Psyllid ID: psy7682

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380---
Protein Sequence
AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIRL
Secondary Structure (PSIPRED)
ccccHHHHHHHHHcHHHHHHHHHccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHcccEEEEcccccEEEEEccHHHHcccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccccccccccccccccccccEEEEEEEccccccccccccccEEEEccccccEEEEEEcccccccccccHHHHHHHccccEEEccccccccHHHHHHHHHHHHcccccEEEEccccccccccccccccccccccccEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccHccccccccccccccccccHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHcHcHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHcccEEEEEEccccEEEEEccccHHccccHHHHccccHHccccHcHHHHHHHHccccccccccccccEEEccccccEEEccccccEEEEEEEEEccccccccccccccccccccccccccccEEEEEEEEccccccccccccccEEEEEcccccEEEEEccHHccccHHHHccccEEEEcccEEEccccccccHHHHHHHHHHHHHHccEEEEEcccccEcccccccccccccHcHHHHHHcc
Coil and Loop (DISEMBL)
AKCLNEKRRREQENNYIEELAELISAASFAESmsslavkpdkcAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESmsslavkpdkcAILQETVNQIRNIKqqetssdavqqgevssskptvitnevLGPLLLEALEGFLfvvnpdgyvnfCTENIKSFIRYSRQEVLGKSVYNLihhgdharfhnclvpsshqvnawtsdsggqagkrpsltastpnrtFNIRLLISSTHltaglsraggengqddsgdvsseggpclmcvarripptdkqlsapieqFTMKldrsgtiigmdtsgvsqTHTQYLNKAVAcktsatvwtcpnspltSTKLLLKALLLSICTDYALvqtdtcmyrsspscfglqgasrTSLWQRIRL
Flexible Loop (DISEMBL)
akclnekrrreqENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQqetssdavqqgevssskptviTNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIpptdkqlsapIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYrsspscfglqgasrtslwqrirl
Low Complexity Region (SEG)
AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPltstklllkalllsICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIRL
Disordered region (IsUnstruct)
*******************LAELISA*********LAVKPDKCAILQETVNQCL***********YIEELAELISAASF******LAVKPDKCAILQETVN**************************VITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA**********************TFNIRLLISSTHL*************************CLMCVARRI**********IEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGA***********
Disordered Region (DISOPRED)
*****************************************************************YIEELAELISAASFAESM**LAVKPDKCAILQETVNQIRNIK**********************TNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN*********************************TFNIRLLISSTHLT************************CLMCVARRIPP************TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIRL
Disordered Region (DISEMBL)
***********QENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIK*****************KPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWT***********SLTASTPNRTFNIRLLISSTHLTAGLS****************EGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIRL
Disordered Region (DISPRO)
********************************************************KRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIK***************SSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS**Q**AWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSS**C**LQ*ASRTS*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIRL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	383	2.2.26 [Sep-21-2011]
Q98TW1	1505	Nuclear receptor coactiva	yes	N/A	0.579	0.147	0.407	2e-44
Q9W705	1516	Nuclear receptor coactiva	N/A	N/A	0.595	0.150	0.397	5e-44
B5DE09	1440	Nuclear receptor coactiva	yes	N/A	0.595	0.158	0.394	9e-44
Q4PJW2	1440	Nuclear receptor coactiva	yes	N/A	0.582	0.154	0.414	1e-43
Q9WUI9	1465	Nuclear receptor coactiva	yes	N/A	0.590	0.154	0.410	2e-43
Q15596	1464	Nuclear receptor coactiva	yes	N/A	0.595	0.155	0.398	2e-43
Q61026	1462	Nuclear receptor coactiva	no	N/A	0.603	0.158	0.406	2e-43
Q15788	1441	Nuclear receptor coactiva	no	N/A	0.582	0.154	0.414	4e-43
P70365	1447	Nuclear receptor coactiva	no	N/A	0.582	0.154	0.414	7e-43
Q9Y6Q9	1424	Nuclear receptor coactiva	no	N/A	0.665	0.179	0.363	3e-42

>sp|Q98TW1|NCOA2_DANRE Nuclear receptor coactivator 2 OS=Danio rerio GN=ncoa2 PE=1 SV=1

 Score =  179 bits (455), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 112/275 (40%), Positives = 159/275 (57%), Gaps = 53/275 (19%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR RE E+ YIEELAELI  A+F + + +  VKPDKCAIL+ETV QIR IK+QE ++  
Sbjct: 36  EKRNREHESKYIEELAELI-FANFND-IDNFNVKPDKCAILKETVKQIRQIKEQEKAAAA 93

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVN +G + F +EN+  ++RY+++
Sbjct: 94  NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNMEGNIVFVSENVTQYLRYNQE 153

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA--WTSDSGGQAGKRPSLTASTPNR---T 226
           E++  SVY+++H GDHA F   L+P SH VN   W+S++              P R   T
Sbjct: 154 ELMNTSVYSILHVGDHAEFIKNLLPKSH-VNGVPWSSEN--------------PRRNSHT 198

Query: 227 FNIRLLISSTHLTAGLSRAGGENGQD----------------DSGDVSSEG---GPCLMC 267
           FN R+L+ + H  A       E  QD                +   +  EG     CL+C
Sbjct: 199 FNCRMLV-NPHSEA-------EETQDHEAQQKYETMQCFAVSEPKSIKEEGEDFQSCLIC 250

Query: 268 VARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTS 302
           VARR+P  ++ +    E FT + D  G I  +DTS
Sbjct: 251 VARRVPMKERPMLPTQESFTTRQDLQGKITSLDTS 285

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1) (By similarity). Has a role in primitive myelopoiesis in the differentiation of granulocytes and macrophages.
Danio rerio (taxid: 7955)

>sp|Q9W705|NCOA2_XENLA Nuclear receptor coactivator 2 OS=Xenopus laevis GN=ncoa2 PE=2 SV=1

 Score =  179 bits (453), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 150/269 (55%), Gaps = 41/269 (15%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR REQEN YIEELAELI  A+F + + +L  KPDKCAIL+ETV QIR IK+ E ++  
Sbjct: 32  EKRNREQENKYIEELAELI-FANFND-IDNLNFKPDKCAILKETVKQIRQIKEHEKTAAA 89

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct: 90  NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNREGNVVFVSENVTQYLRYNQE 149

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNR---TFN 228
           E++  SVY+++H GDH+ F   L+P                    SL    P R   TFN
Sbjct: 150 ELMNTSVYSILHVGDHSEFIKNLLPK-------------------SLVNGVPRRNSHTFN 190

Query: 229 IRLLISSTHLTAGLSRAGGENGQ----------DDSGDVSSEG---GPCLMCVARRIPPT 275
            R+L+            G E  Q               +  EG     CL+CVARR+P  
Sbjct: 191 CRMLVKPMMECEEERHDGQETHQKYESMQCFAVSQPKSIKEEGEDFQSCLICVARRVPVK 250

Query: 276 DKQLSAPIEQFTMKLDRSGTIIGMDTSGV 304
           ++ +  P E FT + D  G I  +DT+ +
Sbjct: 251 ERPVPPPSESFTTRQDFQGKITSLDTTSM 279

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1) (By similarity). Required in a nuclear receptor pathway to suppress expression of dorsal mesoderm genes.

Xenopus laevis (taxid: 8355)

>sp|B5DE09|NCOA2_XENTR Nuclear receptor coactivator 2 OS=Xenopus tropicalis GN=ncoa2 PE=2 SV=1

 Score =  177 bits (450), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 150/269 (55%), Gaps = 41/269 (15%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR REQEN YIEELAELI  A+F + + +L  KPDKCAIL+ETV QIR IK+ E ++  
Sbjct: 35  EKRNREQENKYIEELAELI-FANFND-IDNLNFKPDKCAILKETVKQIRQIKEHEKTAAA 92

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct: 93  NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNREGNVVFVSENVTQYLRYNQE 152

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNR---TFN 228
           E++  SVY+++H GDH+ F   L+P                    S+    P R   TFN
Sbjct: 153 ELMNTSVYSILHVGDHSEFIKNLLPK-------------------SIVNGGPRRNSHTFN 193

Query: 229 IRLLISSTHLTAGLSRAGGENGQ----------DDSGDVSSEG---GPCLMCVARRIPPT 275
            R+L+            G E  Q               +  EG     CL+CVARR+P  
Sbjct: 194 CRMLVKPMMECEEEGHDGQETHQKYETMQCFAVSQPKSIKEEGEDFQSCLICVARRVPMK 253

Query: 276 DKQLSAPIEQFTMKLDRSGTIIGMDTSGV 304
           ++ +  P E FT + D  G I  +DT+ +
Sbjct: 254 ERPVPPPSESFTTRQDLQGKITSLDTTNM 282

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required in a nuclear receptor pathway to suppress expression of dorsal mesoderm genes.

Xenopus tropicalis (taxid: 8364)

>sp|Q4PJW2|NCOA1_PIG Nuclear receptor coactivator 1 OS=Sus scrofa GN=NCOA1 PE=2 SV=1

 Score =  177 bits (448), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 114/275 (41%), Positives = 156/275 (56%), Gaps = 52/275 (18%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE----T 111
           EKRRREQEN Y+EELAEL+SA      + SL+VKPDKC IL++TV+QI+ +K+ E    T
Sbjct: 32  EKRRREQENKYLEELAELLSAN--ISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEKST 89

Query: 112 SSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
           + D VQ+ ++SSS   VI  E LGPLLLEAL+GF FVVN +G + F +EN+ S++ Y+++
Sbjct: 90  TDDEVQKSDISSSSQGVIEKESLGPLLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQE 149

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA--WTSDSGGQAGKRPSLTASTPNRTFNI 229
           E++  SVY+++H GDHA F   L+P S  VN   W  +    A +R S        TFN 
Sbjct: 150 ELMNTSVYSILHVGDHAEFVKNLLPKSL-VNGVPWPQE----ATRRNS-------HTFNC 197

Query: 230 RLLISSTHLTAGLSRAGGENG--------------------QDDSGDVSSEGGPCLMCVA 269
           R+LI            G EN                     Q+D  D  S    CL+C+A
Sbjct: 198 RMLIHPP------DEPGTENQEACQRYEVMQCFTVSQPKSIQEDGEDFQS----CLICIA 247

Query: 270 RRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGV 304
           RR+P     +   +E F  K D +G II +DTS +
Sbjct: 248 RRLPRPPAIMG--VESFMTKQDTTGKIISIDTSSL 280

Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response.

Sus scrofa (taxid: 9823)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9WUI9|NCOA2_RAT Nuclear receptor coactivator 2 OS=Rattus norvegicus GN=Ncoa2 PE=1 SV=1

 Score =  177 bits (448), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 112/273 (41%), Positives = 155/273 (56%), Gaps = 47/273 (17%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR REQEN YIEELAELI  A+F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct: 35  EKRNREQENKYIEELAELI-FANFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct: 93  NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVN--AWTSDSGGQAGKRPSLTASTPNRTFNI 229
           E++ KSVY+++H GDH  F   L+P S  VN  +WT    G+  +R S        TFN 
Sbjct: 153 ELMNKSVYSILHVGDHTEFVKNLLPKS-MVNGGSWT----GEPPRRNS-------HTFNC 200

Query: 230 RLLISSTHLTAGLSRAGGENGQDD-----------------SGDVSSEG---GPCLMCVA 269
           R+L+     +        E G D+                    +  EG     CL+CVA
Sbjct: 201 RMLVKPLPDSE-------EEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDKQSCLICVA 253

Query: 270 RRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTS 302
           RR+P  ++      E FT + D  G I  +DTS
Sbjct: 254 RRVPMKERPALPSSESFTTRQDLQGKITFLDTS 286

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.

Rattus norvegicus (taxid: 10116)

>sp|Q15596|NCOA2_HUMAN Nuclear receptor coactivator 2 OS=Homo sapiens GN=NCOA2 PE=1 SV=2

 Score =  177 bits (448), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 108/271 (39%), Positives = 153/271 (56%), Gaps = 43/271 (15%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR REQEN YIEELAELI  A+F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct: 35  EKRNREQENKYIEELAELI-FANFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct: 93  NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
           E++ KSVY+++H GDH  F   L+P S        + G  +G+ P   +     TFN R+
Sbjct: 153 ELMNKSVYSILHVGDHTEFVKNLLPKS------IVNGGSWSGEPPRRNS----HTFNCRM 202

Query: 232 LISSTHLTAGLSRAGGENGQDD-----------------SGDVSSEG---GPCLMCVARR 271
           L+     +        E G D+                    +  EG     CL+CVARR
Sbjct: 203 LVKPLPDSE-------EEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARR 255

Query: 272 IPPTDKQLSAPIEQFTMKLDRSGTIIGMDTS 302
           +P  ++ +    E FT + D  G I  +DTS
Sbjct: 256 VPMKERPVLPSSESFTTRQDLQGKITSLDTS 286

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.

Homo sapiens (taxid: 9606)

>sp|Q61026|NCOA2_MOUSE Nuclear receptor coactivator 2 OS=Mus musculus GN=Ncoa2 PE=1 SV=3

 Score =  176 bits (447), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 109/268 (40%), Positives = 154/268 (57%), Gaps = 37/268 (13%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
           EKR REQEN YIEELAELI  A+F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct: 35  EKRNREQENKYIEELAELI-FANFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query: 114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
             D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct: 93  NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGSVVFVSENVTQYLRYNQE 152

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
           E++ KSVY+++H GDH  F   L+P S  VN      G  +G+ P  ++     TFN R+
Sbjct: 153 ELMNKSVYSILHVGDHTEFVKNLLPKS-MVNG-----GSWSGEPPRRSS----HTFNCRM 202

Query: 232 LISSTHLTAGLSRAGGENGQ-----------------DDSGDVSSEGGPCLMCVARRIPP 274
           L+     +        E  Q                 ++  D+ S    CL+CVARR+P 
Sbjct: 203 LVKPLPDSEEEGHDSQEAHQKYEAMQCFAVSQPKSIKEEGEDLQS----CLICVARRVPM 258

Query: 275 TDKQLSAPIEQFTMKLDRSGTIIGMDTS 302
            ++      E FT + D  G I  +DTS
Sbjct: 259 KERPTLPSSESFTTRQDLQGKITSLDTS 286

Transcriptional coactivator for steroid receptors and nuclear receptors. Coactivator of the steroid binding domain (AF-2) but not of the modulating N-terminal domain (AF-1). Required with NCOA1 to control energy balance between white and brown adipose tissues.

Mus musculus (taxid: 10090)

>sp|Q15788|NCOA1_HUMAN Nuclear receptor coactivator 1 OS=Homo sapiens GN=NCOA1 PE=1 SV=3

 Score =  175 bits (444), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 114/275 (41%), Positives = 157/275 (57%), Gaps = 52/275 (18%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE----T 111
           EKRRREQEN Y+EELAEL+SA      + SL+VKPDKC IL++TV+QI+ +K+ E    T
Sbjct: 32  EKRRREQENKYLEELAELLSAN--ISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEKST 89

Query: 112 SSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
           + D VQ+ ++SSS   VI  E LGPLLLEAL+GF FVVN +G + F +EN+ S++ Y+++
Sbjct: 90  TDDDVQKSDISSSSQGVIEKESLGPLLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQE 149

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA--WTSDSGGQAGKRPSLTASTPNRTFNI 229
           E++  SVY+++H GDHA F   L+P S  VN   W  +    A +R S        TFN 
Sbjct: 150 ELMNTSVYSILHVGDHAEFVKNLLPKSL-VNGVPWPQE----ATRRNS-------HTFNC 197

Query: 230 RLLISSTHLTAGLSRAGGENG--------------------QDDSGDVSSEGGPCLMCVA 269
           R+LI            G EN                     Q+D  D  S    CL+C+A
Sbjct: 198 RMLIHPP------DEPGTENQEACQRYEVMQCFTVSQPKSIQEDGEDFQS----CLICIA 247

Query: 270 RRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGV 304
           RR+ P    ++  +E F  K D +G II +DTS +
Sbjct: 248 RRL-PRPPAITG-VESFMTKQDTTGKIISIDTSSL 280

Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|P70365|NCOA1_MOUSE Nuclear receptor coactivator 1 OS=Mus musculus GN=Ncoa1 PE=1 SV=2

 Score =  175 bits (443), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 114/275 (41%), Positives = 157/275 (57%), Gaps = 52/275 (18%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE----T 111
           EKRRREQEN Y+EELAEL+SA      + SL+VKPDKC IL++TV+QI+ +K+ E    T
Sbjct: 32  EKRRREQENKYLEELAELLSAN--ISDIDSLSVKPDKCKILKKTVDQIQLMKRMEQEKST 89

Query: 112 SSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
           + D VQ+ ++SSS   VI  E LGPLLLEAL+GF FVVN +G + F +EN+ S++ Y+++
Sbjct: 90  TDDDVQKSDISSSSQGVIEKESLGPLLLEALDGFFFVVNCEGRIVFVSENVTSYLGYNQE 149

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA--WTSDSGGQAGKRPSLTASTPNRTFNI 229
           E++  SVY+++H GDHA F   L+P S  VN   W  +    A +R S        TFN 
Sbjct: 150 ELMNTSVYSILHVGDHAEFVKNLLPKSL-VNGVPWPQE----ATRRNS-------HTFNC 197

Query: 230 RLLISSTHLTAGLSRAGGENG--------------------QDDSGDVSSEGGPCLMCVA 269
           R+LI            G EN                     Q+D  D  S    CL+C+A
Sbjct: 198 RMLIHPPE------DPGTENQEACQRYEVMQCFTVSQPKSIQEDGEDFQS----CLICIA 247

Query: 270 RRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGV 304
           RR+ P    ++  +E F  K D +G II +DTS +
Sbjct: 248 RRL-PRPPAITG-VESFMTKQDTTGKIISIDTSSL 280

Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

>sp|Q9Y6Q9|NCOA3_HUMAN Nuclear receptor coactivator 3 OS=Homo sapiens GN=NCOA3 PE=1 SV=1

 Score =  172 bits (437), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 110/303 (36%), Positives = 161/303 (53%), Gaps = 48/303 (15%)

Query: 27  ASFAESMSSLAVKPDKCAILQETVNQ---CLNEKRRREQENNYIEELAELISAASFAESM 83
           +   E++  LA    K  +  +T  Q   C  EKRRREQE+ YIEELAELISA      +
Sbjct: 2   SGLGENLDPLASDSRKRKLPCDTPGQGLTCSGEKRRREQESKYIEELAELISAN--LSDI 59

Query: 84  SSLAVKPDKCAILQETVNQIRNIKQQE---TSSDAVQQGEVSSSKPTVITNEVLGPLLLE 140
            +  VKPDKCAIL+ETV QIR IK+Q    ++ D VQ+ +VSS+   VI  + LGPLLL+
Sbjct: 60  DNFNVKPDKCAILKETVRQIRQIKEQGKTISNDDDVQKADVSSTGQGVIDKDSLGPLLLQ 119

Query: 141 ALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQ 200
           AL+GFLFVVN DG + F +EN+  +++Y +++++  SVYN++H  D   F   L  S+  
Sbjct: 120 ALDGFLFVVNRDGNIVFVSENVTQYLQYKQEDLVNTSVYNILHEEDRKDFLKNLPKSTVN 179

Query: 201 VNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTH---------------------LT 239
             +WT+++  Q            + TFN R+L+ + H                       
Sbjct: 180 GVSWTNETQRQK-----------SHTFNCRMLMKTPHDILEDINASPEMRQRYETMQCFA 228

Query: 240 AGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGM 299
               RA  E G+D           C++CVARRI   ++   +  E F  + D SG ++ +
Sbjct: 229 LSQPRAMMEEGEDLQS--------CMICVARRITTGERTFPSNPESFITRHDLSGKVVNI 280

Query: 300 DTS 302
           DT+
Sbjct: 281 DTN 283

Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Plays a central role in creating a multisubunit coactivator complex, which probably acts via remodeling of chromatin. Involved in the coactivation of different nuclear receptors, such as for steroids (GR and ER), retinoids (RARs and RXRs), thyroid hormone (TRs), vitamin D3 (VDR) and prostanoids (PPARs). Displays histone acetyltransferase activity. Also involved in the coactivation of the NF-kappa-B pathway via its interaction with the NFKB1 subunit. Interacts with PSMB9.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 4

EC: 8

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	383
242019472	363	Neuronal PAS domain-containing protein,	0.647	0.683	0.551	5e-76
270007579	1460	hypothetical protein TcasGA2_TC014256 [T	0.668	0.175	0.514	3e-71
91082795	1504	PREDICTED: similar to transcriptional in	0.668	0.170	0.514	5e-71
241244650	1337	nuclear receptor coactivator, putative [	0.686	0.196	0.515	5e-69
427796185	1504	Putative transcriptional intermediary fa	0.720	0.183	0.495	8e-65
328782966	1617	PREDICTED: hypothetical protein LOC41063	0.647	0.153	0.482	2e-64
340723192	1594	PREDICTED: hypothetical protein LOC10064	0.647	0.155	0.479	5e-64
350418715	1606	PREDICTED: hypothetical protein LOC10074	0.647	0.154	0.479	5e-64
328711465	1437	PREDICTED: hypothetical protein LOC10016	0.691	0.184	0.478	4e-63
328711463	1395	PREDICTED: hypothetical protein LOC10016	0.684	0.187	0.483	5e-63

>gi|242019472|ref|XP_002430185.1| Neuronal PAS domain-containing protein, putative [Pediculus humanus corporis] gi|212515276|gb|EEB17447.1| Neuronal PAS domain-containing protein, putative [Pediculus humanus corporis]

 Score =  291 bits (744), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 161/292 (55%), Positives = 193/292 (66%), Gaps = 44/292 (15%)

Query: 49  TVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ 108
           + N+CLNEKRRREQEN YIEELAELISA SFA+ MSSL+VKPDKCAILQETVNQIR+IKQ
Sbjct: 12  SFNKCLNEKRRREQENIYIEELAELISA-SFAD-MSSLSVKPDKCAILQETVNQIRHIKQ 69

Query: 109 QETSSD--AVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFI 166
           QE  S   AVQQGEVSSS PTV+ NEV GPLLLEAL+GFLF+VN +G + F T+N+  FI
Sbjct: 70  QENCSGDAAVQQGEVSSSNPTVLRNEVFGPLLLEALDGFLFIVNLEGKIEFVTDNVHQFI 129

Query: 167 RYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRT 226
           ++++ ++ GKS+YN+IHHGDHARF + L+P +     W           P        RT
Sbjct: 130 KFTKDDLFGKSIYNIIHHGDHARFSSSLLPMTI---GW-----------PEPNPQNSRRT 175

Query: 227 FNIRLLIS--------------------STHLTAGLSRAGGENGQDDSGDVSSE----GG 262
           FN RLLI                     +  +     +   E G  DS DV+SE    G 
Sbjct: 176 FNCRLLIKPPDDQEETMEEKQQRISKYENMQIQCTQVQLNKEKG--DSDDVTSESSEIGS 233

Query: 263 PCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNK 314
             LMCVARRIP  +K +  PIEQFTMKLD SG IIG+DT GVS T++QYLNK
Sbjct: 234 GTLMCVARRIPQNEKSVGTPIEQFTMKLDTSGKIIGIDTIGVSATYSQYLNK 285

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270007579|gb|EFA04027.1| hypothetical protein TcasGA2_TC014256 [Tribolium castaneum]

 Score =  275 bits (703), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 162/315 (51%), Positives = 204/315 (64%), Gaps = 59/315 (18%)

Query: 33  MSSLAVKPDKCAILQET-----VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLA 87
           MS+LA   +K     ET     +N+C NEKRRREQEN YIEELAELISA +FA+ MSSL+
Sbjct: 1   MSALATGVNKKRKKSETKPQAQINKCNNEKRRREQENIYIEELAELISA-NFAD-MSSLS 58

Query: 88  VKPDKCAILQETVNQIRNIKQQET---SSDAVQQGEVSSSKPTVITNEVLGPLLLEALEG 144
           VKPDKCAILQETVNQIR+IKQ+E+   SSD VQQGEVSSS+PT+++NEV GPLLLEALEG
Sbjct: 59  VKPDKCAILQETVNQIRSIKQRESASQSSDPVQQGEVSSSRPTILSNEVYGPLLLEALEG 118

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAW 204
           FLFVVN +G V   TEN+ ++I+++R E+ G S+YN IH GDHARF   L+P    +  W
Sbjct: 119 FLFVVNAEGKVEHVTENVSNYIKFTRDEIFGNSIYNFIHLGDHARFTTSLMP----MIGW 174

Query: 205 TSDSGGQAGKRPSLTASTPNRTFNIRLL-------------------------ISSTHLT 239
            S+S          T +T +R+F++R L                         ISST L 
Sbjct: 175 GSES----------TTTTRSRSFSVRFLVKPPDDQDETVEEKQQRVNCYELMHISSTQLR 224

Query: 240 AGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGM 299
             +S +      DD G   ++ GP L+CVA RI   DK +S  IEQFT KLD SG IIG+
Sbjct: 225 DQVSVS------DDDG---ADSGPYLLCVASRISHRDKVISG-IEQFTTKLDTSGKIIGV 274

Query: 300 DTSGVSQTHTQYLNK 314
           D SGVS  ++Q++NK
Sbjct: 275 DASGVSAPYSQFINK 289

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91082795|ref|XP_967666.1| PREDICTED: similar to transcriptional intermediary factor 2 [Tribolium castaneum]

 Score =  274 bits (701), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 162/315 (51%), Positives = 204/315 (64%), Gaps = 59/315 (18%)

Query: 33  MSSLAVKPDKCAILQET-----VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLA 87
           MS+LA   +K     ET     +N+C NEKRRREQEN YIEELAELISA +FA+ MSSL+
Sbjct: 141 MSALATGVNKKRKKSETKPQAQINKCNNEKRRREQENIYIEELAELISA-NFAD-MSSLS 198

Query: 88  VKPDKCAILQETVNQIRNIKQQET---SSDAVQQGEVSSSKPTVITNEVLGPLLLEALEG 144
           VKPDKCAILQETVNQIR+IKQ+E+   SSD VQQGEVSSS+PT+++NEV GPLLLEALEG
Sbjct: 199 VKPDKCAILQETVNQIRSIKQRESASQSSDPVQQGEVSSSRPTILSNEVYGPLLLEALEG 258

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAW 204
           FLFVVN +G V   TEN+ ++I+++R E+ G S+YN IH GDHARF   L+P    +  W
Sbjct: 259 FLFVVNAEGKVEHVTENVSNYIKFTRDEIFGNSIYNFIHLGDHARFTTSLMP----MIGW 314

Query: 205 TSDSGGQAGKRPSLTASTPNRTFNIRLL-------------------------ISSTHLT 239
            S+S          T +T +R+F++R L                         ISST L 
Sbjct: 315 GSES----------TTTTRSRSFSVRFLVKPPDDQDETVEEKQQRVNCYELMHISSTQLR 364

Query: 240 AGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGM 299
             +S +      DD G   ++ GP L+CVA RI   DK +S  IEQFT KLD SG IIG+
Sbjct: 365 DQVSVS------DDDG---ADSGPYLLCVASRISHRDKVISG-IEQFTTKLDTSGKIIGV 414

Query: 300 DTSGVSQTHTQYLNK 314
           D SGVS  ++Q++NK
Sbjct: 415 DASGVSAPYSQFINK 429

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241244650|ref|XP_002402360.1| nuclear receptor coactivator, putative [Ixodes scapularis] gi|215496326|gb|EEC05966.1| nuclear receptor coactivator, putative [Ixodes scapularis]

 Score =  268 bits (684), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 150/291 (51%), Positives = 194/291 (66%), Gaps = 28/291 (9%)

Query: 52  QCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET 111
           +CLNEK RREQEN Y+EELAELISA+     M+SL+VKPDKCAILQETVNQIR IKQQE+
Sbjct: 22  KCLNEKHRREQENIYLEELAELISAS--ISDMNSLSVKPDKCAILQETVNQIRRIKQQES 79

Query: 112 S-SDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSR 170
             SD +QQ EVSSSKPT++ ++VLGPLLLEAL+GFLFVVN DG + F +ENI SFI+Y++
Sbjct: 80  GQSDDLQQSEVSSSKPTILGSDVLGPLLLEALDGFLFVVNTDGKIEFVSENITSFIKYTQ 139

Query: 171 QEVLGKSVYNLIHHGDHARFHNCLVPSS-HQVNAWTSDSGGQAGKRPSLTASTPNRTFNI 229
            ++ GKS+YN+IHHGDH RF + L+P S      WTSD    A   P    S  +R+F+ 
Sbjct: 140 DDLDGKSIYNIIHHGDHGRFSSNLLPMSIGNGFGWTSDLAPPALALPGGPNSK-SRSFHC 198

Query: 230 RLLIS--------------------STHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVA 269
           R L+                     + H++A      G+  + +  D  SE   CL+CVA
Sbjct: 199 RFLVKPPDAAEETVEEKQTRISQYENMHISAIFLPYPGD--KSEGTDSESEVQNCLVCVA 256

Query: 270 RRIPPTDK-QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACK 319
           RRIP  +K   S  +EQFT +LD SG I+ +DTSGVS T++QYLNK++  +
Sbjct: 257 RRIPANEKIPSSVGVEQFTTRLDLSGKILAVDTSGVSSTYSQYLNKSLVGR 307

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427796185|gb|JAA63544.1| Putative transcriptional intermediary factor 2, partial [Rhipicephalus pulchellus]

 Score =  253 bits (647), Expect = 8e-65,   Method: Compositional matrix adjust.
 Identities = 149/301 (49%), Positives = 195/301 (64%), Gaps = 25/301 (8%)

Query: 39  KPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQE 98
           KP K  +      +CLNEK RREQEN Y+EELAELISA+     M+SL+VKPDKCAILQE
Sbjct: 27  KPGKMMLPVLARKKCLNEKHRREQENVYLEELAELISAS--LSDMNSLSVKPDKCAILQE 84

Query: 99  TVNQIRNIKQQETSSDA----VQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGY 154
           TVNQIR IKQQE S       +QQ EVSSSKPT++ ++VLGPLLLEAL+GFLFVVN +G 
Sbjct: 85  TVNQIRRIKQQEASGGGGLGELQQSEVSSSKPTILGSDVLGPLLLEALDGFLFVVNTEGR 144

Query: 155 VNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVN--AWTSDSGGQA 212
           + F +EN+ SF++Y + E+ G S+YN++HHGDH RF + L+P S   N   WT ++GG++
Sbjct: 145 IEFVSENVSSFLQYGQGELDGTSIYNILHHGDHGRFSSNLLPMSLGANGLGWT-EAGGKS 203

Query: 213 GK-------RPSLTASTPNRTFNIRLLISSTHLTA------GLSRAGGENGQDDSGDVSS 259
                    RP   A     +  +  L  + H++A        S  GG    D+SG   S
Sbjct: 204 RSFQCRFLLRPP-DAEDKQNSARVAPLYENMHISAIFLPYPNGSGTGGAGSGDESG-ADS 261

Query: 260 EGGPCLMCVARRIPPTDK-QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVAC 318
           E   CL+CVARRIP  +K   S  +EQFT +LD  G I+ +DTSGVS T++QYLNK++  
Sbjct: 262 EVQNCLVCVARRIPANEKIPASVGVEQFTTRLDLVGKILAVDTSGVSSTYSQYLNKSLVG 321

Query: 319 K 319
           +
Sbjct: 322 R 322

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782966|ref|XP_394114.4| PREDICTED: hypothetical protein LOC410637 [Apis mellifera]

 Score =  252 bits (643), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 186/290 (64%), Gaps = 42/290 (14%)

Query: 47  QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI 106
           Q  +N+CLNEKRRR QEN +I+ELAELISA   +        K DKC ILQ TV+QIR+I
Sbjct: 43  QSQINKCLNEKRRRNQENLFIDELAELISATDMSSG------KTDKCQILQRTVDQIRHI 96

Query: 107 KQQETS-SDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSF 165
           ++QE S S AVQQGEVSSS P +++N+ +GP+LLEAL+GFLFVVN +G V + T+NI  +
Sbjct: 97  REQEGSNSHAVQQGEVSSSNPNILSNDQVGPILLEALDGFLFVVNTEGRVEYVTDNITQY 156

Query: 166 IRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNR 225
           I Y++ +VLGK +YN+IHHGDH  F   L+P   Q+  WT++   Q  +R        NR
Sbjct: 157 INYTKDDVLGKDIYNIIHHGDHNTFMPSLLP--MQL-GWTNE---QQPQR--------NR 202

Query: 226 TFNIRLLIS----------------STHLTAGLSRAGGENGQD--DSGDVSSE---GGPC 264
           TFN R L+                 S + +  +  A   N  D  +SGDVSSE    GPC
Sbjct: 203 TFNCRFLVKPPDDKEETMEEKQQRVSKYESMQICSALLPNNSDRLESGDVSSESSDNGPC 262

Query: 265 LMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNK 314
           +MCVARRIPP +K +  PIEQFT+KLD +G II +D   +S  +++YL+K
Sbjct: 263 VMCVARRIPPNEKPIGTPIEQFTVKLDTTGKIIAVDVIWLSSPYSEYLSK 312

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340723192|ref|XP_003399979.1| PREDICTED: hypothetical protein LOC100648067 [Bombus terrestris]

 Score =  251 bits (640), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 184/290 (63%), Gaps = 42/290 (14%)

Query: 47  QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI 106
           Q  +N+CLNEKRRR QEN +I+ELAELISA   +        K DKC ILQ TV+QIR+I
Sbjct: 37  QSQINKCLNEKRRRNQENLFIDELAELISATDMSSG------KTDKCQILQRTVDQIRHI 90

Query: 107 KQQETS-SDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSF 165
           ++QE S S AVQQGEVSSS P +++N+ +GP+LLEAL+GFLFVVN +G V + T+NI  +
Sbjct: 91  REQEGSNSHAVQQGEVSSSNPNILSNDQVGPILLEALDGFLFVVNTEGRVEYVTDNITQY 150

Query: 166 IRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNR 225
           I Y++ +VLGK +YN+IHHGDH  F   L+P      AW ++   Q  +R        NR
Sbjct: 151 INYTKDDVLGKDIYNIIHHGDHNTFMPSLLPIPL---AWMNE---QPPQR--------NR 196

Query: 226 TFNIRLLIS----------------STHLTAGLSRAGGENGQD--DSGDVSSE---GGPC 264
           TFN R L+                 S + +  +  A   N  D  +SGDVSSE    GPC
Sbjct: 197 TFNCRFLVKPPDDKEETMEEKQQRVSKYESMQICSALLPNNSDRLESGDVSSESSDNGPC 256

Query: 265 LMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNK 314
           +MCVARRIPP +K +  PIEQFT+KLD +G II +D   +S  +++YL+K
Sbjct: 257 VMCVARRIPPNEKPIGTPIEQFTVKLDTTGKIIAVDVIWLSSPYSEYLSK 306

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418715|ref|XP_003491944.1| PREDICTED: hypothetical protein LOC100747735 [Bombus impatiens]

 Score =  251 bits (640), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 184/290 (63%), Gaps = 42/290 (14%)

Query: 47  QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI 106
           Q  +N+CLNEKRRR QEN +I+ELAELISA   +        K DKC ILQ TV+QIR+I
Sbjct: 37  QSQINKCLNEKRRRNQENLFIDELAELISATDMSSG------KTDKCQILQRTVDQIRHI 90

Query: 107 KQQETS-SDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSF 165
           ++QE S S AVQQGEVSSS P +++N+ +GP+LLEAL+GFLFVVN +G V + T+NI  +
Sbjct: 91  REQEGSNSHAVQQGEVSSSNPNILSNDQVGPILLEALDGFLFVVNTEGRVEYVTDNITQY 150

Query: 166 IRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNR 225
           I Y++ +VLGK +YN+IHHGDH  F   L+P      AW ++   Q  +R        NR
Sbjct: 151 INYTKDDVLGKDIYNIIHHGDHNTFMPSLLPIPL---AWMNE---QPPQR--------NR 196

Query: 226 TFNIRLLIS----------------STHLTAGLSRAGGENGQD--DSGDVSSE---GGPC 264
           TFN R L+                 S + +  +  A   N  D  +SGDVSSE    GPC
Sbjct: 197 TFNCRFLVKPPDDKEETMEEKQQRVSKYESMQICSALLPNNSDRLESGDVSSESSDNGPC 256

Query: 265 LMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNK 314
           +MCVARRIPP +K +  PIEQFT+KLD +G II +D   +S  +++YL+K
Sbjct: 257 VMCVARRIPPNEKPIGTPIEQFTVKLDTTGKIIAVDVIWLSSPYSEYLSK 306

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328711465|ref|XP_001944363.2| PREDICTED: hypothetical protein LOC100161757 isoform 1 [Acyrthosiphon pisum]

 Score =  248 bits (632), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 146/305 (47%), Positives = 187/305 (61%), Gaps = 40/305 (13%)

Query: 47  QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI 106
           Q  +N+C NEKRRREQEN YIEELAELISA SFA+ M+SL+VKPDKCAILQETVNQ+R  
Sbjct: 23  QSQLNKCRNEKRRREQENIYIEELAELISA-SFAD-MNSLSVKPDKCAILQETVNQVR-A 79

Query: 107 KQQETSSD----------AVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVN 156
                SSD          AVQQGEVSSSKPT I+N  L PLLL AL+GFLFVVN DG + 
Sbjct: 80  GTHRLSSDQTESLISTEAAVQQGEVSSSKPTRISNTELAPLLLSALDGFLFVVNADGQIE 139

Query: 157 FCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF----HNCLVPSSHQVNAWTSDSGGQA 212
           F TENI+ F+ Y+++E+LGKSVYN+IHHGDH +F    +N L+     + +  S+     
Sbjct: 140 FVTENIQQFLHYNKEELLGKSVYNIIHHGDHTKFGVLLNNPLLIYDSPIGSLGSNVPTTP 199

Query: 213 GKRPSLTASTPN-------RTFNIRLLIS----------------STHLTAGLSRAGGEN 249
               S + S  N       + FN RLLI                 S + T  +S      
Sbjct: 200 LMEQSPSGSKGNNWNQRFTKKFNCRLLIKPPSDQDQTIEEKQTRVSQYETLQISSTKING 259

Query: 250 GQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHT 309
           G  D  D +      L+C+ARR+P  +K LS P+EQFT+KLD++G I+ +DT  VS+ + 
Sbjct: 260 GMVDDEDSTDGISQNLLCIARRVPYNEKHLSPPLEQFTIKLDQNGKILALDTKDVSEAYA 319

Query: 310 QYLNK 314
           Q++NK
Sbjct: 320 QHINK 324

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328711463|ref|XP_003244545.1| PREDICTED: hypothetical protein LOC100161757 isoform 2 [Acyrthosiphon pisum]

 Score =  247 bits (631), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 149/308 (48%), Positives = 191/308 (62%), Gaps = 46/308 (14%)

Query: 47  QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI 106
           Q  +N+C NEKRRREQEN YIEELAELISA SFA+ M+SL+VKPDKCAILQETVNQ+R  
Sbjct: 23  QSQLNKCRNEKRRREQENIYIEELAELISA-SFAD-MNSLSVKPDKCAILQETVNQVR-A 79

Query: 107 KQQETSSD----------AVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVN 156
                SSD          AVQQGEVSSSKPT I+N  L PLLL AL+GFLFVVN DG + 
Sbjct: 80  GTHRLSSDQTESLISTEAAVQQGEVSSSKPTRISNTELAPLLLSALDGFLFVVNADGQIE 139

Query: 157 FCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF----HNCLVPSSHQVNAWTSDSGGQA 212
           F TENI+ F+ Y+++E+LGKSVYN+IHHGDH +F    +N L+     + +  S+     
Sbjct: 140 FVTENIQQFLHYNKEELLGKSVYNIIHHGDHTKFGVLLNNPLLIYDSPIGSLGSNVPTTP 199

Query: 213 GKRPSLTASTPN-------RTFNIRLLIS----------------STHLTAGLSRA---G 246
               S + S  N       + FN RLLI                 S + T  +S     G
Sbjct: 200 LMEQSPSGSKGNNWNQRFTKKFNCRLLIKPPSDQDQTIEEKQTRVSQYETLQISSTKING 259

Query: 247 GENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQ 306
           G    +DS D  S+    L+C+ARR+P  +K LS P+EQFT+KLD++G I+ +DT  VS+
Sbjct: 260 GMVDDEDSTDGISQN---LLCIARRVPYNEKHLSPPLEQFTIKLDQNGKILALDTKDVSE 316

Query: 307 THTQYLNK 314
            + Q++NK
Sbjct: 317 AYAQHINK 324

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	383
UNIPROTKB|I3LNS5	1428	I3LNS5 "Uncharacterized protei	0.613	0.164	0.412	6.3e-42
UNIPROTKB|D4A3M5	1396	Ncoa2 "Nuclear receptor coacti	0.608	0.166	0.417	9.7e-42
UNIPROTKB|F1NDP9	395	NCOA2 "Uncharacterized protein	0.618	0.6	0.415	1.1e-41
RGD|620108	1465	Ncoa2 "nuclear receptor coacti	0.608	0.159	0.417	2.4e-41
UNIPROTKB|Q9WUI9	1465	Ncoa2 "Nuclear receptor coacti	0.608	0.159	0.417	2.4e-41
ZFIN|ZDB-GENE-010406-3	1505	ncoa2 "nuclear receptor coacti	0.608	0.154	0.420	1.4e-40
UNIPROTKB|E1BPY4	1465	NCOA2 "Uncharacterized protein	0.613	0.160	0.412	2.1e-40
UNIPROTKB|E2QXC0	1465	NCOA2 "Uncharacterized protein	0.613	0.160	0.412	2.1e-40
UNIPROTKB|E2QY25	1465	NCOA2 "Uncharacterized protein	0.613	0.160	0.412	2.1e-40
UNIPROTKB|F1NDQ6	1463	NCOA2 "Uncharacterized protein	0.618	0.161	0.415	2.8e-40

UNIPROTKB|I3LNS5 I3LNS5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 434 (157.8 bits), Expect = 6.3e-42, Sum P(3) = 6.3e-42
 Identities = 109/264 (41%), Positives = 152/264 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++ KSVY+++H GDH  F   L+P S  VN      G  +G+ P  ++     TFN R+
Sbjct:   153 ELMNKSVYSILHVGDHTEFVKNLLPKSI-VNG-----GSWSGEPPRRSS----HTFNCRM 202

Query:   232 LISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTDKQ 278
             L+              E  Q               +  EG     CL+CVARR+P  ++ 
Sbjct:   203 LVKPLPDPEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARRVPMKERP 262

Query:   279 LSAPIEQFTMKLDRSGTIIGMDTS 302
             +    E FT + D  G I  +DTS
Sbjct:   263 VLPSSESFTTRQDLQGKITSLDTS 286

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

UNIPROTKB|D4A3M5 Ncoa2 "Nuclear receptor coactivator 2" [Rattus norvegicus (taxid:10116)]

 Score = 437 (158.9 bits), Expect = 9.7e-42, Sum P(2) = 9.7e-42
 Identities = 111/266 (41%), Positives = 153/266 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVN--AWTSDSGGQAGKRPSLTASTPNRTFNI 229
             E++ KSVY+++H GDH  F   L+P S  VN  +WT    G+  +R S        TFN 
Sbjct:   153 ELMNKSVYSILHVGDHTEFVKNLLPKS-MVNGGSWT----GEPPRRNS-------HTFNC 200

Query:   230 RLLISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTD 276
             R+L+     +        E  Q               +  EG     CL+CVARR+P  +
Sbjct:   201 RMLVKPLPDSEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARRVPMKE 260

Query:   277 KQLSAPIEQFTMKLDRSGTIIGMDTS 302
             +      E FT + D  G I  +DTS
Sbjct:   261 RPALPSSESFTTRQDLQGKITSLDTS 286

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

UNIPROTKB|F1NDP9 NCOA2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 110/265 (41%), Positives = 154/265 (58%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    34 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 91

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVNP+G V F +EN+  ++RY+++
Sbjct:    92 NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNPEGNVVFVSENVTQYLRYNQE 151

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++  S+Y+++H GDH  F   L+P S  VN      G  +G  P   + T N    ++ 
Sbjct:   152 ELMNTSIYSILHVGDHNEFVKILLPKS-LVNG-----GSWSGDTPRRNSHTFNCRMLVKP 205

Query:   232 LISS--------THL---TAGLSRAGGENG-QDDSGDVSSEGGPCLMCVARRIPPTDKQL 279
             L  S         H    T         N  ++D  D+ S    CL+CVARR P  ++ L
Sbjct:   206 LADSEEGHDNQEAHQKYETMQCFAVSQPNSFKEDGEDLQS----CLICVARRAPMKERPL 261

Query:   280 SAPIEQFTMKLDRSGTIIGMDTSGV 304
                 E FT + D  G I  +DTS +
Sbjct:   262 LPSSESFTTRQDLQGKITSLDTSSM 286

GO:0004871 "signal transducer activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IEA

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

RGD|620108 Ncoa2 "nuclear receptor coactivator 2" [Rattus norvegicus (taxid:10116)]

 Score = 434 (157.8 bits), Expect = 2.4e-41, Sum P(2) = 2.4e-41
 Identities = 111/266 (41%), Positives = 153/266 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVN--AWTSDSGGQAGKRPSLTASTPNRTFNI 229
             E++ KSVY+++H GDH  F   L+P S  VN  +WT    G+  +R S        TFN 
Sbjct:   153 ELMNKSVYSILHVGDHTEFVKNLLPKS-MVNGGSWT----GEPPRRNS-------HTFNC 200

Query:   230 RLLISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTD 276
             R+L+     +        E  Q               +  EG     CL+CVARR+P  +
Sbjct:   201 RMLVKPLPDSEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDKQSCLICVARRVPMKE 260

Query:   277 KQLSAPIEQFTMKLDRSGTIIGMDTS 302
             +      E FT + D  G I  +DTS
Sbjct:   261 RPALPSSESFTTRQDLQGKITFLDTS 286

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0003682 "chromatin binding" evidence=ISO

GO:0003713 "transcription coactivator activity" evidence=IEA;ISO

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005102 "receptor binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA;ISO;IDA

GO:0005737 "cytoplasm" evidence=ISO

GO:0005791 "rough endoplasmic reticulum" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0005874 "microtubule" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISO

GO:0008584 "male gonad development" evidence=IEP

GO:0014069 "postsynaptic density" evidence=IDA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=ISO;IPI

GO:0021549 "cerebellum development" evidence=IEP

GO:0030165 "PDZ domain binding" evidence=IPI

GO:0030331 "estrogen receptor binding" evidence=IPI

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=ISO

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=ISO

GO:0030425 "dendrite" evidence=IDA

GO:0032403 "protein complex binding" evidence=IPI

GO:0033142 "progesterone receptor binding" evidence=IPI

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0035259 "glucocorticoid receptor binding" evidence=IPI

GO:0042974 "retinoic acid receptor binding" evidence=IPI

GO:0043025 "neuronal cell body" evidence=IDA

GO:0043197 "dendritic spine" evidence=IDA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISO

GO:0045925 "positive regulation of female receptivity" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO;IMP

GO:0046965 "retinoid X receptor binding" evidence=IPI

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0048786 "presynaptic active zone" evidence=IDA

GO:0070182 "DNA polymerase binding" evidence=IPI

GO:2000324 "positive regulation of glucocorticoid receptor signaling pathway" evidence=IMP

UNIPROTKB|Q9WUI9 Ncoa2 "Nuclear receptor coactivator 2" [Rattus norvegicus (taxid:10116)]

 Score = 434 (157.8 bits), Expect = 2.4e-41, Sum P(2) = 2.4e-41
 Identities = 111/266 (41%), Positives = 153/266 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVN--AWTSDSGGQAGKRPSLTASTPNRTFNI 229
             E++ KSVY+++H GDH  F   L+P S  VN  +WT    G+  +R S        TFN 
Sbjct:   153 ELMNKSVYSILHVGDHTEFVKNLLPKS-MVNGGSWT----GEPPRRNS-------HTFNC 200

Query:   230 RLLISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTD 276
             R+L+     +        E  Q               +  EG     CL+CVARR+P  +
Sbjct:   201 RMLVKPLPDSEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDKQSCLICVARRVPMKE 260

Query:   277 KQLSAPIEQFTMKLDRSGTIIGMDTS 302
             +      E FT + D  G I  +DTS
Sbjct:   261 RPALPSSESFTTRQDLQGKITFLDTS 286

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

ZFIN|ZDB-GENE-010406-3 ncoa2 "nuclear receptor coactivator 2" [Danio rerio (taxid:7955)]

 Score = 445 (161.7 bits), Expect = 1.4e-40, P = 1.4e-40
 Identities = 111/264 (42%), Positives = 160/264 (60%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR RE E+ YIEELAELI A +F + + +  VKPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    36 EKRNREHESKYIEELAELIFA-NFND-IDNFNVKPDKCAILKETVKQIRQIKEQEKAAAA 93

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVN +G + F +EN+  ++RY+++
Sbjct:    94 NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNMEGNIVFVSENVTQYLRYNQE 153

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA--WTSDSGGQAGKRPSLTASTPNRTFNI 229
             E++  SVY+++H GDHA F   L+P SH VN   W+S++     +R S        TFN 
Sbjct:   154 ELMNTSVYSILHVGDHAEFIKNLLPKSH-VNGVPWSSENP----RRNS-------HTFNC 201

Query:   230 RLLI---SSTHLTAGL-SRAGGENGQ----DDSGDVSSEGGP---CLMCVARRIPPTDKQ 278
             R+L+   S    T    ++   E  Q     +   +  EG     CL+CVARR+P  ++ 
Sbjct:   202 RMLVNPHSEAEETQDHEAQQKYETMQCFAVSEPKSIKEEGEDFQSCLICVARRVPMKERP 261

Query:   279 LSAPIEQFTMKLDRSGTIIGMDTS 302
             +    E FT + D  G I  +DTS
Sbjct:   262 MLPTQESFTTRQDLQGKITSLDTS 285

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0007165 "signal transduction" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0009790 "embryo development" evidence=IMP

GO:0030099 "myeloid cell differentiation" evidence=IMP

GO:0030851 "granulocyte differentiation" evidence=IMP

GO:0060215 "primitive hemopoiesis" evidence=IMP

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=ISS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E1BPY4 NCOA2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 434 (157.8 bits), Expect = 2.1e-40, Sum P(2) = 2.1e-40
 Identities = 109/264 (41%), Positives = 151/264 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++ KSVY+++H GDH  F   L+P S  VN      G  +G+ P   +     TFN R+
Sbjct:   153 ELMNKSVYSILHVGDHTEFVKNLLPKSI-VNG-----GAWSGEPPRRNS----HTFNCRM 202

Query:   232 LISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTDKQ 278
             L+     +        E  Q               +  EG     CL+CVARR+P  ++ 
Sbjct:   203 LVKPLPESEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARRVPMKERP 262

Query:   279 LSAPIEQFTMKLDRSGTIIGMDTS 302
                  E FT + D  G I  +DTS
Sbjct:   263 ALPSSESFTTRQDLQGKITSLDTS 286

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=IEA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

UNIPROTKB|E2QXC0 NCOA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 434 (157.8 bits), Expect = 2.1e-40, Sum P(2) = 2.1e-40
 Identities = 109/264 (41%), Positives = 151/264 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++ KSVY ++H GDH  F   L+P S  VN      G  +G+ P   +     TFN R+
Sbjct:   153 ELMNKSVYGILHVGDHTEFVKNLLPKSI-VNG-----GSWSGEPPRRNS----HTFNCRM 202

Query:   232 LISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTDKQ 278
             L+     +        E  Q               +  EG     CL+CVARR+P  ++ 
Sbjct:   203 LVKPLPDSEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARRVPMKERP 262

Query:   279 LSAPIEQFTMKLDRSGTIIGMDTS 302
             +    E FT + D  G I  +DTS
Sbjct:   263 VLPSSESFTTRQDLQGKITSLDTS 286

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

UNIPROTKB|E2QY25 NCOA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 434 (157.8 bits), Expect = 2.1e-40, Sum P(2) = 2.1e-40
 Identities = 109/264 (41%), Positives = 151/264 (57%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    35 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 92

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+   VI  + LGP++LEAL+GF FVVN +G V F +EN+  ++RY+++
Sbjct:    93 NIDEVQKSDVSSTGQGVIDKDALGPMMLEALDGFFFVVNLEGNVVFVSENVTQYLRYNQE 152

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++ KSVY ++H GDH  F   L+P S  VN      G  +G+ P   +     TFN R+
Sbjct:   153 ELMNKSVYGILHVGDHTEFVKNLLPKSI-VNG-----GSWSGEPPRRNS----HTFNCRM 202

Query:   232 LISSTHLTAGLSRAGGENGQ----------DDSGDVSSEGGP---CLMCVARRIPPTDKQ 278
             L+     +        E  Q               +  EG     CL+CVARR+P  ++ 
Sbjct:   203 LVKPLPDSEEEGHDNQEAHQKYETMQCFAVSQPKSIKEEGEDLQSCLICVARRVPMKERP 262

Query:   279 LSAPIEQFTMKLDRSGTIIGMDTS 302
             +    E FT + D  G I  +DTS
Sbjct:   263 VLPSSESFTTRQDLQGKITSLDTS 286

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=IEA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

UNIPROTKB|F1NDQ6 NCOA2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 442 (160.7 bits), Expect = 2.8e-40, P = 2.8e-40
 Identities = 110/265 (41%), Positives = 154/265 (58%)

Query:    56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSS-- 113
             EKR REQEN YIEELAELI A +F + + +   KPDKCAIL+ETV QIR IK+QE ++  
Sbjct:    34 EKRNREQENKYIEELAELIFA-NFND-IDNFNFKPDKCAILKETVKQIRQIKEQEKAAAA 91

Query:   114 --DAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQ 171
               D VQ+ +VSS+  +VI  + LGP++LEAL+GF FVVNP+G V F +EN+  ++RY+++
Sbjct:    92 NEDEVQKADVSSTGQSVIDKDALGPMMLEALDGFFFVVNPEGNVVFVSENVTQYLRYNQE 151

Query:   172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
             E++  S+Y+++H GDH  F   L+P S  VN      G  +G  P   + T N    ++ 
Sbjct:   152 ELMNTSIYSILHVGDHNEFVKILLPKS-LVNG-----GSWSGDTPRRNSHTFNCRMLVKP 205

Query:   232 LISS--------THL---TAGLSRAGGENG-QDDSGDVSSEGGPCLMCVARRIPPTDKQL 279
             L  S         H    T         N  ++D  D+ S    CL+CVARR P  ++ L
Sbjct:   206 LADSEEGHDNQEAHQKYETMQCFAVSQPNSFKEDGEDLQS----CLICVARRAPMKERPL 261

Query:   280 SAPIEQFTMKLDRSGTIIGMDTSGV 304
                 E FT + D  G I  +DTS +
Sbjct:   262 LPSSESFTTRQDLQGKITSLDTSSM 286

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0035257 "nuclear hormone receptor binding" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016922 "ligand-dependent nuclear receptor binding" evidence=IEA

GO:0030375 "thyroid hormone receptor coactivator activity" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

---

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!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	383
smart00091	67	smart00091, PAS, PAS domain	7e-10
cd00130	103	cd00130, PAS, PAS domain; PAS motifs appear in arc	3e-08
smart00353	53	smart00353, HLH, helix loop helix domain	1e-07
pfam00989	113	pfam00989, PAS, PAS fold	1e-07
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-07
smart00353	53	smart00353, HLH, helix loop helix domain	2e-05
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-05
pfam13426	101	pfam13426, PAS_9, PAS domain	2e-04

>gnl|CDD|214512 smart00091, PAS, PAS domain

 Score = 54.3 bits (131), Expect = 7e-10
 Identities = 19/58 (32%), Positives = 32/58 (55%)

Query: 137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
            +LE+L   +FV++ DG + +     +  + YS +E++GKS+  LIH  D  R    L
Sbjct: 5   AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEAL 62

PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. Length = 67

>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

 Score = 51.1 bits (122), Expect = 3e-08
 Identities = 13/47 (27%), Positives = 25/47 (53%)

Query: 144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF 190
             + V++ DG + +     +  + YS +E++GKS+ +LIH  D    
Sbjct: 3   DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREEL 49

Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. Length = 103

>gnl|CDD|197674 smart00353, HLH, helix loop helix domain

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 54  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
             E+RRR + N   +EL  L+      +       K  K  IL+  +  I++++++ 
Sbjct: 2   ARERRRRRKINEAFDELRSLLPTLPKNK-------KLSKAEILRLAIEYIKSLQEEL 51

Length = 53

>gnl|CDD|216228 pfam00989, PAS, PAS fold

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
           +LE+L   +FVV+ DG + +     +  +  SR+EV+GKS+ +LI   D A     L
Sbjct: 6   ILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEDDDAEVAELL 62

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 = 113

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 7/55 (12%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           E+RRRE+ N+  +EL  L+     ++       K  K  IL++ V+ I+++++  
Sbjct: 12  ERRRRERINDAFDELRSLLPTLPPSK-------KLSKAEILRKAVDYIKSLQELL 59

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60

>gnl|CDD|197674 smart00353, HLH, helix loop helix domain

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 7/48 (14%)

Query: 4  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVN 51
            E+RRR + N   +EL  L+      +       K  K  IL+  + 
Sbjct: 2  ARERRRRRKINEAFDELRSLLPTLPKNK-------KLSKAEILRLAIE 42

Length = 53

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)

Query: 1  AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRR 60
          A  L E+RRRE+ N+  +EL  L+     ++       K  K  IL++ V+   + +   
Sbjct: 7  AHNLRERRRRERINDAFDELRSLLPTLPPSK-------KLSKAEILRKAVDYIKSLQELL 59

Query: 61 E 61
          +
Sbjct: 60 Q 60

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60

>gnl|CDD|222120 pfam13426, PAS_9, PAS domain

 Score = 39.7 bits (93), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 27/49 (55%)

Query: 146 LFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
           + V++PDG + +  +     + Y+R+E+LGKS+ +L   GD       L
Sbjct: 1   ILVLDPDGRIVYANDAALRLLGYTREELLGKSIRDLFGPGDDEEAVARL 49

Length = 101

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	383
KOG3558|consensus	768		100.0
KOG3559|consensus	598		100.0
KOG3561|consensus	803		100.0
KOG3560|consensus	712		100.0
KOG3753|consensus	1114		99.9
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	99.71
KOG3561|consensus	803		98.97
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.93
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	98.89
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	98.81
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	98.75
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	98.66
smart00353	53	HLH helix loop helix domain.	98.61
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	98.54
KOG4304|consensus	250		98.53
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	98.47
PRK13560	807	hypothetical protein; Provisional	98.27
KOG1318|consensus	411		98.23
PRK13560	807	hypothetical protein; Provisional	98.1
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.02
PRK09776	1092	putative diguanylate cyclase; Provisional	97.9
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	97.87
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	97.64
KOG3558|consensus	768		97.63
PRK09776	1092	putative diguanylate cyclase; Provisional	97.54
KOG1319|consensus	229		97.28
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	97.24
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	97.21
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	97.17
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.02
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	97.02
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	96.55
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	96.37
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	96.35
PRK13557	540	histidine kinase; Provisional	96.31
PRK11091	779	aerobic respiration control sensor protein ArcB; P	96.21
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	96.2
PRK10060	663	RNase II stability modulator; Provisional	96.08
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	95.63
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	95.15
PRK13559	361	hypothetical protein; Provisional	95.09
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	94.97
KOG3753|consensus	1114		94.94
smart00353	53	HLH helix loop helix domain.	94.92
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	94.84
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	94.83
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	94.49
KOG3559|consensus	598		94.35
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	94.03
KOG4029|consensus	228		93.8
KOG0561|consensus	373		93.72
KOG1318|consensus	411		93.68
KOG2483|consensus	232		92.97
PRK13558	665	bacterio-opsin activator; Provisional	92.91
PRK11360	607	sensory histidine kinase AtoS; Provisional	91.91
KOG3960|consensus	284		91.89
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	91.73
KOG2588|consensus	953		91.5
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	91.33
PLN03217	93	transcription factor ATBS1; Provisional	90.79
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	90.41
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	89.45
PF12860	115	PAS_7: PAS fold	88.96
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	85.71
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	85.7
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	84.92
PRK11086	542	sensory histidine kinase DcuS; Provisional	84.67
PRK13557	540	histidine kinase; Provisional	84.33
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	83.58
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	83.38
PRK10060	663	RNase II stability modulator; Provisional	82.86
KOG3560|consensus	712		80.78

>KOG3558|consensus

Probab=100.00  E-value=1.7e-59  Score=477.83  Aligned_cols=289  Identities=19%  Similarity=0.233  Sum_probs=221.4

Q ss_pred             hhhhhhhhhhHH-HHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCCCcccccCccCC
Q psy7682          45 ILQETVNQCLNE-KRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSS  123 (383)
Q Consensus        45 ~~~~~~~~~~~e-k~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~~~~~~~~~~~~  123 (383)
                      +...+++++|.+ |.||.|||.+|+|||.+||+   +.   ++..+|||++|||+||+|||.++..+....+    +.+ 
T Consensus        42 ~~~~rkEkSRdAARsRRsKEn~~FyeLa~~lPl---p~---aisshLDkaSimRLtISyLRlrk~a~~g~~p----~~e-  110 (768)
T KOG3558|consen   42 LQELRKEKSRDAARSRRSKENEEFYELAKLLPL---PA---AISSHLDKASIMRLTISYLRLRKFAGAGDPP----RAE-  110 (768)
T ss_pred             HHHHHhhhhhhhhhhhcccchHHHHHHHHhCCC---cc---hhhhhhhhHHHHHHHHHHHHHHHHhhcCCcc----ccc-
Confidence            444467888885 55999999999999999999   65   4568999999999999999987776553221    111 


Q ss_pred             CCCCcCCccchhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCC
Q psy7682         124 SKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNA  203 (383)
Q Consensus       124 ~~P~~~~~~~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~  203 (383)
                       .+.......++.+||++||||++||+.||+|+|+||+|..|||++|.||+|.|||||+||+||+++.++|......+..
T Consensus       111 -~~~~~~e~~l~~~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~~p~~  189 (768)
T KOG3558|consen  111 -GEPENLEQHLGDHILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLTTPEV  189 (768)
T ss_pred             -CCCcchhhhhhhhHHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhccccCCCcc
Confidence             1111113357899999999999999999999999999999999999999999999999999999999999877521111


Q ss_pred             CCCCCCCCCCCCCCCCCCCCceeEEEEEEEcCC--------------eeeeee-ecCCCCCC-CCCCCCCCCCCCceEEE
Q psy7682         204 WTSDSGGQAGKRPSLTASTPNRTFNIRLLISST--------------HLTAGL-SRAGGENG-QDDSGDVSSEGGPCLMC  267 (383)
Q Consensus       204 ~~s~s~~~~g~~~~~~~~~~~rsF~cRmk~~~~--------------~i~~~~-~~~~~~~g-~d~~~~~~~~~~~~LVa  267 (383)
                      .       ..     .....+|+||+|||+..+              +++|+. .+.....+ ...-. ....+..|||+
T Consensus       190 ~-------es-----~~~~teRsFflRMKsTLT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~-g~~~Pl~~lV~  256 (768)
T KOG3558|consen  190 K-------ES-----TDTSTERSFFLRMKSTLTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLC-GYKEPLLGLVA  256 (768)
T ss_pred             c-------cc-----ccCccceeEEEEeeeeeccCCceeeeeccceeEEEEeeeeeeccCCCCCCccc-Cccccchheee
Confidence            0       01     134568999999998432              234432 12111000 00000 01133789999


Q ss_pred             EEeecCCCCc-ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhh
Q psy7682         268 VARRIPPTDK-QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSI  346 (383)
Q Consensus       268 v~r~ip~~~~-~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~  346 (383)
                      +|.++|++.. ++.-.+.+|+|||++||||+|||+|+  +.++||.|+||+|+|+|+||   |. +|.++     +.++.
T Consensus       257 ~a~alp~ps~~EipL~~~~FvtRhs~DmkityCedRi--sdlm~y~PeeLvGrS~Ye~~---Ha-~Ds~~-----v~KSh  325 (768)
T KOG3558|consen  257 LAEALPPPSYTEIPLDCHMFVTRHSLDMKITYCEDRI--SDLMDYEPEELVGRSCYEFV---HA-LDSDR-----VRKSH  325 (768)
T ss_pred             eeccCCCCcccccccCCceeEEeeecceeEEEEchhH--HHHhcCCHHHhhchhHHHhh---hH-hhhhH-----HHHHH
Confidence            9999999875 34444579999999999999999999  99999999999999999998   34 55544     35566


Q ss_pred             hcccceeecccceecccCCcccc
Q psy7682         347 CTDYALVQTDTCMYRSSPSCFGL  369 (383)
Q Consensus       347 ~~~~~~~q~~t~~yR~~~~~~~~  369 (383)
                      .+|+.|||+.|+|||+++++||+
T Consensus       326 ~dL~~KGQv~TgyYR~lak~GGy  348 (768)
T KOG3558|consen  326 HDLLTKGQVVTGYYRLLAKNGGY  348 (768)
T ss_pred             HHHHhcCccchhHHHHHHhcCCe
Confidence            78999999999999999999986

>KOG3559|consensus

Probab=100.00  E-value=1.2e-46  Score=363.63  Aligned_cols=283  Identities=24%  Similarity=0.303  Sum_probs=217.5

Q ss_pred             hHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCCCcccccCccCCCCCCcCCccc
Q psy7682          54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSKPTVITNEV  133 (383)
Q Consensus        54 ~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~~~~~~~~~~~~~~P~~~~~~~  133 (383)
                      +++|.||++||.+|.||+.+||+   +.   ++.+++||++|+|+|.+|||+...+.... ...+|..++..|-.-.+.+
T Consensus         7 naA~tRRekEN~EF~eLAklLPL---a~---AItsQlDKasiiRLtTsYlKmr~vFPeGL-Geawg~~S~a~~~~g~~~e   79 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPL---AS---AITSQLDKASIIRLTTSYLKMRNVFPEGL-GEAWGASSRADPLDGVDKE   79 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccc---hh---hhhhccchhhhhhHHHHHHHHHHhccccc-chhccCCCccccccchHHH
Confidence            45788999999999999999999   43   45689999999999999999877664311 1112222334444445678


Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAG  213 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g  213 (383)
                      |+..+|+.+||||+||+.||+|+|+||+++-+||.+|.||.|.++||||||.|++++...|+...+              
T Consensus        80 lgshlLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~H--------------  145 (598)
T KOG3559|consen   80 LGSHLLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQH--------------  145 (598)
T ss_pred             HHHhHHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHhhhhh--------------
Confidence            999999999999999999999999999999999999999999999999999999999999986542              


Q ss_pred             CCCCCCCCCCceeEEEEEEEcC----C--------eeee-eeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc-cc
Q psy7682         214 KRPSLTASTPNRTFNIRLLISS----T--------HLTA-GLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK-QL  279 (383)
Q Consensus       214 ~~~~~~~~~~~rsF~cRmk~~~----~--------~i~~-~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~-~i  279 (383)
                          .....-+|+||.||+|-.    .        .++| +|.+.... ..+.++..+......|||+|.++|.+.. +|
T Consensus       146 ----~qeyeIErsfflrmkCvlakrnaglt~sg~kvihcSgylKir~y-~~~m~p~dscyqn~glvAvG~slP~saitei  220 (598)
T KOG3559|consen  146 ----LQEYEIERSFFLRMKCVLAKRNAGLTCSGYKVIHCSGYLKIRQY-ELDMSPNDSCYQNVGLVAVGHSLPPSAITEI  220 (598)
T ss_pred             ----hhhhhhhhhhhhhhhhhheeccccccccCcceEeecCcceEEEE-eeccCCccchhheeeeEEecCCCCcccceEE
Confidence                012456899999999832    1        3555 23321110 0111111223567889999999988764 45


Q ss_pred             CCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhhhcccceeecccce
Q psy7682         280 SAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCM  359 (383)
Q Consensus       280 ~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~  359 (383)
                      ..+.++|+.|-++|++++|.|.|+  .+++||.|+||+|+++|+++   |. -|..++.-.   |  ..++.|||+.|.+
T Consensus       221 kl~sNmFmfraslDlkliF~D~rv--~qltgYepqdliektLY~~i---h~-~D~~~lr~~---H--~~ll~kGqvtTkY  289 (598)
T KOG3559|consen  221 KLHSNMFMFRASLDLKLIFLDSRV--HQLTGYEPQDLIEKTLYHHI---HG-CDSFHLRCA---H--HLLLVKGQVTTKY  289 (598)
T ss_pred             EeccceEEEEeecceEEEeehhhH--HHhhCCCchhhhhHHHHHHh---hh-hhHHHHHHH---H--HHHHhccccccHH
Confidence            556699999999999999999999  89999999999999987665   44 455443211   1  1467899999999


Q ss_pred             ecccCCccccccCCcceEEEE
Q psy7682         360 YRSSPSCFGLQGASRTSLWQR  380 (383)
Q Consensus       360 yR~~~~~~~~~~~~~~~~~~~  380 (383)
                      |||+.+.+|       |+||.
T Consensus       290 YR~l~k~gg-------wvwvq  303 (598)
T KOG3559|consen  290 YRFLLKQGG-------WVWVQ  303 (598)
T ss_pred             HHHHHcCCc-------eEEEE
Confidence            999988765       88874

>KOG3561|consensus

Probab=100.00  E-value=5.3e-44  Score=377.19  Aligned_cols=311  Identities=26%  Similarity=0.392  Sum_probs=219.6

Q ss_pred             hhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCCCcccccCccCCCC
Q psy7682          46 LQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSK  125 (383)
Q Consensus        46 ~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~~~~~~~~~~~~~~  125 (383)
                      ..++++|+++|||||||+|.+|+||++|||.+      +++.+|+||++|||+||.+||.++.++.....    ...+|+
T Consensus        18 r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~------~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~~----~~~d~K   87 (803)
T KOG3561|consen   18 RKKRENRSEIEKRRRDQMNKYIEELSEMVPTN------ASLSRKPDKLTVLRMAVDHLRLIKEQESENSS----IDQDYK   87 (803)
T ss_pred             hhccccchhHHHHHHHHHHHHHHHHHHhhhcc------hhcccCchHHHHHHHHHHHHHHHhhhhccccc----cccccc
Confidence            34488999999999999999999999999993      35779999999999999999999987521111    125799


Q ss_pred             CCcCCccchhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCC-----
Q psy7682         126 PTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQ-----  200 (383)
Q Consensus       126 P~~~~~~~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~-----  200 (383)
                      |+++++++++++||||+|||+|||++||+|+|||+||+.+|||.|+||+|+|||+|+||.|.+.++.++.+....     
T Consensus        88 pSflS~~eL~~LmLeAlDGF~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql~~r~~e~~f~~  167 (803)
T KOG3561|consen   88 PSFLSNDELTHLILEALDGFLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQLSPRSNEHTFNC  167 (803)
T ss_pred             ccccchHHHHHHHHHHhcCeEEEEecCceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcccccccccccccccch
Confidence            999999999999999999999999999999999999999999999999999999999999999999999854311     


Q ss_pred             -CCCCCCCC----------------------------------CCCCCCC--------------------CCCCCCCCce
Q psy7682         201 -VNAWTSDS----------------------------------GGQAGKR--------------------PSLTASTPNR  225 (383)
Q Consensus       201 -~~~~~s~s----------------------------------~~~~g~~--------------------~~~~~~~~~r  225 (383)
                       .+..+.+.                                  ....+.+                    ......+.+|
T Consensus       168 r~l~~~~~~~~~E~~~~~~~~~~~~~~~~~s~e~~~~~i~~~~~~~~~~~~~~~~~r~~~p~~~~~~~~id~~~~~~aRr  247 (803)
T KOG3561|consen  168 RLLDGKTGPPPEEAVKFYGNFQCFTNSQPKSIEGFQSTICRQRRKAEGDRVCFGVSRLTTPQLIGEMCIIDTRLCEGARR  247 (803)
T ss_pred             hhhccCCCCchHHhhhhhhhcccccccCccccccccccceeeccccccCccccccccccchhhccceecccccccccccc
Confidence             11111111                                  0000110                    0011233489


Q ss_pred             eEEEEEEEcCC--------------------------------eeeee-eec-CC-C-----------CCCCCCC---CC
Q psy7682         226 TFNIRLLISST--------------------------------HLTAG-LSR-AG-G-----------ENGQDDS---GD  256 (383)
Q Consensus       226 sF~cRmk~~~~--------------------------------~i~~~-~~~-~~-~-----------~~g~d~~---~~  256 (383)
                      +|+|||++...                                .++|+ |.. +. +           -.....|   ..
T Consensus       248 sfe~r~r~~~~r~~p~~gy~~~~~~g~~~~~~~~~~~~~~~y~~~h~~g~~~s~~~~c~~~~~t~~~q~~~~~~d~~i~~  327 (803)
T KOG3561|consen  248 SFECRMRFCDHRAPPIIGYEPFEVLGTSRNYDYYHKDDLPNYRVIHCTGYIKSAGPSCKYRFLTKGQQWIWLPQDDYISY  327 (803)
T ss_pred             chhhhhhhccccCCccccccceeeccccccccccccCcccceEEEeeeeeEeccCCcceeccccccccccccCccccccc
Confidence            99999997421                                12332 211 11 0           0001111   11


Q ss_pred             CCCCCCceEEEEEeecCCCC-------cc--c--------CCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCC
Q psy7682         257 VSSEGGPCLMCVARRIPPTD-------KQ--L--------SAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACK  319 (383)
Q Consensus       257 ~~~~~~~~LVav~r~ip~~~-------~~--i--------~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~  319 (383)
                      ....+..|+|++++......       .+  +        ......|.+||..||+|++||.++  ..++||.+.++.|+
T Consensus       328 ~~~~s~p~~v~~~~~~vs~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~sr~~~~g~~~~~dqr~--~~i~~~~~~~~~g~  405 (803)
T KOG3561|consen  328 HQWNSKPCLVAIGRLVVSYAEVRVPSRADMSIEGPRQQPSSPQSSEFISRSSSDGSFTFVDQRA--SAILGYQPQELLGR  405 (803)
T ss_pred             cccCCCcceeEecccccchhhccCcccccCccccccccccCcccchhhcccCcCCceecccccc--ccccccCchhhcCc
Confidence            23345669999988765332       11  1        112378999999999999999998  89999999999999


Q ss_pred             CccceecCCCCchhHHHHHHHHHHhhhhcccceeecccceecccCCccccccCCcce
Q psy7682         320 TSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTS  376 (383)
Q Consensus       320 S~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~~~~~~~~~~~~~~~  376 (383)
                      |.|.|. |++++....-.+ +.+.      ....|..+..||+..+++.+.-.-.+|
T Consensus       406 ss~~s~-h~~d~~~~~~s~-~~~~------~~s~~~~~~~yr~~~~n~~~~~~~~~~  454 (803)
T KOG3561|consen  406 SSYESS-HPADSSPLSESL-KQVQ------ALSEQRSTLLYRFRSKNGSSIPNKSSA  454 (803)
T ss_pred             cccccc-CccccchhhchH-HHHH------HhcccccccccccccCCCCcccccccc
Confidence            999998 444423321111 1111      124567788888888887665444433

>KOG3560|consensus

Probab=100.00  E-value=9.5e-38  Score=310.69  Aligned_cols=276  Identities=21%  Similarity=0.286  Sum_probs=195.5

Q ss_pred             hhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCC--CcccccC
Q psy7682          42 KCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETS--SDAVQQG  119 (383)
Q Consensus        42 ~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~--~~~~~~~  119 (383)
                      |-+-+-+.+.+++.+||.||++|.+++-||+|||.   +.+|   .+||||+||||++|+|||....++..  .+..+.+
T Consensus        19 k~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPf---pqdi---isKLDkLSVLRLSVSyLr~KSfFqvvl~~s~~~~~   92 (712)
T KOG3560|consen   19 KQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPF---PQDI---ISKLDKLSVLRLSVSYLRVKSFFQVVLHQSSRQPA   92 (712)
T ss_pred             ccCCCccccccCCcchhHHHHhhhHHHHHHHhcCC---CHHH---HhhhhhhhhhhhhHHHHHHHHHHHHHHhcCccccC
Confidence            33444444789999999999999999999999999   5544   58999999999999999986665431  0111111


Q ss_pred             cc-C---CCCCCc-CCccchhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         120 EV-S---SSKPTV-ITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       120 ~~-~---~~~P~~-~~~~~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .. .   +..|-- -..-..++++|++++||++||+++|.|.|+|.+|.+|||+.|.|++.+|+||+||.+|+++|.++|
T Consensus        93 gg~~s~~a~~~yr~gl~llege~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQL  172 (712)
T KOG3560|consen   93 GGPPSPHASCPYRNGLALLEGELLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQL  172 (712)
T ss_pred             CCCCCccccchhhccccccchHHHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHH
Confidence            10 0   001000 001234789999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCC-----CCCCCCCCC-------C-CCCCCCCCCCceeEEEEEEEcCCeeeeeeecC-----CC-CCCCCC--
Q psy7682         195 VPSSHQVNA-----WTSDSGGQA-------G-KRPSLTASTPNRTFNIRLLISSTHLTAGLSRA-----GG-ENGQDD--  253 (383)
Q Consensus       195 ~~~~~~~~~-----~~s~s~~~~-------g-~~~~~~~~~~~rsF~cRmk~~~~~i~~~~~~~-----~~-~~g~d~--  253 (383)
                      ......+-.     .+-+.++..       | ..++..+.-.+|+|+||+||-... +|+++..     .+ ..|+..  
T Consensus       173 hwa~~ppq~~~s~q~~~e~~~~~~~~~~~~~d~~ppens~yleRcficR~RCLLDn-TsGFLamdfqGklk~LhGqkkk~  251 (712)
T KOG3560|consen  173 HWAMDPPQVVFSQQPPLETGDDAILRAQEWGDGTPPENSAYLERCFICRFRCLLDN-TSGFLAMDFQGKLKFLHGQKKKA  251 (712)
T ss_pred             hhccCCchhhccCCCccccccccceeeeccCccCCcccchHHhhhheeeEEEeecC-CcceeeeecccceeeecCCcccC
Confidence            755321100     000000000       0 112223455789999999994321 1222110     00 011100  


Q ss_pred             CCCCCCCCCceEEEEEeecCCCC-cccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         254 SGDVSSEGGPCLMCVARRIPPTD-KQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       254 ~~~~~~~~~~~LVav~r~ip~~~-~~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      ......++.+.|+|+|.|+-.++ .+|......|.|||.+|+..+.+|+++  ..+|||.-.||.|.+.|+|+|
T Consensus       252 ~~g~~lpP~LaLf~iatP~~pPS~lEi~~k~~i~rtKhklDfa~vs~Dak~--k~~lgy~eaEL~~m~gY~lvH  323 (712)
T KOG3560|consen  252 PSGAMLPPRLALFCIATPFLPPSALEIKMKSAILRTKHKLDFALVSMDAKV--KATLGYCEAELHGMPGYNLVH  323 (712)
T ss_pred             CCCccCCCceeEEEEecCCCCchhhhhhhhhhhhhcccccccceeccchhh--hhhhccchhhccCCCccceee
Confidence            01123477899999999995554 366666789999999999999999999  899999999999999999984

>KOG3753|consensus

Probab=99.90  E-value=1.5e-23  Score=218.41  Aligned_cols=308  Identities=15%  Similarity=0.178  Sum_probs=193.6

Q ss_pred             cccCCCchhhhhhhhhhhh------hHHHH-HHHhhhH---hHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHH
Q psy7682          35 SLAVKPDKCAILQETVNQC------LNEKR-RREQENN---YIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIR  104 (383)
Q Consensus        35 ~~~~k~~~~~~~~~~~~~~------~~ek~-RR~~~n~---~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr  104 (383)
                      +++.+||.-...+...+|+      ..|.. |-+-..+   .+.||+.-||.   ..   ..+.++.-+.+|..+....+
T Consensus        73 ~~~qsP~~~~l~~~~sehsP~ts~~~seq~~~~~t~~El~~~~~e~K~~~p~---~~---~~kg~~stl~~l~yal~cv~  146 (1114)
T KOG3753|consen   73 SARQSPDTFSLQMAKSEHSPSTSGCSSEQSDRVRTHKELIKVLKELKVHLPA---ER---RAKGKASTLATLKYALRCVK  146 (1114)
T ss_pred             ccccCchHHHHHhhhccCCccccccchhhhhhcchHHHHHHHHHHHHhhccc---cc---cCCCCchhhhhhHHHhhhhh
Confidence            3457777555566666665      22222 2222222   56778888888   22   23467888888888877755


Q ss_pred             hhhhccCCCcccccCccCCCCCCcCC-----cc----chhhHHHHhhcCcEEEEcC-CccEEEeecccccccCccccccc
Q psy7682         105 NIKQQETSSDAVQQGEVSSSKPTVIT-----NE----VLGPLLLEALEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVL  174 (383)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~P~~~~-----~~----~~~~lll~aldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~  174 (383)
                      +..   ...+..+.-...+-.|....     -+    -.++...++.|.|+++|+. ||+|+|+|+.++.+|||..+.|.
T Consensus       147 qv~---anse~~q~~~~~eg~Pcg~d~s~ytveE~~a~tSe~~~kn~DsF~~~vS~~dG~iLyis~q~a~ilg~krDv~s  223 (1114)
T KOG3753|consen  147 QVQ---ANSEYYQLLSSSEGHPCGADVSMYTVEELEAITSEHTVKNADSFVVAVSFLDGRILYISEQAALILGCKRDVLS  223 (1114)
T ss_pred             hcc---cchHHHhhhhcccCCCCCCCccchhHHHhhhccCCCccccccceEEEEeccCCcEEEeechhhhhccCchhhhc
Confidence            422   21122222111222332111     11    1355667788999999998 99999999999999999999999


Q ss_pred             CCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEEEcCCeee-eeeecCC-----CC
Q psy7682         175 GKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISSTHLT-AGLSRAG-----GE  248 (383)
Q Consensus       175 G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~~~~~rsF~cRmk~~~~~i~-~~~~~~~-----~~  248 (383)
                      |..|.||+||.|...|...+....  +..|...++.+++.    ......++||||+.....+.. -.|.++.     ..
T Consensus       224 ~a~FvdflapqD~~vF~sfta~~~--lp~ws~~s~~ds~~----~~c~~~ks~fcRisgr~~~~~~~~y~PFRl~pyl~e  297 (1114)
T KOG3753|consen  224 SAKFVDFLAPQDVGVFYSFTARYK--LPLWSMGSSADSFT----QECAEEKSFFCRISGRKDRENEIRYHPFRLTPYLVE  297 (1114)
T ss_pred             cchhhhhcchhhhhhhhhcccccc--Cccccccccccchh----hhhhhhcceeeeeecccCCcCccccCcccccceeEE
Confidence            999999999999999999998764  44565443222221    134567999999987544221 1121110     00


Q ss_pred             CCCCCCCCCCCCCCceEEEEEeecCCCCc--ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         249 NGQDDSGDVSSEGGPCLMCVARRIPPTDK--QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       249 ~g~d~~~~~~~~~~~~LVav~r~ip~~~~--~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +. +   ....+.+.|+..++..|...+.  .|..+..+|+|||+.+|.|.+||.++  .++|||+|+||||+|+.+|||
T Consensus       298 v~-~---~~~~~s~~ccLllaerihSgYeAPrIps~KriFtT~HTptClf~hVDeaA--Vp~LGyLPqDLIG~sil~f~H  371 (1114)
T KOG3753|consen  298 VR-D---QQGAESQPCCLLLAERIHSGYEAPRIPSNKRIFTTTHTPTCLFQHVDEAA--VPLLGYLPQDLIGTSILAFVH  371 (1114)
T ss_pred             ec-c---ccccCcCcceeehhhhhhcccccCcCCcccceeEeccCCcceeeecchhh--hhhhccCchhhhccchhhhhc
Confidence            10 0   0012334444444444654443  46666689999999999999999998  799999999999999999996


Q ss_pred             CCCCchhHHHHHHHHHHhhhhcccceeecccceecccCCccccccCCc
Q psy7682         327 CPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASR  374 (383)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~~~~~~~~~~~~~  374 (383)
                      ++|-++-..      +..   ++..+++.-.  |-..++||-.|||+.
T Consensus       372 ~eDr~vm~q------~H~---~v~q~~G~p~--F~~sp~Rf~aqNG~y  408 (1114)
T KOG3753|consen  372 PEDRHVMVQ------IHQ---KVLQSGGKPV--FSHSPIRFCAQNGSY  408 (1114)
T ss_pred             CCchHHHHH------HHH---HHHHhCCCCc--ccccceeeeecCCcE
Confidence            655433221      111   2222332221  667778888888874

>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

Probab=99.71  E-value=6.7e-18  Score=141.55  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=62.9

Q ss_pred             ceeEEEeCCCCcEEEEcCC-CCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhhhcccceeecccceecc
Q psy7682         284 EQFTMKLDRSGTIIGMDTS-GVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRS  362 (383)
Q Consensus       284 ~~F~tRHsldgkf~~vD~r-~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~  362 (383)
                      ++|+|||++||||+|||++ +  ..+|||+|+||+|+|+|+|+ ||+| +.  ..    +......++.+||+.++.|||
T Consensus         2 ~~F~trhs~dgki~~~d~~~v--~~~lgy~~~eLvG~s~y~~~-H~~D-~~--~~----~~~~~~~~~~~g~~~~~~yR~   71 (111)
T PF14598_consen    2 EEFTTRHSLDGKITYVDSRAV--SSLLGYLPEELVGRSIYDFV-HPDD-LQ--RV----LKQHHREVLQKGQSVSPYYRF   71 (111)
T ss_dssp             -EEEEEEETTSBEEEEETTHH--HHHHSS-HHHHTTSBGGGGB-SCCT-HH--HH----HHHHHHHHHHHSSEEEEEEEE
T ss_pred             ceEEEEECCCcEEEEEcCccC--hhhcCCCcHHHcCCchHHhC-CHhh-hh--hH----HHHHHHHHhhCCCcCcceEEE
Confidence            6899999999999999999 6  79999999999999999997 7777 32  11    112222456799999999997


Q ss_pred             cCCccccccCCcceEEEEee
Q psy7682         363 SPSCFGLQGASRTSLWQRIR  382 (383)
Q Consensus       363 ~~~~~~~~~~~~~~~~~~~~  382 (383)
                      +.++       +.|+|++.+
T Consensus        72 ~~k~-------g~~vwvqt~   84 (111)
T PF14598_consen   72 RTKN-------GGYVWVQTK   84 (111)
T ss_dssp             E-TT-------SSEEEEEEE
T ss_pred             EecC-------CcEEEEEEE
Confidence            6654       478998864

...

>KOG3561|consensus

Probab=98.97  E-value=3.1e-10  Score=121.62  Aligned_cols=49  Identities=45%  Similarity=0.632  Sum_probs=44.8

Q ss_pred             CcchhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhH
Q psy7682           1 AKCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLN   55 (383)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~   55 (383)
                      +.|..|||||+|||.||+||||||++|  +    .++||+|||+||+++|.|.+.
T Consensus        23 ~~~~~EKrRRdq~N~yI~ELs~Mvp~~--~----~~~RK~DK~tVLr~aV~~lr~   71 (803)
T KOG3561|consen   23 NRSEIEKRRRDQMNKYIEELSEMVPTN--A----SLSRKPDKLTVLRMAVDHLRL   71 (803)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHhhhcc--h----hcccCchHHHHHHHHHHHHHH
Confidence            469999999999999999999999999  2    388999999999999999953

>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

Probab=98.93  E-value=1.1e-09  Score=91.80  Aligned_cols=73  Identities=19%  Similarity=0.347  Sum_probs=58.7

Q ss_pred             cCcEEEEcCCccEEEeecc-cccccCcccccccCCccccccCCCChHH-HHhhcCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         143 EGFLFVVNPDGYVNFCTEN-IKSFIRYSRQEVLGKSVYNLIHHGDHAR-FHNCLVPSSHQVNAWTSDSGGQAGKRPSLTA  220 (383)
Q Consensus       143 dgfi~vvs~dG~i~yvS~s-v~~~LGy~~~el~G~s~~d~iHp~D~~~-~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~  220 (383)
                      +.|+.-.+.||+|+|+.++ +..+|||.++||+|+|+|+|+||+|... +...+...-                     .
T Consensus         2 ~~F~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~---------------------~   60 (111)
T PF14598_consen    2 EEFTTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVL---------------------Q   60 (111)
T ss_dssp             -EEEEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHH---------------------H
T ss_pred             ceEEEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHh---------------------h
Confidence            4688999999999999999 8999999999999999999999999997 766654321                     1


Q ss_pred             CCCceeEEEEEEEcCC
Q psy7682         221 STPNRTFNIRLLISST  236 (383)
Q Consensus       221 ~~~~rsF~cRmk~~~~  236 (383)
                      .++..+...||+.+.+
T Consensus        61 ~g~~~~~~yR~~~k~g   76 (111)
T PF14598_consen   61 KGQSVSPYYRFRTKNG   76 (111)
T ss_dssp             HSSEEEEEEEEE-TTS
T ss_pred             CCCcCcceEEEEecCC
Confidence            2334677899999886

...

>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt)

Probab=98.89  E-value=3.1e-09  Score=77.69  Aligned_cols=53  Identities=28%  Similarity=0.471  Sum_probs=45.9

Q ss_pred             hhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhh
Q psy7682          49 TVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNI  106 (383)
Q Consensus        49 ~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~  106 (383)
                      +..|+..||+||+.+|..|++|+++||.+ .    .+...++||++||+.||+||+.+
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~-~----~~~~~k~~K~~iL~~ai~yI~~L   54 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSC-S----AGSSRKLSKASILQKAIDYIKQL   54 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSH-H----CCTTSSSSHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccch-h----ccccccCCHHHHHHHHHHHHHHh
Confidence            56889999999999999999999999992 1    12357999999999999999975

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=98.81  E-value=5.5e-09  Score=106.82  Aligned_cols=150  Identities=11%  Similarity=0.145  Sum_probs=98.6

Q ss_pred             HhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         140 EALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLT  219 (383)
Q Consensus       140 ~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~  219 (383)
                      ++..+.++++|.+|+|++++++...++||..+||+|+++.+|+||+|.+.+...+.....      .      +      
T Consensus         3 ~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~------~------~------   64 (442)
T TIGR02040         3 ATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALR------T------G------   64 (442)
T ss_pred             cccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhc------c------C------
Confidence            344456889999999999999999999999999999999999999998888877643210      0      0      


Q ss_pred             CCCCceeEEEEEEEcCC-e--eeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCC----------c---------
Q psy7682         220 ASTPNRTFNIRLLISST-H--LTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTD----------K---------  277 (383)
Q Consensus       220 ~~~~~rsF~cRmk~~~~-~--i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~----------~---------  277 (383)
                        .....+..+.+.+.+ .  +.++..+.    +          ....++++++.+....          .         
T Consensus        65 --~~~~~~e~~~~~~~g~~~~~~~~~~~~----~----------~~~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l  128 (442)
T TIGR02040        65 --RGAVRVELNHIDPSSFELPMRFILVRL----G----------ADRGVLALGRDLRAVAELQQQLVAAQQAMERDYWTL  128 (442)
T ss_pred             --CCcceEeeccCCCCCCccCeEEEEEEe----C----------CCCeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              001122233333322 0  11111111    0          0124677888763100          0         


Q ss_pred             --------ccCCCCceeEEEeCC-CCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         278 --------QLSAPIEQFTMKLDR-SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       278 --------~i~~~~~~F~tRHsl-dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                              .+-......+.-.+. +|+++++++..  ..++||.++|++|+++.+++
T Consensus       129 ~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~--~~l~G~~~~el~g~~~~~~~  183 (442)
T TIGR02040       129 REMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAA--AALLGGVGQSLVGRAFPQEF  183 (442)
T ss_pred             HHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHH--HHHhCcCHHHHcCCCHHHhC
Confidence                    011112344555676 89999999998  79999999999999988876

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

Probab=98.75  E-value=1.9e-08  Score=74.31  Aligned_cols=55  Identities=29%  Similarity=0.465  Sum_probs=47.9

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      .++..|+..||+||+++|..|.+|..+||..   .    ...++||++||+.|+.||+.++.
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~---~----~~~k~~k~~iL~~a~~yI~~L~~   57 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTL---P----PSKKLSKAEILRKAVDYIKSLQE   57 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCC---C----CCCCCCHHHHHHHHHHHHHHHHH
Confidence            3456889999999999999999999999993   1    24899999999999999998764

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=98.66  E-value=3.1e-08  Score=101.24  Aligned_cols=158  Identities=16%  Similarity=0.114  Sum_probs=99.4

Q ss_pred             hhhHHHHhhcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQA  212 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~  212 (383)
                      ....+++++...++++|. +|+|+|+++++..++||++++++|+++.+++||+|.+.+...+.....             
T Consensus       134 r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~-------------  200 (442)
T TIGR02040       134 RYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRA-------------  200 (442)
T ss_pred             HHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHh-------------
Confidence            345677777778999997 899999999999999999999999999999999999988877743210             


Q ss_pred             CCCCCCCCCCCceeEEEEEEEcCCeeeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc----------ccCCC
Q psy7682         213 GKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK----------QLSAP  282 (383)
Q Consensus       213 g~~~~~~~~~~~rsF~cRmk~~~~~i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~----------~i~~~  282 (383)
                              .+....+.++++.....+....... .   .        .+...+++..+.+.....          .+-..
T Consensus       201 --------~g~~~~~~~~~~~~~~~~~~~~~~~-~---~--------~~~~~~l~~~~dit~~~~~e~~~~~~~~~l~e~  260 (442)
T TIGR02040       201 --------TGSAAPVRILLRRSQKRLLVVVSVF-R---Q--------DGESLFLCQLSPAGATQPVGDELSENLARLYHE  260 (442)
T ss_pred             --------cCCCcceEEEEcCCCeEEEEEEEEE-E---e--------CCceEEEEEEcccchhhhhhHHHHHHHHHHHHh
Confidence                    0001112222221111110100000 0   0        011233333444432211          01011


Q ss_pred             CceeEEEeCCCCcEEEEcCCCCccccCCcc-cccccCCCccceec
Q psy7682         283 IEQFTMKLDRSGTIIGMDTSGVSQTHTQYL-NKAVACKTSATVWT  326 (383)
Q Consensus       283 ~~~F~tRHsldgkf~~vD~r~l~~~ilGY~-p~eLiG~S~yd~~~  326 (383)
                      ...-+.-.+.+|.|++|++..  ..++||. +++|+|+++.+|+.
T Consensus       261 ~~d~I~v~D~~G~I~~~N~a~--~~l~G~~~~~~l~G~~~~~~~~  303 (442)
T TIGR02040       261 APDAIVFSDADGTIRGANEAF--LELTDSSSLEAVRGRTLDRWLG  303 (442)
T ss_pred             CCceEEEEcCCCcEEehhHHH--HHHhCCCChHHHcCCCHHHHhC
Confidence            233445578999999999998  8999997 47799999988774

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>smart00353 HLH helix loop helix domain

Probab=98.61  E-value=8.6e-08  Score=69.24  Aligned_cols=48  Identities=27%  Similarity=0.428  Sum_probs=42.0

Q ss_pred             hHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        54 ~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      ..||+||+++|+.|.+|+.+||..   .    ...++||++||..|++|++.++.
T Consensus         2 ~~Er~RR~~~n~~~~~L~~lip~~---~----~~~k~~k~~iL~~ai~yi~~L~~   49 (53)
T smart00353        2 ARERRRRRKINEAFDELRSLLPTL---P----NNKKLSKAEILRLAIEYIKSLQE   49 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC---C----CCCCCCHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999982   1    24799999999999999998764

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []

Probab=98.54  E-value=5e-08  Score=78.90  Aligned_cols=61  Identities=30%  Similarity=0.555  Sum_probs=53.6

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      .+.+++++...++++|.+|+|+|+|+++..+|||++++++|+++++++||+|...+...+.
T Consensus         3 ~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~   63 (113)
T PF00989_consen    3 YRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLR   63 (113)
T ss_dssp             HHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHH
T ss_pred             HHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHH
Confidence            4567888999999999999999999999999999999999999999999998766555554

PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....

>KOG4304|consensus

Probab=98.53  E-value=7.4e-08  Score=91.58  Aligned_cols=68  Identities=28%  Similarity=0.406  Sum_probs=54.9

Q ss_pred             hhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccC
Q psy7682          42 KCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET  111 (383)
Q Consensus        42 ~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~  111 (383)
                      .+....+.++|-..|||||++||+.|.||+.|||. .+..+ .....||+|+.||.+||.|||+++....
T Consensus        26 ~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e-~~~~~-~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   26 SKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPE-ALKKD-GQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             hhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHH-HHhhc-chhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            44555667789999999999999999999999998 33332 1234799999999999999999886554

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=98.47  E-value=9.9e-07  Score=96.13  Aligned_cols=167  Identities=16%  Similarity=0.166  Sum_probs=105.8

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGK  214 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~  214 (383)
                      ...+.++.++ +++++.+|.|+|+++++..++||+++|++|+++.+++||++.......+.....      .      +.
T Consensus        15 ~~~le~~~~~-i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~------~------~~   81 (799)
T PRK11359         15 FPALEQNMMG-AVLINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNRE------G------GK   81 (799)
T ss_pred             HHHHHhhcCc-EEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhc------c------CC
Confidence            3444455555 778899999999999999999999999999999999999887554443322110      0      00


Q ss_pred             CCCCCCCCCceeEEEEEEEcCCeeeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc---------ccCCCCce
Q psy7682         215 RPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK---------QLSAPIEQ  285 (383)
Q Consensus       215 ~~~~~~~~~~rsF~cRmk~~~~~i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~---------~i~~~~~~  285 (383)
                           .......+-+|++++.+......... ...  +      ..+....+++.+.+.....         .+-.....
T Consensus        82 -----~~~~~~~~e~~~~~~dG~~~~v~~~~-~~~--~------~~g~~~~~~~~~DiT~~~~~~~~~~~~~~~~~~~~~  147 (799)
T PRK11359         82 -----ARVEGMSRELQLEKKDGSKIWTRFAL-SKV--S------AEGKVYYLALVRDASVEMAQKEQTRQLIIAVDHLDR  147 (799)
T ss_pred             -----ccccccceeeEEecCCcCEEEEEEEe-eee--c------cCCceEEEEEEeeccchhhhHHHHHHHHHHHhcCCC
Confidence                 00111233456666554211100000 000  1      1223456777777754321         01112234


Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      .+.-.+.+|+++++++..  ..++||.+++++|+...++++++++
T Consensus       148 ~i~~~d~~g~i~~~N~~~--~~l~G~~~~e~~g~~~~~~~~~~~~  190 (799)
T PRK11359        148 PVIVLDPERRIVQCNRAF--TEMFGYCISEASGMQPDTLLNIPEF  190 (799)
T ss_pred             cEEEEcCCCcEEEEChhh--HhhhCCCHHHHCCCChHHhcCCCCC
Confidence            456678999999999998  8999999999999999888766655

>PRK13560 hypothetical protein; Provisional

Probab=98.27  E-value=3e-06  Score=91.85  Aligned_cols=163  Identities=12%  Similarity=0.078  Sum_probs=105.8

Q ss_pred             hHHHHhhcCcEEEEcCCcc----EEEeecccccccCcccccccCC--ccccccCCCChHHHHhhcCCCCCCCCCCCCCCC
Q psy7682         136 PLLLEALEGFLFVVNPDGY----VNFCTENIKSFIRYSRQEVLGK--SVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSG  209 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~----i~yvS~sv~~~LGy~~~el~G~--s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~  209 (383)
                      ..+++++.+.+++.+.+|.    +.|++++...++||.+.++++.  .+..++||+|.+.+......... ...  .   
T Consensus        71 r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~-~~~--~---  144 (807)
T PRK13560         71 RNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAE-TIA--M---  144 (807)
T ss_pred             HHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHH-HHH--H---
Confidence            5577888888887766555    3448999999999999998863  46689999999876543211100 000  0   


Q ss_pred             CCCCCCCCCCCCCCceeEEEEEEEcCCe-eeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc-----------
Q psy7682         210 GQAGKRPSLTASTPNRTFNIRLLISSTH-LTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK-----------  277 (383)
Q Consensus       210 ~~~g~~~~~~~~~~~rsF~cRmk~~~~~-i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~-----------  277 (383)
                              ....+....|..|++++.+. +.+...+..     +      ..+...++++++.|.....           
T Consensus       145 --------~~~~~~~~~~e~r~~~~dg~~~~~~~~~~~-----~------~~g~~~~~g~~~DIT~rk~ae~~l~~~~~~  205 (807)
T PRK13560        145 --------ALQSDDWQEEEGHFRCGDGRFIDCCLRFER-----H------AHADDQVDGFAEDITERKRAEERIDEALHF  205 (807)
T ss_pred             --------HhccCcccceEEEEEeCCccEEEEEeeeee-----c------CCCceEEEEEEEccchHHHHHHHHHHHHHH
Confidence                    00112345788899987752 222221110     1      1123467888888864331           


Q ss_pred             --ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         278 --QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       278 --~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                        .+-......+.-.+.+|+|+++++.+  ..++||.++|++|+++++++
T Consensus       206 l~~l~e~~~~~i~~~d~~g~i~~~N~~~--~~~~G~~~~e~~g~~~~~~~  253 (807)
T PRK13560        206 LQQLLDNIADPAFWKDEDAKVFGCNDAA--CLACGFRREEIIGMSIHDFA  253 (807)
T ss_pred             HHHHHhhCCCeEEEEcCCCCEEEEhHHH--HHHhCCCHHHHcCCcchhcC
Confidence              01112234455679999999999998  89999999999999998886

>KOG1318|consensus

Probab=98.23  E-value=1.3e-06  Score=87.68  Aligned_cols=62  Identities=31%  Similarity=0.399  Sum_probs=52.5

Q ss_pred             hhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          42 KCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        42 ~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .-+-.+++-+|+..|||||++||..|.||..|||-++.++      .+..|-.||.-+++|+|.++.-
T Consensus       227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~------~~~nKgtILk~s~dYIr~Lqq~  288 (411)
T KOG1318|consen  227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSED------MKSNKGTILKASCDYIRELQQT  288 (411)
T ss_pred             hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcch------hhcccchhhHHHHHHHHHHHHH
Confidence            3345567889999999999999999999999999954333      5888999999999999998754

>PRK13560 hypothetical protein; Provisional

Probab=98.10  E-value=5.5e-06  Score=89.84  Aligned_cols=163  Identities=12%  Similarity=0.091  Sum_probs=103.0

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGK  214 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~  214 (383)
                      ...+++++...++++|.+|+|+|+|+++..++||+++|++|+++.++.++.+...+........                
T Consensus       206 l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~----------------  269 (807)
T PRK13560        206 LQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKF----------------  269 (807)
T ss_pred             HHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHh----------------
Confidence            3467778888899999999999999999999999999999999999987766655433221110                


Q ss_pred             CCCCCCCCCceeEEEEEEEcCCeeeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc-------------ccCC
Q psy7682         215 RPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK-------------QLSA  281 (383)
Q Consensus       215 ~~~~~~~~~~rsF~cRmk~~~~~i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~-------------~i~~  281 (383)
                           ..+....|-.+++.+.+....-........-.+     .......++++++.|+....             .+-.
T Consensus       270 -----~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-----~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~  339 (807)
T PRK13560        270 -----DADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-----KENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIE  339 (807)
T ss_pred             -----ccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-----CCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHH
Confidence                 001123455566555432110000000000001     01233568888888864321             0111


Q ss_pred             CCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccce
Q psy7682         282 PIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATV  324 (383)
Q Consensus       282 ~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~  324 (383)
                      .....+...+.+|.+++++.... ..++||.+.|++|+++.++
T Consensus       340 ~~~~~i~~~d~~g~i~~~nn~~~-~~~~G~~~~e~~g~~~~~~  381 (807)
T PRK13560        340 AAPIAAIGLDADGNICFVNNNAA-ERMLGWSAAEVMGKPLPGM  381 (807)
T ss_pred             hCcccEEEEcCCCCEEEecCHHH-HHHhCCCHHHHcCCCcccc
Confidence            22345666789999999965542 5699999999999987654

>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

Probab=98.02  E-value=6.1e-06  Score=65.35  Aligned_cols=51  Identities=25%  Similarity=0.630  Sum_probs=44.5

Q ss_pred             EEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCC
Q psy7682         146 LFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       146 i~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~  196 (383)
                      ++++|.+|.|+|+|+++..++||+++|++|+++.+++++++...+...+..
T Consensus         4 i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~   54 (104)
T PF13426_consen    4 IFILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIER   54 (104)
T ss_dssp             EEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHH
T ss_pred             EEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHH
Confidence            788999999999999999999999999999999999999888777776654

...

>PRK09776 putative diguanylate cyclase; Provisional

Probab=97.90  E-value=8.4e-06  Score=91.99  Aligned_cols=151  Identities=12%  Similarity=0.024  Sum_probs=97.1

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRP  216 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~  216 (383)
                      .++++...-++++|.+|+|+|+|+++..++||+++|++|+++.+++||+|.+.....+.....             +   
T Consensus       287 ~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~-------------~---  350 (1092)
T PRK09776        287 NAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLS-------------G---  350 (1092)
T ss_pred             HHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHc-------------C---
Confidence            445555555889999999999999999999999999999999999999998877665532210             0   


Q ss_pred             CCCCCCCceeEEEEEEEcCCee---eeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc---c----------cC
Q psy7682         217 SLTASTPNRTFNIRLLISSTHL---TAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK---Q----------LS  280 (383)
Q Consensus       217 ~~~~~~~~rsF~cRmk~~~~~i---~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~---~----------i~  280 (383)
                          ......+..|++++.+..   .....+...   .       ......++++.+.+.....   .          +.
T Consensus       351 ----~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~---~-------~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~  416 (1092)
T PRK09776        351 ----EINSYSMEKRYYRRDGEVVWALLAVSLVRD---T-------DGTPLYFIAQIEDINELKRTEQVNERLMERITLAN  416 (1092)
T ss_pred             ----CccceeeeeEEEcCCCCEEEEEEEEEEEEC---C-------CCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence                011234556666655421   111111100   0       0222456666666543211   0          00


Q ss_pred             CCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCC
Q psy7682         281 APIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACK  319 (383)
Q Consensus       281 ~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~  319 (383)
                      ......+..-++++.+++++++.  ..++||.+++..+.
T Consensus       417 ~~~~~~i~~~d~~~~~~~~n~~~--~~l~G~~~~~~~~~  453 (1092)
T PRK09776        417 EAGGIGIWEWDLKPNIISWDKRM--FELYEIPPHIKPTW  453 (1092)
T ss_pred             HhcCceEEEEecCCCeEeeCHHH--HHHhCCCcccCCCH
Confidence            11233456668999999999998  79999999995553

>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 []

Probab=97.87  E-value=7.2e-06  Score=64.43  Aligned_cols=60  Identities=18%  Similarity=0.311  Sum_probs=45.4

Q ss_pred             EEEeecccccccCcccccccCCc----cccccCCCChHHHHhhcCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCceeEEE
Q psy7682         155 VNFCTENIKSFIRYSRQEVLGKS----VYNLIHHGDHARFHNCLVP-SSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNI  229 (383)
Q Consensus       155 i~yvS~sv~~~LGy~~~el~G~s----~~d~iHp~D~~~~~~~l~~-~~~~~~~~~s~s~~~~g~~~~~~~~~~~rsF~c  229 (383)
                      |+|+|+++..++||+++++ |..    +++++||+|.+.+.+.+.. ..                     ..+....+.+
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~---------------------~~~~~~~~e~   58 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAAL---------------------QNGEPFEIEY   58 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHH---------------------HTT-EEEEEE
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhh---------------------ccCcceEEEE
Confidence            6899999999999999999 777    8999999999999998875 21                     1234567788


Q ss_pred             EEEEcCC
Q psy7682         230 RLLISST  236 (383)
Q Consensus       230 Rmk~~~~  236 (383)
                      |++++.+
T Consensus        59 R~~~~~G   65 (91)
T PF08447_consen   59 RIRRKDG   65 (91)
T ss_dssp             EEEGTTS
T ss_pred             EEECCCC
Confidence            8888765

The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.

>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 []

Probab=97.64  E-value=3e-05  Score=62.06  Aligned_cols=58  Identities=24%  Similarity=0.545  Sum_probs=51.9

Q ss_pred             HHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCC
Q psy7682         139 LEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       139 l~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~  196 (383)
                      ++++...++++|.+|+|+|+|++...++|++..+++|+++.+++++.+.+.+...+..
T Consensus         1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~   58 (110)
T PF08448_consen    1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRR   58 (110)
T ss_dssp             HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHH
T ss_pred             CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHH
Confidence            4667778999999999999999999999999999999999999999999888887754

The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.

>KOG3558|consensus

Probab=97.63  E-value=8e-06  Score=85.68  Aligned_cols=53  Identities=23%  Similarity=0.490  Sum_probs=49.5

Q ss_pred             cCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         143 EGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       143 dgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      +.|+.-++.|=+|.|+.+.|+.++||+++||+|+|+|+|+|+.|.+.++.-..
T Consensus       274 ~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~  326 (768)
T KOG3558|consen  274 HMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHH  326 (768)
T ss_pred             ceeEEeeecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHH
Confidence            37899999999999999999999999999999999999999999999987654

>PRK09776 putative diguanylate cyclase; Provisional

Probab=97.54  E-value=8.8e-05  Score=83.79  Aligned_cols=158  Identities=9%  Similarity=0.023  Sum_probs=106.0

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCC-ccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCC
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGK-SVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKR  215 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~-s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~  215 (383)
                      .+.++....++.++.+|.++|+|++...++||++++..+. .+.+++||+|.+.+...+....                 
T Consensus       414 ~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~-----------------  476 (1092)
T PRK09776        414 LANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDAL-----------------  476 (1092)
T ss_pred             HHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHH-----------------
Confidence            4445556668899999999999999999999999986553 4677999999998877664321                 


Q ss_pred             CCCCCCCCceeEEEEEEEcCCeeeeeeecCCC--CCCCCCCCCCCCCCCceEEEEEeecCCCCc-------------ccC
Q psy7682         216 PSLTASTPNRTFNIRLLISSTHLTAGLSRAGG--ENGQDDSGDVSSEGGPCLMCVARRIPPTDK-------------QLS  280 (383)
Q Consensus       216 ~~~~~~~~~rsF~cRmk~~~~~i~~~~~~~~~--~~g~d~~~~~~~~~~~~LVav~r~ip~~~~-------------~i~  280 (383)
                          ..+....+-.|++++.+     +.|...  ..-.+.     ......++++.+.+.....             .+-
T Consensus       477 ----~~~~~~~~e~r~~~~dG-----~~w~~~~~~~~~d~-----~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l  542 (1092)
T PRK09776        477 ----QGRSPFKLEFRIVVKDG-----VRHIRALANRVLNK-----DGEVERLLGINMDMTEVRQLNEALFQEKERLHITL  542 (1092)
T ss_pred             ----hcCCCeeEEEEEEcCCc-----eEEEEEeeEEEECC-----CCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHH
Confidence                01122345566666553     111100  000011     1223467888888764321             011


Q ss_pred             CCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecC
Q psy7682         281 APIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTC  327 (383)
Q Consensus       281 ~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~  327 (383)
                      ......+...+.+|+++++++..  ..++||.++|++|+++.++++.
T Consensus       543 ~~~~~~i~~~D~~g~i~~~N~a~--~~l~G~~~~e~iG~~~~~~~~~  587 (1092)
T PRK09776        543 DSIGEAVVCTDMAMKVTFMNPVA--EKMTGWTQEEALGVPLLTVLHI  587 (1092)
T ss_pred             hccccEEEEECCCCeEEEEcHHH--HHHhCCCHHHHcCCCHHHHccc
Confidence            12345566789999999999998  8999999999999998887743

>KOG1319|consensus

Probab=97.28  E-value=0.00026  Score=63.57  Aligned_cols=59  Identities=22%  Similarity=0.357  Sum_probs=49.0

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      +++..|.++|++|||.+|.-...|.+|+|-|--.+   +...|+.|+.||..+|.||..++.
T Consensus        61 rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~d---s~g~KlskA~ILqksidyi~~L~~  119 (229)
T KOG1319|consen   61 RRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQD---SIGQKLSKAIILQKTIDYIQFLHK  119 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhchHHHHHhcccccccc---chhHHHHHHHHHHHHHHHHHHHHH
Confidence            34678999999999999999999999999952222   234599999999999999987764

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=97.24  E-value=0.00014  Score=73.64  Aligned_cols=160  Identities=10%  Similarity=0.068  Sum_probs=96.0

Q ss_pred             chhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCC
Q psy7682         133 VLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQA  212 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~  212 (383)
                      ++...+++++..-+++++.+|+++|+|+++..++||++++++|++...+.++.+.......+.....      .      
T Consensus         4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~------~------   71 (494)
T TIGR02938         4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLA------E------   71 (494)
T ss_pred             HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHH------h------
Confidence            3455677777777999999999999999999999999999999998888877665544433321100      0      


Q ss_pred             CCCCCCCCCCCceeEEEEEEEcCCe---eeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc------------
Q psy7682         213 GKRPSLTASTPNRTFNIRLLISSTH---LTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK------------  277 (383)
Q Consensus       213 g~~~~~~~~~~~rsF~cRmk~~~~~---i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~------------  277 (383)
                               +.......+.+.+.+.   +.....+..     +     .......++++.+.+.....            
T Consensus        72 ---------~~~~~~~~~~~~~~g~~~~~~~~~~~~~-----~-----~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~  132 (494)
T TIGR02938        72 ---------QKPWAGKLLNRRKDGELYLAELTVAPVL-----N-----EAGETTHFLGMHRDITELHRLEQVVANQKLLI  132 (494)
T ss_pred             ---------CCcccceeeccCCCccchhhheeeEEEE-----C-----CCCCEEEEEEehhhhhHHHHHHHHHHHHHHHH
Confidence                     0000111122222210   001111110     0     01223467777777653211            


Q ss_pred             -ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         278 -QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       278 -~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                       .+......-+...+.+|.++++++..  ..++||.+.+..+..+.+++
T Consensus       133 ~~~~~~~~~~i~~~d~~~~i~~~N~~~--~~~~g~~~~~~~~~~~~~~~  179 (494)
T TIGR02938       133 ESVVDAAPVAFVLLDPTGRVILDNQEY--KKLATDLRVKEPAHTVLDLL  179 (494)
T ss_pred             HHHHhcccceEEEEcCCCCEEEechhH--HHhhchhhhhHHHHHHHHHh
Confidence             01111223345567899999999998  78899999888877655443

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

Probab=97.21  E-value=0.00024  Score=50.93  Aligned_cols=52  Identities=27%  Similarity=0.503  Sum_probs=46.9

Q ss_pred             CcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       144 gfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..+++++.+|.++++++++..++|+.+.+++|.++++++|+.+...+...+.
T Consensus         3 ~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~   54 (103)
T cd00130           3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLE   54 (103)
T ss_pred             ceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHH
Confidence            4578899999999999999999999999999999999999999887766554

Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.

>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 []

Probab=97.17  E-value=0.00033  Score=58.55  Aligned_cols=56  Identities=23%  Similarity=0.415  Sum_probs=50.2

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcc---cccccCCccccccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYS---RQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~---~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .-|++++++. +++|+++|+|+..+||.+   .++++|+++.+++-+.....+++.+...
T Consensus        14 phG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~~~~~~   73 (110)
T PF08446_consen   14 PHGALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLREALQSE   73 (110)
T ss_dssp             TTSEEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHHHCTCC
T ss_pred             CCEEEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHHhhhcc
Confidence            4689999986 799999999999999999   9999999999999999999999887654

The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....

>smart00091 PAS PAS domain

Probab=97.02  E-value=0.00069  Score=45.00  Aligned_cols=58  Identities=31%  Similarity=0.582  Sum_probs=50.4

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .+++++...+++++.+|.+.++++.+..++|+...++.|.++.+++||.|...+...+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   62 (67)
T smart00091        5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEAL   62 (67)
T ss_pred             HHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHH
Confidence            3456666678889999999999999999999999999999999999999988776654

PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).

>TIGR00229 sensory_box PAS domain S-box

Probab=97.02  E-value=0.00065  Score=51.28  Aligned_cols=59  Identities=19%  Similarity=0.437  Sum_probs=51.2

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ..+++++...+++++.+|.|+|+++.+..++|+...+++|.++.+++|+.+...+...+
T Consensus         6 ~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (124)
T TIGR00229         6 RAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERI   64 (124)
T ss_pred             HHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHH
Confidence            34566677778899999999999999999999999999999999999999887766554

The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.

>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

Probab=96.55  E-value=0.0022  Score=50.42  Aligned_cols=37  Identities=16%  Similarity=0.205  Sum_probs=30.9

Q ss_pred             EeCCCCcEEEEcCCCCccccCCcccccccCCCccceecC
Q psy7682         289 KLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTC  327 (383)
Q Consensus       289 RHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~  327 (383)
                      -.+.+|+|+++++..  ..++||.++|++|+++.+++..
T Consensus         6 i~d~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~~~   42 (104)
T PF13426_consen    6 ILDPDGRILYVNPAF--ERLFGYSREELIGKSISDFFPE   42 (104)
T ss_dssp             EEETTSBEEEE-HHH--HHHHTS-HHHHTTSBGGGGCST
T ss_pred             EECCcCcEEehhHHH--HHHHCcCHHHHcCCCcccccCc
Confidence            456799999999998  8999999999999999988853

...

>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 []

Probab=96.37  E-value=0.002  Score=50.25  Aligned_cols=69  Identities=14%  Similarity=0.107  Sum_probs=39.4

Q ss_pred             EEEEcCCCCccccCCcccccccCCC----ccceecCCCCchhHHHHHHHHHHhhhhcccceeecccceecccCCcccccc
Q psy7682         296 IIGMDTSGVSQTHTQYLNKAVACKT----SATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQG  371 (383)
Q Consensus       296 f~~vD~r~l~~~ilGY~p~eLiG~S----~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~~~~~~~~~~  371 (383)
                      ++|+++++  ..++||.|+|+ |..    +++++ ||+|...+...+.++       ....++.-+..||       +..
T Consensus         1 ~i~~s~~~--~~i~G~~~~~~-~~~~~~~~~~~i-hpdD~~~~~~~~~~~-------~~~~~~~~~~e~R-------~~~   62 (91)
T PF08447_consen    1 IIYWSDNF--YEIFGYSPEEI-GKPDFEEWLERI-HPDDRERVRQAIQQA-------ALQNGEPFEIEYR-------IRR   62 (91)
T ss_dssp             -EEE-THH--HHHHTS-HHHH-TCBEHHHHHHHB--TTTHHHHHHHHHHH-------HHHTT-EEEEEEE-------EEG
T ss_pred             CEEEeHHH--HHHhCCCHHHh-ccCCHHHHHhhc-CHHHHHHHHHHHHHH-------hhccCcceEEEEE-------EEC
Confidence            57999998  79999999999 776    56655 666633332222211       1223444555666       556


Q ss_pred             CCcceEEEEee
Q psy7682         372 ASRTSLWQRIR  382 (383)
Q Consensus       372 ~~~~~~~~~~~  382 (383)
                      .++.+.|++.+
T Consensus        63 ~~G~~~wi~~~   73 (91)
T PF08447_consen   63 KDGEYRWIEVR   73 (91)
T ss_dssp             TTSTEEEEEEE
T ss_pred             CCCCEEEEEEE
Confidence            66667777654

The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []

Probab=96.35  E-value=0.0029  Score=50.61  Aligned_cols=42  Identities=12%  Similarity=0.145  Sum_probs=34.7

Q ss_pred             eeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCC
Q psy7682         285 QFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCP  328 (383)
Q Consensus       285 ~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~  328 (383)
                      ..+.-.+.+|+|+|+++.+  ..++||.++|++|++++++++.+
T Consensus        12 ~~i~~~d~~g~I~~~N~a~--~~l~g~~~~~~~g~~~~~~~~~~   53 (113)
T PF00989_consen   12 DGIFVIDEDGRILYVNQAA--EELLGYSREELIGKSLFDLIHPE   53 (113)
T ss_dssp             SEEEEEETTSBEEEECHHH--HHHHSS-HHHHTTSBGGGGCSGG
T ss_pred             ceEEEEeCcCeEEEECHHH--HHHHccCHHHHcCCcHHHhcCch
Confidence            3344556899999999998  89999999999999999998443

PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....

>PRK13557 histidine kinase; Provisional

Probab=96.31  E-value=0.0029  Score=65.25  Aligned_cols=62  Identities=15%  Similarity=0.156  Sum_probs=50.3

Q ss_pred             chhhHHHHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         133 VLGPLLLEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .+-..+++++..-+++++.   +|.|+|+|+++..++||+.+|++|+++.+++||++.......+
T Consensus        30 ~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~   94 (540)
T PRK13557         30 DIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEV   94 (540)
T ss_pred             HHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHH
Confidence            3445566666666888885   8999999999999999999999999999999998766554433

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=96.21  E-value=0.0067  Score=66.57  Aligned_cols=62  Identities=15%  Similarity=0.213  Sum_probs=54.2

Q ss_pred             chhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         133 VLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .+...+++++.+.|+++|.+|+|+|+|+++..++||+.++++|+++.++++|++...+....
T Consensus       155 ~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~  216 (779)
T PRK11091        155 SLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETD  216 (779)
T ss_pred             HHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHH
Confidence            34566788888889999999999999999999999999999999999999998877665443

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=96.20  E-value=0.0031  Score=60.41  Aligned_cols=58  Identities=19%  Similarity=0.428  Sum_probs=50.3

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhh
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNC  193 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~  193 (383)
                      ..+++++..-++++|.+|+|+|+|+++..++||++++++|+.+.+++++.|.......
T Consensus         9 ~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~l~~   66 (333)
T TIGR02966         9 RAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPEFVEYLAA   66 (333)
T ss_pred             HHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHHHHHHHHh
Confidence            4566777777999999999999999999999999999999999999998876655443

Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).

>PRK10060 RNase II stability modulator; Provisional

Probab=96.08  E-value=0.0033  Score=68.12  Aligned_cols=61  Identities=11%  Similarity=0.322  Sum_probs=49.1

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCcccccc-CCCChHHHHhhc
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLI-HHGDHARFHNCL  194 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~i-Hp~D~~~~~~~l  194 (383)
                      +...+++++..-|+++|.+|+|+|+++++..++||+.+|++|+++++++ ||+|...+...+
T Consensus       112 ~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~  173 (663)
T PRK10060        112 FAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNI  173 (663)
T ss_pred             HHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHH
Confidence            3344667677779999999999999999999999999999999998865 566655554444

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D

Probab=95.63  E-value=0.014  Score=47.46  Aligned_cols=58  Identities=7%  Similarity=0.177  Sum_probs=44.4

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      .++++++.=++++|.+++|.|.++++..+++..+. .+|+++.++.++.+.+.+...+.
T Consensus         3 ~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~-~iGr~l~~~~~~~~~~~l~~~i~   60 (106)
T PF13596_consen    3 NILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPS-DIGRPLFDIHPPLSYPNLKKIIE   60 (106)
T ss_dssp             HHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GG-GTTSBCCCSS-HHHHHHHHHHHH
T ss_pred             HHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChH-HCCCCHHHcCCccchHHHHHHHH
Confidence            46788888899999999999999999999997764 57999999988877777777664

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional

Probab=95.15  E-value=0.013  Score=57.35  Aligned_cols=53  Identities=11%  Similarity=0.234  Sum_probs=46.7

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      ..+.+++++..-++++|.+|.|+|+|+++..++||+..+++|+.+.++.++.+
T Consensus         8 ~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~   60 (348)
T PRK11073          8 DAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS   60 (348)
T ss_pred             hHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch
Confidence            34567777777799999999999999999999999999999999999887654

>PRK13559 hypothetical protein; Provisional

Probab=95.09  E-value=0.02  Score=56.48  Aligned_cols=60  Identities=13%  Similarity=0.149  Sum_probs=47.6

Q ss_pred             hhHHHHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         135 GPLLLEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ...++++...-++++|.   +|.|+|+++++..++||+.++++|+++.++.++.+.......+
T Consensus        45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~  107 (361)
T PRK13559         45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKI  107 (361)
T ss_pred             HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHH
Confidence            34456666666888986   6789999999999999999999999998888877765544433

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A

Probab=94.97  E-value=0.015  Score=42.81  Aligned_cols=41  Identities=12%  Similarity=0.308  Sum_probs=31.3

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccc
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVY  179 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~  179 (383)
                      .+.+++++..-|++++ +|+|+|+++++..++||+   +.|+.+.
T Consensus         3 ~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~   43 (64)
T PF13188_consen    3 YRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIG   43 (64)
T ss_dssp             HHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred             HHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHH
Confidence            3456777777799999 899999999999999998   5555544

>KOG3753|consensus

Probab=94.94  E-value=0.014  Score=63.26  Aligned_cols=50  Identities=18%  Similarity=0.327  Sum_probs=43.1

Q ss_pred             cEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       145 fi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      |+.--+..+.|..|-++...+|||.+.||||+++.+|+||.|+..+...-
T Consensus       333 FtT~HTptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H  382 (1114)
T KOG3753|consen  333 FTTTHTPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIH  382 (1114)
T ss_pred             eEeccCCcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHH
Confidence            44555668999999999999999999999999999999999977666543

>smart00353 HLH helix loop helix domain

Probab=94.92  E-value=0.052  Score=38.70  Aligned_cols=43  Identities=28%  Similarity=0.363  Sum_probs=37.7

Q ss_pred             hHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhh
Q psy7682           5 NEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCL   54 (383)
Q Consensus         5 ~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~   54 (383)
                      .|++||++.|..+++|.+++...  .     -..+.+|+.|+..+++.+.
T Consensus         3 ~Er~RR~~~n~~~~~L~~lip~~--~-----~~~k~~k~~iL~~ai~yi~   45 (53)
T smart00353        3 RERRRRRKINEAFDELRSLLPTL--P-----NNKKLSKAEILRLAIEYIK   45 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC--C-----CCCCCCHHHHHHHHHHHHH
Confidence            59999999999999999999986  1     3488999999999988774

>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

Probab=94.84  E-value=0.048  Score=39.75  Aligned_cols=46  Identities=33%  Similarity=0.451  Sum_probs=39.4

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhH
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLN   55 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~   55 (383)
                      ...||+||++++.++++|.++++...       ...+.+|..|+..+++.+..
T Consensus         9 ~~~Er~RR~~~n~~~~~L~~llp~~~-------~~~k~~k~~iL~~a~~yI~~   54 (60)
T cd00083           9 NLRERRRRERINDAFDELRSLLPTLP-------PSKKLSKAEILRKAVDYIKS   54 (60)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHCCCCC-------CCCCCCHHHHHHHHHHHHHH
Confidence            35799999999999999999999871       35889999999999887753

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and

>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt)

Probab=94.83  E-value=0.033  Score=40.29  Aligned_cols=46  Identities=33%  Similarity=0.494  Sum_probs=38.3

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhh
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQC   53 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~   53 (383)
                      ...|++||++.+.++++|.+++....     ..-..|.+|+.|++.+++.+
T Consensus         6 ~~~Er~RR~~i~~~~~~L~~llp~~~-----~~~~~k~~K~~iL~~ai~yI   51 (55)
T PF00010_consen    6 NERERRRRDRINDCFDELRELLPSCS-----AGSSRKLSKASILQKAIDYI   51 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCCSSHH-----CCTTSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccchh-----ccccccCCHHHHHHHHHHHH
Confidence            35799999999999999999999861     22347899999999987765

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=94.49  E-value=0.018  Score=58.52  Aligned_cols=56  Identities=14%  Similarity=0.301  Sum_probs=48.2

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHH
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF  190 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~  190 (383)
                      .+.+++++..-++++|.+|+|+|+++++..+|||+..+++|+++.+++.+.|....
T Consensus       100 ~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~~~~  155 (430)
T PRK11006        100 FRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEFTQY  155 (430)
T ss_pred             HHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHHHHH
Confidence            34567788888999999999999999999999999999999999998876665443

>KOG3559|consensus

Probab=94.35  E-value=0.019  Score=57.48  Aligned_cols=51  Identities=22%  Similarity=0.370  Sum_probs=47.5

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHh
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN  192 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~  192 (383)
                      .+.|++..+.|-+|+|..+.|.+++||++.+|+|+++|.+||-+|...++.
T Consensus       224 sNmFmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~  274 (598)
T KOG3559|consen  224 SNMFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRC  274 (598)
T ss_pred             cceEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHH
Confidence            577888889999999999999999999999999999999999999887765

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=94.03  E-value=0.027  Score=59.43  Aligned_cols=58  Identities=19%  Similarity=0.219  Sum_probs=50.3

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHh
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN  192 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~  192 (383)
                      -..+++++..=|+++|.+|+|+++|+++..+||++.++++|+++.++++..+...+.+
T Consensus        82 L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~l~~~le  139 (520)
T PRK10820         82 LSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFNFLRWLE  139 (520)
T ss_pred             HHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcchHHHHHH
Confidence            3567888777799999999999999999999999999999999999999877554433

>KOG4029|consensus

Probab=93.80  E-value=0.054  Score=51.00  Aligned_cols=59  Identities=19%  Similarity=0.223  Sum_probs=47.1

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccC
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET  111 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~  111 (383)
                      ..+...+..|+.|=...|.-|.+|..+||..  +.    -..||.|..+||+|+.||+.+..+..
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~--~~----~~kklSKveTLr~A~~YI~~L~~lL~  166 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTE--PP----QSKKLSKVETLRLATSYIRYLTKLLA  166 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCC--CC----cccccCcccchHHHHHHHHHHHHHhc
Confidence            3344555558888899999999999999993  11    04899999999999999999876543

>KOG0561|consensus

Probab=93.72  E-value=0.079  Score=51.23  Aligned_cols=48  Identities=33%  Similarity=0.408  Sum_probs=41.1

Q ss_pred             hhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          53 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        53 ~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      +-+||||=.-+|+-|.-|+.|||-   .+     ..||.|++||+.|.+|+-.+..
T Consensus        65 NsNERRRMQSINAGFqsLr~LlPr---~e-----GEKLSKAAILQQTa~yI~~Le~  112 (373)
T KOG0561|consen   65 NSNERRRMQSINAGFQSLRALLPR---KE-----GEKLSKAAILQQTADYIHQLEG  112 (373)
T ss_pred             cchHHHHHHhhhHHHHHHHHhcCc---cc-----chhhHHHHHHHHHHHHHHHHHh
Confidence            345888889999999999999999   33     3799999999999999987653

>KOG1318|consensus

Probab=93.68  E-value=0.19  Score=51.12  Aligned_cols=84  Identities=21%  Similarity=0.339  Sum_probs=58.0

Q ss_pred             hHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhccccccccccc
Q psy7682           5 NEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMS   84 (383)
Q Consensus         5 ~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~   84 (383)
                      .|+|||+.=|.+|-||..||.-+. .++     .|..|-.||++.++-++.-++-+++.- ++...+..|          
T Consensus       240 VERRRR~nIN~~IkeLg~liP~~~-~~~-----~~~nKgtILk~s~dYIr~Lqq~~q~~~-E~~~rqk~l----------  302 (411)
T KOG1318|consen  240 VERRRRENINDRIKELGQLIPKCN-SED-----MKSNKGTILKASCDYIRELQQTLQRAR-ELENRQKKL----------  302 (411)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCC-cch-----hhcccchhhHHHHHHHHHHHHHHHHHH-HHHhhhhHH----------
Confidence            699999999999999999999761 222     344488999999998865443333222 222222222          


Q ss_pred             ccCCCCChhhhhHHHHHHHHhhhhcc
Q psy7682          85 SLAVKPDKCAILQETVNQIRNIKQQE  110 (383)
Q Consensus        85 ~~~~klDK~siLr~ai~~lr~~~~~~  110 (383)
                          . -+..+|++.|++|+.+....
T Consensus       303 ----e-~~n~~L~~rieeLk~~~~~~  323 (411)
T KOG1318|consen  303 ----E-STNQELALRIEELKSEAGRH  323 (411)
T ss_pred             ----H-hHHHHHHHHHHHHHHHHHHh
Confidence                1 46789999999999866543

>KOG2483|consensus

Probab=92.97  E-value=0.15  Score=48.27  Aligned_cols=56  Identities=18%  Similarity=0.351  Sum_probs=44.5

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhcc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE  110 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~  110 (383)
                      .+..|+.-||+||+++...|+.|+..+|.   .++.    ..=+.++||+-|..|+..+....
T Consensus        59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~---~~~~----~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   59 SRAHHNALEKRRRAHLKDCFESLKDSVPL---LNGE----TRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             chhhhhhhhHHHHHHHHHHHHHHHHhCCC---CCCc----chhhhhHhhhhHHHHHHHHHhHH
Confidence            35567777999999999999999999999   3322    22238999999999999877543

>PRK13558 bacterio-opsin activator; Provisional

Probab=92.91  E-value=0.25  Score=53.20  Aligned_cols=59  Identities=19%  Similarity=0.222  Sum_probs=47.4

Q ss_pred             hHHHHhhcCcEEEEc---CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         136 PLLLEALEGFLFVVN---PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       136 ~lll~aldgfi~vvs---~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ..+++.....+++++   .+|.|+|+|+.+..++||++++++|+++.++.||++.......+
T Consensus       151 ~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~  212 (665)
T PRK13558        151 ERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAEL  212 (665)
T ss_pred             HHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHH
Confidence            345555555577776   37999999999999999999999999999999988876655443

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=91.91  E-value=0.096  Score=54.34  Aligned_cols=52  Identities=17%  Similarity=0.309  Sum_probs=45.5

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      ..++++++.-++++|.+|.|++++++...++||.+.+++|+++.+++++++.
T Consensus       265 ~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~  316 (607)
T PRK11360        265 ELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP  316 (607)
T ss_pred             HHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh
Confidence            4556677777999999999999999999999999999999999998876543

>KOG3960|consensus

Probab=91.89  E-value=0.28  Score=46.40  Aligned_cols=48  Identities=23%  Similarity=0.343  Sum_probs=39.2

Q ss_pred             hHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          54 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        54 ~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .-||||=.|.|+.|+.|+.---.+  |      ..+|=|..|||-||+||-.+..+
T Consensus       124 MRERRRLkKVNEAFE~LKRrT~~N--P------NQRLPKVEILRsAI~YIE~Lq~L  171 (284)
T KOG3960|consen  124 MRERRRLKKVNEAFETLKRRTSSN--P------NQRLPKVEILRSAIRYIERLQAL  171 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCCC--c------cccccHHHHHHHHHHHHHHHHHH
Confidence            347888899999999999875442  3      37999999999999999876643

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya

Probab=91.73  E-value=0.32  Score=33.99  Aligned_cols=39  Identities=15%  Similarity=0.161  Sum_probs=34.0

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      ++...+.+|.++++++..  ..++||.+.+++|.+++++++
T Consensus         4 ~i~~~d~~~~~~~~n~~~--~~~~g~~~~~~~~~~~~~~~~   42 (103)
T cd00130           4 GVIVLDLDGRILYANPAA--EQLLGYSPEELIGKSLLDLIH   42 (103)
T ss_pred             eEEEECCCCcEEEECHHH--HHHhCCCHHHHcCccHHHhcC
Confidence            456678899999999998  789999999999999888763

Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.

>KOG2588|consensus

Probab=91.50  E-value=0.15  Score=56.36  Aligned_cols=53  Identities=26%  Similarity=0.422  Sum_probs=46.7

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+.+|||=|.-+|.-|.||+.++|.   .      ..|+-|.++||.|++|++-....
T Consensus       276 kRtAHN~IEKRYRsSINDKI~eLk~lV~g---~------~aKl~kSavLr~ai~~i~dl~~~  328 (953)
T KOG2588|consen  276 KRTAHNIIEKRYRSSINDKIIELKDLVPG---T------EAKLNKSAVLRKAIDYIEDLQGY  328 (953)
T ss_pred             ccchhhHHHHHhhcchhHHHHHHHHhcCc---c------HhhhhhhhhHHHHHHHHHHhhcc
Confidence            36789999999999999999999999998   2      37999999999999999965443

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=91.33  E-value=0.15  Score=55.84  Aligned_cols=54  Identities=17%  Similarity=0.281  Sum_probs=45.6

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCC-CChHHH
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHH-GDHARF  190 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp-~D~~~~  190 (383)
                      .++++....+++++.+|.|+|+++++..++||+.++++|+.+.+++|+ .+....
T Consensus       140 ~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~  194 (799)
T PRK11359        140 IAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADN  194 (799)
T ss_pred             HHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHH
Confidence            456777778999999999999999999999999999999999998764 444333

>PLN03217 transcription factor ATBS1; Provisional

Probab=90.79  E-value=0.33  Score=38.42  Aligned_cols=45  Identities=31%  Similarity=0.430  Sum_probs=34.6

Q ss_pred             HHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          60 REQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        60 R~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      -|++|+.+..|..+||..   .. ..-..|..-+-||++||.|||.++.
T Consensus        19 ddqi~dLvsKLq~llPe~---r~-~r~s~k~saskvLqEtC~YIrsLhr   63 (93)
T PLN03217         19 EDQINDLIIKLQQLLPEL---RD-SRRSDKVSAARVLQDTCNYIRNLHR   63 (93)
T ss_pred             HHHHHHHHHHHHHHChHH---Hh-hhccccccHHHHHHHHHHHHHHHHH
Confidence            478999999999999992   11 0123577778899999999998763

>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 []

Probab=90.41  E-value=0.2  Score=39.47  Aligned_cols=38  Identities=8%  Similarity=0.096  Sum_probs=32.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +.-.+.||+|+++++..  ..++|+.+++++|+++.++++
T Consensus         8 i~v~D~~~~i~~~N~~~--~~~~~~~~~~~~G~~~~~~~~   45 (110)
T PF08448_consen    8 IFVIDPDGRIVYANQAA--AELFGVSPEELIGRSLFDLLP   45 (110)
T ss_dssp             EEEEETTSBEEEE-HHH--HHHHTSTHHHHTTSBHHHHSC
T ss_pred             eEEECCCCEEEEEHHHH--HHHhCCCHHHHhhccchhccc
Confidence            33448999999999998  789999999999999999873

The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=89.45  E-value=0.21  Score=52.43  Aligned_cols=47  Identities=26%  Similarity=0.540  Sum_probs=42.7

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCcccccc
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLI  182 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~i  182 (383)
                      +.+++.++.=|+|+|.+|+++|.|......+|+++++++|+++.|++
T Consensus       120 ~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~  166 (560)
T COG3829         120 EAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVV  166 (560)
T ss_pred             HHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence            45667777779999999999999999999999999999999999886

>PF12860 PAS_7: PAS fold

Probab=88.96  E-value=0.13  Score=42.18  Aligned_cols=42  Identities=19%  Similarity=0.334  Sum_probs=36.3

Q ss_pred             hhcCcEEEEcCCccEEEeecccccccCcccccc-cCCcccccc
Q psy7682         141 ALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEV-LGKSVYNLI  182 (383)
Q Consensus       141 aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el-~G~s~~d~i  182 (383)
                      +++.=|++.|.+|+++|.|+.+..++|+++..+ .|.++-+++
T Consensus         3 ~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~   45 (115)
T PF12860_consen    3 SLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLL   45 (115)
T ss_pred             CcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHH
Confidence            444448899999999999999999999999998 798886664

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]

Probab=85.71  E-value=0.72  Score=37.73  Aligned_cols=52  Identities=31%  Similarity=0.528  Sum_probs=43.9

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      ..++++....+++++.+|.++|+++.+..++||...+..+....++.+....
T Consensus       115 ~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~  166 (232)
T COG2202         115 RALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDE  166 (232)
T ss_pred             HHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCC
Confidence            4577777777888999999999999999999999888888888887665554

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=85.70  E-value=0.59  Score=48.81  Aligned_cols=51  Identities=24%  Similarity=0.460  Sum_probs=42.7

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCccc--ccccCCccccccCCCC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSR--QEVLGKSVYNLIHHGD  186 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~--~el~G~s~~d~iHp~D  186 (383)
                      +.+++++..=++++|.+|+|+++++++..+||+..  .+++|+.+.+++++.+
T Consensus       225 ~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~  277 (545)
T PRK15053        225 EALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPAD  277 (545)
T ss_pred             HHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCch
Confidence            34566656668899999999999999999999976  4799999999887654

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=84.92  E-value=0.41  Score=51.75  Aligned_cols=46  Identities=17%  Similarity=0.398  Sum_probs=40.6

Q ss_pred             HHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccC
Q psy7682         138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIH  183 (383)
Q Consensus       138 ll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iH  183 (383)
                      ++++++.=|+++|.+|+|+|+|+++..+||++..+++|+++.++++
T Consensus       208 il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~  253 (638)
T PRK11388        208 LLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLT  253 (638)
T ss_pred             HHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence            4555555589999999999999999999999999999999999875

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=84.67  E-value=0.91  Score=46.99  Aligned_cols=56  Identities=16%  Similarity=0.299  Sum_probs=45.6

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcc---cccccCCccccccCCCChHHHH
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYS---RQEVLGKSVYNLIHHGDHARFH  191 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~---~~el~G~s~~d~iHp~D~~~~~  191 (383)
                      +.++++++.-|+++|.+|+|+|+++++..+||++   ..+.+|..+.++.++.+...+.
T Consensus       224 ~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~~~~~~~  282 (542)
T PRK11086        224 QAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVSRLKEVL  282 (542)
T ss_pred             HHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCchhHHHHH
Confidence            4567777777999999999999999999999765   4578899998888766654443

>PRK13557 histidine kinase; Provisional

Probab=84.33  E-value=0.77  Score=47.27  Aligned_cols=33  Identities=9%  Similarity=0.044  Sum_probs=30.0

Q ss_pred             CCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         291 DRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       291 sldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.||+++|+++.+  ..++||.++|++|++++.++
T Consensus        50 ~~~g~i~~~N~a~--~~~~G~~~~e~~g~~~~~l~   82 (540)
T PRK13557         50 QPDNPIVFANRAF--LEMTGYAAEEIIGNNCRFLQ   82 (540)
T ss_pred             CCCCCEEEEcHHH--HHHhCCCHHHhcCCChHhhc
Confidence            4689999999998  89999999999999988776

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=83.58  E-value=0.46  Score=48.00  Aligned_cols=58  Identities=14%  Similarity=0.186  Sum_probs=49.7

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhh
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNC  193 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~  193 (383)
                      +.+++++..-+++++.+|.++|+++++..++|+...+..+..+.+++||++...+...
T Consensus       133 ~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  190 (494)
T TIGR02938       133 ESVVDAAPVAFVLLDPTGRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWREALAEN  190 (494)
T ss_pred             HHHHhcccceEEEEcCCCCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhhhhhhc
Confidence            4566666667889999999999999999999999999999999999999887766544

NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.

>TIGR00229 sensory_box PAS domain S-box

Probab=83.38  E-value=2.2  Score=31.26  Aligned_cols=37  Identities=11%  Similarity=0.165  Sum_probs=31.7

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.+|+++++++..  ..++||.+.+++|+++.+++
T Consensus        16 ~~~~d~~~~i~~~n~~~--~~~~g~~~~~~~~~~~~~~~   52 (124)
T TIGR00229        16 IIVIDLEGNILYVNPAF--EEIFGYSAEELIGRNVLELI   52 (124)
T ss_pred             EEEEcCCCcEEEEchHH--HHHhCCChHHhcCcchhhhc
Confidence            33457889999999998  79999999999999988865

The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.

>PRK10060 RNase II stability modulator; Provisional

Probab=82.86  E-value=0.79  Score=49.77  Aligned_cols=43  Identities=14%  Similarity=0.156  Sum_probs=36.3

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      -+.-.+.+|+|+++++..  ..++||.++||+|+++++++.++++
T Consensus       123 gI~i~D~~g~I~~~N~a~--~~l~Gy~~~eliG~~~~~l~~~~~~  165 (663)
T PRK10060        123 VIVILDSRGNIQRFNRLC--EEYTGLKEHDVIGQSVFKLFMSRRE  165 (663)
T ss_pred             eEEEEeCCCCEEEEcHHH--HHHHCcCHHHHcCCCHHHHhCChhh
Confidence            344557899999999998  8999999999999999888755554

>KOG3560|consensus

Probab=80.78  E-value=0.98  Score=47.23  Aligned_cols=51  Identities=8%  Similarity=0.118  Sum_probs=44.1

Q ss_pred             CceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHH
Q psy7682         283 IEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTK  336 (383)
Q Consensus       283 ~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~  336 (383)
                      ++.|..-.+.+|.+.|..+.+  ..||||...|++-.|+||++ |.+|..|+-+
T Consensus       120 LnGF~lVvt~eg~ifyAS~tI--edYLGFhQSDV~HQsVYdlI-HseDR~dfqr  170 (712)
T KOG3560|consen  120 LNGFALVVTAEGEIFYASATI--EDYLGFHQSDVMHQSVYDLI-HSEDRQDFQR  170 (712)
T ss_pred             cCCeEEEEecCceEEEehhhH--HhhhcccccchhhhhHHHHh-hhhhHHHHHH
Confidence            578999999999999999999  89999999999999999998 4555455544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	383
4f3l_A	361	Crystal Structure Of The Heterodimeric Clock:bmal1		1e-14
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		1e-13

>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 361

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 81/145 (55%), Gaps = 11/145 (7%)
Query: 50  VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ 109
           V++  +EK+RR+Q N  I+EL  ++            A K DK  +LQ++++ +R  K+ 
Sbjct: 14  VSRNKSEKKRRDQFNVLIKELGSMLPGN---------ARKMDKSTVLQKSIDFLRKHKET 64
Query: 110 ETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYS 169
              SDA +  +    KPT ++NE    L+LEAL+GF   +  DG + + +E++ S + + 
Sbjct: 65  TAQSDASEIRQ--DWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHL 122
Query: 170 RQEVLGKSVYNLIHHGDHARFHNCL 194
             +++ +S++N I  G+H+  +  L
Sbjct: 123 PSDLVDQSIFNFIPEGEHSEVYKIL 147

>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 387

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/135 (30%), Positives = 80/135 (59%), Gaps = 13/135 (9%)
Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDA 115
           EKRRR++ N++I+ELA L+   +      +++ K DK  +L+  V  ++ ++       A
Sbjct: 21  EKRRRDKMNSFIDELASLVPTCN------AMSRKLDKLTVLRMAVQHMKTLR------GA 68
Query: 116 VQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVL 174
                 ++ KPT ++++ L  L+L A +GFLFVV  D G + F +E++   + YS+ +++
Sbjct: 69  TNPYTEANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLI 128
Query: 175 GKSVYNLIHHGDHAR 189
           G+S+++ +H  D A+
Sbjct: 129 GQSLFDYLHPKDIAK 143

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	383
4f3l_A	361	Mclock, circadian locomoter output cycles protein	4e-44
4f3l_A	361	Mclock, circadian locomoter output cycles protein	1e-04
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	9e-36
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	2e-04
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	1e-21
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	9e-20
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	3e-04
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	6e-17
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	1e-04
3rty_A	339	Period circadian protein; PAS domain, signalling,	3e-15
3rty_A	339	Period circadian protein; PAS domain, signalling,	1e-04
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	2e-07
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	7e-07
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	1e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	1e-04
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	1e-06
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	3e-06
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	6e-05
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	5e-04
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-04
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	4e-04
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	9e-04

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score =  155 bits (393), Expect = 4e-44
 Identities = 59/285 (20%), Positives = 114/285 (40%), Gaps = 27/285 (9%)

Query: 50  VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ 109
           V++  +EK+RR+Q N  I+EL  ++         +    K DK  +LQ++++ +R  K+ 
Sbjct: 14  VSRNKSEKKRRDQFNVLIKELGSMLPG------NAR---KMDKSTVLQKSIDFLRKHKET 64

Query: 110 ETSSDAVQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYS 169
              SDA +  +    KPT ++NE    L+LEAL+GF   +  DG + + +E++ S + + 
Sbjct: 65  TAQSDASEIRQ--DWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHL 122

Query: 170 RQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTA--------- 220
             +++ +S++N I  G+H+  +  L     + ++ T +      +               
Sbjct: 123 PSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPK 182

Query: 221 -STPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPP----T 275
             +            S    +  +  G E     +   S E   C +   R   P     
Sbjct: 183 EPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKE 242

Query: 276 DKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
              +  P E+FT +       + +D          YL   V   +
Sbjct: 243 MCTVEEPNEEFTSRHSLEWKFLFLDHRAPP--IIGYLPFEVLGTS 285

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 3/54 (5%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLV 195
           F    + +    F        I Y   EVLG S Y+  H  D    A+ H  L+
Sbjct: 253 FTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHEHLM 306

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score =  133 bits (336), Expect = 9e-36
 Identities = 57/291 (19%), Positives = 121/291 (41%), Gaps = 53/291 (18%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDA 115
           EKRRR++ N++I+ELA L+   +      +++ K DK  +L+  V  ++ ++    +++ 
Sbjct: 21  EKRRRDKMNSFIDELASLVPTCN------AMSRKLDKLTVLRMAVQHMKTLRG---ATNP 71

Query: 116 VQQGEVSSSKPTVITNEVLGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVL 174
             +   ++ KPT ++++ L  L+L A +GFLFVV  D G + F +E++   + YS+ +++
Sbjct: 72  YTE---ANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLI 128

Query: 175 GKSVYNLIHHGDHARFHNCLVPS--SHQVNAWTSDSGGQAGK----RPSLTASTPNRTFN 228
           G+S+++ +H  D A+    L  S  + +     + +G          PS   S   R+F 
Sbjct: 129 GQSLFDYLHPKDIAKVKEQLSSSDTAPRERLIDAKTGLPVKTDITPGPSRLCSGARRSFF 188

Query: 229 IRLLISSTHLTAGLSRAGGENGQ-----------------------------DDSGDVSS 259
            R+  +   +            +                             D+  D   
Sbjct: 189 CRMKCNRPSVKVEDKDFASTCSKKKADRKSFCTIHSTGYLKSWPPTKMGLDEDNEPDNEG 248

Query: 260 EGGPCLMCVAR-----RIPPTDKQLSAPIEQFTMKLDRSGTIIGMDTSGVS 305
               CL+ + R        P + ++     ++  +    G  + +D    +
Sbjct: 249 CNLSCLVAIGRLHSHMVPQPANGEIRVKSMEYVSRHAIDGKFVFVDQRATA 299

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPSSHQV 201
           ++     DG   F  +   + + Y  QE+LG S Y   H  D    A  H  ++ +  ++
Sbjct: 280 YVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQTREKI 339

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Length = 309

 Score = 93.1 bits (231), Expect = 1e-21
 Identities = 26/212 (12%), Positives = 65/212 (30%), Gaps = 33/212 (15%)

Query: 126 PTVITNE----VLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYN 180
            +  + E    +    +++  + F   V+   G + + +  + S     +          
Sbjct: 4   GSSYSMEQVEGITSEYIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDAKFVE 63

Query: 181 LIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISST---- 236
            +   D + FH+    + +++  W+  SG  +  +         ++F  R+ +       
Sbjct: 64  FLAPHDVSVFHSYT--TPYKLPPWSVCSGLDSFTQE----CMEEKSFFCRVSVGKHHENE 117

Query: 237 ------HLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSAPI--EQFTM 288
                  +T  L +   + G +           C + +A R+    +    P     FT 
Sbjct: 118 IRYQPFRMTPYLVKVQEQQGAESQ--------LCCLLLAERVHSGYEAPRIPPEKRIFTT 169

Query: 289 KLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
               +     +D   V      YL + +    
Sbjct: 170 THTPNCLFQAVDERAVP--LLGYLPQDLIETP 199

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus} Length = 320

 Score = 88.1 bits (218), Expect = 9e-20
 Identities = 35/224 (15%), Positives = 61/224 (27%), Gaps = 33/224 (14%)

Query: 114 DAVQQGEVSSSKPTVITNE----VLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRY 168
               + E  +   +  T E    +     L   + F   V+   G + + +E     +R 
Sbjct: 3   LGSPEFEPCAMDMSTYTLEELEHITSEYTLRNQDTFSVAVSFLTGRIVYISEQAGVLLRC 62

Query: 169 SRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFN 228
            R    G     L+   D   F+    PS           G        L   T  ++  
Sbjct: 63  KRDVFRGARFSELLAPQDVGVFYGSTTPS------RLPTWGTGTSAGSGLKDFTQEKSVF 116

Query: 229 IRLLISST----------HLTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQ 278
            R+                LT  +++    +G            PC + +A RI    + 
Sbjct: 117 CRIRGGPDRDPGPRYQPFRLTPYVTKIRVSDGAPAQ--------PCCLLIAERIHSGYEA 168

Query: 279 LSAPI--EQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT 320
              P     FT +   S     +D          YL + +    
Sbjct: 169 PRIPPDKRIFTTRHTPSCLFQDVDERAA--PLLGYLPQDLLGAP 210

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus} Length = 320

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 12/60 (20%), Positives = 19/60 (31%), Gaps = 3/60 (5%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPSSHQV 201
           F     P        E     + Y  Q++LG  V   +H  D       H  ++  + Q 
Sbjct: 178 FTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHKKILQLAGQP 237

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus} Length = 317

 Score = 79.7 bits (196), Expect = 6e-17
 Identities = 29/197 (14%), Positives = 50/197 (25%), Gaps = 15/197 (7%)

Query: 117 QQGEVSSSKPTVITNEVLGPL----LLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQ 171
            +        TV + E L  L      +  + F  V +   G +   +E     +   R 
Sbjct: 6   PEFPGRLEDVTVYSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRG 65

Query: 172 EVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRL 231
            +      +L+   D   F+    P+                +R S     P + F  R+
Sbjct: 66  FLKSVHFVDLLAPQDVRAFYAHTAPTQLPFWN-------NWTQRASQYECAPAKPFFCRI 118

Query: 232 LISSTHLTAGLS--RAGGENGQDDSGDVSSEGGPCLMCVARRIPP-TDKQLSAPIEQFTM 288
                      S  R         S         CL  V +        ++      FT 
Sbjct: 119 CGGGDREKRHYSPFRILPYLVHVHSSAQPEPEPCCLTLVEKIHSGYEAPRIPVDKRIFTT 178

Query: 289 KLDRSGTIIGMDTSGVS 305
                   + +D   V 
Sbjct: 179 THTPGCVFLEVDERAVP 195

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus} Length = 317

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 3/54 (5%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLV 195
           F     P        E     + Y  Q+++G S+   +H  D       H  ++
Sbjct: 176 FTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQKVL 229

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A Length = 339

 Score = 75.1 bits (184), Expect = 3e-15
 Identities = 38/188 (20%), Positives = 69/188 (36%), Gaps = 12/188 (6%)

Query: 143 EGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQV 201
           + F  V++  DG V + T +I   + Y R   LG+S  + +H  D A F + +       
Sbjct: 3   DSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIA 62

Query: 202 NAWTSDSGGQA-----GKRPSLTASTPNRTFNIRLLISSTHLTAGLSRAGGENGQDDSGD 256
            +  S             R      +       R +           R   E  + D+  
Sbjct: 63  ESRGSVPKDAKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYM 122

Query: 257 VSSEGGPCLMCVARRIPPT----DKQLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYL 312
           VS+     L+  A  I  +    D+ LS    +F ++   +G I  +D++ VS     YL
Sbjct: 123 VSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVS--ALGYL 180

Query: 313 NKAVACKT 320
            + +  ++
Sbjct: 181 PQDLIGRS 188

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A Length = 339

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 3/56 (5%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH---ARFHNCLVPS 197
           F       G ++       S + Y  Q+++G+S+ +  HH D       +  ++  
Sbjct: 156 FAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKK 211

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis} Length = 111

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 12/68 (17%), Positives = 26/68 (38%)

Query: 135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
           G   L+       V+  +G + + + N K  + Y + E++G  +   +H  D     +  
Sbjct: 1   GEFPLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYF 60

Query: 195 VPSSHQVN 202
               H + 
Sbjct: 61  YNEHHLMP 68

>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

 Score = 46.9 bits (112), Expect = 7e-07
 Identities = 13/58 (22%), Positives = 22/58 (37%)

Query: 137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
           L +     F+   N +G   F      + + Y  QE+LGK++    H  D     +  
Sbjct: 6   LNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSF 63

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 44.6 bits (106), Expect = 1e-06
 Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           E+RRR++ NN+I +L+++I       SM S      K  IL +  + I+ ++Q  
Sbjct: 13  ERRRRDKINNWIVQLSKIIP----DSSMESTKSGQSKGGILSKASDYIQELRQSN 63

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)

Query: 6  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETV 50
          E+RRR++ NN+I +L+++I       SM S      K  IL +  
Sbjct: 13 ERRRRDKINNWIVQLSKIIP----DSSMESTKSGQSKGGILSKAS 53

>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

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 14/42 (33%), Positives = 20/42 (47%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
           FL   + D    +C + I   I Y  +E+LG+S Y   H  D
Sbjct: 11  FLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALD 52

>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

 Score = 45.0 bits (107), Expect = 3e-06
 Identities = 11/42 (26%), Positives = 18/42 (42%)

Query: 145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD 186
           F+     +G   +  +   + + Y  QE+LG S Y   H  D
Sbjct: 15  FITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDD 56

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 9/57 (15%)

Query: 54  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
             EKR R   N+ I EL +L+              K +K A+L++ ++ IR ++   
Sbjct: 12  AIEKRYRSSINDKIIELKDLVVG---------TEAKLNKSAVLRKAIDYIRFLQHSN 59

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 12/72 (16%)

Query: 4  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVN--QCLNEKRRR- 60
            EKR R   N+ I EL +L+              K +K A+L++ ++  + L    ++ 
Sbjct: 12 AIEKRYRSSINDKIIELKDLVVG---------TEAKLNKSAVLRKAIDYIRFLQHSNQKL 62

Query: 61 EQENNYIEELAE 72
          +QEN  +     
Sbjct: 63 KQENLSLRTAVH 74

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 8/58 (13%)

Query: 54  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQET 111
             E++RR+   +    L + + +            K  +  IL +    I+ ++++  
Sbjct: 18  ALERKRRDHIKDSFHSLRDSVPSLQ--------GEKASRAQILDKATEYIQYMRRKNH 67

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui} Length = 125

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 3/57 (5%), Positives = 18/57 (31%)

Query: 138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
           L+      +  +  +G +     ++   +      ++G+ +  ++      +     
Sbjct: 24  LVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQRLEAG 80

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis} Length = 129

 Score = 38.2 bits (89), Expect = 9e-04
 Identities = 11/57 (19%), Positives = 25/57 (43%)

Query: 138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL 194
            ++ L   + +VN +G++  C +     +   +  + G+   N +     AR+ N L
Sbjct: 12  FIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLL 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	383
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	100.0
4f3l_A	361	Mclock, circadian locomoter output cycles protein	100.0
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	100.0
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	100.0
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	100.0
3rty_A	339	Period circadian protein; PAS domain, signalling,	99.96
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	99.61
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.56
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.33
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.28
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.23
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.23
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.2
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.1
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.02
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	98.88
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.88
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	98.84
4ati_A	118	MITF, microphthalmia-associated transcription fact	98.71
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	98.67
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	98.64
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.63
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	98.63
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.62
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	98.57
3rty_A	339	Period circadian protein; PAS domain, signalling,	98.56
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	98.56
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.52
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	98.52
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	98.48
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.33
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	98.29
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	98.29
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	98.29
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	98.27
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.25
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.16
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	98.12
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	98.11
3nja_A	125	Probable ggdef family protein; structural genomics	98.06
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	98.04
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	98.02
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.02
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	97.98
3mr0_A	142	Sensory box histidine kinase/response regulator; P	97.95
3eeh_A	125	Putative light and redox sensing histidine kinase;	97.95
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	97.93
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	97.92
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	97.92
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	97.89
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	97.87
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	97.85
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	97.83
3olo_A	118	Two-component sensor histidine kinase; structural	97.76
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	97.74
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	97.74
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	97.7
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	97.67
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	97.67
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	97.65
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.6
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	97.57
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	97.56
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	97.56
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	97.55
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	97.48
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	97.42
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	97.4
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	97.37
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	97.36
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	97.35
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	97.27
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	97.25
4ath_A	83	MITF, microphthalmia-associated transcription fact	97.19
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	97.18
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	97.16
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	97.15
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	97.06
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	97.01
4h10_B	71	Circadian locomoter output cycles protein kaput; B	96.98
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	96.94
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	96.93
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	96.92
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	96.8
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	96.77
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	96.63
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	96.53
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	96.51
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	96.4
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	96.37
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	96.35
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	96.21
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	96.18
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	96.11
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	96.03
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	95.97
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	95.92
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	95.89
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	95.82
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	95.71
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	95.67
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	95.58
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	95.55
3olo_A	118	Two-component sensor histidine kinase; structural	95.48
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	95.47
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	95.41
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	95.38
3s7o_A	343	Bacteriophytochrome; biliverdin, PAS, GAF, photore	95.3
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	95.15
3cax_A	369	Uncharacterized protein PF0695; structural genomic	95.14
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	95.1
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	94.96
4e04_A	327	Bacteriophytochrome (light-regulated signal trans	94.95
3mr0_A	142	Sensory box histidine kinase/response regulator; P	94.75
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.67
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	94.62
3nja_A	125	Probable ggdef family protein; structural genomics	94.5
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	94.29
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	94.13
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	94.1
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	93.78
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	93.34
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	93.25
3zq5_A	520	Phytochrome-like protein CPH1; arginine finger, ta	93.1
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	92.93
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	92.89
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	92.75
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	92.52
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	92.37
1a0a_A	63	BHLH, protein (phosphate system positive regulator	91.96
4ati_A	118	MITF, microphthalmia-associated transcription fact	91.67
3eeh_A	125	Putative light and redox sensing histidine kinase;	91.6
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	91.59
3nhq_A	505	Bacteriophytochrome; photoreceptor, PAS, signaling	91.5
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	91.15
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	90.94
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	90.86
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	90.81
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	90.46
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	90.06
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	89.89
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	89.22
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	89.25
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	88.08
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	87.49
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	85.7
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	81.99
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	80.54

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=100.00  E-value=8.6e-50  Score=400.21  Aligned_cols=312  Identities=21%  Similarity=0.315  Sum_probs=216.5

Q ss_pred             hhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCCCcccccCcc
Q psy7682          42 KCAILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEV  121 (383)
Q Consensus        42 ~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~~~~~~~~~~  121 (383)
                      .++..+++.+|+.+||+||+++|+.|.||+.|||.   ++   +...||||++||++||+|||+++....   +..+   
T Consensus         7 ~~~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~---~~---~~~~k~dk~~il~~~~~~l~~~~~~~~---~~~~---   74 (387)
T 4f3l_B            7 QGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPT---CN---AMSRKLDKLTVLRMAVQHMKTLRGATN---PYTE---   74 (387)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH---HH---HCSSCCCHHHHHHHHHHHHHHHHCC------------
T ss_pred             cchhhhhcccccchhhcchHHHHHHHHHHHHhcCC---CC---ccccccCHHHHHHHHHHHHHHhhcccc---cccc---
Confidence            45667788899999999999999999999999998   33   245899999999999999999875432   1111   


Q ss_pred             CCCCCCcCCccchhhHHHHhhcCcEEEEcCC-ccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCC
Q psy7682         122 SSSKPTVITNEVLGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQ  200 (383)
Q Consensus       122 ~~~~P~~~~~~~~~~lll~aldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~  200 (383)
                      .+++|++++++++.++++++++||++|++.+ |+|+|||++++.+|||+++||+|++++||+||+|++.+.++|......
T Consensus        75 ~~~~~~~~~~~~~~~~ll~~~~gfi~v~~~~~G~i~yvs~~~~~~lG~~~~el~g~~~~~~ihp~D~~~~~~~L~~~~~~  154 (387)
T 4f3l_B           75 ANYKPTFLSDDELKHLILRAADGFLFVVGCDRGKILFVSESVFKILNYSQNDLIGQSLFDYLHPKDIAKVKEQLSSSDTA  154 (387)
T ss_dssp             CCSSCTTSCHHHHHHHHHHTCCSEEEEEETTTCBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHSCC---
T ss_pred             cccCcccCCHHHHHHHHHhcCCCEEEEEecCCeEEEEEchhhHHHcCCCHHHHCCCcHHHhcCCCCHHHHHHHhcccccC
Confidence            3578999999999999999999999999997 999999999999999999999999999999999999999999754211


Q ss_pred             C----CCCCCCCCCCCC--CCCCCCCCCCceeEEEEEEEcCC------------------------eeeee-eec-CC-C
Q psy7682         201 V----NAWTSDSGGQAG--KRPSLTASTPNRTFNIRLLISST------------------------HLTAG-LSR-AG-G  247 (383)
Q Consensus       201 ~----~~~~s~s~~~~g--~~~~~~~~~~~rsF~cRmk~~~~------------------------~i~~~-~~~-~~-~  247 (383)
                      +    +...+.......  ........+.+|+|+|||+|...                        .++|+ +.. ++ .
T Consensus       155 p~~~~~~~~tg~~~~~e~~~~~~~~~~g~~rsF~cRmr~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~G~l~~~~~~  234 (387)
T 4f3l_B          155 PRERLIDAKTGLPVKTDITPGPSRLCSGARRSFFCRMKCNRPSVKVEDKDFASTCSKKKADRKSFCTIHSTGYLKSWPPT  234 (387)
T ss_dssp             -----------------------CCCGGGEEEEEEEEECSCC-------------------CCSEEEEEEEEEEEC----
T ss_pred             ccccccCcccCCccCCCCCCcccccccCCceeEEEeeecccCCcccccccccccccccccCCCceEEEEEEEEEeccccc
Confidence            1    000000000000  00011124678999999999642                        24453 332 21 1


Q ss_pred             CCCCCCC--CCCCCCCCceEEEEEeecCCCCc-----ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCC
Q psy7682         248 ENGQDDS--GDVSSEGGPCLMCVARRIPPTDK-----QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKT  320 (383)
Q Consensus       248 ~~g~d~~--~~~~~~~~~~LVav~r~ip~~~~-----~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S  320 (383)
                      ..+.+.+  .+....+..||||++++++++..     ++..+..+|++||++||+|+|||+++  ..+|||.|+||+|++
T Consensus       235 ~~~~~~~~~~~~~~~~~~~lvai~r~~~~~~~~~~~~ei~~~~~~fi~~~~~dg~~~~vn~~~--~~ilGY~~eEl~g~~  312 (387)
T 4f3l_B          235 KMGLDEDNEPDNEGCNLSCLVAIGRLHSHMVPQPANGEIRVKSMEYVSRHAIDGKFVFVDQRA--TAILAYLPQELLGTS  312 (387)
T ss_dssp             ---------------CCCEEEEEEEECCCSCCSCCCSSSCBCCCEEEEEECTTSBEEEECTHH--HHHHCCCHHHHTTSB
T ss_pred             ccccccccccccCCCcceEEEEEEecccCCCCCCcccccccCCceEEEEECCCCEEEEECCCc--ccccCCCHHHHcCCc
Confidence            1111111  11123456799999999765432     34445689999999999999999998  899999999999999


Q ss_pred             ccceecCCCCchhHHHHHHHHHHhhhhcccceeecccceecccCCccccccCCcceEEEEee
Q psy7682         321 SATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIR  382 (383)
Q Consensus       321 ~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~~~~~~~~~~~~~~~~~~~~~  382 (383)
                      +|+|+ ||+|   ...+ .+.+.+.   +-..++..+..|||+.+       +++|+|+..+
T Consensus       313 ~~~~i-HpdD---~~~~-~~~~~~~---l~~~~~~~~~eyR~~~k-------dG~~vWv~~~  359 (387)
T 4f3l_B          313 CYEYF-HQDD---IGHL-AECHRQV---LQTREKITTNCYKFKIK-------DGSFITLRSR  359 (387)
T ss_dssp             GGGTB-CHHH---HHHH-HHHHHHH---TTCSSCEECCCEEEECT-------TSCEEEEEEE
T ss_pred             HHHee-CHHH---HHHH-HHHHHHH---HhcCCCeeeEEEEEEcc-------CCCEEEEEEE
Confidence            99988 5655   3222 1112121   11356677778886554       4578888753

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=100.00  E-value=9.6e-47  Score=374.42  Aligned_cols=298  Identities=23%  Similarity=0.356  Sum_probs=211.6

Q ss_pred             hhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhccCCCcccccCccCCCC
Q psy7682          46 LQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQETSSDAVQQGEVSSSK  125 (383)
Q Consensus        46 ~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~~~~~~~~~~~~~~~~  125 (383)
                      ..++..|+.+||+||+++|..|.+|++|||.   .      .+||||++||++||+|||.++.+.......  ....+|+
T Consensus        10 ~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~---~------~~~~dk~~il~~~~~~~~~~~~~~~~~~~~--~~~~~~~   78 (361)
T 4f3l_A           10 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPG---N------ARKMDKSTVLQKSIDFLRKHKETTAQSDAS--EIRQDWK   78 (361)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCCS---S------SCCCCHHHHHHHHHHHHHHHHHHHTSCSCG--GGTSCCS
T ss_pred             chhhhhhhHHHHHHHHHHHHHHHHHHHhCCC---C------CCCcCHHHHHHHHHHHHHHHHhhccccccc--ccccccC
Confidence            3456688899999999999999999999995   1      379999999999999999988775422111  1124689


Q ss_pred             CCcCCccchhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCC
Q psy7682         126 PTVITNEVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWT  205 (383)
Q Consensus       126 P~~~~~~~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~  205 (383)
                      |++++++++.++++++++||++|++.+|+|+|+|+++..+|||+++||+|+++++|+||+|++.+.+++.........+.
T Consensus        79 ~~~~~~~~~~~~~l~a~~~~i~v~~~~G~i~yvs~~~~~~lGy~~~el~g~~~~~~ihp~D~~~~~~~l~~~~~~~~~~~  158 (361)
T 4f3l_A           79 PTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLT  158 (361)
T ss_dssp             CTTSCHHHHHHHHHHHTTEEEEEEETTSBEEEECTTHHHHHCCCHHHHTTSBGGGGSCGGGHHHHHHHHHHCCCCCCSSS
T ss_pred             cccccHHHHHHHHHHhcCceEEEEcCCccEEEEechhhhhcCCCHHHhcCCcHHHhcCHHHHHHHHHHhccCCCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999975431100000


Q ss_pred             CCCCCCCCCCCCCCCCCCceeEEEEEEEcCC---------eeee-e-eecCC-----CCCCCCCC----CCCCCCCCceE
Q psy7682         206 SDSGGQAGKRPSLTASTPNRTFNIRLLISST---------HLTA-G-LSRAG-----GENGQDDS----GDVSSEGGPCL  265 (383)
Q Consensus       206 s~s~~~~g~~~~~~~~~~~rsF~cRmk~~~~---------~i~~-~-~~~~~-----~~~g~d~~----~~~~~~~~~~L  265 (383)
                                +........++|+|||++...         .++| + +.++.     ...|...+    .....++..||
T Consensus       159 ----------~~~~~~~~~~~f~cr~~~~~~~~~~~~~y~~i~~~G~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~l  228 (361)
T 4f3l_A          159 ----------PEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCF  228 (361)
T ss_dssp             ----------CGGGCGGGEEEEEEEEECCCSCSSSCCCEEEEEEEEEEEECC------------------------CEEE
T ss_pred             ----------cccccccCceeEEEEEeccCCCCCCCCceEEEEEEEEEEeccCCCcccccCcccccccccCccCCCceEE
Confidence                      001123457899999998642         1222 2 22221     11121111    01123457899


Q ss_pred             EEEEeecCCCCc----ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHH
Q psy7682         266 MCVARRIPPTDK----QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKA  341 (383)
Q Consensus       266 Vav~r~ip~~~~----~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~  341 (383)
                      ||++|+++....    .++.+..+|+++|++||+|+|||+++  ..++||.|+||+|+++|+|+ ||+|   ...+    
T Consensus       229 vai~r~~~~~~~~e~~~i~~~~~~f~~~~~~dg~~~~vn~~~--~~ilGY~~eEl~g~~~~~~i-HpdD---~~~~----  298 (361)
T 4f3l_A          229 VATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRA--PPIIGYLPFEVLGTSGYDYY-HVDD---LENL----  298 (361)
T ss_dssp             EEEEEESSCCSSEEECSCSSSCCEEEEEECTTSBEEEECTTS--HHHHCCCHHHHTTSBGGGGB-CHHH---HHHH----
T ss_pred             EEEEecCCCCcccccccccCCcceeEEEEcCCceEEEECChh--hhhhCcCHHHHcCCCHHHeE-CHHH---HHHH----
Confidence            999999865542    25556689999999999999999998  89999999999999999987 5555   2222    


Q ss_pred             HHhhhhcccceeecccceecccCCccccccCCcceEEEEee
Q psy7682         342 LLLSICTDYALVQTDTCMYRSSPSCFGLQGASRTSLWQRIR  382 (383)
Q Consensus       342 ~~~~~~~~~~~~q~~t~~yR~~~~~~~~~~~~~~~~~~~~~  382 (383)
                       ...+..++..|+..+..||+..+       +++|+|+..+
T Consensus       299 -~~~~~~~l~~g~~~~~eyR~~~k-------dG~~vWv~~~  331 (361)
T 4f3l_A          299 -AKCHEHLMQYGKGKSCYYRFLTK-------GQQWIWLQTH  331 (361)
T ss_dssp             -HHHHHHHHHHSEEECCCEEEECT-------TSEEEEEEEE
T ss_pred             -HHHHHHHHhCCCcceEEEEEEec-------CCCEEEEEEE
Confidence             11122334567777778886554       4578888643

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=100.00  E-value=1.4e-37  Score=304.40  Aligned_cols=228  Identities=17%  Similarity=0.166  Sum_probs=157.3

Q ss_pred             CCCCCcCCccchhhH----HHHhhcCcEEEEcCC-ccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         123 SSKPTVITNEVLGPL----LLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       123 ~~~P~~~~~~~~~~l----ll~aldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      +..+++++++++.++    +|+|+|||++||+++ |+|+|+|++|+.+|||+|+||+|+|+|||+||+|+++|+++|++.
T Consensus        12 ~~~~~~~s~eel~~l~~e~lLqaldGF~~vvs~~~G~i~yvS~sv~~~Lg~~~~~l~g~s~~d~iHp~D~~~f~~qL~~~   91 (320)
T 4dj2_A           12 AMDMSTYTLEELEHITSEYTLRNQDTFSVAVSFLTGRIVYISEQAGVLLRCKRDVFRGARFSELLAPQDVGVFYGSTTPS   91 (320)
T ss_dssp             --CCSEECHHHHHHHHHHHTTSCSSEEEEEEETTTCBEEEECTHHHHHHTSCSTTTTTSBGGGGBCHHHHHHHHHHCCTT
T ss_pred             ccCccccCHHHHHHHHHHHHHhccCCEEEEEECCCceEEEECcHHHHHhCcCHHHHcCCcHHHhcCHHHHHHHHHhhccc
Confidence            345788899999887    699999999999995 999999999999999999999999999999999999999999875


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEEEcCC--------eeeee-eecCCCCCCCCCCCCCCCCCCceEEEE
Q psy7682         198 SHQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISST--------HLTAG-LSRAGGENGQDDSGDVSSEGGPCLMCV  268 (383)
Q Consensus       198 ~~~~~~~~s~s~~~~g~~~~~~~~~~~rsF~cRmk~~~~--------~i~~~-~~~~~~~~g~d~~~~~~~~~~~~LVav  268 (383)
                      .  ...|.+.+  +.+..  ....+.+|+|+|||||+..        .++|+ +.+...  ..+     ......++|++
T Consensus        92 ~--lp~~~~~~--~~~~~--~~~~~~~rsF~CRmr~~l~k~~~~~Y~~~~~~g~lk~~~--~~~-----g~~~~~~~li~  158 (320)
T 4dj2_A           92 R--LPTWGTGT--SAGSG--LKDFTQEKSVFCRIRGGPDRDPGPRYQPFRLTPYVTKIR--VSD-----GAPAQPCCLLI  158 (320)
T ss_dssp             T--CCBTTC-----------------CCCEEEEECCC-------CCEEEEEEEEEEEEC--C--------CCCEEEEEEE
T ss_pred             C--CCCcccCc--ccccc--cccCCCceeEEEEEEEeccCCCcccEEEEEEEEEecccc--cCC-----CCcccceeeee
Confidence            2  22232211  00000  0124578999999999642        24453 332111  111     11234566666


Q ss_pred             EeecCCCCc--ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhh
Q psy7682         269 ARRIPPTDK--QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSI  346 (383)
Q Consensus       269 ~r~ip~~~~--~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~  346 (383)
                      +.|++++..  .+.....+|++||++||+|+|||+++  ..+|||.|+||+|+++|+|+ ||+| +.  .+ .++    +
T Consensus       159 a~~~~s~~~~~~i~~~~~~Fitrh~~dG~~~yvd~~~--~~lLGY~peELig~s~~~~v-HPdD-~~--~~-~~~----~  227 (320)
T 4dj2_A          159 AERIHSGYEAPRIPPDKRIFTTRHTPSCLFQDVDERA--APLLGYLPQDLLGAPVLLFL-HPED-RP--LM-LAI----H  227 (320)
T ss_dssp             EEECCCSSSSSCCCGGGCEEEEEECTTCBEEEECTTH--HHHHSCCHHHHTTSBGGGGB-CGGG-HH--HH-HHH----H
T ss_pred             eeeccCccccccccCCCceEEEEecCCceEEEcCcce--eccCCcChHHHcCCcHHHhC-CHHH-HH--HH-HHH----H
Confidence            778866532  23344589999999999999999998  89999999999999999998 5666 32  21 111    1


Q ss_pred             hcccc-eeecc-cceecccCCccccccCCcceEEEEe
Q psy7682         347 CTDYA-LVQTD-TCMYRSSPSCFGLQGASRTSLWQRI  381 (383)
Q Consensus       347 ~~~~~-~~q~~-t~~yR~~~~~~~~~~~~~~~~~~~~  381 (383)
                      ..+.. +||.. +..|||+.++       ++|+|++.
T Consensus       228 ~~~l~~~g~~~~~~~yR~~~kd-------G~~vwvet  257 (320)
T 4dj2_A          228 KKILQLAGQPFDHSPIRFCARN-------GEYVTMDT  257 (320)
T ss_dssp             HHHTTSSSCCEECCCEEEECSS-------SCEEEEEC
T ss_pred             HHHHhcCCCcccceEEEEEccC-------CCEEEEEE
Confidence            12222 56766 5688866554       46888753

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=100.00  E-value=1.2e-36  Score=297.41  Aligned_cols=191  Identities=16%  Similarity=0.140  Sum_probs=140.5

