synechocystis sp. p 95.95
d2o9ca2127 Bacteriophytochrome BphP {Deinococcus radiodurans 95.73
d3c2wa3113 Bacteriophytochrome BphP {Pseudomonas aeruginosa [ 83.56
>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=3.4e-25  Score=140.42  Aligned_cols=102  Identities=17%  Similarity=0.220  Sum_probs=86.9

Q ss_pred             EEEEEecC--CEEEEcCCcccccCcCc-chhcCCCcceeeCccCHH--HHHHHHHHHHHcCCcccEEeeeEecCCcEEEE
Q psy10825          8 TFCMSDLM--NSTIYDLVAPPIIGYLP-FEVLGTSGYDYYHVDDLD--SVVTCHEALMQKGEGTSCYYRFLTKGQQWIWL   82 (140)
Q Consensus         8 ~~v~~~d~--~i~~~n~a~~~~lGy~~-~el~g~~~~~~vhpdd~~--~~~~~~~~~~~~g~~~~~e~r~~~~~G~~~wv   82 (140)
                      .|+++++.  +++++|+++..++||.+ +||+|+++++++||||++  .....++.+...|+....+||++++||+|+|+
T Consensus         3 ~F~trh~~~g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~vWv   82 (109)
T d1oj5a_           3 SFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSA   82 (109)
T ss_dssp             EEEEEECTTCCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEE
T ss_pred             eEEEEECCCceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEEEE
Confidence            57777655  69999999999999986 899999999999999975  34456778888888888889999999999999


Q ss_pred             EEEEEEEEecCCCCceEEEEEeEEccc
Q psy10825         83 QTRFYITYHQWNSKPEFIVCTHRVVSY  109 (140)
Q Consensus        83 ~~~~~~~~~~~~~~~~~iv~~~~~it~  109 (140)
                      ++++.++++++++++.+|+|+++++.+
T Consensus        83 ~t~~~~~~~~~~~~~~~Ii~~h~i~~~  109 (109)
T d1oj5a_          83 HTRCKLCYPQSPDMQPFIMGIHIIDRE  109 (109)
T ss_dssp             EEEEEEECC----CCCEEEEEEEEECC
T ss_pred             EEEEEEEECCCCCcccEEEEEEEEecC
Confidence            999999999999999999999998764
>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Back     information, alignment and structure
>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]} Back     information, alignment and structure
>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]} Back     information, alignment and structure
>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]} Back     information, alignment and structure
>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]} Back     information, alignment and structure
>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]} Back     information, alignment and structure
>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]} Back     information, alignment and structure
>d2veaa3 d.110.3.9 (A:4-130) Phytochrome-like protein Cph1 {Synechocystis sp. pcc 6803 [TaxId: 1148]} Back     information, alignment and structure
>d2o9ca2 d.110.3.9 (A:4-130) Bacteriophytochrome BphP {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d3c2wa3 d.110.3.9 (A:5-117) Bacteriophytochrome BphP {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure