Psyllid ID: psy8548

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
Protein Sequence
MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEEEEEEEEKEEDKNLLK
Secondary Structure (PSIPRED)
ccccEEEEcccccccccEEEEEHHHHHHHcccHHHHHcccccccccccccccHHHHHHHHHHHHHcccEEEEEEccccccccccHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEcccccccEEEEEcccccHcccccHHHHHcccccccccccccccHHHHHHHHHHHHcccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mnsnfvlgnaqvpslypivycsdgfcelSGFARAQIMQKGCAckflygpdtseeHKTQIEKALESKTELKLEVIFYKkngyheeeeeeeeeEEKEEDKNLLK
Flexible Loop (DISEMBL)
mnsnfvlgnaqvpSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKalesktelklEVIFYKKNgyheeeeeeeeeeekeedknllk
Low Complexity Region (SEG)
MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHeeeeeeeeeeekeeDKNLLK
Disordered region (IsUnstruct)
****FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGP*******************LKLEVIFYK*************************
Disordered Region (DISOPRED)
*NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY******************L**
Disordered Region (DISEMBL)
MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG**********************
Disordered Region (DISPRO)
*NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH*E*EEEEEEEEKE*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTxxxxxxxxxxxxxxxxxxxxxVIFYKxxxxxxxxxxxxxxxxxxxxxxxxK
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	102	2.2.26 [Sep-21-2011]
O89047	1087	Potassium voltage-gated c	yes	N/A	0.774	0.072	0.658	7e-29
Q9WVJ0	1087	Potassium voltage-gated c	yes	N/A	0.774	0.072	0.658	7e-29
Q9ULD8	1083	Potassium voltage-gated c	yes	N/A	0.774	0.072	0.658	7e-29
Q96L42	1107	Potassium voltage-gated c	no	N/A	0.774	0.071	0.658	2e-27
Q9QWS8	1102	Potassium voltage-gated c	no	N/A	0.774	0.071	0.645	8e-27
P59111	1102	Potassium voltage-gated c	no	N/A	0.774	0.071	0.645	9e-27
Q9R1T9	1017	Potassium voltage-gated c	no	N/A	0.774	0.077	0.569	1e-24
Q9UQ05	1017	Potassium voltage-gated c	no	N/A	0.774	0.077	0.556	2e-23
O54852	1195	Potassium voltage-gated c	no	N/A	0.764	0.065	0.481	3e-17
Q9ER47	1195	Potassium voltage-gated c	no	N/A	0.764	0.065	0.481	3e-17

>sp|O89047|KCNH3_RAT Potassium voltage-gated channel subfamily H member 3 OS=Rattus norvegicus GN=Kcnh3 PE=2 SV=1

 Score =  125 bits (314), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct: 26  HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL+   E K E+I Y+K+G
Sbjct: 86  ALDEHKEFKAELILYRKSG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current with fast inactivation. Channel properties may be modulated by cAMP and subunit assembly.
Rattus norvegicus (taxid: 10116)

>sp|Q9WVJ0|KCNH3_MOUSE Potassium voltage-gated channel subfamily H member 3 OS=Mus musculus GN=Kcnh3 PE=2 SV=2

 Score =  125 bits (314), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct: 26  HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL+   E K E+I Y+K+G
Sbjct: 86  ALDEHKEFKAELILYRKSG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current with fast inactivation. Channel properties may be modulated by cAMP and subunit assembly.

Mus musculus (taxid: 10090)

>sp|Q9ULD8|KCNH3_HUMAN Potassium voltage-gated channel subfamily H member 3 OS=Homo sapiens GN=KCNH3 PE=2 SV=2

 Score =  125 bits (314), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct: 26  HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL+   E K E+I Y+K+G
Sbjct: 86  ALDEHKEFKAELILYRKSG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current with fast inactivation. Channel properties may be modulated by cAMP and subunit assembly.

Homo sapiens (taxid: 9606)

>sp|Q96L42|KCNH8_HUMAN Potassium voltage-gated channel subfamily H member 8 OS=Homo sapiens GN=KCNH8 PE=2 SV=2

 Score =  120 bits (302), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNF+L NAQV   +PIVYCSDGFCEL+GFAR ++MQK C+CKFL+G +T+E+   QIEK
Sbjct: 26  HSNFILANAQVAKGFPIVYCSDGFCELAGFARTEVMQKSCSCKFLFGVETNEQLMLQIEK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LE KTE K E++FYKKNG
Sbjct: 86  SLEEKTEFKGEIMFYKKNG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits a slowly activating, outward rectifying current. Channel properties may be modulated by cAMP and subunit assembly.

Homo sapiens (taxid: 9606)

>sp|Q9QWS8|KCNH8_RAT Potassium voltage-gated channel subfamily H member 8 OS=Rattus norvegicus GN=Kcnh8 PE=2 SV=2

 Score =  118 bits (296), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 51/79 (64%), Positives = 65/79 (82%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNF+L NAQV   +PIVYCSDGFCEL+GFAR ++MQK C+CKFL+G +T+E+   QIEK
Sbjct: 26  HSNFILANAQVAKGFPIVYCSDGFCELAGFARTEVMQKSCSCKFLFGVETNEQLMLQIEK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LE K E K E++FYKKNG
Sbjct: 86  SLEEKVEFKGEIMFYKKNG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits a slowly activating, outward rectifying current. Channel properties may be modulated by cAMP and subunit assembly.

Rattus norvegicus (taxid: 10116)

>sp|P59111|KCNH8_MOUSE Potassium voltage-gated channel subfamily H member 8 OS=Mus musculus GN=Kcnh8 PE=2 SV=2

 Score =  118 bits (296), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 51/79 (64%), Positives = 65/79 (82%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNF+L NAQV   +PIVYCSDGFCEL+GFAR ++MQK C+CKFL+G +T+E+   QIEK
Sbjct: 26  HSNFILANAQVAKGFPIVYCSDGFCELAGFARTEVMQKSCSCKFLFGVETNEQLMLQIEK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LE K E K E++FYKKNG
Sbjct: 86  SLEEKVEFKGEIMFYKKNG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits a slowly activating, outward rectifying current (By similarity). Channel properties may be modulated by cAMP and subunit assembly.

Mus musculus (taxid: 10090)

>sp|Q9R1T9|KCNH4_RAT Potassium voltage-gated channel subfamily H member 4 OS=Rattus norvegicus GN=Kcnh4 PE=2 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 45/79 (56%), Positives = 62/79 (78%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNF+L NAQ P  +PIVYCSDGFCEL+G+ R ++MQK C+C+FLYGP+TSE    +++K
Sbjct: 26  HSNFLLANAQGPRGFPIVYCSDGFCELTGYGRTEVMQKTCSCRFLYGPETSEPALQRLQK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           ALE   E + E+ FY+K+G
Sbjct: 86  ALEGHQEHRAEICFYRKDG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current, but shows no inactivation. Channel properties may be modulated by cAMP and subunit assembly.

Rattus norvegicus (taxid: 10116)

>sp|Q9UQ05|KCNH4_HUMAN Potassium voltage-gated channel subfamily H member 4 OS=Homo sapiens GN=KCNH4 PE=2 SV=1

 Score =  107 bits (267), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 44/79 (55%), Positives = 60/79 (75%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNF+L NAQ    +PIVYCSDGFCEL+G+ R ++MQK C+C+FLYGP+TSE    ++ K
Sbjct: 26  HSNFLLANAQGTRGFPIVYCSDGFCELTGYGRTEVMQKTCSCRFLYGPETSEPALQRLHK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           ALE   E + E+ FY+K+G
Sbjct: 86  ALEGHQEHRAEICFYRKDG 104

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current, but shows no inactivation. Channel properties may be modulated by cAMP and subunit assembly.

Homo sapiens (taxid: 9606)

>sp|O54852|KCNH7_RAT Potassium voltage-gated channel subfamily H member 7 OS=Rattus norvegicus GN=Kcnh7 PE=1 SV=1

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 38/79 (48%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           N  F++ NA+V +   I+YC+DGFCE++GF+R  +MQK C C FL+GP+T      QI +
Sbjct: 26  NKKFIIANARVQNC-AIIYCNDGFCEMTGFSRPDVMQKPCTCDFLHGPETKRHDIAQIAQ 84

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL    E K+EV +Y KNG
Sbjct: 85  ALLGSEERKVEVTYYHKNG 103

Pore-forming (alpha) subunit of voltage-gated potassium channel. Channel properties may be modulated by cAMP and subunit assembly.

Rattus norvegicus (taxid: 10116)

>sp|Q9ER47|KCNH7_MOUSE Potassium voltage-gated channel subfamily H member 7 OS=Mus musculus GN=Kcnh7 PE=2 SV=2

 Score = 87.0 bits (214), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 38/79 (48%), Positives = 53/79 (67%), Gaps = 1/79 (1%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           N  F++ NA+V +   I+YC+DGFCE++GF+R  +MQK C C FL+GP+T      QI +
Sbjct: 26  NKKFIIANARVQNC-AIIYCNDGFCEMTGFSRPDVMQKPCTCDFLHGPETKRHDIAQIAQ 84

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL    E K+EV +Y KNG
Sbjct: 85  ALLGSEERKVEVTYYHKNG 103

Pore-forming (alpha) subunit of voltage-gated potassium channel (By similarity). Channel properties may be modulated by cAMP and subunit assembly.

Mus musculus (taxid: 10090)

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	102
189240721	900	PREDICTED: similar to AGAP005251-PA [Tri	0.764	0.086	0.884	5e-36
270012947	1034	hypothetical protein TcasGA2_TC004313 [T	0.764	0.075	0.884	1e-35
307166687	928	Potassium voltage-gated channel subfamil	0.774	0.085	0.835	1e-35
380022535	999	PREDICTED: potassium voltage-gated chann	0.774	0.079	0.848	1e-35
328776551	992	PREDICTED: potassium voltage-gated chann	0.774	0.079	0.848	1e-35
383857459	988	PREDICTED: potassium voltage-gated chann	0.774	0.079	0.822	4e-35
350426330	990	PREDICTED: potassium voltage-gated chann	0.774	0.079	0.835	5e-35
345481594	1008	PREDICTED: potassium voltage-gated chann	0.774	0.078	0.835	5e-35
242006252	770	voltage-gated channel, putative [Pedicul	0.774	0.102	0.848	7e-35
340723656	990	PREDICTED: potassium voltage-gated chann	0.774	0.079	0.822	1e-34

>gi|189240721|ref|XP_967544.2| PREDICTED: similar to AGAP005251-PA [Tribolium castaneum]

 Score =  154 bits (390), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 69/78 (88%), Positives = 75/78 (96%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+G+ARAQIMQKGCACKFLYGP+T +EHK QI+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGYARAQIMQKGCACKFLYGPETKDEHKAQIDK 85

Query: 62  ALESKTELKLEVIFYKKN 79
           ALESK ELKLEVIFYKKN
Sbjct: 86  ALESKIELKLEVIFYKKN 103

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270012947|gb|EFA09395.1| hypothetical protein TcasGA2_TC004313 [Tribolium castaneum]

 Score =  153 bits (387), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 69/78 (88%), Positives = 75/78 (96%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+G+ARAQIMQKGCACKFLYGP+T +EHK QI+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGYARAQIMQKGCACKFLYGPETKDEHKAQIDK 85

Query: 62  ALESKTELKLEVIFYKKN 79
           ALESK ELKLEVIFYKKN
Sbjct: 86  ALESKIELKLEVIFYKKN 103

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307166687|gb|EFN60684.1| Potassium voltage-gated channel subfamily H member 8 [Camponotus floridanus]

 Score =  153 bits (387), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 66/79 (83%), Positives = 75/79 (94%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
          +SNFVLGNAQVP++YPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE K  I+K
Sbjct: 5  DSNFVLGNAQVPTIYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEEKAMIDK 64

Query: 62 ALESKTELKLEVIFYKKNG 80
          +LESKTELK+EV+FYKKNG
Sbjct: 65 SLESKTELKMEVVFYKKNG 83

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380022535|ref|XP_003695098.1| PREDICTED: potassium voltage-gated channel subfamily H member 8 [Apis florea]

 Score =  153 bits (386), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 67/79 (84%), Positives = 75/79 (94%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE +  I+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEERAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELK+EV+FYKKNG
Sbjct: 86  SLESKTELKMEVVFYKKNG 104

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328776551|ref|XP_003249178.1| PREDICTED: potassium voltage-gated channel subfamily H member 8 [Apis mellifera]

 Score =  153 bits (386), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 67/79 (84%), Positives = 75/79 (94%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE +  I+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEERAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELK+EV+FYKKNG
Sbjct: 86  SLESKTELKMEVVFYKKNG 104

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857459|ref|XP_003704222.1| PREDICTED: potassium voltage-gated channel subfamily H member 8 [Megachile rotundata]

 Score =  151 bits (382), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 65/79 (82%), Positives = 75/79 (94%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVP++YPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE +  I+K
Sbjct: 26  HSNFVLGNAQVPTIYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEERAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELK+EV+FYKKNG
Sbjct: 86  SLESKTELKMEVVFYKKNG 104

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350426330|ref|XP_003494406.1| PREDICTED: potassium voltage-gated channel subfamily H member 8-like [Bombus impatiens]

 Score =  151 bits (382), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 66/79 (83%), Positives = 74/79 (93%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE +  I+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEERAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELK+EV+FYKK G
Sbjct: 86  SLESKTELKMEVVFYKKTG 104

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345481594|ref|XP_003424408.1| PREDICTED: potassium voltage-gated channel subfamily H member 8-like [Nasonia vitripennis]

 Score =  151 bits (381), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 66/79 (83%), Positives = 75/79 (94%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVP++YPIVYCSDGFCEL+GFARAQIMQKGCACKFLYGP+T EE K  I+K
Sbjct: 26  HSNFVLGNAQVPTIYPIVYCSDGFCELTGFARAQIMQKGCACKFLYGPETKEEEKAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELKLEV+FYKK+G
Sbjct: 86  SLESKTELKLEVVFYKKSG 104

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242006252|ref|XP_002423966.1| voltage-gated channel, putative [Pediculus humanus corporis] gi|212507248|gb|EEB11228.1| voltage-gated channel, putative [Pediculus humanus corporis]

 Score =  150 bits (380), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 67/79 (84%), Positives = 74/79 (93%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
          NSNFVLGNAQVPSLYPIVYCSDGFCEL+GF+RAQIMQK CACKFLYGP+T++E+K QI+K
Sbjct: 4  NSNFVLGNAQVPSLYPIVYCSDGFCELTGFSRAQIMQKSCACKFLYGPETNDENKAQIDK 63

Query: 62 ALESKTELKLEVIFYKKNG 80
          ALE K ELKLEVIFYKK G
Sbjct: 64 ALECKIELKLEVIFYKKTG 82

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340723656|ref|XP_003400205.1| PREDICTED: potassium voltage-gated channel subfamily H member 8-like [Bombus terrestris]

 Score =  150 bits (379), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/79 (82%), Positives = 74/79 (93%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +SNFVLGNAQVPSLYPIVYCSDGFCEL+GFARAQIMQ+GCACKFLYGP+T EE +  I+K
Sbjct: 26  HSNFVLGNAQVPSLYPIVYCSDGFCELTGFARAQIMQRGCACKFLYGPETKEEERAMIDK 85

Query: 62  ALESKTELKLEVIFYKKNG 80
           +LESKTELK+EV+FYKK G
Sbjct: 86  SLESKTELKMEVVFYKKTG 104

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

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	102
FB|FBgn0011589	1284	Elk "Eag-like K[+] channel" [D	0.764	0.060	0.746	2.1e-26
UNIPROTKB|F8WCG6	195	KCNH8 "Potassium voltage-gated	0.774	0.405	0.658	5.2e-26
ZFIN|ZDB-GENE-070912-23	914	kcnh3 "potassium voltage-gated	0.774	0.086	0.683	6.8e-26
UNIPROTKB|J9P8R4	433	KCNH8 "Uncharacterized protein	0.764	0.180	0.666	6.9e-26
UNIPROTKB|F1SHB2	642	KCNH3 "Uncharacterized protein	0.774	0.123	0.658	1.4e-25
UNIPROTKB|E1B760	1074	KCNH3 "Uncharacterized protein	0.774	0.073	0.658	3.9e-25
UNIPROTKB|Q9ULD8	1083	KCNH3 "Potassium voltage-gated	0.774	0.072	0.658	4e-25
MGI|MGI:1341723	1087	Kcnh3 "potassium voltage-gated	0.774	0.072	0.658	4e-25
RGD|71070	1087	Kcnh3 "potassium voltage-gated	0.774	0.072	0.658	4e-25
UNIPROTKB|F1P602	1056	KCNH3 "Uncharacterized protein	0.764	0.073	0.666	4.9e-25

FB|FBgn0011589 Elk "Eag-like K[+] channel" [Drosophila melanogaster (taxid:7227)]

 Score = 311 (114.5 bits), Expect = 2.1e-26, P = 2.1e-26
 Identities = 59/79 (74%), Positives = 67/79 (84%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQ     PIVYCSDGF +L+G++RAQIMQKGC+C FLYGPDT EEHK QIEK
Sbjct:    26 HSNFVLGNAQANG-NPIVYCSDGFVDLTGYSRAQIMQKGCSCHFLYGPDTKEEHKQQIEK 84

Query:    62 ALESKTELKLEVIFYKKNG 80
             +L +K ELKLEVIFYKK G
Sbjct:    85 SLSNKMELKLEVIFYKKEG 103

GO:0005267 "potassium channel activity" evidence=NAS

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA;NAS

GO:0008076 "voltage-gated potassium channel complex" evidence=NAS

GO:0006813 "potassium ion transport" evidence=IEA;NAS

GO:0055085 "transmembrane transport" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

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

UNIPROTKB|F8WCG6 KCNH8 "Potassium voltage-gated channel subfamily H member 8" [Homo sapiens (taxid:9606)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNF+L NAQV   +PIVYCSDGFCEL+GFAR ++MQK C+CKFL+G +T+E+   QIEK
Sbjct:    26 HSNFILANAQVAKGFPIVYCSDGFCELAGFARTEVMQKSCSCKFLFGVETNEQLMLQIEK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             +LE KTE K E++FYKKNG
Sbjct:    86 SLEEKTEFKGEIMFYKKNG 104

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

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

ZFIN|ZDB-GENE-070912-23 kcnh3 "potassium voltage-gated channel, subfamily H (eag-related), member 3" [Danio rerio (taxid:7955)]

 Score = 304 (112.1 bits), Expect = 6.8e-26, P = 6.8e-26
 Identities = 54/79 (68%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV SLYPIVYCSDGFCEL+G+ARA++MQK CAC FLYGP+TS+    QI+ 
Sbjct:    26 HSNFVLGNAQVQSLYPIVYCSDGFCELTGYARAELMQKSCACHFLYGPETSDRLMAQIQG 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+ + E K E++FYKK G
Sbjct:    86 ALDERREFKTELVFYKKGG 104

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA;IDA

GO:0006813 "potassium ion transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0005216 "ion channel activity" evidence=IEA

GO:0006811 "ion transport" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0055085 "transmembrane transport" evidence=IEA

GO:0034765 "regulation of ion transmembrane transport" evidence=IDA

GO:0034220 "ion transmembrane transport" evidence=IDA

GO:0071805 "potassium ion transmembrane transport" evidence=IDA

GO:0043855 "cyclic nucleotide-gated ion channel activity" evidence=IDA

GO:0006810 "transport" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|J9P8R4 KCNH8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 293 (108.2 bits), Expect = 6.9e-26, P = 6.9e-26
 Identities = 52/78 (66%), Positives = 65/78 (83%)

Query:     3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKA 62
             SNF+L NAQV   +PIVYCSDGFCEL+GFAR ++MQK C+CKFL+G +T+E+   QIEK+
Sbjct:     1 SNFILANAQVAKGFPIVYCSDGFCELAGFARTEVMQKSCSCKFLFGVETNEQLMLQIEKS 60

Query:    63 LESKTELKLEVIFYKKNG 80
             LE KTE K E++FYKKNG
Sbjct:    61 LEEKTEFKGEIMFYKKNG 78

GO:0016021 "integral to membrane" evidence=IEA

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

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

UNIPROTKB|F1SHB2 KCNH3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 298 (110.0 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct:    26 HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+   E K E+I Y+K+G
Sbjct:    86 ALDEHKEFKAELILYRKSG 104

GO:0016021 "integral to membrane" evidence=IEA

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

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

UNIPROTKB|E1B760 KCNH3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 298 (110.0 bits), Expect = 3.9e-25, P = 3.9e-25
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct:    26 HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+   E K E+I Y+K+G
Sbjct:    86 ALDEHKEFKAELILYRKSG 104

GO:0016021 "integral to membrane" evidence=IEA

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

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

UNIPROTKB|Q9ULD8 KCNH3 "Potassium voltage-gated channel subfamily H member 3" [Homo sapiens (taxid:9606)]

 Score = 298 (110.0 bits), Expect = 4.0e-25, P = 4.0e-25
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct:    26 HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+   E K E+I Y+K+G
Sbjct:    86 ALDEHKEFKAELILYRKSG 104

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

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

GO:0005249 "voltage-gated potassium channel activity" evidence=TAS

GO:0016021 "integral to membrane" evidence=NAS

GO:0006813 "potassium ion transport" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0007268 "synaptic transmission" evidence=TAS

MGI|MGI:1341723 Kcnh3 "potassium voltage-gated channel, subfamily H (eag-related), member 3" [Mus musculus (taxid:10090)]

 Score = 298 (110.0 bits), Expect = 4.0e-25, P = 4.0e-25
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct:    26 HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+   E K E+I Y+K+G
Sbjct:    86 ALDEHKEFKAELILYRKSG 104

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0000160 "phosphorelay signal transduction system" evidence=IEA

GO:0004871 "signal transducer activity" evidence=IEA

GO:0005216 "ion channel activity" evidence=IEA

GO:0005244 "voltage-gated ion channel activity" evidence=IEA

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0005267 "potassium channel activity" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0006811 "ion transport" evidence=IEA

GO:0006813 "potassium ion transport" evidence=IEA

GO:0007165 "signal transduction" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0023014 "signal transduction by phosphorylation" evidence=IEA

GO:0034765 "regulation of ion transmembrane transport" evidence=IEA

GO:0055085 "transmembrane transport" evidence=IEA

GO:0071805 "potassium ion transmembrane transport" evidence=IEA

RGD|71070 Kcnh3 "potassium voltage-gated channel, subfamily H (eag-related), member 3" [Rattus norvegicus (taxid:10116)]

 Score = 298 (110.0 bits), Expect = 4.0e-25, P = 4.0e-25
 Identities = 52/79 (65%), Positives = 66/79 (83%)

Query:     2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             +SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI K
Sbjct:    26 HSNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRK 85

Query:    62 ALESKTELKLEVIFYKKNG 80
             AL+   E K E+I Y+K+G
Sbjct:    86 ALDEHKEFKAELILYRKSG 104

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

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

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|F1P602 KCNH3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 297 (109.6 bits), Expect = 4.9e-25, P = 4.9e-25
 Identities = 52/78 (66%), Positives = 65/78 (83%)

Query:     3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKA 62
             SNFVLGNAQV  L+P+VYCSDGFC+L+GF+RA++MQ+GCAC FLYGPDTSE  + QI KA
Sbjct:     1 SNFVLGNAQVAGLFPVVYCSDGFCDLTGFSRAEVMQRGCACSFLYGPDTSELVRQQIRKA 60

Query:    63 LESKTELKLEVIFYKKNG 80
             L+   E K E+I Y+K+G
Sbjct:    61 LDEHKEFKAELILYRKSG 78

GO:0016021 "integral to membrane" evidence=IEA

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

GO:0005249 "voltage-gated potassium channel activity" evidence=IEA

GO:0000155 "phosphorelay sensor kinase activity" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O89047	KCNH3_RAT	No assigned EC number	0.6582	0.7745	0.0726	yes	N/A
Q9WVJ0	KCNH3_MOUSE	No assigned EC number	0.6582	0.7745	0.0726	yes	N/A
Q9ULD8	KCNH3_HUMAN	No assigned EC number	0.6582	0.7745	0.0729	yes	N/A

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	102
pfam13426	101	pfam13426, PAS_9, PAS domain	1e-12
PRK13559	361	PRK13559, PRK13559, hypothetical protein; Provisio	1e-11
PRK13557	540	PRK13557, PRK13557, histidine kinase; Provisional	2e-11
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	9e-08
cd00130	103	cd00130, PAS, PAS domain; PAS motifs appear in arc	5e-06

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

 Score = 58.2 bits (141), Expect = 1e-12
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIF 75
            IVY +D    L G+ R +++ K  + + L+GP   EE   ++ +AL +  E+++E+  
Sbjct: 8  GRIVYANDAALRLLGYTREELLGK--SIRDLFGPGDDEEAVARLREALRNGGEVEVELEL 65

Query: 76 YKKNG 80
           +K+G
Sbjct: 66 RRKDG 70

Length = 101

>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional

 Score = 58.7 bits (142), Expect = 1e-11
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 6   VLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALES 65
            + +   P L PIV  +  F +L+G+A  +++  G  C+FL G  T      +I  A+ +
Sbjct: 57  CITDPHQPDL-PIVLANQAFLDLTGYAAEEVV--GRNCRFLQGAATDPIAVAKIRAAIAA 113

Query: 66  KTELKLEVIFYKKNG 80
           + E+ +E++ Y+K+G
Sbjct: 114 EREIVVELLNYRKDG 128

Length = 361

>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional

 Score = 58.5 bits (142), Expect = 2e-11
 Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 2/64 (3%)

Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFY 76
           PIV+ +  F E++G+A  +I+  G  C+FL GP+T      ++  A+  + E+  E++ Y
Sbjct: 54  PIVFANRAFLEMTGYAAEEII--GNNCRFLQGPETDRATVAEVRDAIAERREIATEILNY 111

Query: 77  KKNG 80
           +K+G
Sbjct: 112 RKDG 115

Length = 540

>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional

 Score = 47.9 bits (114), Expect = 9e-08
 Identities = 19/64 (29%), Positives = 41/64 (64%), Gaps = 2/64 (3%)

Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFY 76
           P++Y +D F  ++G++  +++  G  C+FL G DT+EE   ++ +A++ +    +E+  Y
Sbjct: 172 PLIYINDAFERITGYSPDEVL--GRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNY 229

Query: 77  KKNG 80
           +K+G
Sbjct: 230 RKDG 233

Length = 665

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

 Score = 41.1 bits (96), Expect = 5e-06
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 18 IVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK 77
          I+Y +    +L G++  +++ K      L  P+  EE + ++E  L     + LEV   +
Sbjct: 14 ILYANPAAEQLLGYSPEELIGKSLL--DLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71

Query: 78 KNG 80
          K+G
Sbjct: 72 KDG 74

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	102
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.55
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.21
PRK13557	540	histidine kinase; Provisional	99.03
PRK10060	663	RNase II stability modulator; Provisional	98.93
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.92
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.91
PRK13559	361	hypothetical protein; Provisional	98.88
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	98.76
PRK13560	807	hypothetical protein; Provisional	98.71
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	98.63
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	98.63
PRK13558	665	bacterio-opsin activator; Provisional	98.57
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.57
PF14598	111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.55
KOG0501|consensus	971		98.54
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	98.39
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	98.38
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	98.36
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	98.34
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	98.34
PRK09776	1092	putative diguanylate cyclase; Provisional	98.31
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.0
PF13188	64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	97.98
KOG1229|consensus	775		97.96
PF12860	115	PAS_7: PAS fold	97.9
PRK09776	1092	putative diguanylate cyclase; Provisional	97.79
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	97.3
PRK11360	607	sensory histidine kinase AtoS; Provisional	97.3
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	97.22
PRK11006	430	phoR phosphate regulon sensor protein; Provisional	97.19
smart00091	67	PAS PAS domain. PAS motifs appear in archaea, euba	97.18
PRK13560	807	hypothetical protein; Provisional	97.06
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.02
KOG3558|consensus	768		96.96
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	96.91
PF08670	148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	96.55
TIGR02373	124	photo_yellow photoactive yellow protein. Members o	96.07
PRK15053	545	dpiB sensor histidine kinase DpiB; Provisional	95.67
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	95.05
COG3852	363	NtrB Signal transduction histidine kinase, nitroge	94.92
PRK11086	542	sensory histidine kinase DcuS; Provisional	94.44
COG5002	459	VicK Signal transduction histidine kinase [Signal	94.41
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	94.06
KOG3559|consensus	598		93.22
KOG3560|consensus	712		92.81
PF08446	110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	92.61
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	92.51
COG3290	537	CitA Signal transduction histidine kinase regulati	91.77
PRK09959	1197	hybrid sensory histidine kinase in two-component r	91.26
KOG3561|consensus	803		91.15
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	90.26
KOG3558|consensus	768		89.79
PF07310	137	PAS_5: PAS domain; InterPro: IPR009922 This family	87.46
KOG3560|consensus	712		84.3
COG5000	712	NtrY Signal transduction histidine kinase involved	83.16

>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=99.55  E-value=1.9e-13  Score=77.61  Aligned_cols=79  Identities=24%  Similarity=0.331  Sum_probs=67.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +.+++++|.+    ++|+++|++|++++|++.++++|+  +...+..+.........+.+.+..+..+..++.+++++|+
T Consensus         1 p~~i~i~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~   74 (104)
T PF13426_consen    1 PDGIFILDPD----GRILYVNPAFERLFGYSREELIGK--SISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGE   74 (104)
T ss_dssp             -SEEEEEETT----SBEEEE-HHHHHHHTS-HHHHTTS--BGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSE
T ss_pred             CEEEEEECCc----CcEEehhHHHHHHHCcCHHHHcCC--CcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCC
Confidence            3689999998    999999999999999999999999  6666666666778888889999988889999999999999


Q ss_pred             eeeec
Q psy8548          82 HEEEE   86 (102)
Q Consensus        82 ~~~~~   86 (102)
                      .+|+.
T Consensus        75 ~~~~~   79 (104)
T PF13426_consen   75 TFWVE   79 (104)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            98875

...