Q ss_pred             CCCCcCCccchhhH----HHHhhcCcEEEEcCC-ccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCC
Q psy7682         124 SKPTVITNEVLGPL----LLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSS  198 (383)
Q Consensus       124 ~~P~~~~~~~~~~l----ll~aldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~  198 (383)
                      ..+++++++|+.++    +|+|+|||++||+.+ |+|+|||++++.+|||+|+||+|++++||+||+|+++|+++|+...
T Consensus        13 ~~~~~~s~~el~~~~~e~~L~aldgF~~vvs~~~G~i~yvS~~~~~~Lg~~~~el~g~s~~d~ihp~D~~~f~~ql~~~~   92 (317)
T 4dj3_A           13 EDVTVYSLEDLTALASEHTSKNTDTFAAVFSFLSGRLVHISEQAALILNSKRGFLKSVHFVDLLAPQDVRAFYAHTAPTQ   92 (317)
T ss_dssp             CCCCBCCTTTTTSTTHHHHTSCTTEEEEEEETTTCBEEEECTTHHHHTTCCHHHHHTSBGGGGBCGGGHHHHHHHTCTTT
T ss_pred             cCccccCHHHHHhhhhHHHHhccCCEEEEEEcCCcEEEEECCHHHHHcCCCHHHHcCCchhhhcChhhHHHHHHhhcccC
Confidence            34567788888766    999999999999996 9999999999999999999999999999999999999999995332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCceeEEEEEEEcCC-------eeeee-eecCCCCCCCCCCCCCCCCCCceEEEEEe
Q psy7682         199 HQVNAWTSDSGGQAGKRPSLTASTPNRTFNIRLLISST-------HLTAG-LSRAGGENGQDDSGDVSSEGGPCLMCVAR  270 (383)
Q Consensus       199 ~~~~~~~s~s~~~~g~~~~~~~~~~~rsF~cRmk~~~~-------~i~~~-~~~~~~~~g~d~~~~~~~~~~~~LVav~r  270 (383)
                        ...+....  + ++  .......+|+|+|||||+.+       .++|+ |.....  +..    ...+...||||+++
T Consensus        93 --lP~~~~~~--~-~~--~~~~~~~~rsF~CRmr~g~~~~~~~y~~~~~~g~l~~~~--~~~----~~~~~~~clv~v~~  159 (317)
T 4dj3_A           93 --LPFWNNWT--Q-RA--SQYECAPAKPFFCRICGGGDREKRHYSPFRILPYLVHVH--SSA----QPEPEPCCLTLVEK  159 (317)
T ss_dssp             --CCCCC---------------CCCCCCEEEEECCCCCSSSCCCEEEEEEEEEEECC--CCS----SSCSCEEEEEEEEE
T ss_pred             --CCCcCCCc--c-cc--cccCCCCCceEEEEEeCCCCCCCCceEEEEEEeEEEecc--CCC----CCCCCceEEEEEEe
Confidence              11111100  0 00  01135678999999999654       34553 332111  100    01234579999987


Q ss_pred             ecCCCCc-ccCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         271 RIPPTDK-QLSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       271 ~ip~~~~-~i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      ..|.+.. .+.....+|++||++||+|+|||+++  ..+|||.|+||+|+++|+|+ ||+|
T Consensus       160 ~~~~~~~~~~~~~~~~Fitrh~~dG~~~yvs~~~--~~lLGY~peELig~s~~~~v-HPdD  217 (317)
T 4dj3_A          160 IHSGYEAPRIPVDKRIFTTTHTPGCVFLEVDERA--VPLLGYLPQDLIGTSILTYL-HPED  217 (317)
T ss_dssp             CCCTTSSSCCCGGGCEEEEEECTTSBEEEECTTH--HHHHSCCHHHHTTSBGGGGB-CTTT
T ss_pred             cCCCcCCCCcccCCCceEEEecCCCeEEEEChHH--hhhcCcChHHHcCCCHHHeE-CHHH
Confidence            6664432 11112369999999999999999998  89999999999999999998 6777

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=100.00  E-value=4.4e-36  Score=292.46  Aligned_cols=218  Identities=13%  Similarity=0.114  Sum_probs=136.8

Q ss_pred             hhhHHHHhhcCcEEEEcCC-ccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQA  212 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~  212 (383)
                      .++++|+|+|||++||+++ |+|+|+|++++.+|||+|+||+|+|++||+||+|+++++++|++..  ...+....+.+.
T Consensus        16 ~~~lll~a~dgF~~vvs~~~G~i~yvS~s~~~~Lg~~~~el~g~s~~d~iHp~D~~~~~~~L~~~~--lp~~~~~~~~~~   93 (309)
T 3gdi_A           16 TSEYIVKNADMFAVAVSLVSGKILYISNQVASIFHCKKDAFSDAKFVEFLAPHDVSVFHSYTTPYK--LPPWSVCSGLDS   93 (309)
T ss_dssp             SCC----CTTEEEEEECTTTCBEEEECTTTTTTC-------CCSBGGGGBCTTTHHHHHHHTCTTS--SCBCC-------
T ss_pred             HHHHHHHhcCCEEEEEECCCceEEEECCHHHHHcCCCHHHHcCCchhhccCHhHHHHHHHhccccC--CCCcccccCccc
Confidence            5689999999999999996 9999999999999999999999999999999999999999997632  111211110000


Q ss_pred             CCCCCCCCCCCceeEEEEEEEcCC--------eeeee-eecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCcccCC--
Q psy7682         213 GKRPSLTASTPNRTFNIRLLISST--------HLTAG-LSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDKQLSA--  281 (383)
Q Consensus       213 g~~~~~~~~~~~rsF~cRmk~~~~--------~i~~~-~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~~i~~--  281 (383)
                      .  +  .....+|+|+||||++..        .++|+ +.+...  ..+     ......|||+++.++++.......  
T Consensus        94 ~--~--~~~~~~rsF~CRmr~~~~~~~~~~Y~~~~~~g~lk~~~--~~~-----g~~~~~~lv~~a~~~~s~~~~p~~~~  162 (309)
T 3gdi_A           94 F--T--QECMEEKSFFCRVSVGKHHENEIRYQPFRMTPYLVKVQ--EQQ-----GAESQLCCLLLAERVHSGYEAPRIPP  162 (309)
T ss_dssp             -----------CCCEEEEECCCC----CCCCEEEEEEEEEEECC---------------EEEEEEEEECCCTTSSSCCCG
T ss_pred             c--c--cccCCceeEEEEEEccccCCCccceEEEEEEeeecccc--CCC-----CCcCccEEEEEEEecCCCccCCCcCC
Confidence            0  0  012357999999998631        24553 332111  011     113457888888888654321111  


Q ss_pred             CCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhhhcccceeeccc-cee
Q psy7682         282 PIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDT-CMY  360 (383)
Q Consensus       282 ~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t-~~y  360 (383)
                      ...+|++||++||+|+|||+++  ..+|||.|+||+|+++|+|+ ||+| +....   ++... +.  -.++|..+ ..|
T Consensus       163 ~~~~Fitrh~~dG~~~yvd~~~--~~lLGY~peELig~s~~~~i-HpdD-~~~~~---~~~~~-~l--~~~g~~~~~~~y  232 (309)
T 3gdi_A          163 EKRIFTTTHTPNCLFQAVDERA--VPLLGYLPQDLIETPVLVQL-HPSD-RPLML---AIHKK-IL--QAGGQPFDYSPI  232 (309)
T ss_dssp             GGCEEEEEECTTCBEEEECTTH--HHHHSCCHHHHTTSBHHHHB-CTTS-HHHHH---HHHHH-HH--HTTTCCEEEEEE
T ss_pred             CCceEEEEecCCCeEEEECccc--ccccCcCHHHHcCCCHHHhC-CHHH-HHHHH---HHHHH-HH--hcCCceeeceEE
Confidence            2258999999999999999998  89999999999999999998 6777 33211   11111 11  12466555 578


Q ss_pred             cccCCccccccCCcceEEEEe
Q psy7682         361 RSSPSCFGLQGASRTSLWQRI  381 (383)
Q Consensus       361 R~~~~~~~~~~~~~~~~~~~~  381 (383)
                      ||+.++       ++|+|++-
T Consensus       233 R~~~kd-------G~~vwvet  246 (309)
T 3gdi_A          233 RFRTRN-------GEYITLDT  246 (309)
T ss_dssp             EEECTT-------SCEEEEEE
T ss_pred             EEEccC-------CCEEEEEE
Confidence            876554       46888763

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=99.96  E-value=1.7e-30  Score=256.05  Aligned_cols=173  Identities=20%  Similarity=0.288  Sum_probs=123.2

Q ss_pred             hcCcEEEEc-CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         142 LEGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTA  220 (383)
Q Consensus       142 ldgfi~vvs-~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~  220 (383)
                      .|||++||+ .+|+|+|+|+++..+|||+++||+|++++||+||+|++.+.++|+...    +++...+         ..
T Consensus         2 ~dgF~~vv~~~~G~i~yvS~~~~~~LGy~~~el~G~s~~d~ihp~D~~~f~~~L~~gl----~~~~~~~---------~~   68 (339)
T 3rty_A            2 EDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGI----PIAESRG---------SV   68 (339)
T ss_dssp             CSCEEEEEETTTCBEEEECTTHHHHHCCCTTSSTTSBGGGGBCHHHHHHHHHHHHTTS----CCC---------------
T ss_pred             CcEEEEEEECCCcEEEEEChHHHHHcCCCHHHHCCCcHHHhcCHHHHHHHHHHHhcCC----CCCcccc---------CC
Confidence            489999999 599999999999999999999999999999999999999999998653    1211100         01


Q ss_pred             CCCceeEEEEEEEcCCeeee----------eeecC-----CCCCCCCCCCC---CCCCCCceEEEEEeecCCCCcc---c
Q psy7682         221 STPNRTFNIRLLISSTHLTA----------GLSRA-----GGENGQDDSGD---VSSEGGPCLMCVARRIPPTDKQ---L  279 (383)
Q Consensus       221 ~~~~rsF~cRmk~~~~~i~~----------~~~~~-----~~~~g~d~~~~---~~~~~~~~LVav~r~ip~~~~~---i  279 (383)
                      ...+++|||||+++..++.+          .|.++     ......+...+   ...+...|||++|+|++++...   +
T Consensus        69 ~~~~rsffcR~~rr~~~l~s~gy~v~~~~~~~~p~~l~~~~~~~~~e~~~~~~~~~~g~~~~lv~~a~~i~s~~~~p~e~  148 (339)
T 3rty_A           69 PKDAKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEI  148 (339)
T ss_dssp             ----CCEEEEEEECCC-------------CCEEEEEEEEEEEECCCC----------CCCEEEEEEEEECCCSCSSTTBB
T ss_pred             CCCCceEEEEEEeccCCCCcCCcceecccccceeEEEEEEEeccccccccccccccCCceEEEEEEcccCCccccccchh
Confidence            34578999999865332111          12221     01111111000   0123457899999999876541   1


Q ss_pred             -CCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         280 -SAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       280 -~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                       ......|++||++||+|+|||+++  ..+|||.|+||+|+++|+|+ ||+|
T Consensus       149 ~~~~~~~fi~r~~~dG~~~yvn~~~--~~lLGY~peELiG~s~~~~v-HPdD  197 (339)
T 3rty_A          149 LSQKSPKFAIRHTATGIISHVDSAA--VSALGYLPQDLIGRSIMDFY-HHED  197 (339)
T ss_dssp             CCSSCCEEEEEEETTCBEEEECTTH--HHHHCCCHHHHTTSBGGGGB-CGGG
T ss_pred             hccCCceEEEEECCCCeEEEcChhh--hcccCCCHHHHcCCcHHHEE-CHHH
Confidence             123489999999999999999998  89999999999999999998 6776

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=99.61  E-value=5.2e-17  Score=137.66  Aligned_cols=81  Identities=21%  Similarity=0.176  Sum_probs=61.5

Q ss_pred             CCceeEEEeCCCCcEEEEcCCCCccccCCccc--ccccCCCccceecCCCCch--hHHHHHHHHHHhhhhcccceeeccc
Q psy7682         282 PIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLN--KAVACKTSATVWTCPNSPL--TSTKLLLKALLLSICTDYALVQTDT  357 (383)
Q Consensus       282 ~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p--~eLiG~S~yd~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~q~~t  357 (383)
                      +.++|++||++||||+|||++++   ..+|.|  +||+|+|+|+|+ |++|..  .++++        +..++.+||+.|
T Consensus         5 ~~e~F~sRh~~dGKf~~vDq~~~---r~~~~~g~qdLlGrsiy~f~-H~~D~~~s~l~~h--------~~~vl~~Gq~~S   72 (132)
T 1oj5_A            5 GVESFMTKQDTTGKIISIDTSSL---RAAGRTGWEDLVRKCIYAFF-QPQGREPSYARQL--------FQEVMTRGTASS   72 (132)
T ss_dssp             -CCEEEEEECTTCCEEEEECHHH---HTTCCSCHHHHHHHHHHHHT-SCBTTBCCHHHHH--------HHHHHHHSEEEC
T ss_pred             CceeeEEeecCCCcEEEEecccc---cccccccHHHHHHHHHHHHh-CcccchHHHHHHH--------HHHHHHcCCccc
Confidence            45899999999999999999862   366666  999999999998 455512  33332        234557899999


Q ss_pred             ceecccCCccccccCCcceEEEEe
Q psy7682         358 CMYRSSPSCFGLQGASRTSLWQRI  381 (383)
Q Consensus       358 ~~yR~~~~~~~~~~~~~~~~~~~~  381 (383)
                      ..|||+.+.+       +|+|++-
T Consensus        73 ~~YRfr~k~g-------~~V~~qT   89 (132)
T 1oj5_A           73 PSYRFILNDG-------TMLSAHT   89 (132)
T ss_dssp             CCEEEECTTS-------CEEEEEE
T ss_pred             cceEEEecCC-------cEEEEEE
Confidence            9999887743       6889874

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=99.56  E-value=1.5e-15  Score=125.43  Aligned_cols=60  Identities=17%  Similarity=0.307  Sum_probs=51.2

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..+++++++||++++.+|+|+|+|+++..+|||+++|++|+++++|+||+|++.+.+.+.
T Consensus         2 ~~lle~~~d~i~v~d~~G~i~yvn~~~~~~lGy~~~el~G~~~~~~ihp~D~~~~~~~~~   61 (111)
T 2vlg_A            2 EFPLQTKTDIHAVLASNGRIIYISANSKLHLGYLQGEMIGSFLKTFLHEEDQFLVESYFY   61 (111)
T ss_dssp             -------CCEEEEECTTSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHH
T ss_pred             cchhhcCCCEEEEEcCCCeEEEEChHHHHHhCCCHHHHcCCcHHHeECHhHHHHHHHHHh
Confidence            568899999999999999999999999999999999999999999999999999988774

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.33  E-value=1e-12  Score=100.64  Aligned_cols=61  Identities=28%  Similarity=0.465  Sum_probs=52.7

Q ss_pred             hhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhcc
Q psy7682          44 AILQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE  110 (383)
Q Consensus        44 ~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~  110 (383)
                      ++.+++..|+.+||+||+++|..|.+|+.|||.+   .   ....|+||++||++||.|||.++.+.
T Consensus         5 k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~---~---~~~~KldKasIL~~tV~ylk~l~~~~   65 (73)
T 4h10_A            5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTC---N---AMSRKLDKLTVLRMAVQHMKTLRGAW   65 (73)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHH---H---TCSSCCCHHHHHHHHHHHHHHHSCC-
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHcccc---c---cccccccHHHHHHHHHHHHHHHhcCc
Confidence            4567788999999999999999999999999983   1   23479999999999999999887664

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.28  E-value=9.3e-13  Score=131.44  Aligned_cols=105  Identities=14%  Similarity=0.171  Sum_probs=73.0

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTAS  221 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~~  221 (383)
                      ...|++..+.||+|+|+|+++..+|||+++||+|+++++|+||+|.+.+...+.....                    ..
T Consensus       277 ~~~fi~~~~~dg~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~~~l~--------------------~~  336 (387)
T 4f3l_B          277 SMEYVSRHAIDGKFVFVDQRATAILAYLPQELLGTSCYEYFHQDDIGHLAECHRQVLQ--------------------TR  336 (387)
T ss_dssp             CCEEEEEECTTSBEEEECTHHHHHHCCCHHHHTTSBGGGTBCHHHHHHHHHHHHHHTT--------------------CS
T ss_pred             CceEEEEECCCCEEEEECCCcccccCCCHHHHcCCcHHHeeCHHHHHHHHHHHHHHHh--------------------cC
Confidence            4558888999999999999999999999999999999999999999999877643210                    01


Q ss_pred             CCceeEEEEEEEcCCeeeeeeecCCCCC--CCCCCCCCCCCCCceEEEEEeecCC
Q psy7682         222 TPNRTFNIRLLISSTHLTAGLSRAGGEN--GQDDSGDVSSEGGPCLMCVARRIPP  274 (383)
Q Consensus       222 ~~~rsF~cRmk~~~~~i~~~~~~~~~~~--g~d~~~~~~~~~~~~LVav~r~ip~  274 (383)
                      +...++..|++++.+.    |.|.....  -.+.    ......++|++.+.|..
T Consensus       337 ~~~~~~eyR~~~kdG~----~vWv~~~~~~~~~~----~~g~~~~ivg~~~dIT~  383 (387)
T 4f3l_B          337 EKITTNCYKFKIKDGS----FITLRSRWFSFMNP----WTKEVEYIVSTNTVVLA  383 (387)
T ss_dssp             SCEECCCEEEECTTSC----EEEEEEEEEEEEET----TTTEEEEEEEEEEECC-
T ss_pred             CCeeeEEEEEEccCCC----EEEEEEEEEEEECC----CCCCEEEEEEEEEEcch
Confidence            1234567899988752    22211000  0000    01233588999888753

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.23  E-value=1.4e-11  Score=121.57  Aligned_cols=53  Identities=26%  Similarity=0.305  Sum_probs=48.9

Q ss_pred             cCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         143 EGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       143 dgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..|++..+.||+|+|+|+++..+|||+++||+|+++++|+||+|.+.+...+.
T Consensus       251 ~~f~~~~~~dg~~~~vn~~~~~ilGY~~eEl~g~~~~~~iHpdD~~~~~~~~~  303 (361)
T 4f3l_A          251 EEFTSRHSLEWKFLFLDHRAPPIIGYLPFEVLGTSGYDYYHVDDLENLAKCHE  303 (361)
T ss_dssp             CEEEEEECTTSBEEEECTTSHHHHCCCHHHHTTSBGGGGBCHHHHHHHHHHHH
T ss_pred             ceeEEEEcCCceEEEECChhhhhhCcCHHHHcCCCHHHeECHHHHHHHHHHHH
Confidence            56788889999999999999999999999999999999999999998877664

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.23  E-value=1.2e-11  Score=93.95  Aligned_cols=54  Identities=33%  Similarity=0.491  Sum_probs=48.5

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      +++..|+.+||+||+++|..|.+|+.|||.   +      ..|+||++||+.||.|||.++..
T Consensus         7 ~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~---~------~~K~dK~sIL~~aI~yik~Lq~~   60 (71)
T 4h10_B            7 AKRVSRNKSEKKRRDQFNVLIKELGSMLPG---N------ARKMDKSTVLQKSIDFLRKHKEI   60 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSSS---C------CSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhHHHhhHHHHHHHHHHHHHHhCCC---C------CCCCcHHHHHHHHHHHHHHHHHh
Confidence            556799999999999999999999999997   2      26999999999999999988754

>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

Probab=99.20  E-value=4.2e-11  Score=96.76  Aligned_cols=112  Identities=14%  Similarity=0.208  Sum_probs=78.5

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAG  213 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g  213 (383)
                      +..++++++..+|++++.+|+|+|+|+++..+|||+++|++|+++++++||+|.+.+...+.....              
T Consensus         3 ~~~ll~e~~~d~i~~~d~~g~i~~~n~~~~~~~G~~~~el~g~~~~~~i~p~d~~~~~~~~~~~~~--------------   68 (121)
T 3f1p_B            3 FKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVK--------------   68 (121)
T ss_dssp             -----CCCCCEEEEEECTTSBEEEECTTHHHHHSCCGGGTTTSBGGGGBCTTTHHHHHHHHHHHTT--------------
T ss_pred             cccceecCCCceEEEECCCceEEEECcchhhhhCCChHHHcCCCHHHeECHHHHHHHHHHHHHHHh--------------
Confidence            455778889999999999999999999999999999999999999999999999998877643210              


Q ss_pred             CCCCCCCCCCceeEEEEEEEcCCe---eeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCC
Q psy7682         214 KRPSLTASTPNRTFNIRLLISSTH---LTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPP  274 (383)
Q Consensus       214 ~~~~~~~~~~~rsF~cRmk~~~~~---i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~  274 (383)
                            ..+....+.+|++++.+.   +.+...+..     +.    ......++|++++.|..
T Consensus        69 ------~~~~~~~~e~r~~~~dG~~~w~~~~~~~~~-----~~----~~g~~~~iv~~~~DIT~  117 (121)
T 3f1p_B           69 ------LKGQVLSVMFRFRSKNQEWLWMRTSSFTFQ-----NP----YSDEIEYIICTNTNVKN  117 (121)
T ss_dssp             ------STTCCEEEEEEEECTTSCEEEEEEEEEEEC-----CT----TCCCCCEEEEEEEECCC
T ss_pred             ------cCCCcccEEEEEEecCCCEEEEEEEEEEEE-----CC----CCCceeEEEEEeEEccc
Confidence                  012335678899887752   122222211     00    01234678999988854

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=99.10  E-value=2.3e-10  Score=103.98  Aligned_cols=149  Identities=10%  Similarity=0.101  Sum_probs=99.2

Q ss_pred             cEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q psy7682         145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTPN  224 (383)
Q Consensus       145 fi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~~~~~  224 (383)
                      +|+++|.+|+|+|+|+++..++||+++|++|+++.++.++.+...+...+....                     ..+..
T Consensus         1 ~i~i~D~~g~i~~~N~a~~~l~Gy~~~el~G~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~   59 (227)
T 3ewk_A            1 LVSITDLQGRILYANDNFCAVSRYGREELVGQDHRIVNSGYHGKAYIRDMWRTI---------------------SRGNI   59 (227)
T ss_dssp             CEEEEETTCBEEEECHHHHHHTTCCHHHHTTSBGGGGCCSCSCHHHHHHHHHHH---------------------TTTCC
T ss_pred             CEEEECCCCcEEehHHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHHHHHHHHH---------------------HcCCe
Confidence            378899999999999999999999999999999988877665544433332110                     01122


Q ss_pred             eeEEEEEEEcCCe---eeeeeecCCCCCCCCCCCCCCCCCCceEEEEEeecCCCCc---c------cCCCCceeEEEeCC
Q psy7682         225 RTFNIRLLISSTH---LTAGLSRAGGENGQDDSGDVSSEGGPCLMCVARRIPPTDK---Q------LSAPIEQFTMKLDR  292 (383)
Q Consensus       225 rsF~cRmk~~~~~---i~~~~~~~~~~~g~d~~~~~~~~~~~~LVav~r~ip~~~~---~------i~~~~~~F~tRHsl  292 (383)
                      ..+..+++++.+.   +.....+....          ......++++.+.++....   .      +-......+...+.
T Consensus        60 ~~~e~~~~~~dG~~~~~~~~~~p~~d~----------~g~~~~~~~~~~DIT~~k~~e~~l~~~~~~~~~~~~~i~~~d~  129 (227)
T 3ewk_A           60 WQGEFCNRRKDGTRYWVDSTIVPLMDN----------AGKPRQYISIRRDITAQKEAEAQLARLKQAMDANSEMILLTDR  129 (227)
T ss_dssp             EEEEEEEECSSSCEEEEEEEEEEEECS----------SSCEEEEEEEEEECTTTTHHHHHHHHHHHHHHTCCSEEEEECT
T ss_pred             EEEEEEEEcCCCCEEeeeeEEEEEEcC----------CCCEEEEEEEEEehhhHHHHHHHHHHHHHHHhcCcCeEEEEcC
Confidence            3445566665542   11222221111          1233568899999876542   0      10112334555689


Q ss_pred             CCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         293 SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       293 dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +|+|+++++..  ..++||.++|++|++...+++
T Consensus       130 ~g~i~~~N~~~--~~~~G~~~~e~~g~~~~~l~~  161 (227)
T 3ewk_A          130 AGRIIYANPAL--CRFSGMAEGELLGQSPSILDS  161 (227)
T ss_dssp             TSCEEEECHHH--HHHHTCCTHHHHSSCGGGGBC
T ss_pred             CCcEEEEchHH--HHHhCCCHHHHcCCChhhccC
Confidence            99999999998  899999999999999887763

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=99.02  E-value=2.2e-10  Score=85.21  Aligned_cols=59  Identities=24%  Similarity=0.396  Sum_probs=48.7

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++.+|+.+||+||+++|..|.+|..|||.+ ...  .....+++|++||.+||.|||.++..
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~-~~~--~~~~~k~sKa~iL~~Ai~YIk~Lq~~   60 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAE-WKQ--QNVSAAPSKATTVEAACRYIRHLQQN   60 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHH-HHT--SSCCCCSCTTHHHHHHHHHHHHHHTC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCc-ccc--cccCCcccHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999982 111  11247999999999999999987643

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1

Probab=98.88  E-value=9.2e-10  Score=82.38  Aligned_cols=58  Identities=26%  Similarity=0.397  Sum_probs=47.9

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+..||+||+++|..|.+|..+||.+  .. . +...|+||++||+.||.||+.++..
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~--~~-~-~~~~k~~Ka~IL~~ai~YI~~Lq~~   62 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDS--SM-E-STKSGQSKGGILSKASDYIQELRQS   62 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCC--CC-C-SSTTCCCTTTTTTTTHHHHHHHHTT
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCc--cc-c-cccCCCCHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999983  11 0 1135899999999999999987643

>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

Probab=98.88  E-value=5e-10  Score=89.64  Aligned_cols=54  Identities=26%  Similarity=0.453  Sum_probs=50.0

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ...||+++|.+|+|+|+|+++..+|||+++|++|+++++++||+|.+.+...+.
T Consensus         8 ~~~~i~~~d~~g~i~~~n~~~~~~~Gy~~~el~g~~~~~~~~p~d~~~~~~~~~   61 (117)
T 3f1p_A            8 SKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQ   61 (117)
T ss_dssp             GGEEEEEECTTCBEEEECTHHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHH
T ss_pred             CccEEEEECCCceEEEECcChhhhhCCCHHHHcCCchhheECHHHHHHHHHHHH
Confidence            356799999999999999999999999999999999999999999998887764

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C

Probab=98.84  E-value=3.3e-09  Score=83.05  Aligned_cols=54  Identities=28%  Similarity=0.411  Sum_probs=48.3

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .++..|+.+||+||+++|..|.+|..+||.   +      ..|+||++||..||.||+.++..
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~---~------~~k~~Ka~IL~~Ai~YI~~Lq~~   58 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVG---T------EAKLNKSAVLRKAIDYIRFLQHS   58 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---S------SCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccC---C------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999998   2      26999999999999999987754

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=98.71  E-value=1.3e-08  Score=85.00  Aligned_cols=58  Identities=33%  Similarity=0.444  Sum_probs=44.8

Q ss_pred             hhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          46 LQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        46 ~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      -+++.+|+.+||+||+++|..|.+|..+||.+  .    ....|+||++||..||.||+.++..
T Consensus        25 ~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~--~----~~~~k~~Ka~IL~~aieYIk~Lq~~   82 (118)
T 4ati_A           25 RQKKDNHNLIERRRRFNINDRIKELGTLIPKS--N----DPDMRWNKGTILKASVDYIRKLQRE   82 (118)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHSCCC----------CCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhc--c----CccccCCHHHHHHHHHHHHHHHHHH
Confidence            34677999999999999999999999999983  1    1136999999999999999988653

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1

Probab=98.67  E-value=2.8e-08  Score=77.39  Aligned_cols=56  Identities=14%  Similarity=0.326  Sum_probs=48.8

Q ss_pred             hhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          46 LQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        46 ~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ..++..|+..||+||+.+|..|.+|..+||..  +      ..|++|++||+.|+.||+.+...
T Consensus        10 ~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~--~------~~k~sK~~iL~~Ai~YI~~L~~~   65 (80)
T 1hlo_A           10 ADKRAHHNALERKRRDHIKDSFHSLRDSVPSL--Q------GEKASRAQILDKATEYIQYMRRK   65 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGG--T------TSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCC--C------CCCccHHHHHHHHHHHHHHHHHH
Confidence            35677999999999999999999999999982  1      26999999999999999987643

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=98.64  E-value=3.4e-08  Score=77.36  Aligned_cols=54  Identities=15%  Similarity=0.340  Sum_probs=47.5

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+..||+||+.+|..|.+|..+||..  +      ..|+||++||+.|+.||+.+...
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~--~------~~k~sK~~iL~~Ai~YI~~L~~~   55 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL--Q------GEKASRAQILDKATEYIQYMRRK   55 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGG--T------TSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCC--C------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999982  1      36999999999999999987743

>3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus}

Probab=98.63  E-value=2.3e-08  Score=96.93  Aligned_cols=73  Identities=15%  Similarity=0.128  Sum_probs=60.3

Q ss_pred             CcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTP  223 (383)
Q Consensus       144 gfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~~~~  223 (383)
                      .|+...+.||+|+||++++..+|||.++||+|+++++|+||+|++.+++.+.....                    ..+.
T Consensus       166 ~Fitrh~~dG~~~yvd~~~~~lLGY~peELig~s~~~~iHpdD~~~~~~~~~~~l~--------------------~~g~  225 (309)
T 3gdi_A          166 IFTTTHTPNCLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQ--------------------AGGQ  225 (309)
T ss_dssp             EEEEEECTTCBEEEECTTHHHHHSCCHHHHTTSBHHHHBCTTSHHHHHHHHHHHHH--------------------TTTC
T ss_pred             eEEEEecCCCeEEEECcccccccCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHh--------------------cCCc
Confidence            68999999999999999999999999999999999999999999888776643210                    0122


Q ss_pred             cee-EEEEEEEcCC
Q psy7682         224 NRT-FNIRLLISST  236 (383)
Q Consensus       224 ~rs-F~cRmk~~~~  236 (383)
                      ..+ +..||+++++
T Consensus       226 ~~~~~~yR~~~kdG  239 (309)
T 3gdi_A          226 PFDYSPIRFRTRNG  239 (309)
T ss_dssp             CEEEEEEEEECTTS
T ss_pred             eeeceEEEEEccCC
Confidence            345 6899999886

>4dj3_A Period circadian protein homolog 3; PAS domain, circadian rhythm, protein binding; 2.50A {Mus musculus}

Probab=98.63  E-value=2.1e-08  Score=97.45  Aligned_cols=53  Identities=17%  Similarity=0.214  Sum_probs=49.6

Q ss_pred             cCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         143 EGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       143 dgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..|+...+.||+|+||++++..+|||.++||+|+++++|+||+|++.+.+.+.
T Consensus       174 ~~Fitrh~~dG~~~yvs~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~  226 (317)
T 4dj3_A          174 RIFTTTHTPGCVFLEVDERAVPLLGYLPQDLIGTSILTYLHPEDRPLMVAIHQ  226 (317)
T ss_dssp             CEEEEEECTTSBEEEECTTHHHHHSCCHHHHTTSBGGGGBCTTTTTHHHHHHH
T ss_pred             CceEEEecCCCeEEEEChHHhhhcCcChHHHcCCCHHHeECHHHHHHHHHHHH
Confidence            47999999999999999999999999999999999999999999998887664

>4dj2_A Period circadian protein homolog 1; PAS domains, circadian clock protein, protein binding; 2.75A {Mus musculus}

Probab=98.62  E-value=2.7e-08  Score=96.83  Aligned_cols=54  Identities=19%  Similarity=0.206  Sum_probs=50.4

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ...|+...+.||+|+||++++..+|||.++||+|+++++|+||+|++.+++.+.
T Consensus       175 ~~~Fitrh~~dG~~~yvd~~~~~lLGY~peELig~s~~~~vHPdD~~~~~~~~~  228 (320)
T 4dj2_A          175 KRIFTTRHTPSCLFQDVDERAAPLLGYLPQDLLGAPVLLFLHPEDRPLMLAIHK  228 (320)
T ss_dssp             GCEEEEEECTTCBEEEECTTHHHHHSCCHHHHTTSBGGGGBCGGGHHHHHHHHH
T ss_pred             CceEEEEecCCceEEEcCcceeccCCcChHHHcCCcHHHhCCHHHHHHHHHHHH
Confidence            466899999999999999999999999999999999999999999999887664

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=98.57  E-value=1.8e-08  Score=80.50  Aligned_cols=57  Identities=21%  Similarity=0.358  Sum_probs=51.3

Q ss_pred             HHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         139 LEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       139 l~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      +++...+|++++.+|+|+|+|+++..+|||+++|++|+++.+++||+|...+...+.
T Consensus         9 ~~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~el~g~~~~~~~~p~d~~~~~~~~~   65 (121)
T 2kdk_A            9 NVKPTEFITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHK   65 (121)
T ss_dssp             CCCSSEEEEEECTTSBEEEECTHHHHHTCCCTTTSBTSBTTTTBCSSSHHHHHHHHH
T ss_pred             ccCCccEEEEECCCeeEEEEChhHHHHHCCCHHHHcCCcHHHeeCHHHHHHHHHHHH
Confidence            345677899999999999999999999999999999999999999999988776654

>3rty_A Period circadian protein; PAS domain, signalling, timeless, circadian clock protein; 2.85A {Drosophila melanogaster} PDB: 1wa9_A 3gec_A

Probab=98.56  E-value=2.1e-08  Score=98.42  Aligned_cols=54  Identities=19%  Similarity=0.343  Sum_probs=49.9

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ...|++..+.||+|+|+|+++..+|||.++||+|+++++|+||+|++.+.+.+.
T Consensus       153 ~~~fi~r~~~dG~~~yvn~~~~~lLGY~peELiG~s~~~~vHPdD~~~~~~~~~  206 (339)
T 3rty_A          153 SPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYE  206 (339)
T ss_dssp             CCEEEEEEETTCBEEEECTTHHHHHCCCHHHHTTSBGGGGBCGGGHHHHHHHHH
T ss_pred             CceEEEEECCCCeEEEcChhhhcccCCCHHHHcCCcHHHEECHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999998876654

>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

Probab=98.56  E-value=1.1e-07  Score=76.21  Aligned_cols=46  Identities=13%  Similarity=0.156  Sum_probs=41.7

Q ss_pred             CCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         282 PIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       282 ~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      +...|+..+++||+|+||++.+  ..++||.|+||+|+++++++ ||++
T Consensus        10 ~~~d~i~~~d~~g~i~~~n~~~--~~~~G~~~~el~g~~~~~~i-~p~d   55 (121)
T 3f1p_B           10 QPTRFISRHNIEGIFTFVDHRC--VATVGYQPQELLGKNIVEFC-HPED   55 (121)
T ss_dssp             CCCEEEEEECTTSBEEEECTTH--HHHHSCCGGGTTTSBGGGGB-CTTT
T ss_pred             CCCceEEEECCCceEEEECcch--hhhhCCChHHHcCCCHHHeE-CHHH
Confidence            4578999999999999999998  89999999999999999987 6776

>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

Probab=98.52  E-value=7.4e-08  Score=76.72  Aligned_cols=82  Identities=11%  Similarity=0.041  Sum_probs=56.6

Q ss_pred             CceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCCchhHHHHHHHHHHhhhhcccceeecccceecc
Q psy7682         283 IEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNSPLTSTKLLLKALLLSICTDYALVQTDTCMYRS  362 (383)
Q Consensus       283 ~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~t~~yR~  362 (383)
                      ...|++++++||+|+||++.+  ..++||.|+||+|+++++++ ||++......    .+.    .....++..+..||+
T Consensus         8 ~~~~i~~~d~~g~i~~~n~~~--~~~~Gy~~~el~g~~~~~~~-~p~d~~~~~~----~~~----~~~~~~~~~~~e~r~   76 (117)
T 3f1p_A            8 SKTFLSEHSMDMKFTYCDDRI--TELIGYHPEELLGRSAYEFY-HALDSENMTK----SHQ----NLCTKGQVVSGQYRM   76 (117)
T ss_dssp             GGEEEEEECTTCBEEEECTHH--HHHHCCCHHHHTTSBGGGGB-CGGGHHHHHH----HHH----HHHHHSEEECCCEEE
T ss_pred             CccEEEEECCCceEEEECcCh--hhhhCCCHHHHcCCchhheE-CHHHHHHHHH----HHH----HHHhCCCeeeeEEEE
Confidence            368999999999999999998  89999999999999999887 5665222111    111    222334555556664


Q ss_pred             cCCccccccCCcceEEEEee
Q psy7682         363 SPSCFGLQGASRTSLWQRIR  382 (383)
Q Consensus       363 ~~~~~~~~~~~~~~~~~~~~  382 (383)
                      .       ..+++++|+..+
T Consensus        77 ~-------~~dG~~~w~~~~   89 (117)
T 3f1p_A           77 L-------AKHGGYVWLETQ   89 (117)
T ss_dssp             E-------CTTSSEEEEEEE
T ss_pred             E-------ecCCCEEEEEEe
Confidence            4       444566777643

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=98.52  E-value=1.3e-07  Score=74.98  Aligned_cols=56  Identities=18%  Similarity=0.240  Sum_probs=48.8

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .++..|+..||+||+.+|..|.+|..+||..  ++     ..|+||++||+.|+.||+.+...
T Consensus         5 ~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~--~~-----~~K~sK~~iL~~A~~YI~~L~~~   60 (88)
T 1nkp_A            5 VKRRTHNVLERQRRNELKRSFFALRDQIPEL--EN-----NEKAPKVVILKKATAYILSVQAE   60 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGG--TT-----CTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHCCCC--CC-----CCCCCHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999982  21     36999999999999999987654

>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis}

Probab=98.48  E-value=9.3e-08  Score=78.23  Aligned_cols=45  Identities=18%  Similarity=0.207  Sum_probs=40.0

Q ss_pred             CceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         283 IEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       283 ~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      ...|+..++.+|+|+||++.+  ..+|||.++||+|+++|+|+ ||+|
T Consensus         8 ~~d~i~v~d~~G~i~yvn~~~--~~~lGy~~~el~G~~~~~~i-hp~D   52 (111)
T 2vlg_A            8 KTDIHAVLASNGRIIYISANS--KLHLGYLQGEMIGSFLKTFL-HEED   52 (111)
T ss_dssp             -CCEEEEECTTSBEEEECTTH--HHHHSCCHHHHTTSBGGGGB-CGGG
T ss_pred             CCCEEEEEcCCCeEEEEChHH--HHHhCCCHHHHcCCcHHHeE-CHhH
Confidence            356788899999999999998  89999999999999999987 6666

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=98.33  E-value=6.2e-07  Score=70.28  Aligned_cols=62  Identities=11%  Similarity=0.170  Sum_probs=54.3

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCcc--ccccCCCChHHHHhhcCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSV--YNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~--~d~iHp~D~~~~~~~l~~  196 (383)
                      .+.+++++.+.++.++.+|.++|+|+++..++||++++++|...  .+++||+|.+.+.+.+..
T Consensus         6 ~~~l~~~~~~~i~~~d~~~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~i~p~d~~~~~~~~~~   69 (118)
T 3icy_A            6 LQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDRHMLSNAYSK   69 (118)
T ss_dssp             HHHHHTTCCCCCEEECTTSCEEECCCCCGGGGGGEEEETTEEEEGGGGGBCGGGHHHHHHHHHH
T ss_pred             HHHHHhcCCceEEEEEcCCCceEEechhHhhcCCCHHHccCChhHHHHHcCHHHHHHHHHHHHH
Confidence            45677888888999999999999999999999999999998754  899999999998877643

>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian clock, PAS domain, transcription, activator, biolo rhythms, DNA-binding, nucleus; NMR {Homo sapiens}

Probab=98.29  E-value=1.4e-06  Score=69.22  Aligned_cols=49  Identities=10%  Similarity=0.239  Sum_probs=42.7

Q ss_pred             cCCCCceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         279 LSAPIEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       279 i~~~~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      +-.....++..++.+|+|+|+++.+  ..++||.++|++|+++++++ ||++
T Consensus         8 ~~~~~~~~i~~~d~~g~i~~~N~~~--~~~~G~~~~el~g~~~~~~~-~p~d   56 (121)
T 2kdk_A            8 INVKPTEFITRFAVNGKFVYVDQRA--TAILGYLPQELLGTSCYEYF-HQDD   56 (121)
T ss_dssp             CCCCSSEEEEEECTTSBEEEECTHH--HHHTCCCTTTSBTSBTTTTB-CSSS
T ss_pred             cccCCccEEEEECCCeeEEEEChhH--HHHHCCCHHHHcCCcHHHee-CHHH
Confidence            4445578999999999999999998  89999999999999998887 5666

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=98.29  E-value=1.7e-06  Score=69.41  Aligned_cols=57  Identities=14%  Similarity=0.121  Sum_probs=49.0

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHH
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFH  191 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~  191 (383)
                      ...+++++...|+++|.+|+|+|+|+++..++||+++|++|+++.++.++++.....
T Consensus         7 ~~~~~~~~~~~i~~~d~~g~i~~~N~a~~~~~G~~~~elig~~~~~l~~~~~~~~~~   63 (120)
T 2gj3_A            7 FRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVY   63 (120)
T ss_dssp             HHHHHHHCSSEEEEECTTCBEEEECHHHHHHHCCCTTGGGGCBGGGGCCTTSCHHHH
T ss_pred             HHHHHHhCCCeEEEECCCCCEEeehHHHHHHHCcCHHHHcCCCHHHcCCCCCCHHHH
Confidence            345667777779999999999999999999999999999999999998887765443

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=98.29  E-value=9.7e-07  Score=68.57  Aligned_cols=54  Identities=17%  Similarity=0.269  Sum_probs=47.1

Q ss_pred             hhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          49 TVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        49 ~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      +..|+..||+||+.+|..|..|+++||..  ++     ..|+.|++||+.|+.||+.+...
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~--~~-----~~k~sk~~iL~kA~~yI~~L~~~   55 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLG--PD-----SSRHTTLSLLTKAKLHIKKLEDS   55 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCC--SS-----SCCCTTHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCC--CC-----CCCCCHHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999972  22     47999999999999999987654

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=98.27  E-value=6.4e-07  Score=68.90  Aligned_cols=56  Identities=25%  Similarity=0.301  Sum_probs=43.0

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+..||+||+.+|+.|.+|..+||..  .+    ....+.|..||+.|+.||+.++..
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~--~~----~~K~~sK~~IL~~AieYI~~Lq~~   60 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMH--LK----SDKAQTKLLILQQAVQVILGLEQQ   60 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHH--HC----CCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCC--CC----ccccccHHHHHHHHHHHHHHHHHH
Confidence            456888899999999999999999999951  11    113348999999999999987754

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=98.25  E-value=1.6e-06  Score=65.19  Aligned_cols=56  Identities=20%  Similarity=0.277  Sum_probs=47.6

Q ss_pred             hhhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          46 LQETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        46 ~~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ..++..++.-|++|+..+|..|.+|..+||..  +      ..||+|..||++|+.||+.+...
T Consensus        10 ~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~--~------~~KlSKi~tLr~Ai~YI~~L~~~   65 (68)
T 1mdy_A           10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSN--P------NQRLPKVEILRNAIRYIEGLQAL   65 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSC--T------TSCCCHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCC--C------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            34566788889999999999999999999982  2      26999999999999999987643

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=98.16  E-value=3.7e-06  Score=61.68  Aligned_cols=54  Identities=17%  Similarity=0.193  Sum_probs=46.1

Q ss_pred             hhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          49 TVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        49 ~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      +..++.-|++|+..+|..|+.|...||..  +     ...||.|..||++|+.||+.+...
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~--~-----~~~klSKi~tLr~Ai~YI~~L~~~   56 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCY--S-----KTQKLSKIETLRLAKNYIWALSEI   56 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSC--C-----SSSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCC--C-----CcCcCCHHHHHHHHHHHHHHHHHH
Confidence            44567779999999999999999999982  2     247999999999999999987654

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=98.12  E-value=9.9e-07  Score=73.84  Aligned_cols=59  Identities=20%  Similarity=0.486  Sum_probs=50.9

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ..+++++..-|+++|.+|+|+|+|+++..+|||++++++|+++.++++|++...+...+
T Consensus        10 ~~i~~~~~d~i~~~D~~g~I~~~N~aa~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~   68 (129)
T 3mfx_A           10 ELFIQHLTEAMILVNANGFIRSCNQRSAELLDCPQVSLKGQDWRNFLTEHHQARYDNLL   68 (129)
T ss_dssp             HHHHTTCSSEEEEEETTSBEEEECHHHHHHTTSCHHHHTTSBGGGGBCTTCCGGGGCTT
T ss_pred             HHHHhcCCceEEEECCCCEEEeEhHHHHHHHCcCHHHHcCCcHHHHcChHhHHHHHHHH
Confidence            34566666668999999999999999999999999999999999999999876655444

>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*

Probab=98.11  E-value=1.2e-06  Score=71.27  Aligned_cols=59  Identities=15%  Similarity=0.189  Sum_probs=50.6

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhh
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNC  193 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~  193 (383)
                      ...+++++.+-|+++|.+|.|+|+|+++..++||+++|++|+++.++++|.+.......
T Consensus        18 ~~~l~~~~~d~i~~~d~~g~i~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~   76 (130)
T 1d06_A           18 LRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGY   76 (130)
T ss_dssp             HHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHH
T ss_pred             HHHHHhhCcCeEEEECCCCeEEEEcHHHHHHHCCCHHHHcCCcHHHHCCchhHHHHHHH
Confidence            34567777777899999999999999999999999999999999999998877654433