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

Probab=99.21  E-value=2.3e-10  Score=65.73  Aligned_cols=80  Identities=21%  Similarity=0.282  Sum_probs=57.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEE-EEEEEecC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKL-EVIFYKKN   79 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~-e~~~~~~~   79 (102)
                      ++++++++|.+    |+|+++|+++++++|++.++++|+  +...+..+.........+...+..+..... ......++
T Consensus        10 ~~~~i~~~d~~----g~I~~~N~a~~~l~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (113)
T PF00989_consen   10 SPDGIFVIDED----GRILYVNQAAEELLGYSREELIGK--SLFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRD   83 (113)
T ss_dssp             SSSEEEEEETT----SBEEEECHHHHHHHSS-HHHHTTS--BGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETT
T ss_pred             CCceEEEEeCc----CeEEEECHHHHHHHccCHHHHcCC--cHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecC
Confidence            46799999987    999999999999999999999999  554444443333466677777776665443 44444458


Q ss_pred             CCeeeec
Q psy8548          80 GYHEEEE   86 (102)
Q Consensus        80 G~~~~~~   86 (102)
                      |..+|+.
T Consensus        84 g~~~~~~   90 (113)
T PF00989_consen   84 GRPRWVE   90 (113)
T ss_dssp             SCEEEEE
T ss_pred             CcEEEEE
Confidence            8877764

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=99.03  E-value=3.7e-09  Score=75.27  Aligned_cols=81  Identities=26%  Similarity=0.611  Sum_probs=64.9

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      ..+|++.|....+ ++|+|+|++|++++||+.++++|+  +...+.++.........++..+..+..+..++...+++|+
T Consensus        40 ~~~i~v~d~~~~~-g~i~~~N~a~~~~~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~  116 (540)
T PRK13557         40 RMPMIVTDPNQPD-NPIVFANRAFLEMTGYAAEEIIGN--NCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGS  116 (540)
T ss_pred             cCcEEEEcCCCCC-CCEEEEcHHHHHHhCCCHHHhcCC--ChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEEeCCCC
Confidence            3578888874334 899999999999999999999998  6666666666666677777788888778888888888998


Q ss_pred             eeee
Q psy8548          82 HEEE   85 (102)
Q Consensus        82 ~~~~   85 (102)
                      .+|+
T Consensus       117 ~~~~  120 (540)
T PRK13557        117 SFWN  120 (540)
T ss_pred             EEEE
Confidence            8775

>PRK10060 RNase II stability modulator; Provisional

Probab=98.93  E-value=8e-09  Score=76.44  Aligned_cols=79  Identities=14%  Similarity=0.139  Sum_probs=62.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCc-ccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCAC-KFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~-~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      +++|+++|.+    |+|+++|++|++++||+.++++|+  +. .++.++.........+...+..+..|..+...++++|
T Consensus       121 ~~gI~i~D~~----g~I~~~N~a~~~l~Gy~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G  194 (663)
T PRK10060        121 NSVIVILDSR----GNIQRFNRLCEEYTGLKEHDVIGQ--SVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKTRKG  194 (663)
T ss_pred             CceEEEEeCC----CCEEEEcHHHHHHHCcCHHHHcCC--CHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCC
Confidence            5789999998    899999999999999999999998  54 3343443334445566677778888999999999999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ..+|+.
T Consensus       195 ~~~~~~  200 (663)
T PRK10060        195 QRLFLF  200 (663)
T ss_pred             CEEEEE
Confidence            877653

>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=98.92  E-value=2e-08  Score=57.27  Aligned_cols=78  Identities=19%  Similarity=0.284  Sum_probs=59.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++.+++++|.+    ++++++|+++++++|++.++++|+  ....+.++.........+.+.+..+.....+..... +|
T Consensus         4 ~p~~i~v~D~~----~~i~~~N~~~~~~~~~~~~~~~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~   76 (110)
T PF08448_consen    4 SPDGIFVIDPD----GRIVYANQAAAELFGVSPEELIGR--SLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG   76 (110)
T ss_dssp             CSSEEEEEETT----SBEEEE-HHHHHHHTSTHHHHTTS--BHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred             CCceeEEECCC----CEEEEEHHHHHHHhCCCHHHHhhc--cchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence            46789999998    999999999999999999999999  655566655566677777788877777666555544 66


Q ss_pred             Ceeee
Q psy8548          81 YHEEE   85 (102)
Q Consensus        81 ~~~~~   85 (102)
                      ..+|.
T Consensus        77 ~~~~~   81 (110)
T PF08448_consen   77 EERWF   81 (110)
T ss_dssp             CEEEE
T ss_pred             CcEEE
Confidence            55554

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.

>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=98.91  E-value=7.3e-09  Score=57.85  Aligned_cols=70  Identities=27%  Similarity=0.356  Sum_probs=50.9

Q ss_pred             EEEecHHHHHhhCCChhhhcCCCCC--cccccCCCCCHHHHHHHHH-HHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548          18 IVYCSDGFCELSGFARAQIMQKGCA--CKFLYGPDTSEEHKTQIEK-ALESKTELKLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        18 i~~~N~~~~~i~G~~~~ei~g~~~~--~~~l~~~~~~~~~~~~i~~-~l~~~~~~~~e~~~~~~~G~~~~~~~~   88 (102)
                      |+++|+.|++++||+.+++ +.+..  ...+..|++.....+.+.. ....+..+..++++++++|+.+|++.-
T Consensus         1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~   73 (91)
T PF08447_consen    1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVR   73 (91)
T ss_dssp             -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEE
T ss_pred             CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEE
Confidence            5899999999999999999 54101  2233456667777777777 677788999999999999999998753

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.

>PRK13559 hypothetical protein; Provisional

Probab=98.88  E-value=3.3e-08  Score=67.78  Aligned_cols=81  Identities=25%  Similarity=0.531  Sum_probs=62.8

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      ..+|+++|..... +.++++|++|++++||+.++++|+  ....+..+.........+...+..+..+..+...++++|.
T Consensus        53 ~~~i~i~D~~~~~-g~i~~~N~a~~~l~G~~~~e~iG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~  129 (361)
T PRK13559         53 RMAMCITDPHQPD-LPIVLANQAFLDLTGYAAEEVVGR--NCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGE  129 (361)
T ss_pred             CCcEEEecCCCCC-CcEEEEchHHHHHhCCCHHHHcCC--ChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEEcCCCC
Confidence            4578899975333 789999999999999999999998  6555655555556666677777777777788887888888


Q ss_pred             eeee
Q psy8548          82 HEEE   85 (102)
Q Consensus        82 ~~~~   85 (102)
                      .+|+
T Consensus       130 ~~~~  133 (361)
T PRK13559        130 PFWN  133 (361)
T ss_pred             EEEE
Confidence            7765

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

Probab=98.76  E-value=3.5e-07  Score=48.03  Aligned_cols=80  Identities=20%  Similarity=0.284  Sum_probs=56.0

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++.+++++|..    +.++++|++++.++|++..+++|+  ....+..+.........+......+..+..+......+|
T Consensus         1 ~~~~i~~~d~~----~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (103)
T cd00130           1 LPDGVIVLDLD----GRILYANPAAEQLLGYSPEELIGK--SLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDG   74 (103)
T ss_pred             CCceEEEECCC----CcEEEECHHHHHHhCCCHHHHcCc--cHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCC
Confidence            35688899987    899999999999999999999987  543344444444444444444544555666777777777


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ..+|+.
T Consensus        75 ~~~~~~   80 (103)
T cd00130          75 SVIWVL   80 (103)
T ss_pred             CEEEEE
Confidence            766643

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.

>PRK13560 hypothetical protein; Provisional

Probab=98.71  E-value=1.4e-07  Score=70.10  Aligned_cols=79  Identities=14%  Similarity=0.254  Sum_probs=58.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      ++++++.|.+    ++++++|++++.++||+.++++|+  +...+.++.............+..+.....+....+++|+
T Consensus       214 ~~~i~~~d~~----g~i~~~N~~~~~~~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~  287 (807)
T PRK13560        214 ADPAFWKDED----AKVFGCNDAACLACGFRREEIIGM--SIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKDGR  287 (807)
T ss_pred             CCeEEEEcCC----CCEEEEhHHHHHHhCCCHHHHcCC--cchhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCCCC
Confidence            5688899987    899999999999999999999998  5554554433333323334445566666778888899999


Q ss_pred             eeeec
Q psy8548          82 HEEEE   86 (102)
Q Consensus        82 ~~~~~   86 (102)
                      .+|++
T Consensus       288 ~~~~~  292 (807)
T PRK13560        288 TRPVD  292 (807)
T ss_pred             EEEEE
Confidence            88553

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=98.63  E-value=1.2e-07  Score=66.59  Aligned_cols=78  Identities=17%  Similarity=0.251  Sum_probs=60.1

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +.++++.|.+    ++++++|++++.++|++.++++|+  ....+..+.........+...+..+..+..++...+++|+
T Consensus        14 ~~~i~~~d~~----g~~~~~N~~~~~~~G~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~   87 (494)
T TIGR02938        14 PLAISITDLK----ANILYANDAFTRITGYTKEEIIGK--NESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRRKDGE   87 (494)
T ss_pred             CceEEEECCC----CcEEEEchhheeecCCCHHHHhCC--CchhhcCCCCCHHHHHHHHHHHHhCCcccceeeccCCCcc
Confidence            4678899987    899999999999999999999998  5554554445555666666777777777777777777777


Q ss_pred             eeee
Q psy8548          82 HEEE   85 (102)
Q Consensus        82 ~~~~   85 (102)
                      .+|+
T Consensus        88 ~~~~   91 (494)
T TIGR02938        88 LYLA   91 (494)
T ss_pred             chhh
Confidence            6664

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.

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=98.63  E-value=2.4e-07  Score=65.46  Aligned_cols=78  Identities=13%  Similarity=0.106  Sum_probs=52.5

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCC-hhhhcCCCCCcccccCCCCCHHHHHHHHHHHH-hCCcEEEEEEEEec
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFA-RAQIMQKGCACKFLYGPDTSEEHKTQIEKALE-SKTELKLEVIFYKK   78 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~-~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~-~~~~~~~e~~~~~~   78 (102)
                      +.++|+++|.+    |+|+++|++|++++||+ .++++|+  +...+..+.. .. ...+...+. .+.....+....++
T Consensus       261 ~~d~I~v~D~~----G~I~~~N~a~~~l~G~~~~~~l~G~--~~~~~~~~~~-~~-~~~~~~~~~~~g~~~~~~~~~~~~  332 (442)
T TIGR02040       261 APDAIVFSDAD----GTIRGANEAFLELTDSSSLEAVRGR--TLDRWLGRGG-VD-LRVLLSNVRRTGQVRLYATTLTGE  332 (442)
T ss_pred             CCceEEEEcCC----CcEEehhHHHHHHhCCCChHHHcCC--CHHHHhCCCc-cc-HHHHHHHHhhcCceEEEEEEEEcC
Confidence            35789999987    89999999999999997 5789998  5433332211 11 122233333 33333456667789


Q ss_pred             CCCeeeec
Q psy8548          79 NGYHEEEE   86 (102)
Q Consensus        79 ~G~~~~~~   86 (102)
                      +|+.+|++
T Consensus       333 ~G~~~~ve  340 (442)
T TIGR02040       333 FGAQTEVE  340 (442)
T ss_pred             CCCEEEEE
Confidence            99988885

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).

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.57  E-value=8.6e-07  Score=65.49  Aligned_cols=81  Identities=25%  Similarity=0.599  Sum_probs=63.0

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH   82 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~   82 (102)
                      .++++.|...+. +.++++|++|++++||+.++++|+  ....+.++.........+...+..+..+..+++.++++|..
T Consensus       159 ~gi~~~d~~~~d-g~i~~~N~~~~~l~G~~~eel~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~  235 (665)
T PRK13558        159 VGITIADATLPD-EPLIYINDAFERITGYSPDEVLGR--NCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGST  235 (665)
T ss_pred             ccEEEEcCCCCC-CcEEEEcHHHHHHhCcCHHHHcCC--CHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEECCCCCE
Confidence            467777753334 899999999999999999999998  65555555555555566677777788888898999999988


Q ss_pred             eeec
Q psy8548          83 EEEE   86 (102)
Q Consensus        83 ~~~~   86 (102)
                      +|+.
T Consensus       236 ~~~~  239 (665)
T PRK13558        236 FWNQ  239 (665)
T ss_pred             EEEE
Confidence            8763

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.57  E-value=3.6e-07  Score=68.51  Aligned_cols=79  Identities=18%  Similarity=0.168  Sum_probs=57.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|++.|.+    |+++++|++++.++|++.++++|+  ....+.++.............+..+..+..+....+++|
T Consensus       164 ~~~~i~~~D~~----g~i~~~N~a~~~l~G~~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G  237 (779)
T PRK11091        164 SPDLVYYRNED----GEFSGCNRAMELLTGKSEKQLIGL--TPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDG  237 (779)
T ss_pred             CcceEEEECCC----CcEEeEcHHHHHHhCcCHHHHcCC--ChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCC
Confidence            46789999987    999999999999999999999998  544444443333344444455566667777777777777


Q ss_pred             Ceeee
Q psy8548          81 YHEEE   85 (102)
Q Consensus        81 ~~~~~   85 (102)
                      ..+|+
T Consensus       238 ~~~~~  242 (779)
T PRK11091        238 RKACF  242 (779)
T ss_pred             CEEEE
Confidence            76554

>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=98.55  E-value=1.8e-06  Score=50.70  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=57.8

Q ss_pred             EEeCCCCCCCCEEEecHH-HHHhhCCChhhhcCCCCCcccccCCCCCHH-HHHHHHHHHHhCCcEEEEEEEEecCCCeee
Q psy8548           7 LGNAQVPSLYPIVYCSDG-FCELSGFARAQIMQKGCACKFLYGPDTSEE-HKTQIEKALESKTELKLEVIFYKKNGYHEE   84 (102)
Q Consensus         7 i~d~~~~~~~~i~~~N~~-~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~-~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~   84 (102)
                      -.+.+    +.|+++.+. ...++||..++++|+  ....+.++.+-.. ..+.....+..|.....-+++..++|..+|
T Consensus         7 rhs~d----gki~~~d~~~v~~~lgy~~~eLvG~--s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vw   80 (111)
T PF14598_consen    7 RHSLD----GKITYVDSRAVSSLLGYLPEELVGR--SIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVW   80 (111)
T ss_dssp             EEETT----SBEEEEETTHHHHHHSS-HHHHTTS--BGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEE
T ss_pred             EECCC----cEEEEEcCccChhhcCCCcHHHcCC--chHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEE
Confidence            44555    899999999 699999999999999  4444444545443 556777788888887788999999999999


Q ss_pred             ecch
Q psy8548          85 EEEE   88 (102)
Q Consensus        85 ~~~~   88 (102)
                      +.+.
T Consensus        81 vqt~   84 (111)
T PF14598_consen   81 VQTK   84 (111)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9764

...

>KOG0501|consensus

Probab=98.54  E-value=2.2e-07  Score=67.62  Aligned_cols=83  Identities=42%  Similarity=0.835  Sum_probs=73.0

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH   82 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~   82 (102)
                      ..+++.+++.-+ ..|+|+|+.||++.||.+.+++.+++.+.+.++...+......+++.+.+.+.-++|+..+.++..+
T Consensus        28 tsFlL~NAQiVD-~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TP  106 (971)
T KOG0501|consen   28 TSFLLANAQIVD-WPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTP  106 (971)
T ss_pred             cceeeccceeec-cceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCc
Confidence            356777776666 8999999999999999999999996667888999889999999999999998888999999999999


Q ss_pred             eeec
Q psy8548          83 EEEE   86 (102)
Q Consensus        83 ~~~~   86 (102)
                      +|.-
T Consensus       107 vW~~  110 (971)
T KOG0501|consen  107 VWLL  110 (971)
T ss_pred             eEEE
Confidence            8864

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=98.39  E-value=3.3e-07  Score=64.77  Aligned_cols=78  Identities=9%  Similarity=0.038  Sum_probs=51.3

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCC-cEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKT-ELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~-~~~~e~~~~~~~G   80 (102)
                      +++++++|.+    |+|+++|++++.++||+.++++|+  +...+.++.........+...+..+. .+..+.....++|
T Consensus         6 ~d~~~~~d~~----g~i~~~n~~~~~~~g~~~~el~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g   79 (442)
T TIGR02040         6 ADVTLLLDAE----GVVREVAANPHHPSFEQLSEWEGR--RWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPSS   79 (442)
T ss_pred             CcEEEEECCC----CcEEEEEECCCcccccccccCCCC--cHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCCC
Confidence            5789999988    999999999999999999999999  65444444433333344444444433 3444444444455


Q ss_pred             Ceeee
Q psy8548          81 YHEEE   85 (102)
Q Consensus        81 ~~~~~   85 (102)
                      ..+|+
T Consensus        80 ~~~~~   84 (442)
T TIGR02040        80 FELPM   84 (442)
T ss_pred             CccCe
Confidence            44443

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).

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

Probab=98.38  E-value=2.6e-06  Score=58.04  Aligned_cols=76  Identities=9%  Similarity=0.074  Sum_probs=49.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++++++|.+    ++|+++|+++++++|++..+++|+  +...+.+...  .....+...+..+..+.........+|
T Consensus        16 ~~~gi~~~d~~----~~i~~~N~a~~~~~g~~~~~~~g~--~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~g   87 (348)
T PRK11073         16 LINSILLLDDD----LAIHYANPAAQQLLAQSSRKLFGT--PLPELLSYFS--LNIELMRESLQAGQGFTDNEVTLVIDG   87 (348)
T ss_pred             CcCeEEEECCC----CeEeeEcHHHHHHhCCCHHHHcCC--CHHHHcCcch--hhHHHHHHHHHcCCcccccceEEEECC
Confidence            46789999987    899999999999999999999998  6554443321  122333444544444333333334466


Q ss_pred             Ceee
Q psy8548          81 YHEE   84 (102)
Q Consensus        81 ~~~~   84 (102)
                      +.+|
T Consensus        88 ~~~~   91 (348)
T PRK11073         88 RSHI   91 (348)
T ss_pred             ceEE
Confidence            5555

>TIGR00229 sensory_box PAS domain S-box

Probab=98.36  E-value=8.2e-06  Score=44.60  Aligned_cols=78  Identities=19%  Similarity=0.286  Sum_probs=48.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-CcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~~~~e~~~~~~~G   80 (102)
                      +.+++++|..    +.++++|++++.++|++..+++|+  ....+.++.........+...+... ............+|
T Consensus        13 ~~~~~~~d~~----~~i~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (124)
T TIGR00229        13 PDAIIVIDLE----GNILYVNPAFEEIFGYSAEELIGR--NVLELIPEEDREEVRERIERLLEGEREPVSEERRVRRKDG   86 (124)
T ss_pred             CceEEEEcCC----CcEEEEchHHHHHhCCChHHhcCc--chhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeEcCCC
Confidence            4578888887    899999999999999999999987  4433333333333333344444322 22333444445566


Q ss_pred             Ceeee
Q psy8548          81 YHEEE   85 (102)
Q Consensus        81 ~~~~~   85 (102)
                      ..+|+
T Consensus        87 ~~~~~   91 (124)
T TIGR00229        87 SEIWV   91 (124)
T ss_pred             CEEEE
Confidence            65554

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.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=98.34  E-value=2.9e-06  Score=63.50  Aligned_cols=79  Identities=14%  Similarity=0.254  Sum_probs=59.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcc-cccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACK-FLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~-~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      +.+++++|.+    ++++++|+++++++|++.++++|+  ... ++..+.........+...+..+..+..+++..+++|
T Consensus       146 ~~~i~~~d~~----g~i~~~N~~~~~l~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG  219 (799)
T PRK11359        146 DRPVIVLDPE----RRIVQCNRAFTEMFGYCISEASGM--QPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTG  219 (799)
T ss_pred             CCcEEEEcCC----CcEEEEChhhHhhhCCCHHHHCCC--ChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCC
Confidence            4578888887    899999999999999999999998  433 344444455555556666666666777777888888


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|+.
T Consensus       220 ~~~~~~  225 (799)
T PRK11359        220 EKIWIK  225 (799)
T ss_pred             CEEEEE
Confidence            877763

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=98.34  E-value=1.9e-06  Score=64.47  Aligned_cols=79  Identities=19%  Similarity=0.218  Sum_probs=53.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC----CcEEEEEEEEe
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK----TELKLEVIFYK   77 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~----~~~~~e~~~~~   77 (102)
                      ..+++++|.+    ++++++|+++++++||+.++++|+  +...+.++.........+......+    ..+..+.+.++
T Consensus        22 ~~~i~~~d~~----g~i~~~N~~~~~l~G~s~eeliG~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   95 (799)
T PRK11359         22 MMGAVLINEN----DEVLFFNPAAEKLWGYKREEVIGN--NIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEK   95 (799)
T ss_pred             cCcEEEEcCC----CeEEEEcHHHHHHhCCCHHHHcCC--CHHHhcCccccccchHHHhhhhccCCccccccceeeEEec
Confidence            3567888887    899999999999999999999998  5444444433322222333333322    23445777888


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      ++|+.+|+.
T Consensus        96 ~dG~~~~v~  104 (799)
T PRK11359         96 KDGSKIWTR  104 (799)
T ss_pred             CCcCEEEEE
Confidence            899877764

>PRK09776 putative diguanylate cyclase; Provisional

Probab=98.31  E-value=4.4e-06  Score=64.48  Aligned_cols=79  Identities=15%  Similarity=0.287  Sum_probs=57.1

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-CcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~~~~e~~~~~~~G   80 (102)
                      ..+|++.|.+    |+++++|+++++++||+.++++|+  ....+..+.........+...+... ..+..+.+..+++|
T Consensus       293 ~~~i~~~d~d----G~i~~~N~~~~~l~G~~~~el~g~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG  366 (1092)
T PRK09776        293 AIGMALVGTE----GQWLQVNKALCQFLGYSQEELRGL--TFQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYYRRDG  366 (1092)
T ss_pred             CceEEEEcCC----CcEEehhHHHHHHhCCCHHHHccC--CceeccCcchhHhHHHHHHHHHcCCccceeeeeEEEcCCC
Confidence            3578889987    899999999999999999999998  5444444444333434444333322 34677888889999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|+.
T Consensus       367 ~~~~~~  372 (1092)
T PRK09776        367 EVVWAL  372 (1092)
T ss_pred             CEEEEE
Confidence            888764

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=98.00  E-value=3e-05  Score=51.94  Aligned_cols=40  Identities=15%  Similarity=0.206  Sum_probs=34.6

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFL   46 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l   46 (102)
                      +..+|+++|.+    ++++++|++|++++|++.++.+|+  +...+
T Consensus        15 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~   54 (333)
T TIGR02966        15 LPDAVVVLDEE----GQIEWCNPAAERLLGLRWPDDLGQ--RITNL   54 (333)
T ss_pred             CcCcEEEECCC----CcEEEEcHHHHHHhCCChHHHcCC--cHHHH
Confidence            45789999998    899999999999999999999998  54433

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).

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

Probab=97.98  E-value=2.1e-05  Score=41.16  Aligned_cols=31  Identities=19%  Similarity=0.369  Sum_probs=24.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      ++.+|+++| .    ++|+++|+++++++||+   ..|+
T Consensus        10 ~~~~i~i~d-~----~~i~~~N~~~~~l~g~~---~~~~   40 (64)
T PF13188_consen   10 SPDGILIID-G----GRIIYVNPAFEELFGYS---LEGE   40 (64)
T ss_dssp             SSSEEEEEE-T----SBEEEE-HHHHHHHCS----HTCC
T ss_pred             CccceEEEE-C----CChHHhhHHHHHHhCCC---CCCC
Confidence            467899999 7    79999999999999998   4554

>KOG1229|consensus

Probab=97.96  E-value=1.5e-06  Score=61.73  Aligned_cols=74  Identities=16%  Similarity=0.188  Sum_probs=58.0

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCC-CHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDT-SEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~-~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      ++|=|+|.+    ..|+|+||+|+.|+|+-+.+++|+  +...++..+. ....+..+...++.|..|++++..+++.|.
T Consensus       168 eAiEI~~dd----hViQYVNpAfE~mmG~hkgEliGk--e~adlpkkdknradlldtintcikkgke~qG~~~aRRksgd  241 (775)
T KOG1229|consen  168 EAIEICDDD----HVIQYVNPAFENMMGCHKGELIGK--EEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEARRKSGD  241 (775)
T ss_pred             hhheeccch----hHHHHhcHHHHhhhcchhhhhcCC--chhhccccccchhhhhhhhhHhhhcCccccchHHHhhccCC
Confidence            345566665    788999999999999999999999  6555554433 446777888889999999998888887775


Q ss_pred             e
Q psy8548          82 H   82 (102)
Q Consensus        82 ~   82 (102)
                      .
T Consensus       242 S  242 (775)
T KOG1229|consen  242 S  242 (775)
T ss_pred             c
Confidence            3

>PF12860 PAS_7: PAS fold

Probab=97.90  E-value=0.00015  Score=42.24  Aligned_cols=35  Identities=14%  Similarity=0.243  Sum_probs=31.6

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhh-cCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQI-MQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei-~g~   39 (102)
                      |++||++.|.+    ++++++|++|..++|++...+ .|.
T Consensus         4 l~~Gv~v~D~~----~rl~~~N~~~~~l~~~~~~~~~~G~   39 (115)
T PF12860_consen    4 LPQGVAVFDSD----GRLVFWNQRFRELFGLPPEMLRPGA   39 (115)
T ss_pred             cCceEEEEcCC----CeEEeEcHHHHHHhCCCHHHhcCCC
Confidence            67899999998    899999999999999999887 555

>PRK09776 putative diguanylate cyclase; Provisional

Probab=97.79  E-value=0.00014  Score=56.42  Aligned_cols=79  Identities=10%  Similarity=0.151  Sum_probs=51.1

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCC--CCCHHHHHHHHHHHHhCCc--EEEEEEEEe
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGP--DTSEEHKTQIEKALESKTE--LKLEVIFYK   77 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~--~~~~~~~~~i~~~l~~~~~--~~~e~~~~~   77 (102)
                      +++|+++|.+    ++++++|+++++++||+.++++|+  +...+...  .........+.........  +..+....+
T Consensus       546 ~~~i~~~D~~----g~i~~~N~a~~~l~G~~~~e~iG~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  619 (1092)
T PRK09776        546 GEAVVCTDMA----MKVTFMNPVAEKMTGWTQEEALGV--PLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHC  619 (1092)
T ss_pred             ccEEEEECCC----CeEEEEcHHHHHHhCCCHHHHcCC--CHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEe
Confidence            4678889987    899999999999999999999998  53333221  1111222224444433333  445666677


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      ++|..+|+.
T Consensus       620 ~~G~~~~~~  628 (1092)
T PRK09776        620 RSGGSYDVH  628 (1092)
T ss_pred             CCCcEEEEE
Confidence            788776653

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=97.30  E-value=0.00068  Score=49.46  Aligned_cols=42  Identities=10%  Similarity=0.162  Sum_probs=36.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG   48 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~   48 (102)
                      |.++|+++|.+    |+|+++|+++++++|++.++++|+  +...+.+
T Consensus        89 m~eGVi~vD~~----G~I~~iN~aA~~Llg~~~eel~Gk--~i~eli~  130 (520)
T PRK10820         89 LPEPVLSIDMK----GKVELANPASCQLFGQSEEKLRNH--TAAQLIN  130 (520)
T ss_pred             CCCcEEEECCC----CeeeHhHHHHHHHHCcCHHHHCCC--cHHHHcC
Confidence            67899999998    999999999999999999999998  6554443

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=97.30  E-value=0.0023  Score=46.11  Aligned_cols=58  Identities=16%  Similarity=0.236  Sum_probs=41.5

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK   66 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~   66 (102)
                      ++++++++|.+    ++++++|+++++++|++.++++|+  +...+.++.  ......+...+..+
T Consensus       271 ~~~~i~~~d~~----g~i~~~N~~~~~l~g~~~~~~~g~--~~~~~~~~~--~~~~~~~~~~~~~~  328 (607)
T PRK11360        271 IADGVIAIDRQ----GKITTMNPAAEVITGLQRHELVGK--PYSELFPPN--TPFASPLLDTLEHG  328 (607)
T ss_pred             ccCeEEEEcCC----CCEEEECHHHHHHhCCChHHhcCC--cHHHHcCCc--hhHHHHHHHHHhcC
Confidence            35688999987    899999999999999999999998  655454432  22233444444443

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

Probab=97.22  E-value=0.0012  Score=37.74  Aligned_cols=74  Identities=14%  Similarity=0.180  Sum_probs=42.0

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      |+.+++++|.+    ++|++.|++..+++++.... +|+  +...+.++.. ......+.+.+..+..-..+... ..+|
T Consensus         8 ~~~~i~~vD~~----~~I~~~n~~a~~~f~~~~~~-iGr--~l~~~~~~~~-~~~l~~~i~~~~~~~~~~~~~~~-~~~~   78 (106)
T PF13596_consen    8 MPIGIIFVDRN----LRIRYFNPAAARLFNLSPSD-IGR--PLFDIHPPLS-YPNLKKIIEQVRSGKEEEFEIVI-PNGG   78 (106)
T ss_dssp             SSSEEEEEETT----SBEEEE-SCGC-SS---GGG-TTS--BCCCSS-HHH-HHHHHHHHHHHHTTSBSEEEEEE-EETT
T ss_pred             CCCCEEEEcCC----CeEEEeChhHhhhcCCChHH-CCC--CHHHcCCccc-hHHHHHHHHHHHcCCCceEEEEe-cCCC
Confidence            56789999998    89999999999999976544 788  6555554422 22333444555556543333333 2455


Q ss_pred             Cee
Q psy8548          81 YHE   83 (102)
Q Consensus        81 ~~~   83 (102)
                      +.+
T Consensus        79 ~~~   81 (106)
T PF13596_consen   79 RWY   81 (106)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            543

>PRK11006 phoR phosphate regulon sensor protein; Provisional

Probab=97.19  E-value=0.0025  Score=45.00  Aligned_cols=35  Identities=20%  Similarity=0.277  Sum_probs=32.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      ++++|+++|.+    |+|+++|+++++++|++.+++.|+
T Consensus       107 ~~~~i~~~d~~----g~i~~~N~~a~~l~g~~~~~~~g~  141 (430)
T PRK11006        107 LPDAVVLTTEE----GNIFWCNGLAQQLLGFRWPEDNGQ  141 (430)
T ss_pred             CCCeEEEEcCC----CceeHHHHHHHHHhCCCChHhCCC
Confidence            46789999987    899999999999999999999988

>smart00091 PAS PAS domain

Probab=97.18  E-value=0.0026  Score=30.17  Aligned_cols=34  Identities=18%  Similarity=0.311  Sum_probs=29.0

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      +.++++++..    +.++++|+.+..++|++..++.+.
T Consensus        11 ~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~   44 (67)
T smart00091       11 PDGIFVLDLD----GRILYANPAAEELLGYSPEELIGK   44 (67)
T ss_pred             CceEEEEcCC----CeEEEECHHHHHHhCCCHHHHcCC
Confidence            4567778876    899999999999999999888876

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).