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=98.06  E-value=3.8e-06  Score=65.86  Aligned_cols=60  Identities=10%  Similarity=0.019  Sum_probs=48.8

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccC--CccccccCCCChHHHHhhcC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLG--KSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G--~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..+++++..-+++++.+|.++|+|+++..++||++.+++|  ..+.+++||+|...+...+.
T Consensus        10 ~~~~~~~~~~i~~~d~~~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~   71 (125)
T 3nja_A           10 HTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELD   71 (125)
T ss_dssp             -------CCEEEEEETTTTEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHH
T ss_pred             HHHHHhCCeeEEEEEcCCCcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHH
Confidence            3456666777899999999999999999999999999999  78899999999998887764

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=98.04  E-value=3.7e-06  Score=66.60  Aligned_cols=51  Identities=14%  Similarity=0.330  Sum_probs=44.6

Q ss_pred             hcCcEEEEcCC-ccEEEeecccccccCcccccccCCccccccCCCChHHHHh
Q psy7682         142 LEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN  192 (383)
Q Consensus       142 ldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~  192 (383)
                      .+.-|+++|.+ |+|+|+|+++..+|||+++|++|+++.++++|.+......
T Consensus         7 ~~~~i~~~d~~~g~I~~~N~aa~~l~G~~~~el~g~~~~~l~~~~~~~~~~~   58 (114)
T 1ll8_A            7 FNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEA   58 (114)
T ss_dssp             TTCEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHH
T ss_pred             CCceEEEEECCCCeEEEehHHHHHHhCCCHHHHcCCCHHHhcCcchhHHHHH
Confidence            34448889998 9999999999999999999999999999999988765443

>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*

Probab=98.02  E-value=7.4e-06  Score=63.16  Aligned_cols=56  Identities=21%  Similarity=0.352  Sum_probs=47.9

Q ss_pred             HHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         139 LEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       139 l~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ++++..-+++++.   +|+|+|+|+++..++||++++++|+++.+++||++...+...+
T Consensus         3 l~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~   61 (115)
T 4eet_B            3 PEFIEKNFVITDPRLPDNPIIFASDGFLELTEYSREEILGRNARFLQGPETDQATVQKI   61 (115)
T ss_dssp             --CCCCSEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHH
T ss_pred             cccCCCcEEEEcCCCCCCcEEEEcHHHHHHHCcCHHHHhCCCHHHhcCCCCChHHHHHH
Confidence            4556666899999   9999999999999999999999999999999999877665554

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=98.02  E-value=2.4e-06  Score=67.71  Aligned_cols=52  Identities=12%  Similarity=0.145  Sum_probs=44.7

Q ss_pred             cEEEEc-CCccEEEeecccccccCcccccccCC-ccccccCCCChHHHHhhcCC
Q psy7682         145 FLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGK-SVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       145 fi~vvs-~dG~i~yvS~sv~~~LGy~~~el~G~-s~~d~iHp~D~~~~~~~l~~  196 (383)
                      .++.++ .+|.++|+|+++..+|||++++++|. .+.+++||+|++.+.+.+..
T Consensus         5 giw~~d~~~~~~~~~n~~~~~l~G~~~~e~~~~~~~~~~ihpdd~~~~~~~~~~   58 (115)
T 3h9w_A            5 IPWKINWQTMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVK   58 (115)
T ss_dssp             EEEEEETTTTEEEEECTHHHHHHCSCGGGCCBHHHHHHSBCHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCcEEEEChhHHHHhCCChHHccCHHHHHHhcCHHHHHHHHHHHHH
Confidence            367778 58999999999999999999999995 35789999999998877653

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=97.98  E-value=8.7e-06  Score=69.27  Aligned_cols=60  Identities=13%  Similarity=0.122  Sum_probs=52.2

Q ss_pred             hHHHHhhcCcEEEEcCC---ccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         136 PLLLEALEGFLFVVNPD---GYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       136 ~lll~aldgfi~vvs~d---G~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..+++++..-|+++|.+   |.|+|+|+++..++||++++++|+++.+++||++...+...+.
T Consensus        10 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~   72 (176)
T 4hia_A           10 RAVFDRSGVALTLVDMSLPEQPVVLANPPFLRMTGYTEGQILGFNCRFLQRGDENAQARADIR   72 (176)
T ss_dssp             HHHHHHCSSCCEEEETTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTCCHHHHHHHH
T ss_pred             HHHHhcCCCcEEEEecCCCCCcEEEECHHHHHHHCcCHHHHcCCCcceeeCCCCCHHHHHHHH
Confidence            45667776678889998   9999999999999999999999999999999999877766553

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=97.95  E-value=1.5e-05  Score=66.12  Aligned_cols=63  Identities=21%  Similarity=0.209  Sum_probs=52.1

Q ss_pred             chhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccC--CccccccCCCChHHHHhhcC
Q psy7682         133 VLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLG--KSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G--~s~~d~iHp~D~~~~~~~l~  195 (383)
                      +...+++++....++..+.+|.++|+|+++..++||++.++.+  ..+.+++||+|.+.+...+.
T Consensus         9 ~rl~~~~~~~~~g~w~~d~~~~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~   73 (142)
T 3mr0_A            9 ERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALK   73 (142)
T ss_dssp             CCHHHHHHHTTCEEEEECTTTCCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHH
T ss_pred             HHHHHHHHhCCcEEEEEEcCCCeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHH
Confidence            3445677777777999999999999999999999999999987  45789999999999887774

>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}

Probab=97.95  E-value=4.4e-06  Score=64.81  Aligned_cols=62  Identities=18%  Similarity=0.129  Sum_probs=55.1

Q ss_pred             hhhHHHHhhcCcEEEEcCC-ccEEEeecccccccCcccccccCCc--cccccCCCChHHHHhhcC
Q psy7682         134 LGPLLLEALEGFLFVVNPD-GYVNFCTENIKSFIRYSRQEVLGKS--VYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~d-G~i~yvS~sv~~~LGy~~~el~G~s--~~d~iHp~D~~~~~~~l~  195 (383)
                      ....+++++...+++++.+ |.|+|+|+++..++||++++++|..  +.+++||+|...+...+.
T Consensus        12 ~~~~~~~~~~~~i~~~d~~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (125)
T 3eeh_A           12 RVRELTEATNDILWEFTADLSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDRELMKDTMQ   76 (125)
T ss_dssp             HHHHHHSCCCCEEEEEETTSSCEEEECTHHHHHHSSCHHHHHHCGGGGGGGBCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCceEEEEEcCCCcEEEecHHHHHHHCCCHHHHccCcHHHHHhcCHHHHHHHHHHHH
Confidence            4456778888889999998 9999999999999999999999988  899999999988877764

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=97.93  E-value=4.6e-06  Score=66.96  Aligned_cols=54  Identities=24%  Similarity=0.169  Sum_probs=46.0

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      ..+.+++++...|+++|.+|+|+|+|+++..++||+++|++|+++.++.++.+.
T Consensus        12 ~~~~l~e~~~d~i~~~d~~g~i~~vN~a~~~l~Gy~~~el~g~~~~~~~~~~~~   65 (117)
T 2r78_A           12 AYRALFEHAIDGIFIMDAEGHYLDVNPAICSAIGYTRDEFLALDWGVLSRGVDS   65 (117)
T ss_dssp             HHHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTCBTTTTTTCSTT
T ss_pred             HHHHHHhcCCceEEEECCCCCEEEecHHHHHHHCcCHHHHcCCCHHHhCCccch
Confidence            445667777777899999999999999999999999999999998887666553

>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}

Probab=97.92  E-value=1.8e-05  Score=63.16  Aligned_cols=58  Identities=19%  Similarity=0.245  Sum_probs=48.2

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccc--cCCccccccCCCChHHHHhhc
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEV--LGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el--~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ...+++++...|+++|.+|.|+|+|+++..++||+++|+  +|+++.+++|  |...+...+
T Consensus        19 ~~~l~e~~~~~i~~~d~~g~i~~~N~a~~~~~G~~~~el~g~g~~~~~~~~--~~~~~~~~~   78 (126)
T 3bwl_A           19 LEALFENSPDMIDVLDADGTICEVNQRFCAELGYDESEVLGRSIWEFDLMF--DAEDVQTQL   78 (126)
T ss_dssp             HHHHHHHCSSEEEEECTTCBEEEECHHHHHHHTCCGGGTTTSBGGGTBTTC--CHHHHHHHH
T ss_pred             HHHHHhhCCcEEEEEcCCCCEEEEcHHHHHHhCCCHHHHhhCCCchhhccC--CHHHHHHHH
Confidence            445677777779999999999999999999999999999  6789999888  655555443

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=97.92  E-value=5.9e-06  Score=63.79  Aligned_cols=60  Identities=12%  Similarity=0.079  Sum_probs=51.9

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ....+++++...++++|.+|+|+|+|+++..++|+++++++|+++.+++ |+|...+...+
T Consensus         4 ~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~-~~~~~~~~~~~   63 (114)
T 3luq_A            4 RLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIF-PEIGEEWKSVH   63 (114)
T ss_dssp             HHHHHHHTCSSEEEEEETTCBEEEECHHHHHHTTCCSSCCTTCBHHHHC-TTCCHHHHHHH
T ss_pred             HHHHHHhcCCceEEEEcCCcEEEEECHHHHHHHCCCHHHHcCCcHHHHC-CccHHHHHHHH
Confidence            3456778888889999999999999999999999999999999999987 88877665544

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}

Probab=97.89  E-value=8.4e-06  Score=64.90  Aligned_cols=55  Identities=22%  Similarity=0.347  Sum_probs=48.0

Q ss_pred             HhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         140 EALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       140 ~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      +++...|+++|.   +|.|+|+|+++..++||++++++|+++.+++++++...+...+
T Consensus         4 ~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~e~~g~~~~~~~~~~~~~~~~~~~   61 (128)
T 3t50_A            4 EFTLMPMLITNPHLPDNPIVFANPAFLKLTGYEADEVMGRNCRFLQGHGTDPAHVRAI   61 (128)
T ss_dssp             CCCSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHH
T ss_pred             ccCcccEEEecCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHhhhcCCccCHHHHHHH
Confidence            345556889999   9999999999999999999999999999999998877766555

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=97.87  E-value=2.2e-05  Score=71.94  Aligned_cols=63  Identities=19%  Similarity=0.189  Sum_probs=54.9

Q ss_pred             chhhHHHHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         133 VLGPLLLEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      .....+++++..-|+++|.   +|+|+|+|+++..++||+++|++|+++.+++||+|...+...+.
T Consensus        63 ~~~~~i~~~~~~~i~~~d~~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~~~~~~~~~~  128 (258)
T 3p7n_A           63 QWVLDLIEASPIASVVSDPRLADNPLIAINQAFTDLTGYSEEECVGRNCRFLAGSGTEPWLTDKIR  128 (258)
T ss_dssp             HHHHHHHHTCSSEEEEECTTSTTCCEEEECHHHHHHHCCCGGGTTTSCGGGGCCTTCCHHHHHHHH
T ss_pred             HHHHHHHhcCCccEEEEcCCCCCCcEEEEhHHHHHHcCCCHHHHCCCChhhccCCCCchhHHHHHH
Confidence            3456677888888999999   99999999999999999999999999999999999877766553

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=97.85  E-value=3.2e-06  Score=66.71  Aligned_cols=58  Identities=17%  Similarity=0.439  Sum_probs=52.1

Q ss_pred             HHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       138 ll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      +++++...++++|.+|.|+|+|+++..++||++++++|+++.++++++|...+...+.
T Consensus         4 l~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~   61 (126)
T 3mjq_A            4 FLETIEDMILIINREGRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILA   61 (126)
T ss_dssp             TGGGCSSEEEEEETTSBEEEECTHHHHHHSCCHHHHHHSBHHHHHCTTCHHHHHHHHH
T ss_pred             HHhhCCceEEEEeCCCcEEEEcHHHHHHHCCCHHHHcCCCHHHHcCchhHHHHHHHHH
Confidence            4566777799999999999999999999999999999999999999999987776654

>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*

Probab=97.83  E-value=6.2e-06  Score=65.77  Aligned_cols=48  Identities=19%  Similarity=0.414  Sum_probs=42.7

Q ss_pred             cEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHh
Q psy7682         145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN  192 (383)
Q Consensus       145 fi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~  192 (383)
                      -|+++|.+|.|+|+|+++..++||+++|++|+++.+++++.+......
T Consensus         5 ~i~~~d~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~   52 (119)
T 2vv6_A            5 AMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDS   52 (119)
T ss_dssp             EEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHH
T ss_pred             eEEEECCCCeEEEEhHHHHHHhCCCHHHHcCCCHHHhCCchHHHHHHH
Confidence            478899999999999999999999999999999999998887655443

>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}

Probab=97.76  E-value=1.1e-05  Score=62.89  Aligned_cols=51  Identities=12%  Similarity=0.163  Sum_probs=44.7

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHG  185 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~  185 (383)
                      .+.+++++..-|+++|.+|+|+|+|+++..++||++++++|+++.+++++.
T Consensus        15 ~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~   65 (118)
T 3olo_A           15 AHYLINNAVEASFCLGDNWQFLYVNDATCRMTEYSREQLLSMNLQDIDVDF   65 (118)
T ss_dssp             HHHHHHHCSSEEEEECTTSBEEEECHHHHHHHCCCHHHHTTCBGGGTBTTG
T ss_pred             HHHHHhcCCceEEEECCCCcEEEEHHHHHHHHCCCHHHHhCCChhhccccc
Confidence            446677777778999999999999999999999999999999999987443

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*

Probab=97.74  E-value=1.1e-05  Score=65.71  Aligned_cols=55  Identities=15%  Similarity=0.243  Sum_probs=44.8

Q ss_pred             HHHhhcCcEEEEcCCc---cEEEeecccccccCcccccccCCccccccCCCChHHHHh
Q psy7682         138 LLEALEGFLFVVNPDG---YVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHN  192 (383)
Q Consensus       138 ll~aldgfi~vvs~dG---~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~  192 (383)
                      +++++...|+++|.+|   +|+|+|+++..++||+++|++|+++..+.||++......
T Consensus         4 ~~~~~~~~i~~~d~~g~~~~i~~~N~a~~~~~G~~~~el~g~~~~~l~~~~~~~~~~~   61 (132)
T 2pr5_A            4 MLDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVD   61 (132)
T ss_dssp             --CCCCCEEEEECTTSTTCCEEEECHHHHHHHSCCHHHHTTSCGGGGCCTTCCHHHHH
T ss_pred             HHhcCCCcEEEEeCCCCCCcEEEECHHHHHHhCcCHHHHcCCChhhhCCCCCCHHHHH
Confidence            4566666788999876   999999999999999999999999988888876554433

>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*

Probab=97.74  E-value=2.9e-05  Score=61.45  Aligned_cols=48  Identities=21%  Similarity=0.313  Sum_probs=39.5

Q ss_pred             cCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHH
Q psy7682         143 EGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF  190 (383)
Q Consensus       143 dgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~  190 (383)
                      +.-|+++|.   +|+|+|+|+++..++||+++|++|++...+.||++....
T Consensus         3 ~~~i~i~d~~~~~g~i~~~N~a~~~l~Gy~~~e~~G~~~~~l~~~~~~~~~   53 (109)
T 1n9l_A            3 RHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKE   53 (109)
T ss_dssp             SCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHH
T ss_pred             ccEEEEEcCCCCCCeEEEEchHHHHHHCcCHHHHcCCCchhcCCCCCCHHH
Confidence            344677884   799999999999999999999999998777777764433

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=97.70  E-value=3.8e-05  Score=58.91  Aligned_cols=60  Identities=15%  Similarity=0.274  Sum_probs=50.1

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ...+++++...+++++.+|.|+|+|+++..++|+++.+++|+++..+.++++...+...+
T Consensus         9 ~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~   68 (124)
T 3lyx_A            9 RAKAFDYVFDAIVVTDLQGFIIDWNKGSETLYGYSKEQAIGQPVNMLHVPGDTEHITSEV   68 (124)
T ss_dssp             HHHGGGTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTHHHHHHHH
T ss_pred             HHHHHhhcCceEEEECCCCcEeehhhHHHHHhCCCHHHHcCCCHHHhcCcchhhHHHHHH
Confidence            445667778889999999999999999999999999999999999777777766554443

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}

Probab=97.67  E-value=8.2e-06  Score=64.53  Aligned_cols=56  Identities=5%  Similarity=0.068  Sum_probs=43.9

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHH
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHAR  189 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~  189 (383)
                      ....+++++...|+++|.+|+|+|+|+++..++||++++++|+++.++++++....
T Consensus        20 ~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~   75 (125)
T 3fc7_A           20 KFESLVSDSPDGIVHLTTNGTILSVNPSMAGRLGADPDTLVGQQLSAVMDSEAANQ   75 (125)
T ss_dssp             ------CCSCCEEEEEETTSBEEEECHHHHHHHTSCHHHHTTSBGGGSSCHHHHHH
T ss_pred             HHHHHHhcCCCeEEEEcCCCeEEEECHHHHHHhCCCHHHHcCccHHHhCCHHHHHH
Confidence            34456777888899999999999999999999999999999999999994433333

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=97.67  E-value=1.4e-05  Score=59.63  Aligned_cols=45  Identities=18%  Similarity=0.293  Sum_probs=39.3

Q ss_pred             HHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhh
Q psy7682          56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIK  107 (383)
Q Consensus        56 ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~  107 (383)
                      ||+|+..+|..|++|+.+||..  +.     ..||.|..|||+|++||+.+.
T Consensus        22 ER~Rm~~lN~aF~~LR~~VP~~--p~-----~kKLSKiEtLr~Ai~YI~~Lq   66 (68)
T 2lfh_A           22 PLSLLDDMNHCYSRLRELVPGV--PR-----GTQLSQVEILQRVIDYILDLQ   66 (68)
T ss_dssp             CSCSSSHHHHHHHHHHHHCCCC--CT-----TCCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC--CC-----CCCccHHHHHHHHHHHHHHHH
Confidence            5778999999999999999993  22     479999999999999999765

>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}

Probab=97.65  E-value=5.3e-06  Score=66.70  Aligned_cols=57  Identities=18%  Similarity=0.197  Sum_probs=47.4

Q ss_pred             HHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         138 LLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       138 ll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      +++++..-|+++|.+|+|+|+|+++..++|+++++++|+++.+++++.+...+...+
T Consensus        17 il~~~~~~i~~~D~~g~i~~~N~a~~~l~g~~~~e~~G~~~~~~~~~~~~~~~~~~~   73 (118)
T 3fg8_A           17 LYFQGGLGFMALDEDLRIIYVNSGCLRHVRRSRDELLGRVVTEVLPETQGSYFDALC   73 (118)
T ss_dssp             SSSCTTCEEEEECTTCBEEEECHHHHHHHTCCHHHHTTSBHHHHCGGGTTSHHHHHH
T ss_pred             HHhhCCceEEEECCCCeEEEECHHHHHHhCCCHHHHcCCcHHHHcCccchHHHHHHH
Confidence            445566668999999999999999999999999999999999998877655544433

>1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8

Probab=97.60  E-value=1.3e-05  Score=67.83  Aligned_cols=54  Identities=9%  Similarity=0.136  Sum_probs=44.8

Q ss_pred             hhcCcEEEEcCCccEEEeecccccccCccc--ccccCCccccccCCCChH--HHHhhcC
Q psy7682         141 ALEGFLFVVNPDGYVNFCTENIKSFIRYSR--QEVLGKSVYNLIHHGDHA--RFHNCLV  195 (383)
Q Consensus       141 aldgfi~vvs~dG~i~yvS~sv~~~LGy~~--~el~G~s~~d~iHp~D~~--~~~~~l~  195 (383)
                      ..+.|+.-.+.||+|+||-.++. -.+|.+  +||+|+++|||+||+|..  .+++.+.
T Consensus         5 ~~e~F~sRh~~dGKf~~vDq~~~-r~~~~~g~qdLlGrsiy~f~H~~D~~~s~l~~h~~   62 (132)
T 1oj5_A            5 GVESFMTKQDTTGKIISIDTSSL-RAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQ   62 (132)
T ss_dssp             -CCEEEEEECTTCCEEEEECHHH-HTTCCSCHHHHHHHHHHHHTSCBTTBCCHHHHHHH
T ss_pred             CceeeEEeecCCCcEEEEecccc-cccccccHHHHHHHHHHHHhCcccchHHHHHHHHH
Confidence            45678999999999999999865 467777  999999999999999966  6666543

>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*

Probab=97.57  E-value=4.6e-05  Score=58.80  Aligned_cols=60  Identities=15%  Similarity=0.202  Sum_probs=52.2

Q ss_pred             hhHHHHhhcCcEEEEc---CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         135 GPLLLEALEGFLFVVN---PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       135 ~~lll~aldgfi~vvs---~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ...+++++...+++++   .+|.|+|+|+++..++|++..+++|+++.++++|.+...+...+
T Consensus         8 ~~~~~~~~~~~i~~~d~~d~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~   70 (130)
T 2z6d_A            8 LKTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVAKI   70 (130)
T ss_dssp             HHHHHHHTTCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHH
T ss_pred             HHHHHHhcccceeeeeccCCCCcEEEecHHHHHHhCcCHHHHcCCChhhccCCCCCchHHHHH
Confidence            4567788888899999   89999999999999999999999999999999998876655443

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=97.56  E-value=4.8e-05  Score=63.23  Aligned_cols=61  Identities=13%  Similarity=0.188  Sum_probs=52.0

Q ss_pred             hhhHHHHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         134 LGPLLLEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ....+++++...|+++|.   +|.|+|+|+++..++||++++++|+++.+++||++...+...+
T Consensus        36 ~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~l~~~~~~~~~~~~~   99 (166)
T 3ue6_A           36 SLVKALQMAQQNFVITDASLPDNPIVYASRGFLTLTGYSLDQILGRNCRFLQGPETDPRAVDKI   99 (166)
T ss_dssp             HHHHHHHHTTSCEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHH
T ss_pred             HHHHHHhcCCceEEEEEccCCCCcEEEECHHHHHHhCcCHHHHcCCCHhheeCCCCCHHHHHHH
Confidence            445566777777888998   8999999999999999999999999999999999877666554

>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*

Probab=97.56  E-value=5.9e-05  Score=71.66  Aligned_cols=56  Identities=23%  Similarity=0.398  Sum_probs=48.4

Q ss_pred             HHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         139 LEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       139 l~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ++++..-|+++|.   +|+|+|+|+++..++||+++|++|+++.++.||++.......+
T Consensus        17 ~~~~~~~i~~~D~~~~~g~i~~~N~a~~~l~G~~~~el~G~~~~~l~~~~~~~~~~~~~   75 (332)
T 2wkq_A           17 LERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNARFLQGPETDRATVRKI   75 (332)
T ss_dssp             GGGCCSEEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHH
T ss_pred             hhcCCCcEEEecCCCCCCCEEEeehHHHHHhCCCHHHHcCCCchhhcCCCCCHHHHHHH
Confidence            4566667899999   9999999999999999999999999999999998866554443

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.55  E-value=2.3e-05  Score=61.56  Aligned_cols=53  Identities=13%  Similarity=0.274  Sum_probs=47.1

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      +...+++++..-++++|.+|+|+|+++++..+||+++.+++|+++.+++++.+
T Consensus         8 l~~~il~~~~~~i~~~D~~g~I~~~N~aa~~l~g~~~~~~~g~~~~~~~~~~~   60 (115)
T 3b33_A            8 LPSAILNNMVTATLILDDGLAIRYANPAAELLFSQSAKRIVEQSLSQLIQHAS   60 (115)
T ss_dssp             HHHHHHHHCSSEEEEECTTCBEEEECHHHHHHTTSCHHHHTTCBHHHHCSEEE
T ss_pred             cHHHHHhhcCceEEEECCCCcEEEECHHHHHHhCCCHHHHhCCCHHHHhCccc
Confidence            44567888888899999999999999999999999999999999999887643

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}

Probab=97.48  E-value=4.8e-05  Score=65.68  Aligned_cols=60  Identities=20%  Similarity=0.229  Sum_probs=51.4

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      +-+.++++++.-|+++|.+|+|+++|++...++|++.+|++|+++++++.+ +...+.+.+
T Consensus        23 ~l~~il~~~~~gi~v~D~~g~I~~~N~a~~~~~G~~~~eviG~~~~~~~p~-~~~~~~~~l   82 (152)
T 3mxq_A           23 LLSELLDQLSFALCIVRNDYVIVKVNEYFESRVIFDGETMQGKNILELFPE-SADYLKRKI   82 (152)
T ss_dssp             HHHHHHHHHCCEEEEEETTSBEEEECHHHHHTSSSCHHHHTTSBHHHHSGG-GHHHHHHHH
T ss_pred             HHHHHHhcCCCCEEEEcCCCEEEEECHHHHHHHCcCHHHHCCCCHHHhcCC-hHHHHHHHH
Confidence            345677888777999999999999999999999999999999999998877 766665544

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus}

Probab=97.42  E-value=7.8e-05  Score=67.02  Aligned_cols=59  Identities=14%  Similarity=0.176  Sum_probs=51.6

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      .+++++...|+++|.+|+|+|+|+++..++||+++|++|+++..+.||.+...+...+.
T Consensus       115 ~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~  173 (227)
T 3ewk_A          115 QAMDANSEMILLTDRAGRIIYANPALCRFSGMAEGELLGQSPSILDSPLADQETLAAMQ  173 (227)
T ss_dssp             HHHHTCCSEEEEECTTSCEEEECHHHHHHHTCCTHHHHSSCGGGGBCTTSCHHHHHHHH
T ss_pred             HHHhcCcCeEEEEcCCCcEEEEchHHHHHhCCCHHHHcCCChhhccCCCCCHHHHHHHH
Confidence            45667777789999999999999999999999999999999999999988777666553

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=97.40  E-value=5.6e-05  Score=60.04  Aligned_cols=50  Identities=16%  Similarity=0.255  Sum_probs=39.4

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHG  185 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~  185 (383)
                      ...+++++..-|+ ++.+|+|+|+|+++..++||++++++|+++.++.+++
T Consensus         5 ~~~~~~~~~~~i~-~~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~   54 (120)
T 3mqq_A            5 YKTAFHLAPIGLV-LSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSS   54 (120)
T ss_dssp             HHHHHHHCSSEEE-EEETTEEEEECHHHHHHTTSCHHHHTTCBGGGGSSSH
T ss_pred             HHHHHhcCCceEE-EecCCEEHHHHHHHHHHhCcCHHHhCCCchhhccCCh
Confidence            3445565554454 5779999999999999999999999999988765543

>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*

Probab=97.37  E-value=7.3e-05  Score=59.21  Aligned_cols=57  Identities=23%  Similarity=0.382  Sum_probs=49.7

Q ss_pred             HHHhhcCcEEEEcC---CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         138 LLEALEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       138 ll~aldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      +++++...+++++.   +|.|+|+|+++..++||++.+++|+++.+++||++...+...+
T Consensus         7 ~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~   66 (146)
T 2v0u_A            7 TLERIEKNFVITDPRLPDNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETDRATVRKI   66 (146)
T ss_dssp             TGGGSSSCEEEECTTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTSCHHHHHHH
T ss_pred             HHhcCCCcEEEEcCCCCCceEEEEcHHHHHHHCcCHHHHcCCCHHHhcCCcCChHHHHHH
Confidence            34566777899999   9999999999999999999999999999999999976655544

>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*

Probab=97.36  E-value=3.9e-05  Score=63.01  Aligned_cols=46  Identities=22%  Similarity=0.323  Sum_probs=40.3

Q ss_pred             HhhcCcEEEEc---CCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         140 EALEGFLFVVN---PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       140 ~aldgfi~vvs---~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      ++.++ |+++|   .+|+|+|+|+++..++||+++|++|+++.+++||++
T Consensus        33 ~~~~~-i~~~d~~d~~g~i~~~N~a~~~l~G~~~~el~g~~~~~l~~~~~   81 (149)
T 3d72_A           33 DTSVA-LILCDLKQKDTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPDG   81 (149)
T ss_dssp             CTTSC-EEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGGSTTS
T ss_pred             cCCcc-EEEEeccCCCCcEEEECHHHHHHHCcCHHHHcCCChhHhCCccc
Confidence            34455 66777   799999999999999999999999999999999884

>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*

Probab=97.35  E-value=0.00011  Score=60.61  Aligned_cols=61  Identities=20%  Similarity=0.187  Sum_probs=52.1

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ....+++++...+++++.+|.|+|+++++..++||+..+++|+++.+++++.+...+...+
T Consensus        41 ~~~~~l~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~  101 (167)
T 1v9y_A           41 IFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYI  101 (167)
T ss_dssp             CHHHHHHTCSSEEEEECTTSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHH
T ss_pred             HHHHHHHhCCCCEEEECCCCcEEEECHHHHHHhCCCHHHHcCCChhhccCccccchHHHHH
Confidence            3456777788889999999999999999999999999999999999999998766554443

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=97.27  E-value=9.4e-05  Score=61.31  Aligned_cols=64  Identities=17%  Similarity=0.196  Sum_probs=55.1

Q ss_pred             ccchhhHHHHhhcCcEEEEcCCc---cEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         131 NEVLGPLLLEALEGFLFVVNPDG---YVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       131 ~~~~~~lll~aldgfi~vvs~dG---~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ...+...+++++...|++++.+|   .|+|+|+++..++||+.++++|+++.+++++.+...+...+
T Consensus        23 ~~~~~~~i~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~   89 (162)
T 3sw1_A           23 NAQLLQSMVDASNDGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEILYQDCRFLQGDDRDQLGRARI   89 (162)
T ss_dssp             CHHHHHHHHHTCSSEEEEEEEETTEEEEEEECHHHHHHHTCCHHHHTTSBGGGGTTTCCCCHHHHHH
T ss_pred             hHHHHHHHHhhccCcEEEEeCCCCccEEEEECHHHHHHHCCCHHHHcCCCcceecCCCcCHHHHHHH
Confidence            34456677888888899999999   99999999999999999999999999999998876655544

>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

Probab=97.25  E-value=0.00011  Score=61.08  Aligned_cols=61  Identities=11%  Similarity=0.142  Sum_probs=50.6

Q ss_pred             cchhhHHHHhhcCcEEEEc-CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         132 EVLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       132 ~~~~~lll~aldgfi~vvs-~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      ++....+++++...+++++ .+|+|+|+|+++..++|++  +++|+++.+++++.+...+...+
T Consensus        16 ~~~~~~~~~~~~~~i~~~d~~~~~i~~~N~~~~~~~g~~--~~~G~~~~~~~~~~~~~~~~~~~   77 (158)
T 3k3c_A           16 AEDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQIYEML   77 (158)
T ss_dssp             HHHHHHHHHHCSSEEEEEETTTTEEEEECHHHHHHCTTC--CSTTSBHHHHSGGGGGTTHHHHH
T ss_pred             HHHHHHHHhcCCceEEEEECCCcEeHHHHHHHHHHcCCc--hhcCCcHHHhCCchhHHHHHHHH
Confidence            3445567788888899999 9999999999999999999  99999999999988765544433

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=97.19  E-value=0.00043  Score=53.58  Aligned_cols=44  Identities=30%  Similarity=0.432  Sum_probs=37.5

Q ss_pred             HHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          59 RREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        59 RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      .|..+|..|.||..++|-.  ++    ...+..|.+||+.||+|||.++.
T Consensus         3 ~R~nIN~~I~EL~~LiP~~--~~----~~~k~nKg~IL~ksvdYI~~Lq~   46 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKS--ND----PDMRWNKGTILKASVDYIRKLQR   46 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCC--CC----TTCCCSHHHHHHHHHHHHHHHHH
T ss_pred             chhhHHHhhhhhhccCCCC--CC----cccCcchHHHHHHHHHHHHHHHH
Confidence            4889999999999999973  22    24699999999999999998764

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=97.18  E-value=9.7e-05  Score=57.23  Aligned_cols=52  Identities=15%  Similarity=0.246  Sum_probs=46.5

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCc---ccccccCCccccccCCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRY---SRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy---~~~el~G~s~~d~iHp~D  186 (383)
                      .+.+++++..-++++|.+|+|+|+++++..++||   ++.+++|+++.+++++.+
T Consensus        17 ~~~il~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~g~~~~~~~~~~~   71 (118)
T 2w0n_A           17 RQAMLQSIKEGVVAVDDRGEVTLINDAAQELLNYRKSQDDEKLSTLSHSWSQVVD   71 (118)
T ss_dssp             HHHHHHCCCCCCEEEBTTTBCCCBCHHHHHHHCSCTTTTTSSCCCTTCCCSCTHH
T ss_pred             HHHHHhhccccEEEECCCCcEeehhHHHHHHhCCCccChhhhhccCcccccCchh
Confidence            4567788887799999999999999999999998   889999999999988765

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=97.16  E-value=0.00021  Score=52.18  Aligned_cols=41  Identities=15%  Similarity=0.323  Sum_probs=37.2

Q ss_pred             cEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         145 FLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       145 fi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      -|+++|.+|+|+|+|+++..++||++++++|+++.++  |.+.
T Consensus         4 ~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~--~~~~   44 (96)
T 3a0s_A            4 AIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDL--PDFE   44 (96)
T ss_dssp             EEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGS--TTCH
T ss_pred             eEEEEcCCCCEeehhHHHHHHhCCCHHHhcCCCHHHC--cchH
Confidence            4788999999999999999999999999999999998  5443

>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* ...

Probab=97.15  E-value=0.00014  Score=61.11  Aligned_cols=52  Identities=13%  Similarity=0.112  Sum_probs=46.6

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      ...++++++-=|+++|.+|+|+|.+...+.+.||++++++|+++++.+.|+.
T Consensus        19 ~~~~ld~l~~Gii~lD~~g~I~~~N~~~e~~sG~~~~eviGk~~f~~~~~~~   70 (125)
T 1nwz_A           19 DDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCT   70 (125)
T ss_dssp             CHHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGG
T ss_pred             HHHHHhccCceEEEECCCCEEEEEHHHHHHHhCCCHHHHcCCchhhhccchh
Confidence            3457888887799999999999999999999999999999999999877765

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=97.06  E-value=0.00043  Score=60.01  Aligned_cols=57  Identities=18%  Similarity=0.156  Sum_probs=50.1

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHH
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF  190 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~  190 (383)
                      ..+.+++++..-++++|.+|+|+|+++++..+||++.++++|+++.+++++.+...+
T Consensus        81 ~l~~il~~~~~gvi~~D~~g~I~~~N~aa~~llg~~~~~~~g~~~~~~~~~~~~~~~  137 (190)
T 2jhe_A           81 ALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLDRLRNHTAAQLINGFNFLRW  137 (190)
T ss_dssp             HHHHHHHHCSSCEEEECTTCBEEEECHHHHHHHTSCHHHHTTSBGGGTSTTCCHHHH
T ss_pred             HHHHHHHhCCCcEEEEcCCCCEEEEcHHHHHHhCCCHHHhcCccHHHHhCCCCHHHH
Confidence            345678888888999999999999999999999999999999999999988765443

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=97.01  E-value=0.00015  Score=61.14  Aligned_cols=51  Identities=12%  Similarity=0.139  Sum_probs=45.5

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      ..++++++-=|+++|.+|+|+|.|...+.+.||++++++|+++++.+.|+.
T Consensus        25 ~~~ld~l~~GiivlD~dg~I~~~N~~~e~isG~s~eeviGk~~f~~~~p~~   75 (129)
T 1mzu_A           25 TAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCT   75 (129)
T ss_dssp             CTTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGG
T ss_pred             HHHHhccCceEEEECCCCeEEEEHHHHHHHhCCCHHHHcCCchhhhccchh
Confidence            335777776699999999999999999999999999999999999877765

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=96.98  E-value=0.00067  Score=51.20  Aligned_cols=43  Identities=35%  Similarity=0.486  Sum_probs=37.5

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhH
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLN   55 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~   55 (383)
                      ..|||||+.-|.+|.||+.|++++         ..|.||+.||+.+++.++.
T Consensus        14 ~iErrRRd~IN~~i~eL~~LvP~~---------~~K~dK~sIL~~aI~yik~   56 (71)
T 4h10_B           14 KSEKKRRDQFNVLIKELGSMLPGN---------ARKMDKSTVLQKSIDFLRK   56 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSSSC---------CSCCCHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHHhCCCC---------CCCCcHHHHHHHHHHHHHH
Confidence            469999999999999999999853         2589999999999988753

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=96.94  E-value=0.00039  Score=55.86  Aligned_cols=48  Identities=6%  Similarity=0.258  Sum_probs=41.7

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccC------------cccccccCCccccccC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIR------------YSRQEVLGKSVYNLIH  183 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LG------------y~~~el~G~s~~d~iH  183 (383)
                      ..+++++..-|+++|.+|+|+|+++++..+||            |++++++|+++.++.+
T Consensus         8 ~~il~~~~~gviv~D~~g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~~   67 (121)
T 4hi4_A            8 ASALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHK   67 (121)
T ss_dssp             HHHHTTSSSEEEEEETTCBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGCS
T ss_pred             HHHHhcCCccEEEEcCCCeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCCCHHHhcC
Confidence            34667776679999999999999999999996            8999999999988764

>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

Probab=96.93  E-value=0.0012  Score=51.56  Aligned_cols=56  Identities=18%  Similarity=0.322  Sum_probs=43.1

Q ss_pred             hHHHHh---hcCcEEEEcC---CccEEEeecccccccCcccccccCCcc-cc-ccCCCChHHHH
Q psy7682         136 PLLLEA---LEGFLFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKSV-YN-LIHHGDHARFH  191 (383)
Q Consensus       136 ~lll~a---ldgfi~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s~-~d-~iHp~D~~~~~  191 (383)
                      +.+++.   +..-+++++.   +|.|+|+|+++..++||+.++++|+++ .+ +.+|++...+.
T Consensus        19 ~~~~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~   82 (138)
T 2l0w_A           19 DTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAA   82 (138)
T ss_dssp             HHHHHHHTTTTSEEEEEESSSTTCBEEEECSHHHHHHSCCHHHHTTSBTTCGGGCCTTCCHHHH
T ss_pred             HHHHHHHhcCCCCEEEEecCCCCCEEEEeCHHHHHHhCCCHHHHcCCCCcccccCCcccchhHH
Confidence            444444   6666888999   999999999999999999999999994 55 45555544433

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=96.92  E-value=0.00029  Score=61.03  Aligned_cols=55  Identities=11%  Similarity=0.141  Sum_probs=47.6

Q ss_pred             chhhHHHHhhcCcEEEEc-CCccEEEeecccccccCcccccccCCccccccCCCChHH
Q psy7682         133 VLGPLLLEALEGFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHAR  189 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs-~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~  189 (383)
                      +....+++++...++++| .+|+|+|+|+++..++||+  +++|+++.+++++.+...
T Consensus        37 ~~l~~l~~~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~--~~~G~~~~~~~~~~~~~~   92 (185)
T 3kx0_X           37 EDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLL--DTVGQPAREVYPELEGQQ   92 (185)
T ss_dssp             HHHHHHHHHCSSEEEEEETTTTEEEEECHHHHHHCCCC--SCTTSBHHHHCTTSCSSS
T ss_pred             HHHHHHHhcCCceEEEEECCCcEEEEEcHHHHHHcCCc--cccCCcHHHHCCchhhhh
Confidence            344567788888899999 9999999999999999999  999999999998877543

>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

Probab=96.80  E-value=0.00059  Score=66.65  Aligned_cols=56  Identities=21%  Similarity=0.383  Sum_probs=50.7

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .-|+++|++. +++|+++|+|+..+||+++++++|+++.++++|++...+++.+...
T Consensus        41 p~G~Ll~~~~~~~~i~~~S~N~~~~lg~~~~~llG~~l~~ll~~~~~~~l~~~l~~~   97 (337)
T 2ool_A           41 PHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGG   97 (337)
T ss_dssp             TTSEEEEECTTTCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHHHHHHHCC-
T ss_pred             CCEEEEEEECCCCEEEEEehhHHHHHCcCHHHHcCCCHHHHcCHHHHHHHHHHHhcC
Confidence            4688999997 5999999999999999999999999999999999999999888543

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=96.77  E-value=0.0016  Score=51.87  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=40.2

Q ss_pred             HHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhcc
Q psy7682          56 EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE  110 (383)
Q Consensus        56 ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~~  110 (383)
                      ++.|=..+|..|+.|+..||..  +.     ..||.|..+||+|+.||+.+...-
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~--p~-----~kKLSKIETLRlAi~YI~~Lq~~L   80 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSI--PQ-----NKKVSKMEILQHVIDYILDLQIAL   80 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTS--CS-----SSCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCC--CC-----CCcccHHHHHHHHHHHHHHHHHHH
Confidence            4567778999999999999983  22     479999999999999999887553

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=96.63  E-value=0.0016  Score=55.68  Aligned_cols=51  Identities=18%  Similarity=0.249  Sum_probs=43.8

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecc---cccccCcccccccCCccccccCCCC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTEN---IKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~s---v~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      .-..+|+++..=|+++|.+|+|+|+|++   ...++| ...+++|+++.++ ||..
T Consensus        20 ~l~~IL~~~~~gI~~vD~~g~I~~~N~a~~~~~~i~g-~~~~~iGr~v~~~-~~~~   73 (151)
T 2qkp_A           20 QANLILNHLPLEITFVNKDDIFQYYNDSVPAAEMVFK-RTPSQVGRNVELC-HPPK   73 (151)
T ss_dssp             HHHHHHHHSSSEEEEEETTSBEEEECCCSCGGGCSSC-CCGGGTTSBGGGS-SCHH
T ss_pred             HHHHHHHhCCCceEEEcCCCeEEEEeCCCchhhhhcC-CCHHHcCCCHHHh-CCHH
Confidence            3456788888889999999999999999   999999 6678999999985 5633

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=96.53  E-value=0.00041  Score=65.94  Aligned_cols=55  Identities=18%  Similarity=0.352  Sum_probs=47.9

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHH
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARF  190 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~  190 (383)
                      +.+++++..-|+++|.+|+|+|+|+++..++||++++++|+++.++.++++....
T Consensus        11 ~~i~~~~~~~i~~~d~~g~i~~~N~a~~~l~G~~~~e~~G~~~~~~~~~~~~~~~   65 (349)
T 3a0r_A           11 ESILESLETAIITLSKDGRITEWNKKAEQLFGLKKENVLGRRLKDLPDFEEIGSV   65 (349)
T ss_dssp             CSSGGGSSSEEEEEESSSBCSCBCHHHHHHHSCCSTTTTTCBSTTSTTTTHHHHH
T ss_pred             HHHHhhhcCeEEEECCCCCEEeeHHHHHHHhCCCHHHHcCcCHHHCcChhHHHHH
Confidence            3456777778999999999999999999999999999999999999777765444

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=96.51  E-value=0.0017  Score=49.32  Aligned_cols=45  Identities=36%  Similarity=0.575  Sum_probs=38.6

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhh
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQC   53 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~   53 (383)
                      ...|||||+..|.+++||+.|+..+.      ....|-||..||+.+++..
T Consensus        14 ~~~ERrRR~rIN~~l~eL~~LvP~~~------~~~~KldKasIL~~tV~yl   58 (73)
T 4h10_A           14 SQIEKRRRDKMNSFIDELASLVPTCN------AMSRKLDKLTVLRMAVQHM   58 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSHHHH------TCSSCCCHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHccccc------cccccccHHHHHHHHHHHH
Confidence            46799999999999999999999861      2347899999999998766

>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii}

Probab=96.40  E-value=0.0022  Score=50.71  Aligned_cols=38  Identities=18%  Similarity=0.071  Sum_probs=33.2

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      -+.-.+.+|+|+|+++..  ..++||.++||+|+++.+++
T Consensus        17 ~i~~~d~~g~i~~~N~a~--~~~~G~~~~elig~~~~~l~   54 (120)
T 2gj3_A           17 AISITDLKANILYANRAF--RTITGYGSEEVLGKNESILS   54 (120)
T ss_dssp             EEEEECTTCBEEEECHHH--HHHHCCCTTGGGGCBGGGGC
T ss_pred             eEEEECCCCCEEeehHHH--HHHHCcCHHHHcCCCHHHcC
Confidence            345568899999999998  89999999999999988775

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=96.37  E-value=0.0017  Score=48.18  Aligned_cols=41  Identities=22%  Similarity=0.489  Sum_probs=33.6

Q ss_pred             EEEEcC---CccEEEeecccccccCcccccccCCc-cccccCCCC
Q psy7682         146 LFVVNP---DGYVNFCTENIKSFIRYSRQEVLGKS-VYNLIHHGD  186 (383)
Q Consensus       146 i~vvs~---dG~i~yvS~sv~~~LGy~~~el~G~s-~~d~iHp~D  186 (383)
                      +++++.   +|.|+|+|+++..++||++++++|++ +.+++++.+
T Consensus         4 i~i~d~~~~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~   48 (110)
T 1byw_A            4 FIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPC   48 (110)
T ss_dssp             EEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTT
T ss_pred             EEEEeccCCCCcEEEECHHHHHHhCCCHHHHccCCCccccccCCc
Confidence            566675   59999999999999999999999999 466555443