>PRK13560 hypothetical protein; Provisional

Probab=97.06  E-value=0.0025  Score=47.77  Aligned_cols=34  Identities=18%  Similarity=0.222  Sum_probs=29.5

Q ss_pred             CceEEEEeCCCCCCCCEEEe-cHHHHHhhCCChhhhcCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYC-SDGFCELSGFARAQIMQK   39 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~-N~~~~~i~G~~~~ei~g~   39 (102)
                      +.+|+++|.+    +.++++ |+++++++||+.++++|+
T Consensus       342 ~~~i~~~d~~----g~i~~~nn~~~~~~~G~~~~e~~g~  376 (807)
T PRK13560        342 PIAAIGLDAD----GNICFVNNNAAERMLGWSAAEVMGK  376 (807)
T ss_pred             cccEEEEcCC----CCEEEecCHHHHHHhCCCHHHHcCC
Confidence            4678899987    899987 678888999999999998

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

Probab=97.02  E-value=0.012  Score=34.65  Aligned_cols=79  Identities=16%  Similarity=0.141  Sum_probs=48.2

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHH-HHHH-HHHHHHhCCcEEEEEEEEecC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEE-HKTQ-IEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~-~~~~-i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      ..++++.|..    +.++++|++++.++|++..+.++.  ....+........ .... ..........+..+......+
T Consensus       122 ~~~~~~~d~~----~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (232)
T COG2202         122 PDGIWVLDED----GRILYANPAAEELLGYSPEEELGR--GLSDLIHPEDEERRELELARALAEGRGGPLEIEYRVRRKD  195 (232)
T ss_pred             CceEEEEeCC----CCEEEeCHHHHHHhCCChHHhcCC--ChhheEecCCCchhhHHHHHHhhccCCCCcceEEEEEecC
Confidence            3567788876    899999999999999998877766  3332222211111 1111 111222334466777878888


Q ss_pred             CCe-eeec
Q psy8548          80 GYH-EEEE   86 (102)
Q Consensus        80 G~~-~~~~   86 (102)
                      |.. .+..
T Consensus       196 g~~~~~~~  203 (232)
T COG2202         196 GERVRWIL  203 (232)
T ss_pred             CCEEEEEE
Confidence            885 4443

>KOG3558|consensus

Probab=96.96  E-value=0.00076  Score=50.22  Aligned_cols=71  Identities=15%  Similarity=0.221  Sum_probs=57.1

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~~   88 (102)
                      -+|+||.+.+..++||..++++|+  -+-.+.+..+...+.+.....+..|...++-++...++|-.+|+.+.
T Consensus       284 mkityCedRisdlm~y~PeeLvGr--S~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTq  354 (768)
T KOG3558|consen  284 MKITYCEDRISDLMDYEPEELVGR--SCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQ  354 (768)
T ss_pred             eeEEEEchhHHHHhcCCHHHhhch--hHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEee
Confidence            799999999999999999999999  44334444455556666677788888888888888889998898875

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=96.91  E-value=0.005  Score=45.94  Aligned_cols=41  Identities=12%  Similarity=0.094  Sum_probs=34.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLY   47 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~   47 (102)
                      ++++|+++|.+    |+|+++|+++++++|++..+++|+  +...+.
T Consensus       212 ~~~gVl~vD~~----G~I~~~N~aa~~llg~s~~~l~G~--~i~~l~  252 (638)
T PRK11388        212 MDDGVIAWDEQ----GNLQFLNAQAARLLRLDATASQGR--AITELL  252 (638)
T ss_pred             cCCcEEEECCC----CeEehhhHHHHHHhCcCHHHHCCC--cHHHHh
Confidence            35789999998    999999999999999999999998  544333

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins

Probab=96.55  E-value=0.021  Score=35.25  Aligned_cols=80  Identities=8%  Similarity=0.071  Sum_probs=48.2

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      +|+-.+.. ++ -.++|.|++...|++++-+++.+-  +.+.-..+.......+.+.+...+|-.....=....+.|+++
T Consensus        43 ailsh~~~-~d-P~f~yaN~aaL~l~e~~w~el~~l--Psr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRiss~Grrf  118 (148)
T PF08670_consen   43 AILSHGTK-AD-PIFIYANQAALDLFETTWDELVGL--PSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRISSTGRRF  118 (148)
T ss_pred             EEEEcCCC-CC-CEEEehhHHHHHHhcCCHHHHhcC--cHhhccChhhHHHHHHHHHHHHHhCCccCCCeEEEcCCCCeE
Confidence            34444433 23 689999999999999999999977  666444443344444444444444421111113346778887


Q ss_pred             eecc
Q psy8548          84 EEEE   87 (102)
Q Consensus        84 ~~~~   87 (102)
                      +++.
T Consensus       119 ~ie~  122 (148)
T PF08670_consen  119 RIER  122 (148)
T ss_pred             EEec
Confidence            7654

>TIGR02373 photo_yellow photoactive yellow protein

Probab=96.07  E-value=0.07  Score=31.95  Aligned_cols=59  Identities=10%  Similarity=0.026  Sum_probs=43.0

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCC-CHHHHHHHHHHHHhC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDT-SEEHKTQIEKALESK   66 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~-~~~~~~~i~~~l~~~   66 (102)
                      +-|++-+|.+    |.|+..|.+=..++|++++.++|+  +...=..|+. ...+...+...+.++
T Consensus        26 pFGvI~lD~~----G~V~~YN~aE~~~sg~~p~~vlGr--~FF~eVAPC~~~~~f~gRF~~g~~~g   85 (124)
T TIGR02373        26 PFGAIQLDGS----GVILRYNAAEGRITGRDPERVIGR--NFFKEVAPCTDIPEFSGRFMEGVASG   85 (124)
T ss_pred             CcceEEECCC----CEEEEEecchhhhcCCChhhhhch--hhhhhcccccCCHHHHHHHHhhhhcC
Confidence            4578888887    999999999999999999999999  5332233444 344555666655555

Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional

Probab=95.67  E-value=0.014  Score=42.30  Aligned_cols=35  Identities=11%  Similarity=0.115  Sum_probs=30.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCCh--hhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFAR--AQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~--~ei~g~   39 (102)
                      |.++++++|.+    |+|+++|+++++++|++.  .+++|+
T Consensus       231 ~~egii~~D~~----g~I~~~N~~a~~ll~~~~~~~~~~g~  267 (545)
T PRK15053        231 VYEGLIAVDPH----GYITAINRNARKMLGLSSPGRQWLGK  267 (545)
T ss_pred             hCceEEEECCC----CeEEeecHHHHHHhCCCCcchhhcCC
Confidence            46899999998    999999999999999865  468887

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

Probab=95.05  E-value=0.072  Score=39.27  Aligned_cols=40  Identities=13%  Similarity=0.342  Sum_probs=34.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFL   46 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l   46 (102)
                      +.++++++|..    |+++++|++...++|.+.++++|+  +...+
T Consensus       126 ~~~~l~vvD~~----G~~i~~N~~~~~~~gl~~e~~~gk--~~~~v  165 (560)
T COG3829         126 IDDGLLVVDED----GIIIYYNKAYAKLLGLSPEEVLGK--HLLDV  165 (560)
T ss_pred             ccCceEEEcCC----CcEEEEcHHHHHHhCCCHHHHcCC--cHHHH
Confidence            35788999998    999999999999999999999999  64444

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]

Probab=94.92  E-value=0.14  Score=35.51  Aligned_cols=59  Identities=12%  Similarity=0.116  Sum_probs=39.6

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcE
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTEL   69 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~   69 (102)
                      ..+++.|.+    +.|.|+|++++.++|.+...+.+.  ....+.+.  .......+.+...++..+
T Consensus        18 ~pVl~vd~~----~~i~yaN~aAe~~~~~Sa~~L~~~--~l~~l~~~--gs~ll~ll~q~~~~~~~~   76 (363)
T COG3852          18 NPVLLVDDE----LAIHYANPAAEQLLAVSARRLAGT--RLSELLPF--GSLLLSLLDQVLERGQPV   76 (363)
T ss_pred             CceEEEcCC----CcEEecCHHHHHHHHHHHHHHhcC--ChHHHcCC--CcHHHHHHHHHHHhcCCc
Confidence            356777776    899999999999999999998887  43333332  123344455555555443

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=94.44  E-value=0.049  Score=39.22  Aligned_cols=35  Identities=6%  Similarity=0.121  Sum_probs=28.3

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCCh---hhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFAR---AQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~---~ei~g~   39 (102)
                      |.++|+++|.+    ++|+++|+++++++|++.   .+.+|+
T Consensus       230 ~~~gIi~~D~~----g~I~~~N~~a~~llg~~~~~~~~~~~~  267 (542)
T PRK11086        230 IKEGVIAVDDR----GEVTLINDEAKRLFNYKKGLEDDPLGT  267 (542)
T ss_pred             hcCcEEEECCC----CeEEEEhHHHHHHhCCCcCCcccccCC
Confidence            46799999998    899999999999998753   345554

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]

Probab=94.41  E-value=0.06  Score=37.94  Aligned_cols=36  Identities=8%  Similarity=0.229  Sum_probs=33.5

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKG   40 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~   40 (102)
                      |.+|++.+|..    |.|+.+|....+++|.+.++++|++
T Consensus       120 MtDGViATdRr----G~iI~iN~~A~k~L~~~~E~~~~~~  155 (459)
T COG5002         120 MTDGVIATDRR----GKIILINKPALKMLGVSKEDALGRS  155 (459)
T ss_pred             HcCceEeecCC----CcEEEeccHHHHHhCcCHHHHhccc
Confidence            67899999988    9999999999999999999999983

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=94.06  E-value=0.071  Score=37.57  Aligned_cols=34  Identities=15%  Similarity=0.127  Sum_probs=28.4

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      +.+++++|.+    ++++++|++|+.++|+...+..+.
T Consensus       140 ~~~i~~~d~~----~~i~~~N~~~~~~~g~~~~~~~~~  173 (494)
T TIGR02938       140 PVAFVLLDPT----GRVILDNQEYKKLATDLRVKEPAH  173 (494)
T ss_pred             cceEEEEcCC----CCEEEechhHHHhhchhhhhHHHH
Confidence            4578899987    899999999999999887766543

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.

>KOG3559|consensus

Probab=93.22  E-value=0.07  Score=38.11  Aligned_cols=31  Identities=10%  Similarity=0.401  Sum_probs=26.6

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      +++...+    ..++|......+++||...+++++
T Consensus       228 mfraslD----lkliF~D~rv~qltgYepqdliek  258 (598)
T KOG3559|consen  228 MFRASLD----LKLIFLDSRVHQLTGYEPQDLIEK  258 (598)
T ss_pred             EEEeecc----eEEEeehhhHHHhhCCCchhhhhH
Confidence            3455555    799999999999999999999988

>KOG3560|consensus

Probab=92.81  E-value=0.46  Score=35.29  Aligned_cols=70  Identities=9%  Similarity=0.013  Sum_probs=51.6

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecc
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEE   87 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~   87 (102)
                      +..+.+......++||...|+.|.+ .+.+++-. +-.-...+-.+.++.|++-..-++..+++|++.||-.
T Consensus       293 fa~vs~Dak~k~~lgy~eaEL~~m~-gY~lvH~~-D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqs  362 (712)
T KOG3560|consen  293 FALVSMDAKVKATLGYCEAELHGMP-GYNLVHVE-DKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQS  362 (712)
T ss_pred             cceeccchhhhhhhccchhhccCCC-ccceeehh-hhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeec
Confidence            6778899999999999999999753 45554432 2222334445678888888888888999999999854

>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=92.61  E-value=0.33  Score=28.24  Aligned_cols=41  Identities=20%  Similarity=0.337  Sum_probs=31.7

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCC---hhhhcCCCCCcccccCC
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFA---RAQIMQKGCACKFLYGP   49 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~---~~ei~g~~~~~~~l~~~   49 (102)
                      ..+.+|..  + ++|+.++.+...++|.+   .++++|+  +...+.+.
T Consensus        17 ~LLa~d~~--~-~~I~~~S~N~~~~lg~~~~~~~~llG~--~l~~ll~~   60 (110)
T PF08446_consen   17 ALLALDPD--D-LRIVQASENIAELLGIPPELPEELLGR--PLSELLGA   60 (110)
T ss_dssp             EEEEEETT--T-TBEEEEETTHHHHHSS----HHHHTTC--BHHHHSCC
T ss_pred             EEEEEECC--C-CEEEEEcCCHHHHhCCccccchhhccc--CHHHHhCH
Confidence            34567764  4 89999999999999999   9999999  65555543

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 ....

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=92.51  E-value=0.26  Score=35.14  Aligned_cols=35  Identities=9%  Similarity=0.142  Sum_probs=31.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      |++.++.+|..    |.+..+|++++.++|.+.+.+.|.
T Consensus        89 l~~pVlsvd~k----g~v~~aNpAa~~l~~~~~~~~~g~  123 (511)
T COG3283          89 LPEPVLSVDMK----GKVDMANPAACQLFGRKEDRLRGH  123 (511)
T ss_pred             CCCceEEeccc----CceeecCHHHHHHhCCChhhhcCc
Confidence            56778888887    899999999999999999999987

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]

Probab=91.77  E-value=0.21  Score=36.77  Aligned_cols=42  Identities=10%  Similarity=0.127  Sum_probs=33.9

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChh--hhcCCCCCcccccCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARA--QIMQKGCACKFLYGP   49 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~--ei~g~~~~~~~l~~~   49 (102)
                      .+|++.+|..    |.|+.+|.+.++|+|+...  +++|+  ....+.+|
T Consensus       225 ~EGviAvd~~----G~It~~N~~A~~ll~~~~~~~~~ig~--~i~~v~~p  268 (537)
T COG3290         225 KEGVIAVDKK----GVITLINQAAQKLLGLRQPSGDPIGR--SIVEVLPP  268 (537)
T ss_pred             hceEEEECCC----CeEeehhHHHHHHhcccCcCcccccc--cceEeecc
Confidence            5689999987    9999999999999998775  68887  55544443

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional

Probab=91.26  E-value=1.1  Score=35.88  Aligned_cols=31  Identities=10%  Similarity=-0.047  Sum_probs=26.5

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhh
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQ   35 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~e   35 (102)
                      |+.+|+++|.+    |+|+++|++++.++|++...
T Consensus       585 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~  615 (1197)
T PRK09959        585 LPNPTYVVNWQ----GNVISHNSAFEHYFTADYYK  615 (1197)
T ss_pred             CCCcEEEEcCC----CcEEEehHHHHHHhCccccc
Confidence            46789999987    99999999999999976543

>KOG3561|consensus

Probab=91.15  E-value=0.26  Score=38.04  Aligned_cols=40  Identities=20%  Similarity=0.350  Sum_probs=32.2

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccccc
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLY   47 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~   47 (102)
                      ..+|++.-+    |+|+||+.....++||..++++|+. .+.+++
T Consensus       106 GF~fvV~cd----G~IvyVSeSVT~~L~y~QsDL~~qS-ly~ilh  145 (803)
T KOG3561|consen  106 GFLFVVNCD----GRIVYVSESVTSVLGYLQSDLMGQS-LYDILH  145 (803)
T ss_pred             CeEEEEecC----ceEEEEecchHHhhCcCHHHHhcch-HHHhcC
Confidence            345677776    8999999999999999999999984 344443

>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function

Probab=90.26  E-value=0.37  Score=33.58  Aligned_cols=71  Identities=13%  Similarity=0.178  Sum_probs=44.1

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      ++++-.+.  + .+.+|+|..|...+||+.++++..  ..+++..+.   ..|..-.... ......+.+.+++++|...
T Consensus       299 mlfVYs~k--~-qRllFAN~~fk~wtGy~~edFl~~--~~dIV~eGl---~qW~~dL~~~-s~~E~~grlviKTK~~g~i  369 (401)
T PF06785_consen  299 MLFVYSPK--S-QRLLFANSQFKTWTGYSSEDFLKD--FSDIVQEGL---AQWETDLQLL-SRQERSGRLVIKTKNGGNI  369 (401)
T ss_pred             eEEEecch--h-hHHHHhHHHHHHHhccCHHHHHhc--chHHHHhhH---HHHHHHHHhh-hhhhhhceEEEEecCCCce
Confidence            45566665  3 799999999999999999999865  445444331   1222111122 2223356777778877644

>KOG3558|consensus

Probab=89.79  E-value=0.61  Score=35.51  Aligned_cols=50  Identities=14%  Similarity=0.119  Sum_probs=37.2

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHH
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQ   58 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~   58 (102)
                      ..|++++.+    |.++|++......+|++.=|+.|.  ..+.+.++.+...+...
T Consensus       130 GFVm~l~~d----G~~lYiSEtVS~yLGLSQvELTG~--SvFDfiHP~DheE~~eq  179 (768)
T KOG3558|consen  130 GFVMALTQD----GDFLYISETVSIYLGLSQVELTGS--SVFDFIHPCDHEEIAEQ  179 (768)
T ss_pred             ceEEEEccC----CCEEEEechhHhhhCccceeeecc--hhhhccCccCHHHHHHH
Confidence            345677776    999999999999999999999998  44445555554444433

>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long

Probab=87.46  E-value=4.5  Score=24.30  Aligned_cols=75  Identities=12%  Similarity=0.149  Sum_probs=47.4

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      .++|++...+...++..+=...+.++|+.   +-|+  ....+..+.........+...+...............+|...
T Consensus        39 ~i~ile~~~~~~~r~RLaGt~i~~~~G~d---~tG~--~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~  113 (137)
T PF07310_consen   39 HIFILEVDDPGDFRYRLAGTRIVELFGRD---LTGR--RLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYL  113 (137)
T ss_pred             CeEEEEEeCCCceEEEEecHHHHHHhCCC---CCCC--CHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCee
Confidence            35666654332256667888889999874   4455  544455555555566666777777777666666666666653

>KOG3560|consensus

Probab=84.30  E-value=1.3  Score=33.01  Aligned_cols=43  Identities=19%  Similarity=0.340  Sum_probs=33.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG   48 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~   48 (102)
                      ||..++++..+    |.|.|++......+||...+++.++ .+++++.
T Consensus       120 LnGF~lVvt~e----g~ifyAS~tIedYLGFhQSDV~HQs-VYdlIHs  162 (712)
T KOG3560|consen  120 LNGFALVVTAE----GEIFYASATIEDYLGFHQSDVMHQS-VYDLIHS  162 (712)
T ss_pred             cCCeEEEEecC----ceEEEehhhHHhhhcccccchhhhh-HHHHhhh
Confidence            35556677776    8999999999999999999999883 3444444

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]

Probab=83.16  E-value=1.9  Score=32.79  Aligned_cols=34  Identities=9%  Similarity=0.008  Sum_probs=30.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK   39 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~   39 (102)
                      ..+++..|.+    |++.-+|++.++|+|.+..+++|+
T Consensus       380 taGVi~~d~~----g~i~t~N~~ae~~l~~~~~~~~G~  413 (712)
T COG5000         380 TAGVIGFDNR----GCITTVNPSAEQILGKPFDQLLGQ  413 (712)
T ss_pred             ceeEEEEcCC----CeeEeecchHHHHhcCChhHhhcc
Confidence            4578888887    899999999999999999999998

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	102
2l4r_A	135	Nmr Solution Structure Of The N-Terminal Pas Domain		1e-14
2l0w_A	138	Solution Nmr Structure Of The N-Terminal Pas Domain		1e-14
2l1m_A	150	Solution Structure Of The Eag Domain Of The Herg (K		1e-14
1byw_A	110	Structure Of The N-Terminal Domain Of The Human-Erg		2e-14
2v1a_A	144	N- And C-Terminal Helices Of Oat Lov2 (404-546) Are		1e-10
2v0u_A	146	N- And C-terminal Helices Of Oat Lov2 (404-546) Are		1e-10
4eeu_A	118	Crystal Structure Of Philov2.1 Length = 118		2e-10
4eep_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		3e-10
2wkp_A	332	Structure Of A Photoactivatable Rac1 Containing Lov		8e-10
4ees_A	115	Crystal Structure Of Ilov Length = 115		8e-10
4eer_A	115	Crystal Structure Of Lov2 Domain Of Arabidopsis Tha		2e-09
2wkq_A	332	Structure Of A Photoactivatable Rac1 Containing The		1e-08
2wkr_A	332	Structure Of A Photoactivatable Rac1 Containing The		1e-08
3ulf_A	170	The Light State Structure Of The Blue-light Photore		2e-08
3ue6_A	166	The Dark Structure Of The Blue-light Photoreceptor		2e-08
3rh8_B	148	Crystal Structure Of The Light-State Dimer Of Funga		1e-06
1g28_A	104	Structure Of A Flavin-Binding Domain, Lov2, From Th		2e-06
2z6d_A	130	Crystal Structure Of Lov1 Domain Of Phototropin2 Fr		2e-06
2pd8_A	149	1.8 Angstrom Crystal Structure Of The Cys71ser Muta		2e-06
3d72_A	149	1.65 Angstrom Crystal Structure Of The Cys71val Var		2e-06
3t50_A	128	X-Ray Structure Of The Lov Domain From The Lov-Hk S		2e-06
3is2_A	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		2e-06
2pd7_A	149	2.0 Angstrom Crystal Structure Of The Fungal Blue-L		2e-06
3hjk_A	154	2.0 Angstrom Structure Of The Ile74val Variant Of V		2e-06
3is2_B	154	2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic		2e-06
2pr5_A	132	Structural Basis For Light-dependent Signaling In T		3e-06
3hji_A	154	1.8 Angstrom Crystal Structure Of The I74v:i85v Var		4e-06
2z6c_A	129	Crystal Structure Of Lov1 Domain Of Phototropin1 Fr		1e-05
1n9l_A	109	Crystal Structure Of The Phot-lov1 Domain From Chla		1e-05

>pdb|2L4R|A Chain A, Nmr Solution Structure Of The N-Terminal Pas Domain Of Herg Length = 135

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 53/76 (69%), Gaps = 1/76 (1%)
Query: 5   FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
           F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +AL 
Sbjct: 29  FIIANARVENC-AVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 87
Query: 65  SKTELKLEVIFYKKNG 80
              E K+E+ FY+K+G
Sbjct: 88  GAEERKVEIAFYRKDG 103

>pdb|2L0W|A Chain A, Solution Nmr Structure Of The N-Terminal Pas Domain Of Herg Potassium Channel Length = 138

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 53/76 (69%), Gaps = 1/76 (1%)
Query: 5   FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
           F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +AL 
Sbjct: 32  FIIANARVENC-AVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 90
Query: 65  SKTELKLEVIFYKKNG 80
              E K+E+ FY+K+G
Sbjct: 91  GAEERKVEIAFYRKDG 106

>pdb|2L1M|A Chain A, Solution Structure Of The Eag Domain Of The Herg (Kv11.1) K+ Channel Length = 150

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 53/76 (69%), Gaps = 1/76 (1%)
Query: 5   FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
           F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +AL 
Sbjct: 29  FIIANARVENC-AVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALL 87
Query: 65  SKTELKLEVIFYKKNG 80
              E K+E+ FY+K+G
Sbjct: 88  GAEERKVEIAFYRKDG 103

>pdb|1BYW|A Chain A, Structure Of The N-Terminal Domain Of The Human-Erg Potassium Channel Length = 110

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 53/76 (69%), Gaps = 1/76 (1%)
Query: 5  FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
          F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +AL 
Sbjct: 4  FIIANARVENC-AVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALL 62
Query: 65 SKTELKLEVIFYKKNG 80
             E K+E+ FY+K+G
Sbjct: 63 GAEERKVEIAFYRKDG 78

>pdb|2V1A|A Chain A, N- And C-Terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-Induced Signal Transduction (Room Temperature (293k) Dark Structure Of Lov2 (404-546)) Length = 144

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 52/80 (65%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F +L+ ++R +I+  G  C+FL GP+T      +I 
Sbjct: 9  IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNCRFLQGPETDRATVRKIR 65
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++++TE+ +++I Y K+G
Sbjct: 66 DAIDNQTEVTVQLINYTKSG 85

>pdb|2V0U|A Chain A, N- And C-terminal Helices Of Oat Lov2 (404-546) Are Involved In Light-induced Signal Transduction (cryo Dark Structure Of Lov2 (404-546)) Length = 146

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 52/80 (65%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F +L+ ++R +I+  G  C+FL GP+T      +I 
Sbjct: 11 IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNCRFLQGPETDRATVRKIR 67
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++++TE+ +++I Y K+G
Sbjct: 68 DAIDNQTEVTVQLINYTKSG 87

>pdb|4EEU|A Chain A, Crystal Structure Of Philov2.1 Length = 118

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  +FV+ + ++P  YPI++ SDGF EL+ ++R +IM  G   +FL GP+T +    +I 
Sbjct: 9  IEKSFVITDPRLPD-YPIIFASDGFLELTEYSREEIM--GRNARFLQGPETDQATVQKIR 65
Query: 61 KALESKTELKLEVIFYKKNG 80
           A+  + E  +++I Y K+G
Sbjct: 66 DAIRDQRETTVQLINYTKSG 85

>pdb|4EEP|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 Length = 115

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 50/80 (62%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F EL+ ++R +I+  G  C+FL GP+T +    +I 
Sbjct: 6  IEKNFVISDPRLPD-NPIIFASDSFLELTEYSREEIL--GRNCRFLQGPETDQATVQKIR 62
Query: 61 KALESKTELKLEVIFYKKNG 80
           A+  + E+ +++I Y K+G
Sbjct: 63 DAIRDQREITVQLINYTKSG 82

>pdb|2WKP|A Chain A, Structure Of A Photoactivatable Rac1 Containing Lov2 Wildtype Length = 332

Iteration: 1
 Score = 58.9 bits (141), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 27/80 (33%), Positives = 52/80 (65%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F +L+ ++R +I+  G  C+FL GP+T      +I 
Sbjct: 20 IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNCRFLQGPETDRATVRKIR 76
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++++TE+ +++I Y K+G
Sbjct: 77 DAIDNQTEVTVQLINYTKSG 96

>pdb|4EES|A Chain A, Crystal Structure Of Ilov Length = 115

Iteration: 1
 Score = 58.5 bits (140), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SDGF EL+ ++R +I+  G   +FL GP+T +    +I 
Sbjct: 6  IEKNFVITDPRLPD-NPIIFASDGFLELTEYSREEIL--GRNARFLQGPETDQATVQKIR 62
Query: 61 KALESKTELKLEVIFYKKNG 80
           A+  + E  +++I Y K+G
Sbjct: 63 DAIRDQRETTVQLINYTKSG 82

>pdb|4EER|A Chain A, Crystal Structure Of Lov2 Domain Of Arabidopsis Thaliana Phototropin 2 C426a Mutant Length = 115

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F EL+ ++R +I+  G   +FL GP+T +    +I 
Sbjct: 6  IEKNFVISDPRLPD-NPIIFASDSFLELTEYSREEIL--GRNARFLQGPETDQATVQKIR 62
Query: 61 KALESKTELKLEVIFYKKNG 80
           A+  + E+ +++I Y K+G
Sbjct: 63 DAIRDQREITVQLINYTKSG 82

>pdb|2WKQ|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450a Mutant Length = 332

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/80 (32%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F +L+ ++R +I+  G   +FL GP+T      +I 
Sbjct: 20 IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNARFLQGPETDRATVRKIR 76
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++++TE+ +++I Y K+G
Sbjct: 77 DAIDNQTEVTVQLINYTKSG 96

>pdb|2WKR|A Chain A, Structure Of A Photoactivatable Rac1 Containing The Lov2 C450m Mutant Length = 332

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/80 (32%), Positives = 51/80 (63%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +  NFV+ + ++P   PI++ SD F +L+ ++R +I+  G   +FL GP+T      +I 
Sbjct: 20 IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNMRFLQGPETDRATVRKIR 76
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++++TE+ +++I Y K+G
Sbjct: 77 DAIDNQTEVTVQLINYTKSG 96