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=96.35  E-value=0.0018  Score=59.11  Aligned_cols=48  Identities=6%  Similarity=0.261  Sum_probs=41.6

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeeccccccc------------CcccccccCCccccccC
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFI------------RYSRQEVLGKSVYNLIH  183 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~L------------Gy~~~el~G~s~~d~iH  183 (383)
                      ..+++++..-|+++|.+|+|+|+++++..+|            ||++++++|+++.+|+.
T Consensus        25 ~~iLd~~~~~vii~D~~g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~~~~~~~~   84 (233)
T 3vol_A           25 KSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFHK   84 (233)
T ss_dssp             HHHHTTSSSEEEEEETTSBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTCBGGGGSS
T ss_pred             HHHHhcCCCcEEEECCCCcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCCCHHHHcC
Confidence            3456776666899999999999999999998            89999999999988764

>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase regulation, transferase; NMR {Homo sapiens} SCOP: d.110.3.5

Probab=96.21  E-value=0.0063  Score=47.42  Aligned_cols=40  Identities=8%  Similarity=0.105  Sum_probs=34.5

Q ss_pred             eeEEEeCCC-CcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         285 QFTMKLDRS-GTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       285 ~F~tRHsld-gkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .-+.-.+.+ |+|+++++.+  ..++||.++||+|+++.++++
T Consensus         9 ~~i~~~d~~~g~I~~~N~aa--~~l~G~~~~el~g~~~~~l~~   49 (114)
T 1ll8_A            9 KAIFTVDAKTTEILVANDKA--CGLLGYSSQDLIGQKLTQFFL   49 (114)
T ss_dssp             CEEEEEETTTCBEEEECTTH--HHHHTCCTTTTTTSBGGGGSS
T ss_pred             ceEEEEECCCCeEEEehHHH--HHHhCCCHHHHcCCCHHHhcC
Confidence            344556788 9999999998  899999999999999998873

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=96.18  E-value=0.0016  Score=51.30  Aligned_cols=33  Identities=6%  Similarity=0.052  Sum_probs=29.7

Q ss_pred             CCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         291 DRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       291 sldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.+|+|++|++..  ..++||.++||+|+++.+++
T Consensus        19 ~~~g~i~~~N~a~--~~l~G~~~~el~g~~~~~~~   51 (120)
T 3mqq_A           19 SRDRVIEDCNDEL--AAIFRCARADLIGRSFEVLY   51 (120)
T ss_dssp             EETTEEEEECHHH--HHHTTSCHHHHTTCBGGGGS
T ss_pred             ecCCEEHHHHHHH--HHHhCcCHHHhCCCchhhcc
Confidence            4589999999998  89999999999999987765

>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*

Probab=96.11  E-value=0.0027  Score=50.96  Aligned_cols=37  Identities=16%  Similarity=0.254  Sum_probs=32.5

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.+|+|+++++.+  ..++||.++||+|+++.+++
T Consensus        29 i~~~d~~g~i~~~N~a~--~~l~Gy~~~eliG~~~~~l~   65 (130)
T 1d06_A           29 TVVSATDGTIVSFNAAA--VRQFGYAEEEVIGQNLRILM   65 (130)
T ss_dssp             EEEEETTSBEEEECHHH--HHHHCCCHHHHTTSBGGGGS
T ss_pred             EEEECCCCeEEEEcHHH--HHHHCCCHHHHcCCcHHHHC
Confidence            34457899999999998  89999999999999988776

>3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum}

Probab=96.03  E-value=0.0042  Score=47.77  Aligned_cols=41  Identities=10%  Similarity=-0.006  Sum_probs=32.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCc--cceecCCCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTS--ATVWTCPNS  330 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~--yd~~~~~~~  330 (383)
                      +...+.++.++++++..  ..++||.+++++|...  .+++ ||++
T Consensus        17 i~~~d~~~~~~~~n~~~--~~~~G~~~~~~~~~~~~~~~~i-~p~d   59 (118)
T 3icy_A           17 IYHLDVSGQATIRFRPP--AFLKTLVSEHAGTTRLNTLSMI-HHDD   59 (118)
T ss_dssp             CEEECTTSCEEECCCCC--GGGGGGEEEETTEEEEGGGGGB-CGGG
T ss_pred             EEEEEcCCCceEEechh--HhhcCCCHHHccCChhHHHHHc-CHHH
Confidence            35568899999999998  8999999999988753  4454 4554

>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*

Probab=95.97  E-value=0.0029  Score=49.59  Aligned_cols=32  Identities=9%  Similarity=-0.057  Sum_probs=28.3

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .+|+|+|+++..  ..++||.++|++|++...+.
T Consensus        14 ~~g~i~~~N~a~--~~l~Gy~~~e~~G~~~~~l~   45 (109)
T 1n9l_A           14 PDCPLVYASEGF--YAMTGYGPDEVLGHNCRFLQ   45 (109)
T ss_dssp             TTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGC
T ss_pred             CCCeEEEEchHH--HHHHCcCHHHHcCCCchhcC
Confidence            689999999998  89999999999999975554

>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*

Probab=95.89  E-value=0.0039  Score=49.07  Aligned_cols=36  Identities=11%  Similarity=0.117  Sum_probs=31.8

Q ss_pred             EEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         288 MKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       288 tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .-.+.+|+|+++++.+  ..++||.++||+|+++.+++
T Consensus         7 ~~~d~~g~i~~~N~a~--~~l~G~~~~el~G~~~~~l~   42 (119)
T 2vv6_A            7 IVIDGHGIIQLFSTAA--ERLFGWSELEAIGQNVNILM   42 (119)
T ss_dssp             EEEETTSBEEEECHHH--HHHHCCCHHHHTTSBGGGGS
T ss_pred             EEECCCCeEEEEhHHH--HHHhCCCHHHHcCCCHHHhC
Confidence            3457899999999998  89999999999999987765

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A*

Probab=95.82  E-value=0.0099  Score=47.66  Aligned_cols=35  Identities=14%  Similarity=0.047  Sum_probs=29.2

Q ss_pred             EeCCCC---cEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         289 KLDRSG---TIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       289 RHsldg---kf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      -.+.+|   +|+||++..  ..++||.++|++|+++..++
T Consensus        14 ~~d~~g~~~~i~~~N~a~--~~~~G~~~~el~g~~~~~l~   51 (132)
T 2pr5_A           14 ITDPALEDNPIVYVNQGF--VQMTGYETEEILGKNCRFLQ   51 (132)
T ss_dssp             EECTTSTTCCEEEECHHH--HHHHSCCHHHHTTSCGGGGC
T ss_pred             EEeCCCCCCcEEEECHHH--HHHhCcCHHHHcCCChhhhC
Confidence            345544   999999998  89999999999999986554

>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*

Probab=95.71  E-value=0.0064  Score=46.07  Aligned_cols=36  Identities=14%  Similarity=0.062  Sum_probs=31.1

Q ss_pred             EeCC---CCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         289 KLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       289 RHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      -.+.   +|+++++++..  ..++||.++|++|+++.++++
T Consensus        12 ~~d~~~~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~~   50 (115)
T 4eet_B           12 ITDPRLPDNPIIFASDGF--LELTEYSREEILGRNARFLQG   50 (115)
T ss_dssp             EECTTSTTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGCC
T ss_pred             EEcCCCCCCcEEEEcHHH--HHHHCcCHHHHhCCCHHHhcC
Confidence            3456   99999999998  899999999999999877663

>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Shewanella oneidensis}

Probab=95.67  E-value=0.0054  Score=50.69  Aligned_cols=38  Identities=8%  Similarity=0.056  Sum_probs=33.7

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +.-.+.+|+|+++++.+  ..++||.++||+|+++.+++.
T Consensus        20 i~~~D~~g~I~~~N~aa--~~l~G~~~~el~G~~~~~l~~   57 (129)
T 3mfx_A           20 MILVNANGFIRSCNQRS--AELLDCPQVSLKGQDWRNFLT   57 (129)
T ss_dssp             EEEEETTSBEEEECHHH--HHHTTSCHHHHTTSBGGGGBC
T ss_pred             EEEECCCCEEEeEhHHH--HHHHCcCHHHHcCCcHHHHcC
Confidence            44467899999999998  899999999999999999874

>2r78_A Sensor protein; sensory box sensor histidine kinase/response regulator, structural genomics, PSI, MCSG; 1.60A {Geobacter sulfurreducens pca}

Probab=95.58  E-value=0.011  Score=46.66  Aligned_cols=37  Identities=8%  Similarity=0.093  Sum_probs=31.9

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccce
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATV  324 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~  324 (383)
                      .+.-.+.+|+|++|++.+  ..++||.++||+|+++.++
T Consensus        23 ~i~~~d~~g~i~~vN~a~--~~l~Gy~~~el~g~~~~~~   59 (117)
T 2r78_A           23 GIFIMDAEGHYLDVNPAI--CSAIGYTRDEFLALDWGVL   59 (117)
T ss_dssp             EEEEECTTSBEEEECHHH--HHHHCCCHHHHTTCBTTTT
T ss_pred             eEEEECCCCCEEEecHHH--HHHHCcCHHHHcCCCHHHh
Confidence            345568999999999998  7999999999999987655

>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*

Probab=95.55  E-value=0.0072  Score=57.00  Aligned_cols=38  Identities=16%  Similarity=0.070  Sum_probs=32.7

Q ss_pred             EEEeCC---CCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         287 TMKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       287 ~tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +.-.+.   +|+|+|+++.+  ..++||.++|++|+++.++++
T Consensus        24 i~~~D~~~~~g~i~~~N~a~--~~l~G~~~~el~G~~~~~l~~   64 (332)
T 2wkq_A           24 FVITDPRLPDNPIIFASDSF--LQLTEYSREEILGRNARFLQG   64 (332)
T ss_dssp             EEEECTTSTTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGCC
T ss_pred             EEEecCCCCCCCEEEeehHH--HHHhCCCHHHHcCCCchhhcC
Confidence            334467   99999999998  899999999999999987763

>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}

Probab=95.48  E-value=0.0056  Score=47.02  Aligned_cols=37  Identities=8%  Similarity=0.068  Sum_probs=32.8

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.+|+|+++++.+  ..++||.++||+|+++.+++
T Consensus        26 i~~~d~~g~i~~~N~~~--~~l~G~~~~el~g~~~~~~~   62 (118)
T 3olo_A           26 SFCLGDNWQFLYVNDAT--CRMTEYSREQLLSMNLQDID   62 (118)
T ss_dssp             EEEECTTSBEEEECHHH--HHHHCCCHHHHTTCBGGGTB
T ss_pred             EEEECCCCcEEEEHHHH--HHHHCCCHHHHhCCChhhcc
Confidence            34457899999999998  89999999999999998876

>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein STR initiative; 1.90A {Marinobacter aquaeolei}

Probab=95.47  E-value=0.0067  Score=47.23  Aligned_cols=26  Identities=0%  Similarity=-0.141  Sum_probs=23.8

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCC
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACK  319 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~  319 (383)
                      .+|+|+|+++.+  ..++||.+++++|.
T Consensus        12 ~~~~~~~~n~~~--~~l~G~~~~e~~~~   37 (115)
T 3h9w_A           12 QTMAFEYIGPQI--EALLGWPQGSWKSV   37 (115)
T ss_dssp             TTTEEEEECTHH--HHHHCSCGGGCCBH
T ss_pred             CCCcEEEEChhH--HHHhCCChHHccCH
Confidence            688999999998  89999999999993

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C

Probab=95.41  E-value=0.035  Score=42.80  Aligned_cols=63  Identities=22%  Similarity=0.240  Sum_probs=53.4

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhhcc
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAELIS   75 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~llP   75 (383)
                      ..|++||+.-|..+.+|..+++..         ..|.||..||..+++.+..=+...+.+.+...+|...+-
T Consensus        12 ~~ErrRR~~in~~f~~L~~lvP~~---------~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~   74 (82)
T 1am9_A           12 AIEKRYRSSINDKIIELKDLVVGT---------EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVH   74 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCS---------SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhccCC---------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999853         368999999999999998877777777777777776653

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis}

Probab=95.38  E-value=0.0095  Score=46.63  Aligned_cols=38  Identities=11%  Similarity=0.023  Sum_probs=32.2

Q ss_pred             EEeCC---CCcEEEEcCCCCccccCCcccccccCCCccceecC
Q psy7682         288 MKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTC  327 (383)
Q Consensus       288 tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~  327 (383)
                      .-.+.   +|+++++++..  ..++||.+++++|+++.++++.
T Consensus        11 ~~~d~~~~~g~i~~~N~~~--~~l~g~~~~e~~g~~~~~~~~~   51 (128)
T 3t50_A           11 LITNPHLPDNPIVFANPAF--LKLTGYEADEVMGRNCRFLQGH   51 (128)
T ss_dssp             EEECTTSTTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGCCT
T ss_pred             EEecCCCCCCcEEEEcHHH--HHHhCcCHHHHcCCCHhhhcCC
Confidence            33456   89999999998  8999999999999998877643

>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*

Probab=95.30  E-value=0.0081  Score=58.58  Aligned_cols=55  Identities=18%  Similarity=0.279  Sum_probs=49.8

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .-|++++++. +++|+++|+|+..+||.++++++|+++-+++-+ ....+++.+...
T Consensus        51 phG~LL~l~~~~~~I~~~S~N~~~~lg~~~~~llG~~l~~ll~~-~~~~l~~~l~~~  106 (343)
T 3s7o_A           51 PHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPE-QWPALQAALPPG  106 (343)
T ss_dssp             TTSEEEEEETTTCBEEEEETTHHHHHSSCHHHHTTCBHHHHSTT-THHHHHHHSCTT
T ss_pred             CCeEEEEEECCCCEEEEEcccHHHHhCcChHHHcCCCHHHHHhH-HHHHHHHHhccc
Confidence            4689999997 899999999999999999999999999999988 888888887643

>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*

Probab=95.15  E-value=0.0081  Score=48.75  Aligned_cols=32  Identities=16%  Similarity=0.070  Sum_probs=29.6

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .+|+|+++++..  ..++||.++|++|+++.+++
T Consensus        46 ~~g~i~~~N~a~--~~l~G~~~~el~g~~~~~l~   77 (149)
T 3d72_A           46 KDTPIVYASEAF--LYMTGYSNAEVLGRNCRFLQ   77 (149)
T ss_dssp             TTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGG
T ss_pred             CCCcEEEECHHH--HHHHCcCHHHHcCCChhHhC
Confidence            699999999998  89999999999999987776

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=95.14  E-value=0.022  Score=55.80  Aligned_cols=50  Identities=20%  Similarity=0.211  Sum_probs=43.2

Q ss_pred             hHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         136 PLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       136 ~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      ..+++++..=|+++|.+|+|+|+|++ ..++ +.+.+++|+++.+++.+...
T Consensus       242 ~~IL~~l~dgIivvD~~g~I~~~N~a-e~i~-~~~~e~iGr~v~~~~p~~~~  291 (369)
T 3cax_A          242 KAIFEALPVDVTFIDKDDRVRFFSPG-ERIF-TRTPSVLGRPVQLCHPPKSV  291 (369)
T ss_dssp             HHHHHHSSSEEEEECTTSBEEEECCS-SCSS-CCCGGGTTCBTTTSSCGGGH
T ss_pred             HHHHHhCCCcEEEECCCCcEEEEcCH-HHcc-CChHHHcCCcHHHHCChhhH
Confidence            46788888779999999999999999 9999 99999999999987554433

>4hia_A LOV protein; PAS, HTH, signaling protein; HET: FMN; 1.95A {Rhodobacter sphaeroides} PDB: 4hnb_A* 4hj4_A* 4hj6_A* 4hj3_A*

Probab=95.10  E-value=0.016  Score=48.49  Aligned_cols=35  Identities=11%  Similarity=0.026  Sum_probs=30.4

Q ss_pred             eCCC---CcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         290 LDRS---GTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       290 Hsld---gkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .+.+   |+|+++++..  ..++||.++|++|+++.++++
T Consensus        23 ~d~~~~~g~i~~~N~a~--~~~~G~~~~e~~g~~~~~~~~   60 (176)
T 4hia_A           23 VDMSLPEQPVVLANPPF--LRMTGYTEGQILGFNCRFLQR   60 (176)
T ss_dssp             EETTSTTCCEEEECHHH--HHHHTCCHHHHTTSCGGGGCC
T ss_pred             EecCCCCCcEEEECHHH--HHHHCcCHHHHcCCCcceeeC
Confidence            3455   9999999998  899999999999999877763

>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens}

Probab=94.96  E-value=0.02  Score=43.21  Aligned_cols=40  Identities=8%  Similarity=0.095  Sum_probs=34.6

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      +.-.+.+|+++++++..  ..++||.+++++|+++++++  |++
T Consensus        16 i~~~d~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~--~~~   55 (114)
T 3luq_A           16 LAMFDREMRYLAVSRRW--REDYGLGDGDILGMSHYDIF--PEI   55 (114)
T ss_dssp             EEEEETTCBEEEECHHH--HHHTTCCSSCCTTCBHHHHC--TTC
T ss_pred             EEEEcCCcEEEEECHHH--HHHHCCCHHHHcCCcHHHHC--Ccc
Confidence            44457899999999998  89999999999999999986  454

>4e04_A Bacteriophytochrome (light-regulated signal trans histidine kinase), PHYB1; bacteriophytochrome chromophore binding domain; HET: LBV; 1.79A {Rhodopseudomonas palustris}

Probab=94.95  E-value=0.0065  Score=58.93  Aligned_cols=55  Identities=16%  Similarity=0.309  Sum_probs=49.8

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~  196 (383)
                      .-|++++++.+++|+++|+|+..+||.++++++|+++-+++-+.....+++.+..
T Consensus        28 phG~Ll~~~~~~~I~~~S~N~~~~lg~~~~~~lG~~l~~ll~~~~~~~l~~~l~~   82 (327)
T 4e04_A           28 PHGLLLALAADMTIVAGSDNLPELTGLAIGALIGRSAADVFDSETHNRLTIALAE   82 (327)
T ss_dssp             TTSEEEEECTTCBEEEEETTHHHHHSCCHHHHTTCBHHHHBCHHHHHHHHHHHHS
T ss_pred             CCeEEEEEcCCCeEEEEcccHHHHhCCChHhhcCCCHHHHcCHHHHHHHHHHhhc
Confidence            4689999998899999999999999999999999999999988888888877754

>3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis}

Probab=94.75  E-value=0.041  Score=44.80  Aligned_cols=41  Identities=5%  Similarity=0.021  Sum_probs=30.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCC--CccceecCCCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACK--TSATVWTCPNS  330 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~--S~yd~~~~~~~  330 (383)
                      +...++++..+++++..  ..++||.+.++.+.  ...+++ ||+|
T Consensus        22 ~w~~d~~~~~~~~s~~~--~~~~G~~~~~~~~~~~~~~~~i-hpdD   64 (142)
T 3mr0_A           22 LWDWNPKTGAMYLSPHF--KKIMGYEDHELPDEITGHRESI-HPDD   64 (142)
T ss_dssp             EEEECTTTCCEEECHHH--HHHTTCCGGGSCSEEC---CCB-CTTT
T ss_pred             EEEEEcCCCeEEECHHH--HHHhCCCccccCCCHHHHHhhc-CHHH
Confidence            44567888999999998  89999999999874  334444 6666

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.67  E-value=0.04  Score=49.78  Aligned_cols=40  Identities=10%  Similarity=0.093  Sum_probs=33.8

Q ss_pred             eeEEEeCC---CCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         285 QFTMKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       285 ~F~tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .-+.-.+.   ||+|+||++..  ..++||.++|++|+++.++++
T Consensus        74 ~~i~~~d~~~~~g~i~~~N~a~--~~l~G~~~~el~g~~~~~l~~  116 (258)
T 3p7n_A           74 IASVVSDPRLADNPLIAINQAF--TDLTGYSEEECVGRNCRFLAG  116 (258)
T ss_dssp             SEEEEECTTSTTCCEEEECHHH--HHHHCCCGGGTTTSCGGGGCC
T ss_pred             ccEEEEcCCCCCCcEEEEhHHH--HHHcCCCHHHHCCCChhhccC
Confidence            33455678   89999999998  899999999999999877763

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=94.62  E-value=0.017  Score=47.34  Aligned_cols=37  Identities=14%  Similarity=0.030  Sum_probs=31.5

Q ss_pred             EEeCC---CCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         288 MKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       288 tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .-.+.   ||+|+++++..  ..++||.+++++|+++.++++
T Consensus        49 ~~~d~~~~~g~i~~~N~~~--~~l~G~~~~e~~g~~~~~l~~   88 (166)
T 3ue6_A           49 VITDASLPDNPIVYASRGF--LTLTGYSLDQILGRNCRFLQG   88 (166)
T ss_dssp             EEEETTSTTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGCC
T ss_pred             EEEEccCCCCcEEEECHHH--HHHhCcCHHHHcCCCHhheeC
Confidence            33456   89999999998  899999999999999877763

>3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum}

Probab=94.50  E-value=0.02  Score=43.94  Aligned_cols=41  Identities=5%  Similarity=-0.074  Sum_probs=32.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccC--CCccceecCCCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVAC--KTSATVWTCPNS  330 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG--~S~yd~~~~~~~  330 (383)
                      +...+.++.++++++..  ..++||.+++++|  ..+.+++ ||++
T Consensus        20 i~~~d~~~~~~~~n~~~--~~~~G~~~~~~~~~~~~~~~~~-~~~d   62 (125)
T 3nja_A           20 SWVLHMESGRLEWSQAV--HDIFGTDSATFDATEDAYFQRV-HPDD   62 (125)
T ss_dssp             EEEEETTTTEEEECHHH--HHHHTCCTTTCCCBHHHHHHHB-CTTT
T ss_pred             EEEEEcCCCcEEECHHH--HHHhCCCcccccccHHHHHhhc-ChhH
Confidence            44567899999999998  7999999999999  4555554 4555

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1

Probab=94.29  E-value=0.038  Score=40.55  Aligned_cols=48  Identities=29%  Similarity=0.402  Sum_probs=38.7

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhh
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCL   54 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~   54 (383)
                      -..|++||+.-|..+.||.+|+...  .  ..+-..|.+|..||+.+++.+.
T Consensus        10 ~~~Er~RR~~in~~~~~L~~lvP~~--~--~~~~~~k~~Ka~IL~~ai~YI~   57 (65)
T 1an4_A           10 NEVERRRRDKINNWIVQLSKIIPDS--S--MESTKSGQSKGGILSKASDYIQ   57 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCC--C--CCSSTTCCCTTTTTTTTHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHCcCc--c--cccccCCCCHHHHHHHHHHHHH
Confidence            3579999999999999999999976  1  2222357899999999988764

>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense}

Probab=94.13  E-value=0.02  Score=44.16  Aligned_cols=38  Identities=13%  Similarity=0.239  Sum_probs=33.4

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .+.-.+.+|+|+++++.+  ..++||.+++++|+++.+++
T Consensus        11 ~i~~~d~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~   48 (126)
T 3mjq_A           11 MILIINREGRLLYANTAV--PKKLGYTHEELMSMHILTIT   48 (126)
T ss_dssp             EEEEEETTSBEEEECTHH--HHHHSCCHHHHHHSBHHHHH
T ss_pred             eEEEEeCCCcEEEEcHHH--HHHHCCCHHHHcCCCHHHHc
Confidence            344567899999999998  89999999999999998887

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=94.10  E-value=0.04  Score=40.34  Aligned_cols=36  Identities=11%  Similarity=0.069  Sum_probs=29.5

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCC-ccceecCCC
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKT-SATVWTCPN  329 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S-~yd~~~~~~  329 (383)
                      .+|+++++++..  ..++||.+++++|++ ..+++..++
T Consensus        12 ~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~~~~~~   48 (110)
T 1byw_A           12 ENCAVIYCNDGF--CELCGYSRAEVMQRPCTCDFLHGPC   48 (110)
T ss_dssp             SSCBEEEECHHH--HHHHTCCHHHHTTSBTTCGGGCCTT
T ss_pred             CCCcEEEECHHH--HHHhCCCHHHHccCCCccccccCCc
Confidence            579999999998  899999999999998 355554443

>3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor}

Probab=93.78  E-value=0.033  Score=47.60  Aligned_cols=39  Identities=5%  Similarity=0.039  Sum_probs=34.5

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTC  327 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~  327 (383)
                      +.-.+.||++++++...  ..++||.++|++|+++++++..
T Consensus        35 i~v~D~~g~I~~~N~a~--~~~~G~~~~eviG~~~~~~~p~   73 (152)
T 3mxq_A           35 LCIVRNDYVIVKVNEYF--ESRVIFDGETMQGKNILELFPE   73 (152)
T ss_dssp             EEEEETTSBEEEECHHH--HHTSSSCHHHHTTSBHHHHSGG
T ss_pred             EEEEcCCCEEEEECHHH--HHHHCcCHHHHCCCCHHHhcCC
Confidence            44568899999999998  8999999999999999999843

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=93.34  E-value=0.2  Score=38.43  Aligned_cols=62  Identities=16%  Similarity=0.304  Sum_probs=49.9

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAEL   73 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~l   73 (383)
                      ..|++||+.-|..+++|..+++..  .      ..|.+|-.|+..+++.+..=+.+...+...+++|..-
T Consensus         8 ~~Er~RR~~in~~f~~Lr~lvP~~--~------~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~   69 (83)
T 1nkp_B            8 ALERKRRDHIKDSFHSLRDSVPSL--Q------GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   69 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSGGG--T------TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHCCCC--C------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999965  1      2689999999999999877666666666666666543

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1

Probab=93.25  E-value=0.2  Score=38.17  Aligned_cols=61  Identities=16%  Similarity=0.318  Sum_probs=50.7

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAE   72 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~   72 (383)
                      ..|++||+.-|..+++|..++...  .      ..|.+|-.||+.+++.+..=+.+.+.+.+.+.+|..
T Consensus        18 ~~Er~RR~~in~~f~~Lr~lvP~~--~------~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A           18 ALERKRRDHIKDSFHSLRDSVPSL--Q------GEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSGGG--T------TSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCC--C------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            579999999999999999999975  1      257999999999999998777777777777776653

>3zq5_A Phytochrome-like protein CPH1; arginine finger, tandem GAF domain, receptor, PAS domain, chromophore, sensory transduction; HET: CYC; 1.95A {Synechocystis SP} PDB: 2vea_A*

Probab=93.10  E-value=0.014  Score=59.99  Aligned_cols=53  Identities=15%  Similarity=0.251  Sum_probs=45.1

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .-|++++++. +++|+++|+|+..+||.++++++|+++-+++-++....++..+
T Consensus        28 phG~LLal~~~~~~I~~~S~N~~~~lg~~~~~llG~~l~~ll~~~~~~~l~~~l   81 (520)
T 3zq5_A           28 PHGLVVVLQEPDLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDPIQSRL   81 (520)
T ss_dssp             TTSEEEEEETTTTEEEEEETTHHHHHSCCHHHHTTSBHHHHCEESSCCCCSSCC
T ss_pred             CCeEEEEEECCCCEEEEEcccHHHHhCcChHHHcCCCHHHHcCHHHHHHHHHHh
Confidence            4689999997 8999999999999999999999999999888776555554443

>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*

Probab=92.93  E-value=0.065  Score=41.57  Aligned_cols=37  Identities=16%  Similarity=0.073  Sum_probs=32.2

Q ss_pred             EEEeCC---CCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.   +|+++++++..  ..++||.+.+++|+++.+++
T Consensus        15 i~~~d~~~~~~~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~   54 (146)
T 2v0u_A           15 FVITDPRLPDNPIIFASDSF--LQLTEYSREEILGRNCRFLQ   54 (146)
T ss_dssp             EEEECTTSTTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGC
T ss_pred             EEEEcCCCCCceEEEEcHHH--HHHHCcCHHHHcCCCHHHhc
Confidence            444577   89999999998  79999999999999988776

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=92.89  E-value=0.1  Score=39.05  Aligned_cols=38  Identities=16%  Similarity=0.159  Sum_probs=31.9

Q ss_pred             eEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         286 FTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       286 F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .+.-.+.+|+++++++..  ..++||.+++++|+++..++
T Consensus        19 ~i~~~d~~~~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~   56 (124)
T 3lyx_A           19 AIVVTDLQGFIIDWNKGS--ETLYGYSKEQAIGQPVNMLH   56 (124)
T ss_dssp             EEEEEETTCBEEEECHHH--HHHHCCCHHHHTTSBGGGGS
T ss_pred             eEEEECCCCcEeehhhHH--HHHhCCCHHHHcCCCHHHhc
Confidence            344557899999999998  79999999999999987443

>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}

Probab=92.75  E-value=0.057  Score=42.48  Aligned_cols=40  Identities=18%  Similarity=0.117  Sum_probs=34.7

Q ss_pred             eeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         285 QFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       285 ~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .-+.-.+.+|+|+++++.+  ..++||.+++++|+++.++++
T Consensus        23 ~~i~~~D~~g~i~~~N~a~--~~l~g~~~~e~~G~~~~~~~~   62 (118)
T 3fg8_A           23 LGFMALDEDLRIIYVNSGC--LRHVRRSRDELLGRVVTEVLP   62 (118)
T ss_dssp             CEEEEECTTCBEEEECHHH--HHHHTCCHHHHTTSBHHHHCG
T ss_pred             ceEEEECCCCeEEEECHHH--HHHhCCCHHHHcCCcHHHHcC
Confidence            3345568899999999998  899999999999999998874

>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*

Probab=92.52  E-value=0.058  Score=40.68  Aligned_cols=33  Identities=15%  Similarity=0.065  Sum_probs=30.1

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      .+|+++++++.+  ..++||.+++++|+++.++++
T Consensus        27 ~~~~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~~   59 (130)
T 2z6d_A           27 PHCPIVYASSGF--FTMTGYSSKEIVGRNCRFLQG   59 (130)
T ss_dssp             TTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGCC
T ss_pred             CCCcEEEecHHH--HHHhCcCHHHHcCCChhhccC
Confidence            799999999998  799999999999999887763

>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

Probab=92.37  E-value=0.092  Score=40.34  Aligned_cols=41  Identities=10%  Similarity=0.082  Sum_probs=32.2

Q ss_pred             EEeCC---CCcEEEEcCCCCccccCCcccccccCCCc-cceecCCCC
Q psy7682         288 MKLDR---SGTIIGMDTSGVSQTHTQYLNKAVACKTS-ATVWTCPNS  330 (383)
Q Consensus       288 tRHsl---dgkf~~vD~r~l~~~ilGY~p~eLiG~S~-yd~~~~~~~  330 (383)
                      .-.+.   +|++++++..+  ..++||.+++++|+++ ++++..++.
T Consensus        33 ~~~d~~~~~g~i~~~N~~~--~~l~g~~~~~~~g~~~~~~~~~~~~~   77 (138)
T 2l0w_A           33 IIANARVENCAVIYCNDGF--CELCGYSRAEVMQRPCTCDFLHGPRT   77 (138)
T ss_dssp             EEEESSSTTCBEEEECSHH--HHHHSCCHHHHTTSBTTCGGGCCTTC
T ss_pred             EEEecCCCCCEEEEeCHHH--HHHhCCCHHHHcCCCCcccccCCccc
Confidence            33455   89999999998  7999999999999984 555544444

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=91.96  E-value=0.15  Score=37.32  Aligned_cols=48  Identities=23%  Similarity=0.353  Sum_probs=37.8

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCL   54 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~   54 (383)
                      ..|++||+.-|..++||..||... +..  +.-..+.+|..|+..+++.++
T Consensus         8 ~aEr~RR~rIn~~~~~L~~LlP~~-~~~--~~~~~k~sKa~iL~~Ai~YIk   55 (63)
T 1a0a_A            8 HAEQARRNRLAVALHELASLIPAE-WKQ--QNVSAAPSKATTVEAACRYIR   55 (63)
T ss_dssp             GGTHHHHHHHHHHHHHHHHTSCHH-HHT--SSCCCCSCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCc-ccc--cccCCcccHHHHHHHHHHHHH
Confidence            469999999999999999999976 222  212478889999998876653

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=91.67  E-value=0.15  Score=41.97  Aligned_cols=55  Identities=29%  Similarity=0.401  Sum_probs=42.3

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQEN   64 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n   64 (383)
                      ..|++||+.=|..+.+|.+|+...   .++   ..|.+|..||.++++.+..=+...+++.
T Consensus        33 ~~ERrRR~~In~~~~~L~~lvP~~---~~~---~~k~~Ka~IL~~aieYIk~Lq~~~~~l~   87 (118)
T 4ati_A           33 LIERRRRFNINDRIKELGTLIPKS---NDP---DMRWNKGTILKASVDYIRKLQREQQRAK   87 (118)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCCC----------CCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhc---cCc---cccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999999999976   122   3588999999999999865544444443

>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}

Probab=91.60  E-value=0.043  Score=41.50  Aligned_cols=39  Identities=0%  Similarity=-0.104  Sum_probs=31.3

Q ss_pred             eeEEEeCCC-CcEEEEcCCCCccccCCcccccccCCC--cccee
Q psy7682         285 QFTMKLDRS-GTIIGMDTSGVSQTHTQYLNKAVACKT--SATVW  325 (383)
Q Consensus       285 ~F~tRHsld-gkf~~vD~r~l~~~ilGY~p~eLiG~S--~yd~~  325 (383)
                      ..+...+.+ |+++++++..  ..++||.+++++|..  +.+++
T Consensus        22 ~~i~~~d~~~~~i~~~n~~~--~~~~g~~~~~~~~~~~~~~~~~   63 (125)
T 3eeh_A           22 DILWEFTADLSEVLVINSAY--EDIWGRSVAKLRENPHDFLNGI   63 (125)
T ss_dssp             CEEEEEETTSSCEEEECTHH--HHHHSSCHHHHHHCGGGGGGGB
T ss_pred             ceEEEEEcCCCcEEEecHHH--HHHHCCCHHHHccCcHHHHHhc
Confidence            345566788 9999999998  799999999999987  34443

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=91.59  E-value=0.045  Score=45.92  Aligned_cols=38  Identities=16%  Similarity=0.126  Sum_probs=33.7

Q ss_pred             eeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccce
Q psy7682         285 QFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATV  324 (383)
Q Consensus       285 ~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~  324 (383)
                      .=+...+.+|++++.+...  ..+.||.+++++|+++++.
T Consensus        33 ~GiivlD~dg~I~~~N~~~--e~isG~s~eeviGk~~f~~   70 (129)
T 1mzu_A           33 VGAIQVDGSGVIHRYNRTE--SRLSGRIPERVIGRNFFTE   70 (129)
T ss_dssp             SEEEEEETTCBEEEECHHH--HHHHCCCHHHHTTSBCCCC
T ss_pred             ceEEEECCCCeEEEEHHHH--HHHhCCCHHHHcCCchhhh
Confidence            3466778999999999998  8999999999999999874

>3nhq_A Bacteriophytochrome; photoreceptor, PAS, signaling, signaling protei; HET: BLA; 2.55A {Pseudomonas aeruginosa} PDB: 3c2w_A* 3nop_C* 3not_C* 3nou_C* 3g6o_A* 3ibr_A*

Probab=91.50  E-value=0.056  Score=55.41  Aligned_cols=54  Identities=19%  Similarity=0.244  Sum_probs=47.7

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCcccc-ccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYN-LIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d-~iHp~D~~~~~~~l~~~  197 (383)
                      .-|++++++.++.|+++|+|+..+||.++  ++|+++-+ ++-++....+++.+...
T Consensus        25 phG~Ll~l~~~~~I~~~S~N~~~~lg~~~--~lG~~l~~~ll~~~~~~~l~~~l~~~   79 (505)
T 3nhq_A           25 PHGALVTLRADGMVLAASENIQALLGFVA--SPGSYLTQEQVGPEVLRMLEEGLTGN   79 (505)
T ss_dssp             TTEEEEEECTTSBEEEEETTHHHHHSSCC--CTTCBCCHHHHHHHHHHHHHHHHSCS
T ss_pred             CCeEEEEEcCCCeEEEEcccHHHHhCccc--ccCCchhhhhCCHHHHHHHHHHhhcc
Confidence            46899999999999999999999999998  99999999 88887778888777543

>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*

Probab=91.15  E-value=0.2  Score=40.46  Aligned_cols=38  Identities=5%  Similarity=0.127  Sum_probs=33.0

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +.-.+.+|+++++++.+  ..++||.+.+++|+.+.++++
T Consensus        53 i~~~d~~g~i~~~N~~~--~~l~g~~~~~~~g~~~~~~~~   90 (167)
T 1v9y_A           53 AVLINENDEVMFFNPAA--EKLWGYKREEVIGNNIDMLIP   90 (167)
T ss_dssp             EEEECTTSBEEEECHHH--HHHHSCCGGGTTTSBGGGGSC
T ss_pred             EEEECCCCcEEEECHHH--HHHhCCCHHHHcCCChhhccC
Confidence            34467899999999998  799999999999999888763

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=90.94  E-value=0.11  Score=37.00  Aligned_cols=36  Identities=11%  Similarity=0.176  Sum_probs=31.6

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccce
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATV  324 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~  324 (383)
                      +.-.+.+|+++++++.+  ..++||.+++++|+++.++
T Consensus         5 i~~~d~~g~i~~~N~~~--~~l~g~~~~~~~g~~~~~~   40 (96)
T 3a0s_A            5 IITLSKDGRITEWNKKA--EQLFGLKKENVLGRRLKDL   40 (96)
T ss_dssp             EEEEETTSBEEEECHHH--HHHHCCCHHHHTTSBGGGS
T ss_pred             EEEEcCCCCEeehhHHH--HHHhCCCHHHhcCCCHHHC
Confidence            34457899999999998  8999999999999998776

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=90.86  E-value=0.56  Score=36.49  Aligned_cols=59  Identities=19%  Similarity=0.187  Sum_probs=44.4

Q ss_pred             hHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHH
Q psy7682           5 NEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEEL   70 (383)
Q Consensus         5 ~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL   70 (383)
                      .|++||+.=+.+.++|.+++...  .   .  ..|.+|..||+++.+.+..=..+.......+++|
T Consensus        13 ~ER~RR~~ln~~f~~Lr~~vP~~--~---~--~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L   71 (88)
T 1nkp_A           13 LERQRRNELKRSFFALRDQIPEL--E---N--NEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCGGG--T---T--CTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC--C---C--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999999999999975  1   1  2689999999999988876554444433333333

>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}

Probab=90.81  E-value=0.057  Score=42.17  Aligned_cols=37  Identities=19%  Similarity=0.092  Sum_probs=31.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccc--cCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAV--ACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eL--iG~S~yd~~  325 (383)
                      +.-.+.+|+|+++++..  ..++||.++||  +|++.++++
T Consensus        30 i~~~d~~g~i~~~N~a~--~~~~G~~~~el~g~g~~~~~~~   68 (126)
T 3bwl_A           30 IDVLDADGTICEVNQRF--CAELGYDESEVLGRSIWEFDLM   68 (126)
T ss_dssp             EEEECTTCBEEEECHHH--HHHHTCCGGGTTTSBGGGTBTT
T ss_pred             EEEEcCCCCEEEEcHHH--HHHhCCCHHHHhhCCCchhhcc
Confidence            44568899999999998  79999999999  578777765

>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like protein,haloarcula marismortui ATCC 430 structural genomics, PSI-2; 2.65A {Haloarcula marismortui}

Probab=90.46  E-value=0.067  Score=41.25  Aligned_cols=39  Identities=15%  Similarity=0.133  Sum_probs=34.0

Q ss_pred             eeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         285 QFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       285 ~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      ..+.-.+.+|+|+++++.+  ..++||.+++++|+++.+++
T Consensus        30 ~~i~~~d~~g~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~   68 (125)
T 3fc7_A           30 DGIVHLTTNGTILSVNPSM--AGRLGADPDTLVGQQLSAVM   68 (125)
T ss_dssp             CEEEEEETTSBEEEECHHH--HHHHTSCHHHHTTSBGGGSS
T ss_pred             CeEEEEcCCCeEEEECHHH--HHHhCCCHHHHcCccHHHhC
Confidence            3445568899999999998  89999999999999998876

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=90.06  E-value=0.21  Score=40.42  Aligned_cols=39  Identities=10%  Similarity=0.119  Sum_probs=32.5

Q ss_pred             EEEeCCCC---cEEEEcCCCCccccCCcccccccCCCccceecC
Q psy7682         287 TMKLDRSG---TIIGMDTSGVSQTHTQYLNKAVACKTSATVWTC  327 (383)
Q Consensus       287 ~tRHsldg---kf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~  327 (383)
                      +.-.+.+|   ++++++...  ..++||.+++++|+++.++++.
T Consensus        38 i~~~d~~~~~~~i~~~N~~~--~~~~g~~~~~~~g~~~~~~~~~   79 (162)
T 3sw1_A           38 IVVAEKEGDDTILIYVNAAF--EYLTGYSRDEILYQDCRFLQGD   79 (162)
T ss_dssp             EEEEEEETTEEEEEEECHHH--HHHHTCCHHHHTTSBGGGGTTT
T ss_pred             EEEEeCCCCccEEEEECHHH--HHHHCCCHHHHcCCCcceecCC
Confidence            44456678   999999998  7999999999999998777643

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=89.89  E-value=0.64  Score=35.51  Aligned_cols=61  Identities=16%  Similarity=0.218  Sum_probs=47.6

Q ss_pred             hHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHh
Q psy7682           5 NEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAE   72 (383)
Q Consensus         5 ~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~   72 (383)
                      .|++||++-+.+.++|.++++..  . +    ..|.+|-.|++++.+.+..-+.+..+....+++|..
T Consensus         8 ~ER~RR~~lk~~f~~Lr~~vP~~--~-~----~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~   68 (80)
T 1nlw_A            8 MEKNRRAHLRLSLEKLKGLVPLG--P-D----SSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR   68 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCC--S-S----SCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCC--C-C----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999999999999864  1 1    256778999999999998766666666666666554

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=89.22  E-value=0.064  Score=51.16  Aligned_cols=47  Identities=15%  Similarity=0.137  Sum_probs=39.0

Q ss_pred             HHHhhcCcEEEEcCCccEEEeecccccccC---cccccccCCccccccCCC
Q psy7682         138 LLEALEGFLFVVNPDGYVNFCTENIKSFIR---YSRQEVLGKSVYNLIHHG  185 (383)
Q Consensus       138 ll~aldgfi~vvs~dG~i~yvS~sv~~~LG---y~~~el~G~s~~d~iHp~  185 (383)
                      +++++..-|+++|.+|+|+|+|+++..+||   +. .+++|+++.+++.+.
T Consensus       175 ~~~~~~dGIivvD~~G~Ii~~N~aA~~ll~~lG~~-~~~iGk~l~el~~~~  224 (305)
T 2ykf_A          175 SSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLT-TELEGVNLIDATRPL  224 (305)
Confidence            455666668999999999999999999975   54 789999999988643

>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* ...