>pdb|3ULF|A Chain A, The Light State Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 170

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 4   NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
           NFV+ +A +P   PIVY S GF  L+G++  QI+  G  C+FL GP+T      +I  A+
Sbjct: 51  NFVITDASLPD-NPIVYASRGFLTLTGYSLDQIL--GRNCRFLQGPETDPRAVDKIRNAI 107
Query: 64  ESKTELKLEVIFYKKNG 80
               +  + ++ Y+++G
Sbjct: 108 TKGVDTSVCLLNYRQDG 124

>pdb|3UE6|A Chain A, The Dark Structure Of The Blue-light Photoreceptor Aureochrome1 Lov Length = 166

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 4   NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
           NFV+ +A +P   PIVY S GF  L+G++  QI+  G  C+FL GP+T      +I  A+
Sbjct: 47  NFVITDASLPD-NPIVYASRGFLTLTGYSLDQIL--GRNCRFLQGPETDPRAVDKIRNAI 103
Query: 64  ESKTELKLEVIFYKKNG 80
               +  + ++ Y+++G
Sbjct: 104 TKGVDTSVCLLNYRQDG 120

>pdb|3RH8|B Chain B, Crystal Structure Of The Light-State Dimer Of Fungal Blue-Light Photoreceptor Vivid Length = 148

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            I KA++ 
Sbjct: 48  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTIRKAIDR 105
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 106 NAEVQVEVVNFKKNG 120

>pdb|1G28|A Chain A, Structure Of A Flavin-Binding Domain, Lov2, From The Chimeric PhytochromePHOTOTROPIN PHOTORECEPTOR PHY3 Length = 104

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 4  NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
          +FV+ + ++P   PI++ SD F EL+ + R +++  G  C+FL G  T  +    I  A+
Sbjct: 2  SFVITDPRLPD-NPIIFASDRFLELTEYTREEVL--GNNCRFLQGRGTDRKAVQLIRDAV 58
Query: 64 ESKTELKLEVIFYKKNG 80
          + + ++ ++V+ Y K G
Sbjct: 59 KEQRDVTVQVLNYTKGG 75

>pdb|2Z6D|A Chain A, Crystal Structure Of Lov1 Domain Of Phototropin2 From Arabidopsis Thaliana Length = 130

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +   FV+ +A  P   PIVY S GF  ++G++  +I+  G  C+FL GPDT +    +I 
Sbjct: 15 LQQTFVVSDATQPHC-PIVYASSGFFTMTGYSSKEIV--GRNCRFLQGPDTDKNEVAKIR 71
Query: 61 KALESKTELKLEVIFYKKNG 80
            +++       ++ YKK+G
Sbjct: 72 DCVKNGKSYCGRLLNYKKDG 91

>pdb|2PD8|A Chain A, 1.8 Angstrom Crystal Structure Of The Cys71ser Mutant Of Vivid Length = 149

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 49  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 106
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 107 NAEVQVEVVNFKKNG 121

>pdb|3D72|A Chain A, 1.65 Angstrom Crystal Structure Of The Cys71val Variant In The Fungal Photoreceptor Vvd Length = 149

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 49  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 106
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 107 NAEVQVEVVNFKKNG 121

>pdb|3T50|A Chain A, X-Ray Structure Of The Lov Domain From The Lov-Hk Sensory Protein From Brucella Abortus (Dark State). Length = 128

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 3/76 (3%)
Query: 5  FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
           ++ N  +P   PIV+ +  F +L+G+   ++M  G  C+FL G  T   H   I+ A+ 
Sbjct: 10 MLITNPHLPD-NPIVFANPAFLKLTGYEADEVM--GRNCRFLQGHGTDPAHVRAIKSAIA 66
Query: 65 SKTELKLEVIFYKKNG 80
          ++  + +++I YKK+G
Sbjct: 67 AEKPIDIDIINYKKSG 82

>pdb|3IS2|A Chain A, 2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic Acid Form Of Vivid Length = 154

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 52  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 109
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 110 NAEVQVEVVNFKKNG 124

>pdb|2PD7|A Chain A, 2.0 Angstrom Crystal Structure Of The Fungal Blue-Light Photoreceptor Vivid Length = 149

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 49  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 106
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 107 NAEVQVEVVNFKKNG 121

>pdb|3HJK|A Chain A, 2.0 Angstrom Structure Of The Ile74val Variant Of Vivid (Vvd). Length = 154

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 52  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 109
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 110 NAEVQVEVVNFKKNG 124

>pdb|3IS2|B Chain B, 2.3 Angstrom Crystal Structure Of A Cys71 Sulfenic Acid Form Of Vivid Length = 154

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           PIVY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 52  PIVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 109
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 110 NAEVQVEVVNFKKNG 124

>pdb|2PR5|A Chain A, Structural Basis For Light-dependent Signaling In The Dimeric Lov Photosensor Ytva (dark Structure) Length = 132

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 17 PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFY 76
          PIVY + GF +++G+   +I+  G  C+FL G  T       I  AL++K  + +++  Y
Sbjct: 23 PIVYVNQGFVQMTGYETEEIL--GKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNY 80
Query: 77 KKNG 80
          KK+G
Sbjct: 81 KKDG 84

>pdb|3HJI|A Chain A, 1.8 Angstrom Crystal Structure Of The I74v:i85v Variant Of Vivid (Vvd). Length = 154

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 13/75 (17%)
Query: 17  PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKT-----------QIEKALES 65
           P+VY S+ F  ++G++ A+++  G  C+FL  PD   + K+            + KA++ 
Sbjct: 52  PVVYASEAFLYMTGYSNAEVL--GRNCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDR 109
Query: 66  KTELKLEVIFYKKNG 80
             E+++EV+ +KKNG
Sbjct: 110 NAEVQVEVVNFKKNG 124

>pdb|2Z6C|A Chain A, Crystal Structure Of Lov1 Domain Of Phototropin1 From Arabidopsis Thaliana Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 4  NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
           FV+ +A  P  YPI+Y S GF  ++G+   +++  G  C+FL G  T  +   +I + L
Sbjct: 19 TFVVSDATKPD-YPIMYASAGFFNMTGYTSKEVV--GRNCRFLQGSGTDADELAKIRETL 75
Query: 64 ESKTELKLEVIFYKKNG 80
           +       ++ YKK+G
Sbjct: 76 AAGNNYCGRILNYKKDG 92

>pdb|1N9L|A Chain A, Crystal Structure Of The Phot-lov1 Domain From Chlamydomonas Reinhardtii In The Dark State. Length = 109

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +   FV+ +A +P   P+VY S+GF  ++G+   +++  G  C+FL G  T  +   +I 
Sbjct: 2  LRHTFVVADATLPDC-PLVYASEGFYAMTGYGPDEVL--GHNCRFLQGEGTDPKEVQKIR 58
Query: 61 KALESKTELKLEVIFYKKNG 80
           A++      + ++ Y+K+G
Sbjct: 59 DAIKKGEACSVRLLNYRKDG 78

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	102
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	5e-34
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	1e-33
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	2e-26
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	4e-26
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	6e-24
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	1e-23
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	2e-18
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	3e-18
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	2e-17
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	2e-14
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	2e-14
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	1e-13
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	3e-13
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	1e-06
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	1e-05
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	6e-05

>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 Length = 138

 Score =  113 bits (284), Expect = 5e-34
 Identities = 35/79 (44%), Positives = 54/79 (68%), Gaps = 1/79 (1%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
           +  F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +
Sbjct: 29  SRKFIIANARVEN-CAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQ 87

Query: 62  ALESKTELKLEVIFYKKNG 80
           AL    E K+E+ FY+K+G
Sbjct: 88  ALLGAEERKVEIAFYRKDG 106

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6 Length = 110

 Score =  111 bits (279), Expect = 1e-33
 Identities = 35/79 (44%), Positives = 54/79 (68%), Gaps = 1/79 (1%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
          +  F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T      QI +
Sbjct: 1  SRKFIIANARVEN-CAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQ 59

Query: 62 ALESKTELKLEVIFYKKNG 80
          AL    E K+E+ FY+K+G
Sbjct: 60 ALLGAEERKVEIAFYRKDG 78

>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* Length = 115

 Score = 93.0 bits (232), Expect = 2e-26
 Identities = 27/79 (34%), Positives = 48/79 (60%), Gaps = 3/79 (3%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
            NFV+ + ++P   PI++ SDGF EL+ ++R +I+  G   +FL GP+T +    +I  
Sbjct: 7  EKNFVITDPRLPD-NPIIFASDGFLELTEYSREEIL--GRNARFLQGPETDQATVQKIRD 63

Query: 62 ALESKTELKLEVIFYKKNG 80
          A+  + E  +++I Y K+G
Sbjct: 64 AIRDQRETTVQLINYTKSG 82

>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* Length = 109

 Score = 92.2 bits (230), Expect = 4e-26
 Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             FV+ +A +P   P+VY S+GF  ++G+   +++  G  C+FL G  T  +   +I  
Sbjct: 3  RHTFVVADATLPD-CPLVYASEGFYAMTGYGPDEVL--GHNCRFLQGEGTDPKEVQKIRD 59

Query: 62 ALESKTELKLEVIFYKKNG 80
          A++      + ++ Y+K+G
Sbjct: 60 AIKKGEACSVRLLNYRKDG 78

>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* Length = 146

 Score = 87.7 bits (218), Expect = 6e-24
 Identities = 27/79 (34%), Positives = 51/79 (64%), Gaps = 3/79 (3%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
            NFV+ + ++P   PI++ SD F +L+ ++R +I+  G  C+FL GP+T      +I  
Sbjct: 12 EKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNCRFLQGPETDRATVRKIRD 68

Query: 62 ALESKTELKLEVIFYKKNG 80
          A++++TE+ +++I Y K+G
Sbjct: 69 AIDNQTEVTVQLINYTKSG 87

>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* Length = 130

 Score = 86.5 bits (215), Expect = 1e-23
 Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 3/80 (3%)

Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +   FV+ +A  P   PIVY S GF  ++G++  +I+  G  C+FL GPDT +    +I 
Sbjct: 15 LQQTFVVSDATQPH-CPIVYASSGFFTMTGYSSKEIV--GRNCRFLQGPDTDKNEVAKIR 71

Query: 61 KALESKTELKLEVIFYKKNG 80
            +++       ++ YKK+G
Sbjct: 72 DCVKNGKSYCGRLLNYKKDG 91

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A* Length = 166

 Score = 73.9 bits (182), Expect = 2e-18
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 3/79 (3%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
             NFV+ +A +P   PIVY S GF  L+G++  QI+  G  C+FL GP+T      +I  
Sbjct: 45  QQNFVITDASLPD-NPIVYASRGFLTLTGYSLDQIL--GRNCRFLQGPETDPRAVDKIRN 101

Query: 62  ALESKTELKLEVIFYKKNG 80
           A+    +  + ++ Y+++G
Sbjct: 102 AITKGVDTSVCLLNYRQDG 120

>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* Length = 149

 Score = 73.5 bits (181), Expect = 3e-18
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 14/91 (15%)

Query: 1   MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPD---------- 50
            +   +L + +     PIVY S+ F  ++G++ A+++ +   C+FL  PD          
Sbjct: 34  TSVALILCDLKQKD-TPIVYASEAFLYMTGYSNAEVLGRN--CRFLQSPDGMVKPKSTRK 90

Query: 51  -TSEEHKTQIEKALESKTELKLEVIFYKKNG 80
                    + KA++   E+++EV+ +KKNG
Sbjct: 91  YVDSNTINTMRKAIDRNAEVQVEVVNFKKNG 121

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis} Length = 258

 Score = 73.5 bits (180), Expect = 2e-17
 Identities = 16/79 (20%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 2   NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
               V+ + ++    P++  +  F +L+G++  + + + C  +FL G  T      +I +
Sbjct: 73  PIASVVSDPRLAD-NPLIAINQAFTDLTGYSEEECVGRNC--RFLAGSGTEPWLTDKIRQ 129

Query: 62  ALESKTELKLEVIFYKKNG 80
            +     + +E++ YKK+G
Sbjct: 130 GVREHKPVLVEILNYKKDG 148

>3t50_A Blue-light-activated histidine kinase; PAS superfamily, blue-light photoreceptor, FMN binding, TRAN; HET: FMN; 1.64A {Brucella melitensis} Length = 128

 Score = 62.9 bits (154), Expect = 2e-14
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 5  FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
           ++ N  +P   PIV+ +  F +L+G+   ++M  G  C+FL G  T   H   I+ A+ 
Sbjct: 10 MLITNPHLPD-NPIVFANPAFLKLTGYEADEVM--GRNCRFLQGHGTDPAHVRAIKSAIA 66

Query: 65 SKTELKLEVIFYKKNG--YHEE 84
          ++  + +++I YKK+G  +   
Sbjct: 67 AEKPIDIDIINYKKSGEAFWNR 88

>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV, PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN; 1.45A {Bacillus subtilis} PDB: 2pr6_A* Length = 132

 Score = 62.9 bits (154), Expect = 2e-14
 Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEK 61
              V+ +  +    PIVY + GF +++G+   +I+  G  C+FL G  T       I  
Sbjct: 9  RVGVVITDPALED-NPIVYVNQGFVQMTGYETEEIL--GKNCRFLQGKHTDPAEVDNIRT 65

Query: 62 ALESKTELKLEVIFYKKNG--YHEE 84
          AL++K  + +++  YKK+G  +  E
Sbjct: 66 ALQNKEPVTVQIQNYKKDGTMFWNE 90

>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* Length = 332

 Score = 63.9 bits (155), Expect = 1e-13
 Identities = 26/77 (33%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 4  NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
          NFV+ + ++P   PI++ SD F +L+ ++R +I+  G   +FL GP+T      +I  A+
Sbjct: 23 NFVITDPRLPD-NPIIFASDSFLQLTEYSREEIL--GRNARFLQGPETDRATVRKIRDAI 79

Query: 64 ESKTELKLEVIFYKKNG 80
          +++TE+ +++I Y K+G
Sbjct: 80 DNQTEVTVQLINYTKSG 96

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida} Length = 162

 Score = 60.7 bits (148), Expect = 3e-13
 Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 5   FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE 64
            V+   +      ++Y +  F  L+G++R +I+     C+FL G D  +  + +I KA+ 
Sbjct: 38  IVVAEKEGDD-TILIYVNAAFEYLTGYSRDEIL--YQDCRFLQGDDRDQLGRARIRKAMA 94

Query: 65  SKTELKLEVIFYKKNG--YHEE 84
                +  +  Y+K+G  +  E
Sbjct: 95  EGRPCREVLRNYRKDGSAFWNE 116

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Length = 227

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 18 IVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK 77
          I+Y +D FC +S + R +++ +    + +      + +   + + +      + E    +
Sbjct: 11 ILYANDNFCAVSRYGREELVGQ--DHRIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRR 68