Probab=88.08  E-value=0.34  Score=40.26  Aligned_cols=38  Identities=21%  Similarity=0.106  Sum_probs=33.7

Q ss_pred             eeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccce
Q psy7682         285 QFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATV  324 (383)
Q Consensus       285 ~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~  324 (383)
                      .=+...+.||++++.+...  ..+.||.+++++|+++++.
T Consensus        28 ~Gii~lD~~g~I~~~N~~~--e~~sG~~~~eviGk~~f~~   65 (125)
T 1nwz_A           28 FGAIQLDGDGNILQYNAAE--GDITGRDPKQVIGKNFFKD   65 (125)
T ss_dssp             SEEEEEETTCBEEEECHHH--HHHHCCCHHHHTTSBCCCC
T ss_pred             ceEEEECCCCEEEEEHHHH--HHHhCCCHHHHcCCchhhh
Confidence            3466778999999999998  8999999999999999874

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=87.49  E-value=0.26  Score=45.40  Aligned_cols=54  Identities=17%  Similarity=0.247  Sum_probs=41.5

Q ss_pred             HHHhhcCcEEEEcC-CccEEEeecccccccCcccccc----cC----CccccccCCCChHHHH
Q psy7682         138 LLEALEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEV----LG----KSVYNLIHHGDHARFH  191 (383)
Q Consensus       138 ll~aldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el----~G----~s~~d~iHp~D~~~~~  191 (383)
                      +.....+.++++|. ++.+.|+|+++..+|||+++++    +.    .-++..+||+|.....
T Consensus        38 ~~~~~~~~~~l~D~~~~~~~~~s~~~~~llG~~~~~~~~~~~~~~~~~~ll~~i~p~D~~~~~  100 (258)
T 3clo_A           38 LTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKR  100 (258)
T ss_dssp             HHHHHSSEEEEEETTTTEEEEEECTTCGGGCCCHHHHHCCEESSSSCHHHHTTBCHHHHHHHH
T ss_pred             HHHHcCCeEEEEEcCCCeEEEEeCCHHHHhCCCcccchHHHHhhhHHHHHHHhCChHHHHHHH
Confidence            34445667778885 8999999999999999998877    32    2366788999977543

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=85.70  E-value=0.15  Score=38.97  Aligned_cols=38  Identities=13%  Similarity=0.057  Sum_probs=33.3

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      +.-.+.+|+++++++.+  ..++||.+++++|+++.+++.
T Consensus        20 i~~~D~~g~I~~~N~aa--~~l~g~~~~~~~g~~~~~~~~   57 (115)
T 3b33_A           20 TLILDDGLAIRYANPAA--ELLFSQSAKRIVEQSLSQLIQ   57 (115)
T ss_dssp             EEEECTTCBEEEECHHH--HHHTTSCHHHHTTCBHHHHCS
T ss_pred             EEEECCCCcEEEECHHH--HHHhCCCHHHHhCCCHHHHhC
Confidence            44567899999999998  899999999999999988764

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=81.99  E-value=0.2  Score=39.41  Aligned_cols=37  Identities=14%  Similarity=0.030  Sum_probs=31.2

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCC------------cccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQ------------YLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilG------------Y~p~eLiG~S~yd~~  325 (383)
                      +.--+.+|+++|+++.+  ..++|            |.+++++|+++.+++
T Consensus        18 viv~D~~g~I~~~N~a~--~~llg~~~~~i~~~~~g~~~~~~~G~~~~~~~   66 (121)
T 4hi4_A           18 VMIADNDLNIIYMNRTV--SEMLGRAEADIRKQLPNFDAGRLMGANIDVFH   66 (121)
T ss_dssp             EEEEETTCBEEEECHHH--HHHHHHTHHHHHHHCTTCCGGGCTTCBGGGGC
T ss_pred             EEEEcCCCeEEEecHHH--HHHHHHHHHHHHHhcCCCChHHhcCCCHHHhc
Confidence            44457899999999997  78875            999999999998876

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=80.54  E-value=0.92  Score=38.37  Aligned_cols=38  Identities=8%  Similarity=0.157  Sum_probs=32.1

Q ss_pred             EEEeC-CCCcEEEEcCCCCccccCCcccccccCCCccceecCC
Q psy7682         287 TMKLD-RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCP  328 (383)
Q Consensus       287 ~tRHs-ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~  328 (383)
                      +.-.+ .||+|+++++..  ..++||.  +++|+++.++++..
T Consensus        50 i~~~d~~~g~i~~~N~a~--~~l~G~~--~~~G~~~~~~~~~~   88 (185)
T 3kx0_X           50 LVGLEGPDHRFVAVNAAY--RGFSPLL--DTVGQPAREVYPEL   88 (185)
T ss_dssp             EEEEETTTTEEEEECHHH--HHHCCCC--SCTTSBHHHHCTTS
T ss_pred             EEEEECCCcEEEEEcHHH--HHHcCCc--cccCCcHHHHCCch
Confidence            44456 899999999998  7999998  99999999988543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	383
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	5e-08
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	5e-05
d2oola2	114	d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodops	6e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-06
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	2e-04
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-04
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	0.001
d1mzua_	110	d.110.3.1 (A:) PYP domain of sensor histidine kina	1e-04
d1oj5a_	109	d.110.3.8 (A:) PAS domain of steroid receptor coac	2e-04
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-04
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	0.002
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	7e-04
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	0.003
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	0.003

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.2 bits (112), Expect = 5e-08
 Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 50  VNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ 109
            +    E+ RR +    + ELA LI A    +++S+    P K   ++     IR+++Q 
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSA---APSKATTVEAACRYIRHLQQN 60

Query: 110 ETS 112
            ++
Sbjct: 61  GST 63

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.7 bits (90), Expect = 5e-05
 Identities = 16/72 (22%), Positives = 26/72 (36%), Gaps = 17/72 (23%)

Query: 4  LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQE 63
            E+ RR +    + ELA LI A    +++S+    P K   ++                
Sbjct: 8  HAEQARRNRLAVALHELASLIPAEWKQQNVSA---APSKATTVEAAC------------- 51

Query: 64 NNYIEELAELIS 75
            YI  L +  S
Sbjct: 52 -RYIRHLQQNGS 62

>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]

 Score = 48.3 bits (115), Expect = 6e-08
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 144 GFLFVVN-PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQ-V 201
           G+LFVV+  D  +   + N++  +R     +L   + + +     AR  + L       +
Sbjct: 18  GYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGGDPAAI 77

Query: 202 NAWTSDSGGQAGKRP 216
           N    D     G+R 
Sbjct: 78  NPIRLDVVTPDGERA 92

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 4/55 (7%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           E+RRR++ NN+I +L+++I  +S   + S       K  IL +  + I+ ++Q  
Sbjct: 13  ERRRRDKINNWIVQLSKIIPDSSMESTKS----GQSKGGILSKASDYIQELRQSN 63

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 6/57 (10%)

Query: 6  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVN--QCLNEKRRR 60
          E+RRR++ NN+I +L+++I  +S   + S       K  IL +  +  Q L +   R
Sbjct: 13 ERRRRDKINNWIVQLSKIIPDSSMESTKS----GQSKGGILSKASDYIQELRQSNHR 65

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 9/55 (16%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           EKR R   N+ I EL +L         +     K +K A+L++ ++ IR ++   
Sbjct: 14  EKRYRSSINDKIIELKDL---------VVGTEAKLNKSAVLRKAIDYIRFLQHSN 59

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 12/70 (17%)

Query: 6  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETV---NQCLNEKRRREQ 62
          EKR R   N+ I EL +L         +     K +K A+L++ +       +  ++ +Q
Sbjct: 14 EKRYRSSINDKIIELKDL---------VVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQ 64

Query: 63 ENNYIEELAE 72
          EN  +     
Sbjct: 65 ENLSLRTAVH 74

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]} Length = 110

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 7/60 (11%), Positives = 20/60 (33%)

Query: 132 EVLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFH 191
           + +G    +AL      V+  G ++              + V+G++ +  +    +    
Sbjct: 2   DGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAF 61

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 109

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 = 38.5 bits (89), Expect = 2e-04
 Identities = 5/53 (9%), Positives = 16/53 (30%), Gaps = 1/53 (1%)

Query: 142 LEGFLFVVNPDGYVNFCTENIKSFIRY-SRQEVLGKSVYNLIHHGDHARFHNC 193
           +E F+   +  G +     +          ++++ K +Y           +  
Sbjct: 1   VESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYAR 53

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 8/55 (14%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           E++RR+   +    L + +         S    K  +  IL +    I+ ++++ 
Sbjct: 10  ERKRRDHIKDSFHSLRDSV--------PSLQGEKASRAQILDKATEYIQYMRRKN 56

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 13/64 (20%)

Query: 6  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVN-----QCLNEKRRR 60
          E++RR+   +    L + +         S    K  +  IL +        +  N   ++
Sbjct: 10 ERKRRDHIKDSFHSLRDSV--------PSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ 61

Query: 61 EQEN 64
          + ++
Sbjct: 62 DIDD 65

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (83), Expect = 7e-04
 Identities = 9/55 (16%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           EK RR      +E+L  L+     +        +    ++L +    I+ ++  +
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSS-------RHTTLSLLTKAKLHIKKLEDSD 56

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 10/65 (15%), Positives = 23/65 (35%), Gaps = 7/65 (10%)

Query: 6  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENN 65
          EK RR      +E+L  L+     +        +    ++L +        +    +  +
Sbjct: 9  EKNRRAHLRLSLEKLKGLVPLGPDSS-------RHTTLSLLTKAKLHIKKLEDSDRKAVH 61

Query: 66 YIEEL 70
           I++L
Sbjct: 62 QIDQL 66

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 56  EKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQE 110
           E++RR +       L + I              K  K  IL++    I +++ +E
Sbjct: 14  ERQRRNELKRSFFALRDQI-------PELENNEKAPKVVILKKATAYILSVQAEE 61

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	383
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	99.54
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.03
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.93
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	98.89
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.86
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	98.85
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	98.84
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	98.82
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	98.81
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	98.79
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	98.71
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	98.65
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.31
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	98.27
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	98.17
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	98.13
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	98.09
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	98.08
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	98.08
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	98.07
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	97.89
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	97.56
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	97.53
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	97.48
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	97.27
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	97.22
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	97.04
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	97.02
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	97.01
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	96.93
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	96.72
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	96.53
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	96.34
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	96.11
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	96.07
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	95.64
d3c2wa3	113	Bacteriophytochrome BphP {Pseudomonas aeruginosa [	95.56
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	95.42
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	94.85
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	94.23
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	93.44
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	87.71

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}

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=99.54  E-value=2.9e-16  Score=127.69  Aligned_cols=82  Identities=21%  Similarity=0.180  Sum_probs=63.2

Q ss_pred             ceeEEEeCCCCcEEEEcCCCCccccCCccc-ccccCCCccceecCCCCchh-HHHHHHHHHHhhhhcccceeecccceec
Q psy7682         284 EQFTMKLDRSGTIIGMDTSGVSQTHTQYLN-KAVACKTSATVWTCPNSPLT-STKLLLKALLLSICTDYALVQTDTCMYR  361 (383)
Q Consensus       284 ~~F~tRHsldgkf~~vD~r~l~~~ilGY~p-~eLiG~S~yd~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~q~~t~~yR  361 (383)
                      ++|+|||++||+|++||+++  ..++||.| +||+|+|+|+|+ ||+|... ..+.       .+..+..+||..+..||
T Consensus         2 e~F~trh~~~g~~~~vd~~~--~~~~gy~~~eelig~s~~~f~-HPeD~~~~~~~~-------~~~~~~~~g~~~~~~yR   71 (109)
T d1oj5a_           2 ESFMTKQDTTGKIISIDTSS--LRAAGRTGWEDLVRKCIYAFF-QPQGREPSYARQ-------LFQEVMTRGTASSPSYR   71 (109)
T ss_dssp             CEEEEEECTTCCEEEEECHH--HHTTCCSCHHHHHHHHHHHHT-SCBTTBCCHHHH-------HHHHHHHHSEEECCCEE
T ss_pred             ceEEEEECCCceEEEECHHH--hhHhhcCCHHHHcCCcHHHeE-CcccchHHHhhH-------HHHHHHhhcccchhhhh
Confidence            68999999999999999998  79999997 899999999998 7777211 1111       11134467899999999


Q ss_pred             ccCCccccccCCcceEEEEee
Q psy7682         362 SSPSCFGLQGASRTSLWQRIR  382 (383)
Q Consensus       362 ~~~~~~~~~~~~~~~~~~~~~  382 (383)
                      |+.+       +++|+|+..+
T Consensus        72 ~~~k-------dG~~vWv~t~   85 (109)
T d1oj5a_          72 FILN-------DGTMLSAHTR   85 (109)
T ss_dssp             EECT-------TSCEEEEEEE
T ss_pred             hhhc-------cCcEEEEEEE
Confidence            5554       5679999753

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.03  E-value=8.8e-11  Score=85.69  Aligned_cols=59  Identities=24%  Similarity=0.357  Sum_probs=48.4

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+..||+||+++|..|.+|..+||... ..  .+...|+||++||+.||.||+.++..
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~-~~--~~~~~k~sKa~iL~~Av~yI~~Lq~~   60 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEW-KQ--QNVSAAPSKATTVEAACRYIRHLQQN   60 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHH-HT--SSCCCCSCTTHHHHHHHHHHHHHHTC
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcc-cc--cCCcccccHHHHHHHHHHHHHHHHHh
Confidence            3568999999999999999999999999621 11  12357999999999999999987643

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=2.7e-10  Score=90.81  Aligned_cols=45  Identities=7%  Similarity=0.008  Sum_probs=41.5

Q ss_pred             CceeEEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCCC
Q psy7682         283 IEQFTMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPNS  330 (383)
Q Consensus       283 ~~~F~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~~  330 (383)
                      ...|++||++||+|+||++++  ..++||.++||+|+++++++ +|++
T Consensus         5 ~~~fi~r~~~dG~i~~~N~~~--~~~~G~~~~el~g~~~~~~~-~~ed   49 (114)
T d1p97a_           5 SKTFLSRHSMDMKFTYCDDRI--TELIGYHPEELLGRSAYEFY-HALD   49 (114)
T ss_dssp             CEEEEEEECTTTSCSEECTTH--HHHTSSCHHHHTTSCHHHHS-CSSS
T ss_pred             cCEEEEEECCCCcEEEECHHH--HHHcCCCccccccccccccc-cccc
Confidence            478999999999999999998  89999999999999999987 5666

>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}

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=98.89  E-value=1.1e-10  Score=93.92  Aligned_cols=48  Identities=10%  Similarity=0.193  Sum_probs=44.4

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCccc-ccccCCccccccCCCChHH
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSR-QEVLGKSVYNLIHHGDHAR  189 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~-~el~G~s~~d~iHp~D~~~  189 (383)
                      ++.|+...|.+|+|+||++++..++||.+ +||+|+++++|+||+|++.
T Consensus         1 ~e~F~trh~~~g~~~~vd~~~~~~~gy~~~eelig~s~~~f~HPeD~~~   49 (109)
T d1oj5a_           1 VESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREP   49 (109)
T ss_dssp             CCEEEEEECTTCCEEEEECHHHHTTCCSCHHHHHHHHHHHHTSCBTTBC
T ss_pred             CceEEEEECCCceEEEECHHHhhHhhcCCHHHHcCCcHHHeECcccchH
Confidence            36799999999999999999999999996 8999999999999999753

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=8.8e-10  Score=87.71  Aligned_cols=72  Identities=22%  Similarity=0.335  Sum_probs=59.1

Q ss_pred             CcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy7682         144 GFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPSSHQVNAWTSDSGGQAGKRPSLTASTP  223 (383)
Q Consensus       144 gfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~~~~~~~~~s~s~~~~g~~~~~~~~~~  223 (383)
                      .||+..+.||+|+|+|+++..+|||+++|++|+++++++||+|.+.+.+.+....                     ..+.
T Consensus         7 ~fi~r~~~dG~i~~~N~~~~~~~G~~~~el~g~~~~~~~~~ed~~~~~~~~~~~~---------------------~~~~   65 (114)
T d1p97a_           7 TFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLC---------------------TKGQ   65 (114)
T ss_dssp             EEEEEECTTTSCSEECTTHHHHTSSCHHHHTTSCHHHHSCSSSHHHHHHHHHHHT---------------------TTSE
T ss_pred             EEEEEECCCCcEEEECHHHHHHcCCCccccccccccccccccccccceeeeeecc---------------------cccc
Confidence            4677789999999999999999999999999999999999999999888764331                     1123


Q ss_pred             ceeEEEEEEEcCC
Q psy7682         224 NRTFNIRLLISST  236 (383)
Q Consensus       224 ~rsF~cRmk~~~~  236 (383)
                      .....+|++++.+
T Consensus        66 ~~~~e~~~~~kdG   78 (114)
T d1p97a_          66 VVSGQYRMLAKHG   78 (114)
T ss_dssp             EEEEEEEEECTTS
T ss_pred             eeecceeeeeecC
Confidence            3566788887765

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.85  E-value=1.7e-09  Score=79.83  Aligned_cols=55  Identities=20%  Similarity=0.289  Sum_probs=47.7

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .++..|+..||+||+++|+.|.+|..+||.+  +      ..++||++||+.||.||+.++..
T Consensus        11 ~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~--~------~~k~sK~~iL~~Ai~YI~~Lq~~   65 (68)
T d1mdya_          11 DRRKAATMRERRRLSKVNEAFETLKRSTSSN--P------NQRLPKVEILRNAIRYIEGLQAL   65 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSC--T------TSCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--C------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            3456899999999999999999999999982  1      36999999999999999987643

>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=98.84  E-value=5.3e-10  Score=90.38  Aligned_cols=56  Identities=21%  Similarity=0.383  Sum_probs=52.2

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .-||+++++. +|+|+|+|+|+..+||+++++|+|++++|++||+|...+++.+...
T Consensus        16 phG~Llvld~~d~~I~~vS~N~~~lLG~~~~~llG~~l~dll~~~~~~~i~~~l~~~   72 (114)
T d2oola2          16 PHGYLFVVSETDLRIASVSANVEDLLRQPPASLLNVPIAHYLTAASAARLTHALHGG   72 (114)
T ss_dssp             TTSEEEEECTTTCBEEEEETTHHHHHSSCGGGGTTCBGGGGBCHHHHHHHHHHHCC-
T ss_pred             CCcEEEEEECCCCEEEEEcCCHHHHhCCChHHHcCCCHHHhCCHHHHHHHHHHHhcC
Confidence            4789999997 7999999999999999999999999999999999999999998754

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=9.1e-10  Score=80.65  Aligned_cols=57  Identities=26%  Similarity=0.416  Sum_probs=47.9

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhh
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQ  108 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~  108 (383)
                      ++..|+..||+||+.+|..|.+|..+||..  ..  .+...|+||++||+.|+.||+.++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~--~~--~~~~~k~sK~~iL~~av~yI~~Lq~   61 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDS--SM--ESTKSGQSKGGILSKASDYIQELRQ   61 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCC--CC--CSSTTCCCTTTTTTTTHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccc--cc--cCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999983  11  1224699999999999999998764

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=2.3e-09  Score=82.17  Aligned_cols=54  Identities=15%  Similarity=0.340  Sum_probs=47.4

Q ss_pred             hhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          48 ETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        48 ~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      ++..|+..||+||+++|+.|.+|+++||..  +      ..|+||++||+.|+.||+.+...
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~--~------~~k~sK~~iL~~A~~yI~~L~~~   55 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSL--Q------GEKASRAQILDKATEYIQYMRRK   55 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGG--T------TSCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCC--C------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999972  2      26999999999999999986543

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=3.2e-09  Score=80.82  Aligned_cols=54  Identities=28%  Similarity=0.411  Sum_probs=47.8

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      +++..|+.+||+||+++|..|.+|..+||..         ..|+||++||..|+.||+.+...
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~---------~~k~~K~~iL~~a~~yI~~L~~~   58 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGT---------EAKLNKSAVLRKAIDYIRFLQHS   58 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS---------SCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC---------CCCCCHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999982         26999999999999999987643

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=8.2e-09  Score=78.28  Aligned_cols=54  Identities=17%  Similarity=0.228  Sum_probs=46.8

Q ss_pred             hhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          49 TVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        49 ~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      +..|+..||+||+++|+.|.+|+++||..  +     ...|++|++||+.|+.||+.+...
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~--~-----~~~k~sK~~iL~~A~~yI~~L~~~   55 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLG--P-----DSSRHTTLSLLTKAKLHIKKLEDS   55 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCC--S-----SSCCCTTHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccC--C-----CCCCCCHHHHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999972  2     236899999999999999987643

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=1.5e-08  Score=78.41  Aligned_cols=56  Identities=18%  Similarity=0.217  Sum_probs=48.5

Q ss_pred             hhhhhhhhHHHHHHHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          47 QETVNQCLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        47 ~~~~~~~~~ek~RR~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      .++..|+..||+||+.+|+.|.+|+.+||..  +     ...|++|++||..|+.||+.+...
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~--~-----~~~k~sK~~iL~~A~~yI~~L~~~   60 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPEL--E-----NNEKAPKVVILKKATAYILSVQAE   60 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGG--T-----TCTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC--C-----CCCccCHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999972  2     246899999999999999987654

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=98.31  E-value=3.5e-07  Score=70.95  Aligned_cols=51  Identities=22%  Similarity=0.425  Sum_probs=45.3

Q ss_pred             EEEc---CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         147 FVVN---PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       147 ~vvs---~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      ++.|   .||+|+|+|+++.+++||+++|++|+++.++.+|++.+.+.+.+...
T Consensus         4 vi~d~~~pd~~I~y~N~a~~~~~G~s~~e~~G~~~~~~~~~~~~~~~~~~~~~~   57 (104)
T d1jnua_           4 VITDPRLPDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDA   57 (104)
T ss_dssp             EEECTTSTTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTSCHHHHHHHHHH
T ss_pred             EEEcCCCCCCEEEEEcHHHHHHHCcCHHHHCCccceeccccccchHHHhhhhhh
Confidence            3566   48999999999999999999999999999999999999888877543

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.27  E-value=3.3e-07  Score=72.15  Aligned_cols=50  Identities=22%  Similarity=0.348  Sum_probs=42.5

Q ss_pred             EEEEc---CCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         146 LFVVN---PDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       146 i~vvs---~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      +++.|   .||+|+|+|+++..++||+++|++|+++..+.||++.....+.+.
T Consensus         6 ~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~~~~l~~~~~~~~~~~~~~   58 (109)
T d1n9la_           6 FVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIR   58 (109)
T ss_dssp             EEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHH
T ss_pred             EEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCcceeeecccCCHHHhhhhh
Confidence            44566   489999999999999999999999999998998987766666553

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

Probab=98.17  E-value=1.6e-07  Score=74.79  Aligned_cols=52  Identities=13%  Similarity=0.179  Sum_probs=46.1

Q ss_pred             hhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCC
Q psy7682         135 GPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGD  186 (383)
Q Consensus       135 ~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D  186 (383)
                      .+.+++++..-|+++|.+|+|+|+|++.+.+|||+.+|++|++++++++|++
T Consensus         5 ~~A~ld~~p~gvi~~D~~G~I~~~N~aa~~~~G~~~eellG~~~~~~~~p~~   56 (110)
T d1mzua_           5 GTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCT   56 (110)
T ss_dssp             -CTTGGGCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGG
T ss_pred             HHHHHhCCCcEEEEEcCCCCEEEeHHHHHHHHcCCHHHHcCCCHHHhcCChh
Confidence            3456677777799999999999999999999999999999999999888764

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]

Probab=98.13  E-value=5.7e-07  Score=72.06  Aligned_cols=62  Identities=16%  Similarity=0.184  Sum_probs=53.4

Q ss_pred             hhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         134 LGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       134 ~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      ..+.+++++..-|+++|.+|+|+|+|+++..+|||+++|++|+++.+++++.+.......+.
T Consensus        17 ~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~   78 (130)
T d1ew0a_          17 HLRSILDTVPDATVVSATDGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPEPYRHEHDGYLQ   78 (130)
T ss_dssp             CHHHHHTTCSSEEEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTTGGGHHHHHH
T ss_pred             HHHHHHHcCCCeEEEEeCCccEEEEHHHHHHhhcCCHHHhcCCccccccccchhHHHHHHHH
Confidence            34557777777789999999999999999999999999999999999999999877655443

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=98.09  E-value=5.8e-07  Score=69.69  Aligned_cols=57  Identities=21%  Similarity=0.345  Sum_probs=47.1

Q ss_pred             HHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhc
Q psy7682         137 LLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCL  194 (383)
Q Consensus       137 lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l  194 (383)
                      .+-.+.|| |+++|.+|+|+|+|+++.+++||+++|++|+++.+++++.+.......+
T Consensus         6 ~~e~~~d~-i~~~d~~g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~   62 (113)
T d1v9ya_           6 ALEQNMMG-AVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYI   62 (113)
T ss_dssp             HHHTCSSE-EEEECTTSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHH
T ss_pred             HHHcCcCc-EEEEeCCCCEEEEchhHhhhhccchhhhcCcceeccccccccccccccc
Confidence            33344444 8889999999999999999999999999999999998888766655443

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.08  E-value=8.2e-07  Score=70.24  Aligned_cols=57  Identities=12%  Similarity=0.257  Sum_probs=49.9

Q ss_pred             hhcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         141 ALEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       141 aldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .++.-|+++|. +|.|+|+++++..+|||+.+|++|+++.++++++|...+...+...
T Consensus         6 ~~n~AI~~id~~~G~I~~~N~a~~~l~Gy~~~el~g~~~~~l~~~~~~~~~~~~~~~~   63 (114)
T d1ll8a_           6 EFNKAIFTVDAKTTEILVANDKACGLLGYSSQDLIGQKLTQFFLRSDSDVVEALSEEH   63 (114)
T ss_dssp             TTTCEEEEEETTTCBEEEECTTHHHHHTCCTTTTTTSBGGGGSSCTTTHHHHHTTSST
T ss_pred             hcCcEEEEEECCCCEEEEECHHHHHhhcCCHHHHcCCCeeeecCcccHHHHHHHHHHH
Confidence            34455888995 7999999999999999999999999999999999999888776543

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]

Probab=98.08  E-value=4.6e-07  Score=73.45  Aligned_cols=55  Identities=13%  Similarity=0.116  Sum_probs=48.9

Q ss_pred             chhhHHHHhhcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCCh
Q psy7682         133 VLGPLLLEALEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDH  187 (383)
Q Consensus       133 ~~~~lll~aldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~  187 (383)
                      .+.+.+++++..-++++|.+|+|+|+|++...+|||++++++|+++++++||++.
T Consensus        17 ~~~d~~ld~~p~gi~~lD~~G~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~p~~~   71 (125)
T d1nwza_          17 KMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTD   71 (125)
T ss_dssp             TCCHHHHTTCSSEEEEEETTCBEEEECHHHHHHHCCCHHHHTTSBCCCCCCGGGC
T ss_pred             HHHHHHHhCCCccEEEEeCCCCEEEEcHHHHHhhccchHhhcCCCHHHccCchhh
Confidence            3455678887777999999999999999999999999999999999999988654

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=98.07  E-value=6.3e-07  Score=68.55  Aligned_cols=50  Identities=18%  Similarity=0.422  Sum_probs=46.3

Q ss_pred             EEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcC
Q psy7682         146 LFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLV  195 (383)
Q Consensus       146 i~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~  195 (383)
                      |+++|.+|+|+|+|+++..++||+.+|++|+++..+++|.+.......+.
T Consensus         3 i~~~D~~G~I~~~N~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~   52 (106)
T d1xj3a1           3 MIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYIS   52 (106)
T ss_dssp             EEEEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHH
T ss_pred             EEEECCCCcEEEEcHHHHHHhhhchHhhcCCCcccccccccccchhhhhh
Confidence            78899999999999999999999999999999999999999888776654

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.89  E-value=2.9e-06  Score=60.64  Aligned_cols=41  Identities=27%  Similarity=0.439  Sum_probs=36.4

Q ss_pred             HHhhhHhHHHHHhhcccccccccccccCCCCChhhhhHHHHHHHHhhhhc
Q psy7682          60 REQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQIRNIKQQ  109 (383)
Q Consensus        60 R~~~n~~i~eL~~llP~~~~~~~~~~~~~klDK~siLr~ai~~lr~~~~~  109 (383)
                      |+++|+.|.+|..+||.+         ..|+||++||..||.||+.++..
T Consensus         1 R~~in~~f~~L~~lvP~~---------~~K~~Ka~iL~~Ai~YI~~Lq~~   41 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGT---------DAKMHKSGVLRKAIDYIKYLQQV   41 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCS---------SCCCCTTTHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCC---------CCcccHHHHHHHHHHHHHHHHHH
Confidence            789999999999999982         26999999999999999987654

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.56  E-value=3.7e-05  Score=59.63  Aligned_cols=45  Identities=18%  Similarity=0.313  Sum_probs=35.7

Q ss_pred             CCccEEEeecccccccCcccccccCCcccc-cc-CCCChHHHHhhcC
Q psy7682         151 PDGYVNFCTENIKSFIRYSRQEVLGKSVYN-LI-HHGDHARFHNCLV  195 (383)
Q Consensus       151 ~dG~i~yvS~sv~~~LGy~~~el~G~s~~d-~i-Hp~D~~~~~~~l~  195 (383)
                      .|+.|+|+|+++.+++||+.+|++|+++.+ ++ ||++.......+.
T Consensus        12 ~d~~I~~~N~a~~~l~G~~~~eiiG~~~~~~~~~~~~~~~~~~~~~~   58 (110)
T d1bywa_          12 ENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIA   58 (110)
T ss_dssp             SSCBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHH
T ss_pred             CCCEEEEEcHHHHHHhCCCHHHhcccCcccccceeeheecccccccc
Confidence            378899999999999999999999999876 33 5665555555443

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=97.53  E-value=2.6e-05  Score=60.69  Aligned_cols=35  Identities=9%  Similarity=-0.072  Sum_probs=30.7

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCccceecCCC
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPN  329 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~  329 (383)
                      +||+|+||++..  ..++||.++||+|+++..++ +++
T Consensus        14 pdg~Ii~vN~a~--~~~~Gy~~~El~G~~~~~l~-~~~   48 (109)
T d1n9la_          14 PDCPLVYASEGF--YAMTGYGPDEVLGHNCRFLQ-GEG   48 (109)
T ss_dssp             TTCCEEEECHHH--HHHHCCCHHHHTTSCGGGGC-CTT
T ss_pred             CCCeEEEEcHHH--HHHHCcCHHHHcCCcceeee-ccc
Confidence            599999999998  89999999999999987665 444

>d2veaa3 d.110.3.9 (A:4-130) Phytochrome-like protein Cph1 {Synechocystis sp. pcc 6803 [TaxId: 1148]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Phytochrome-like protein Cph1
species: Synechocystis sp. pcc 6803 [TaxId: 1148]

Probab=97.48  E-value=3.1e-05  Score=63.23  Aligned_cols=56  Identities=14%  Similarity=0.242  Sum_probs=43.9

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVPS  197 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~~  197 (383)
                      .-||+++++. +++|+++|+|+..+||+++++++|+++-+++-++....+++.+...
T Consensus        25 phG~LLald~~~~~I~~aS~N~~~~lG~~~~~lLG~~l~~ll~~~~~~~l~~~l~~~   81 (127)
T d2veaa3          25 PHGLVVVLQEPDLTISQISANCTGILGRSPEDLLGRTLGEVFDSFQIDPIQSRLTAG   81 (127)
T ss_dssp             TTSEEEEEETTTTEEEEEETTHHHHTSCCTTTSSTTTTTTTSBCC--------CCCT
T ss_pred             CCeEEEEEECCCCEEEEEcCCHHHHhCcChHHHcCCCHHHHCCHHHHHHHHHHhhcc
Confidence            4789999986 8999999999999999999999999999999998888888877654

>d2o9ca2 d.110.3.9 (A:4-130) Bacteriophytochrome BphP {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.27  E-value=6e-05  Score=61.41  Aligned_cols=54  Identities=19%  Similarity=0.274  Sum_probs=47.1

Q ss_pred             hcCcEEEEcC-CccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCC
Q psy7682         142 LEGFLFVVNP-DGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       142 ldgfi~vvs~-dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~  196 (383)
                      .-||+++++. +++|+++|+|+..+||+++++++|+++-+++ +++...+.+.+..
T Consensus        34 phG~LLald~~~~~I~~~S~N~~~~lG~~~~~llG~~l~~ll-~~~~~~~~~~~~~   88 (127)
T d2o9ca2          34 PHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALL-PEQWPALQAALPP   88 (127)
T ss_dssp             TTSEEEEEETTTCBEEEEETTHHHHHSSCHHHHTTCBHHHHC-TTTHHHHHHHSCT
T ss_pred             CCeEEEEEECCCCEEEEECCCHHHHhCCChHHHcCCCHHHHC-CHHHHHHHHHhhh
Confidence            4789999996 8999999999999999999999999999998 5677766666654

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=97.22  E-value=8.6e-05  Score=55.99  Aligned_cols=37  Identities=11%  Similarity=0.109  Sum_probs=33.0

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.+|+|+++++.+  ..++||.++||+|+.+..++
T Consensus         3 i~~~D~~G~I~~~N~a~--~~l~Gy~~~el~g~~~~~~~   39 (106)
T d1xj3a1           3 MIVIDGHGIIQLFSTAA--ERLFGWSELEAIGQNVNILM   39 (106)
T ss_dssp             EEEEETTSBEEEECHHH--HHHHCCCHHHHTTSBGGGGS
T ss_pred             EEEECCCCcEEEEcHHH--HHHhhhchHhhcCCCccccc
Confidence            34568899999999998  89999999999999988776

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=97.04  E-value=0.0002  Score=54.58  Aligned_cols=40  Identities=5%  Similarity=0.096  Sum_probs=34.0

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCP  328 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~  328 (383)
                      +.-.+.+|+|+++++.+  ..++||.++|++|+++.+++++.
T Consensus        14 i~~~d~~g~i~~~N~~~--~~l~Gy~~~e~~g~~~~~~~~~~   53 (113)
T d1v9ya_          14 AVLINENDEVMFFNPAA--EKLWGYKREEVIGNNIDMLIPRD   53 (113)
T ss_dssp             EEEECTTSBEEEECHHH--HHHHSCCGGGTTTSBGGGGSCGG
T ss_pred             EEEEeCCCCEEEEchhH--hhhhccchhhhcCcceecccccc
Confidence            33468899999999998  89999999999999998776443

>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]

Probab=97.02  E-value=0.00014  Score=58.25  Aligned_cols=37  Identities=22%  Similarity=0.155  Sum_probs=33.2

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +.-.+.+|+|+++++..  ..++||.++|++|+++++++
T Consensus        30 i~~lD~~G~i~~~N~a~--~~l~G~~~~e~iG~~~~~~~   66 (125)
T d1nwza_          30 AIQLDGDGNILQYNAAE--GDITGRDPKQVIGKNFFKDV   66 (125)
T ss_dssp             EEEEETTCBEEEECHHH--HHHHCCCHHHHTTSBCCCCC
T ss_pred             EEEEeCCCCEEEEcHHH--HHhhccchHhhcCCCHHHcc
Confidence            33468899999999998  89999999999999998877

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=97.01  E-value=0.00022  Score=54.34  Aligned_cols=36  Identities=14%  Similarity=-0.003  Sum_probs=31.3

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCccceecCCC
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPN  329 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~  329 (383)
                      +||+|+||+++.  ..++||.++||+|++..++++.++
T Consensus        11 pd~~I~y~N~a~--~~~~G~s~~e~~G~~~~~~~~~~~   46 (104)
T d1jnua_          11 PDNPIIFASDRF--LELTEYTREEVLGNNCRFLQGRGT   46 (104)
T ss_dssp             TTCCEEEECHHH--HHHHTCCHHHHTTSCGGGGCCTTS
T ss_pred             CCCEEEEEcHHH--HHHHCcCHHHHCCccceecccccc
Confidence            689999999998  899999999999999877764333

>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]

Probab=96.93  E-value=0.0002  Score=56.07  Aligned_cols=37  Identities=16%  Similarity=0.166  Sum_probs=33.2

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      +...+.||+|+++++.+  ..++||.++||+|+++++++
T Consensus        16 vi~~D~~G~I~~~N~aa--~~~~G~~~eellG~~~~~~~   52 (110)
T d1mzua_          16 AIQVDGSGVIHRYNRTE--SRLSGRIPERVIGRNFFTEV   52 (110)
T ss_dssp             EEEEETTCBEEEECHHH--HHHHCCCHHHHTTSBCCCCC
T ss_pred             EEEEcCCCCEEEeHHHH--HHHHcCCHHHHcCCCHHHhc
Confidence            44567899999999998  89999999999999998866

>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]

Probab=96.72  E-value=0.00053  Score=53.84  Aligned_cols=41  Identities=17%  Similarity=0.256  Sum_probs=34.6

Q ss_pred             EEEeCCCCcEEEEcCCCCccccCCcccccccCCCccceecCCC
Q psy7682         287 TMKLDRSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWTCPN  329 (383)
Q Consensus       287 ~tRHsldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~~~~  329 (383)
                      +.-.+.+|+|+++++.+  ..++||.++||+|+++.+++..++
T Consensus        29 i~~~d~~g~i~~~N~~~--~~l~Gy~~~el~g~~~~~~~~~~~   69 (130)
T d1ew0a_          29 TVVSATDGTIVSFNAAA--VRQFGYAEEEVIGQNLRILMPEPY   69 (130)
T ss_dssp             EEEEETTSBEEEECHHH--HHHHCCCHHHHTTSBGGGGSCTTT
T ss_pred             EEEEeCCccEEEEHHHH--HHhhcCCHHHhcCCccccccccch
Confidence            34458899999999998  899999999999999887774433

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.53  E-value=0.00085  Score=52.00  Aligned_cols=33  Identities=6%  Similarity=0.105  Sum_probs=30.5

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCccceec
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVWT  326 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~~  326 (383)
                      -+|+|++|++.+  ..++||..+||+|+++.++++
T Consensus        17 ~~G~I~~~N~a~--~~l~Gy~~~el~g~~~~~l~~   49 (114)
T d1ll8a_          17 KTTEILVANDKA--CGLLGYSSQDLIGQKLTQFFL   49 (114)
T ss_dssp             TTCBEEEECTTH--HHHHTCCTTTTTTSBGGGGSS
T ss_pred             CCCEEEEECHHH--HHhhcCCHHHHcCCCeeeecC
Confidence            379999999998  899999999999999999873

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.34  E-value=0.00054  Score=52.68  Aligned_cols=32  Identities=9%  Similarity=0.036  Sum_probs=28.7

Q ss_pred             CCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         292 RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       292 ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      .|+.|+|+++..  ..++||.++|++|+++++.+
T Consensus        12 ~d~~I~~~N~a~--~~l~G~~~~eiiG~~~~~~~   43 (110)
T d1bywa_          12 ENCAVIYCNDGF--CELCGYSRAEVMQRPCTCDF   43 (110)
T ss_dssp             SSCBEEEECHHH--HHHHTCCHHHHTTSBTTCGG
T ss_pred             CCCEEEEEcHHH--HHHhCCCHHHhcccCccccc
Confidence            689999999998  89999999999999987643

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.11  E-value=0.0059  Score=45.06  Aligned_cols=61  Identities=23%  Similarity=0.232  Sum_probs=48.0

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHHHHHhhhHhHHHHHhh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKRRREQENNYIEELAEL   73 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~RR~~~n~~i~eL~~l   73 (383)
                      ..|++||+.-|.++++|.++++..         ..|.+|..|+..+++.+..=..+.+.+.+....|...
T Consensus        12 ~~Er~RR~~in~~~~~L~~llP~~---------~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~   72 (80)
T d1am9a_          12 AIEKRYRSSINDKIIELKDLVVGT---------EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCS---------SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCC---------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999999999864         2478999999999999977655555555555555443

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.07  E-value=0.0021  Score=45.48  Aligned_cols=48  Identities=23%  Similarity=0.290  Sum_probs=39.4

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhh
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCL   54 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~   54 (383)
                      ..||+||++-|..+++|.++++...   ...+...|.+|..|++.+++.+.
T Consensus         8 ~~Er~RR~~in~~~~~L~~llP~~~---~~~~~~~k~sKa~iL~~Av~yI~   55 (63)
T d1a0aa_           8 HAEQARRNRLAVALHELASLIPAEW---KQQNVSAAPSKATTVEAACRYIR   55 (63)
T ss_dssp             GGTHHHHHHHHHHHHHHHHTSCHHH---HTSSCCCCSCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCcc---cccCCcccccHHHHHHHHHHHHH
Confidence            4699999999999999999998752   12334689999999999987763

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.64  E-value=0.005  Score=43.68  Aligned_cols=48  Identities=31%  Similarity=0.410  Sum_probs=40.2

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhh
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCL   54 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~   54 (383)
                      ...||+||+.-|.++++|.+++++.    ....-..|.+|..||.++++.+.
T Consensus        10 ~~~Er~RR~~in~~f~~L~~lvP~~----~~~~~~~k~sK~~iL~~av~yI~   57 (65)
T d1an4a_          10 NEVERRRRDKINNWIVQLSKIIPDS----SMESTKSGQSKGGILSKASDYIQ   57 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCC----CCCSSTTCCCTTTTTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcccc----cccCCCCCCCHHHHHHHHHHHHH
Confidence            4679999999999999999999976    12334579999999999988774

>d3c2wa3 d.110.3.9 (A:5-117) Bacteriophytochrome BphP {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.56  E-value=0.0019  Score=51.01  Aligned_cols=54  Identities=17%  Similarity=0.160  Sum_probs=44.6

Q ss_pred             hcCcEEEEcCCccEEEeecccccccCcccccccCCccccccCCCChHHHHhhcCC
Q psy7682         142 LEGFLFVVNPDGYVNFCTENIKSFIRYSRQEVLGKSVYNLIHHGDHARFHNCLVP  196 (383)
Q Consensus       142 ldgfi~vvs~dG~i~yvS~sv~~~LGy~~~el~G~s~~d~iHp~D~~~~~~~l~~  196 (383)
                      .-||+++++.+|.|+++|+|+..+||++++ .+|+.+.+.+-++-...+++.+..
T Consensus        21 phG~LLald~~~~I~~~S~N~~~~lg~~~~-~L~~~~~~~~~~~~~~~l~~~~~~   74 (113)
T d3c2wa3          21 PHGALVTLRADGMVLAASENIQALLGFVAS-PGSYLTQEQVGPEVLRMLEEGLTG   74 (113)
T ss_dssp             TTEEEEEECTTSBEEEEETTHHHHTSSCCC-TTCBCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCeEEEEEcCCCeEEEEcCCHHHHhCCChh-HhcccHHHHhCHHHHHHHHhhhhc
Confidence            468999999999999999999999999865 679888888777666666666543

>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=95.42  E-value=0.0036  Score=48.88  Aligned_cols=40  Identities=5%  Similarity=-0.027  Sum_probs=33.9

Q ss_pred             ceeEEEeC-CCCcEEEEcCCCCccccCCcccccccCCCcccee
Q psy7682         284 EQFTMKLD-RSGTIIGMDTSGVSQTHTQYLNKAVACKTSATVW  325 (383)
Q Consensus       284 ~~F~tRHs-ldgkf~~vD~r~l~~~ilGY~p~eLiG~S~yd~~  325 (383)
                      ..|+.-.+ .||+++||++++  ..+|||.|++|+|+++++++
T Consensus        17 hG~Llvld~~d~~I~~vS~N~--~~lLG~~~~~llG~~l~dll   57 (114)
T d2oola2          17 HGYLFVVSETDLRIASVSANV--EDLLRQPPASLLNVPIAHYL   57 (114)
T ss_dssp             TSEEEEECTTTCBEEEEETTH--HHHHSSCGGGGTTCBGGGGB
T ss_pred             CcEEEEEECCCCEEEEEcCCH--HHHhCCChHHHcCCCHHHhC
Confidence            34444444 479999999998  99999999999999999987

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.85  E-value=0.025  Score=41.34  Aligned_cols=48  Identities=17%  Similarity=0.160  Sum_probs=39.4

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHH
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKR   58 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~   58 (383)
                      ..||+||++-|.++++|.++++..     .+  ..|.+|..|+.++++.+..=+.
T Consensus         7 ~~Er~RR~~in~~f~~L~~llP~~-----~~--~~k~sK~~iL~~A~~yI~~L~~   54 (79)
T d1nlwa_           7 EMEKNRRAHLRLSLEKLKGLVPLG-----PD--SSRHTTLSLLTKAKLHIKKLED   54 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCC-----SS--SCCCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCccC-----CC--CCCCCHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999865     11  2578999999999988865433

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.23  E-value=0.052  Score=39.90  Aligned_cols=47  Identities=17%  Similarity=0.294  Sum_probs=39.1

Q ss_pred             hhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHH
Q psy7682           4 LNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKR   58 (383)
Q Consensus         4 ~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~   58 (383)
                      ..||+||++-|.++++|.++++..     .+   .|.+|..|+..+++.+..-+.
T Consensus         8 ~~Er~RR~~in~~f~~L~~llP~~-----~~---~k~sK~~iL~~A~~yI~~L~~   54 (83)
T d1nkpb_           8 ALERKRRDHIKDSFHSLRDSVPSL-----QG---EKASRAQILDKATEYIQYMRR   54 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSGGG-----TT---SCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCC-----CC---CCCCHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999865     11   478999999999988865333

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.44  E-value=0.085  Score=39.10  Aligned_cols=49  Identities=20%  Similarity=0.239  Sum_probs=39.1

Q ss_pred             chhHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhhhHHHH
Q psy7682           3 CLNEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQCLNEKR   58 (383)
Q Consensus         3 ~~~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~~~ek~   58 (383)
                      ...|++||+.-|.++++|.++++..  .   .  ..|.+|..|+..+++.+..=+.
T Consensus        11 n~~Er~RR~~in~~f~~Lr~llP~~--~---~--~~k~sK~~iL~~A~~yI~~L~~   59 (88)
T d1nkpa_          11 NVLERQRRNELKRSFFALRDQIPEL--E---N--NEKAPKVVILKKATAYILSVQA   59 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCGGG--T---T--CTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCC--C---C--CCccCHHHHHHHHHHHHHHHHH
Confidence            3579999999999999999999853  1   1  2578899999999888765333

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.71  E-value=0.2  Score=35.22  Aligned_cols=41  Identities=24%  Similarity=0.288  Sum_probs=34.8

Q ss_pred             hHHHhHHHHhhHHHHHHhHhhhhhhhcccccccCCCchhhhhhhhhhhh
Q psy7682           5 NEKRRREQENNYIEELAELISAASFAESMSSLAVKPDKCAILQETVNQC   53 (383)
Q Consensus         5 ~~~~~~~~~~~~~~e~~~~~~a~~~~~~~~~~~~k~~~~~~~~~~~~~~   53 (383)
                      .|++||+..|.++++|.+++...     .   ..|.+|..|+..+++.+
T Consensus        19 ~Er~Rr~~in~~~~~L~~llP~~-----~---~~k~sK~~iL~~Ai~YI   59 (68)
T d1mdya_          19 RERRRLSKVNEAFETLKRSTSSN-----P---NQRLPKVEILRNAIRYI   59 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCSC-----T---TSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC-----C---CCCCCHHHHHHHHHHHH
Confidence            59999999999999999999976     1   25778999999887655