Query: 78 KNG--YHEE 84
          K+G  Y  +
Sbjct: 69 KDGTRYWVD 77

>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Length = 227

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 18  IVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK 77
           I+Y +   C  SG A  +++  G +   L  P   +E    +++AL++       ++  +
Sbjct: 133 IIYANPALCRFSGMAEGELL--GQSPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRR 190

Query: 78  KNGYHEEEEEE 88
           + G    + E+
Sbjct: 191 RTGPAPHDAED 201

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A Length = 120

 Score = 37.9 bits (89), Expect = 6e-05
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 18 IVYCSDGFCELSGFARAQIMQKGCACKFLY-GPDTSEEHKTQIEKALESKTELKLEVIFY 76
          I  C+D    +   ARA ++  G + + LY   D  E    +I   + +      + I  
Sbjct: 24 IEDCNDELAAIFRCARADLI--GRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMK 81

Query: 77 KKNG 80
          +  G
Sbjct: 82 RAGG 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	102
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.72
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	99.58
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	99.56
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	99.46
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	99.46
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	99.46
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	99.46
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.44
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.43
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.43
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	99.4
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	99.4
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	99.38
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	99.37
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	99.36
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	99.36
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	99.35
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	99.35
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	99.35
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	99.32
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	99.32
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	99.31
3olo_A	118	Two-component sensor histidine kinase; structural	99.26
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	99.25
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	99.19
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	99.18
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	99.17
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	99.15
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	99.11
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	99.11
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	99.1
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	99.08
3nja_A	125	Probable ggdef family protein; structural genomics	99.08
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	99.07
3mr0_A	142	Sensory box histidine kinase/response regulator; P	99.04
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.0
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	98.99
3rty_A	339	Period circadian protein; PAS domain, signalling,	98.98
1nwz_A	125	PYP, photoactive yellow protein; PAS, LOV, GAF, do	98.93
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.93
1mzu_A	129	PPR; photoactive yellow protein, PAS, PYP, signali	98.92
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	98.9
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	98.9
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.86
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	98.86
3eeh_A	125	Putative light and redox sensing histidine kinase;	98.84
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	98.84
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	98.8
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	98.79
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	98.75
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	98.72
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.71
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.65
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.62
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	98.47
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	98.34
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	98.21
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	98.05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.04
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	98.02
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	97.96
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.73
3cax_A	369	Uncharacterized protein PF0695; structural genomic	97.62
3rty_A	339	Period circadian protein; PAS domain, signalling,	97.39
1oj5_A	132	Steroid receptor coactivator 1A; transcriptional c	97.17
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	96.98
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	96.85
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	96.77
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	95.23
2ool_A	337	Sensor protein; bacteriophytochrome, photoconversi	91.56
4e04_A	327	Bacteriophytochrome (light-regulated signal trans	83.92

>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=99.72  E-value=2.8e-16  Score=89.91  Aligned_cols=84  Identities=25%  Similarity=0.576  Sum_probs=73.1

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      |+++|+++|...+. ++|+++|++|++++||+.++++|+  +...+.++.........++..+..+..+..++..++++|
T Consensus         2 ~~~~i~i~d~~~~~-g~i~~~N~a~~~l~Gy~~~e~~G~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG   78 (109)
T 1n9l_A            2 LRHTFVVADATLPD-CPLVYASEGFYAMTGYGPDEVLGH--NCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDG   78 (109)
T ss_dssp             CSCEEEEEETTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTS
T ss_pred             CccEEEEEcCCCCC-CeEEEEchHHHHHHCcCHHHHcCC--CchhcCCCCCCHHHHHHHHHHHHcCCcEEEEEEEEcCCC
Confidence            57899999975444 899999999999999999999999  777777777777777888999999999999999999999


Q ss_pred             Ceeeecc
Q psy8548          81 YHEEEEE   87 (102)
Q Consensus        81 ~~~~~~~   87 (102)
                      +.+|++-
T Consensus        79 ~~~~~~~   85 (109)
T 1n9l_A           79 TPFWNLL   85 (109)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEE
Confidence            9998863

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

Probab=99.58  E-value=4.2e-14  Score=81.54  Aligned_cols=80  Identities=14%  Similarity=0.145  Sum_probs=67.8

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +++|+++|.+    |+|+++|++|++++||+.++++|+  +...+.++.........++..+..+..+..++..++++|+
T Consensus        15 ~~~i~~~d~~----g~i~~~N~a~~~~~G~~~~elig~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~   88 (120)
T 2gj3_A           15 PIAISITDLK----ANILYANRAFRTITGYGSEEVLGK--NESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKT   88 (120)
T ss_dssp             SSEEEEECTT----CBEEEECHHHHHHHCCCTTGGGGC--BGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTTSC
T ss_pred             CCeEEEECCC----CCEEeehHHHHHHHCcCHHHHcCC--CHHHcCCCCCCHHHHHHHHHHHHcCCCEEEEEEEEcCCCC
Confidence            5789999987    899999999999999999999998  6666666555666667778888888899999999999999


Q ss_pred             eeeecc
Q psy8548          82 HEEEEE   87 (102)
Q Consensus        82 ~~~~~~   87 (102)
                      .+|++-
T Consensus        89 ~~~~~~   94 (120)
T 2gj3_A           89 LYLAEL   94 (120)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            888753

>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=99.56  E-value=1.1e-13  Score=80.97  Aligned_cols=82  Identities=29%  Similarity=0.575  Sum_probs=67.9

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +++|+++|.+.++ ++|+++|++|++++||+.++++|+  +...+.++.........+...+..+..+..++..++++|+
T Consensus         9 ~~~i~~~d~~g~~-~~i~~~N~a~~~~~G~~~~el~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~   85 (132)
T 2pr5_A            9 RVGVVITDPALED-NPIVYVNQGFVQMTGYETEEILGK--NCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGT   85 (132)
T ss_dssp             CCEEEEECTTSTT-CCEEEECHHHHHHHSCCHHHHTTS--CGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSC
T ss_pred             CCcEEEEeCCCCC-CcEEEECHHHHHHhCcCHHHHcCC--ChhhhCCCCCCHHHHHHHHHHHHcCCCeEEEEEEEecCCC
Confidence            5789999986222 499999999999999999999998  6666666666666667778888888889999999999999


Q ss_pred             eeeec
Q psy8548          82 HEEEE   86 (102)
Q Consensus        82 ~~~~~   86 (102)
                      .+|++
T Consensus        86 ~~~~~   90 (132)
T 2pr5_A           86 MFWNE   90 (132)
T ss_dssp             EEEEE
T ss_pred             eeeeE
Confidence            88875

>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=99.46  E-value=4.8e-13  Score=76.92  Aligned_cols=81  Identities=10%  Similarity=0.098  Sum_probs=64.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH-hCCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE-SKTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~-~~~~~~~e~~~~~~~G   80 (102)
                      ++.|++.|.+    ++++|+|+++++++||+.++++|+  ....+.+|.+.......+...+. .+..+..++++++++|
T Consensus        12 ~d~i~~~d~~----g~i~~~n~~~~~~~G~~~~el~g~--~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~~~dG   85 (121)
T 3f1p_B           12 TRFISRHNIE----GIFTFVDHRCVATVGYQPQELLGK--NIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQ   85 (121)
T ss_dssp             CEEEEEECTT----SBEEEECTTHHHHHSCCGGGTTTS--BGGGGBCTTTHHHHHHHHHHHTTSTTCCEEEEEEEECTTS
T ss_pred             CceEEEECCC----ceEEEECcchhhhhCCChHHHcCC--CHHHeECHHHHHHHHHHHHHHHhcCCCcccEEEEEEecCC
Confidence            4578888887    899999999999999999999998  55545556555556666666664 4557889999999999


Q ss_pred             Ceeeecch
Q psy8548          81 YHEEEEEE   88 (102)
Q Consensus        81 ~~~~~~~~   88 (102)
                      +.+|++..
T Consensus        86 ~~~w~~~~   93 (121)
T 3f1p_B           86 EWLWMRTS   93 (121)
T ss_dssp             CEEEEEEE
T ss_pred             CEEEEEEE
Confidence            99998753

>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=99.46  E-value=2.1e-12  Score=72.41  Aligned_cols=83  Identities=31%  Similarity=0.650  Sum_probs=68.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|...+. ++++++|++|++++|++.++++|+  ....+.++.........+...+..+..+..++...+++|
T Consensus         6 ~~~~i~~~d~~~~~-g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   82 (115)
T 4eet_B            6 IEKNFVITDPRLPD-NPIIFASDGFLELTEYSREEILGR--NARFLQGPETDQATVQKIRDAIRDQRETTVQLINYTKSG   82 (115)
T ss_dssp             CCCSEEEECTTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTTC
T ss_pred             CCCcEEEEcCCCCC-CcEEEEcHHHHHHHCcCHHHHhCC--CHHHhcCCCCChHHHHHHHHHHHcCCCcceEEEEecCCC
Confidence            46789999982112 899999999999999999999998  666666666677777788888888888999999999999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|+.
T Consensus        83 ~~~~~~   88 (115)
T 4eet_B           83 KKFWNL   88 (115)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            988764

>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=99.46  E-value=1.7e-13  Score=78.31  Aligned_cols=79  Identities=15%  Similarity=0.180  Sum_probs=64.6

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH   82 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~   82 (102)
                      +.|++.|++    ++++++|+++++++||+.++++|+  ....+.+|.+.....+.+...+..+..+..++++++++|+.
T Consensus        10 ~~i~~~d~~----g~i~~~n~~~~~~~Gy~~~el~g~--~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG~~   83 (117)
T 3f1p_A           10 TFLSEHSMD----MKFTYCDDRITELIGYHPEELLGR--SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGY   83 (117)
T ss_dssp             EEEEEECTT----CBEEEECTHHHHHHCCCHHHHTTS--BGGGGBCGGGHHHHHHHHHHHHHHSEEECCCEEEECTTSSE
T ss_pred             cEEEEECCC----ceEEEECcChhhhhCCCHHHHcCC--chhheECHHHHHHHHHHHHHHHhCCCeeeeEEEEEecCCCE
Confidence            466778887    899999999999999999999998  55545555555666667777777788888899999999999


Q ss_pred             eeecc
Q psy8548          83 EEEEE   87 (102)
Q Consensus        83 ~~~~~   87 (102)
                      +|++.
T Consensus        84 ~w~~~   88 (117)
T 3f1p_A           84 VWLET   88 (117)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99864

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

Probab=99.46  E-value=1.1e-12  Score=75.49  Aligned_cols=79  Identities=14%  Similarity=0.145  Sum_probs=60.6

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +++|+++|.+    |+++++|+++++++||+.++++|+  +...+.++... .........+..+..+..+...++++|+
T Consensus        21 ~d~i~~~d~~----g~i~~vN~a~~~l~Gy~~~el~g~--~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~e~~~~~kdG~   93 (117)
T 2r78_A           21 IDGIFIMDAE----GHYLDVNPAICSAIGYTRDEFLAL--DWGVLSRGVDS-GWAAASLARIVGGEPLREERTVWTRNGD   93 (117)
T ss_dssp             SSEEEEECTT----SBEEEECHHHHHHHCCCHHHHTTC--BTTTTTTCSTT-SHHHHHHHHHHTTCCEEEEEEEECTTSC
T ss_pred             CceEEEECCC----CCEEEecHHHHHHHCcCHHHHcCC--CHHHhCCccch-hHHHHHHHHHHcCCcEEEEEEEEecCCC
Confidence            5789999987    899999999999999999999998  55444433222 1223345556677778889999999999


Q ss_pred             eeeecc
Q psy8548          82 HEEEEE   87 (102)
Q Consensus        82 ~~~~~~   87 (102)
                      .+|++.
T Consensus        94 ~~~v~~   99 (117)
T 2r78_A           94 QLTVEL   99 (117)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            988763

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

Probab=99.44  E-value=1.2e-12  Score=83.37  Aligned_cols=79  Identities=18%  Similarity=0.330  Sum_probs=69.9

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      .++|+++|.+    ++|+++|++|++++||+.++++|+  ....+.++.........++..+..+..|.+++..++++|+
T Consensus       121 ~~~i~~~d~~----g~i~~~N~~~~~~~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k~G~  194 (227)
T 3ewk_A          121 SEMILLTDRA----GRIIYANPALCRFSGMAEGELLGQ--SPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRRRTGP  194 (227)
T ss_dssp             CSEEEEECTT----SCEEEECHHHHHHHTCCTHHHHSS--CGGGGBCTTSCHHHHHHHHHHHHHTCCEECCEEEEEECCS
T ss_pred             cCeEEEEcCC----CcEEEEchHHHHHhCCCHHHHcCC--ChhhccCCCCCHHHHHHHHHHHHcCCceeEEEEEECCCCC
Confidence            4678899987    899999999999999999999999  7777777777888888999999999999999999999997


Q ss_pred             ------eeeec
Q psy8548          82 ------HEEEE   86 (102)
Q Consensus        82 ------~~~~~   86 (102)
                            .+|++
T Consensus       195 ~~~dg~~~~~~  205 (227)
T 3ewk_A          195 APHDAEDYWAE  205 (227)
T ss_dssp             SSSCEEEEEEE
T ss_pred             cCcccceEEEE
Confidence                  67764

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

Probab=99.43  E-value=2.1e-12  Score=82.18  Aligned_cols=78  Identities=14%  Similarity=0.232  Sum_probs=68.0

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      .|+++|.+    |+|+++|++|++++||+.++++|+  +...+.++.........++..+..+..+..++..++++|+.+
T Consensus         1 ~i~i~D~~----g~i~~~N~a~~~l~Gy~~~el~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~   74 (227)
T 3ewk_A            1 LVSITDLQ----GRILYANDNFCAVSRYGREELVGQ--DHRIVNSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRY   74 (227)
T ss_dssp             CEEEEETT----CBEEEECHHHHHHTTCCHHHHTTS--BGGGGCCSCSCHHHHHHHHHHHTTTCCEEEEEEEECSSSCEE
T ss_pred             CEEEECCC----CcEEehHHHHHHHHCcCHHHHcCC--CHHHcCCCCCCHHHHHHHHHHHHcCCeEEEEEEEEcCCCCEE
Confidence            37889987    999999999999999999999999  766676666677777888888889999999999999999998


Q ss_pred             eecc
Q psy8548          84 EEEE   87 (102)
Q Consensus        84 ~~~~   87 (102)
                      |+..
T Consensus        75 ~~~~   78 (227)
T 3ewk_A           75 WVDS   78 (227)
T ss_dssp             EEEE
T ss_pred             eeee
Confidence            8763

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

Probab=99.43  E-value=3.8e-12  Score=77.34  Aligned_cols=83  Identities=23%  Similarity=0.421  Sum_probs=70.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|...++ ++|+++|++|++++||+.++++|+  +...+.++.........+...+..+..+..++...+++|
T Consensus        16 ~~~~i~~~d~~~~~-g~i~~~N~a~~~~~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG   92 (176)
T 4hia_A           16 SGVALTLVDMSLPE-QPVVLANPPFLRMTGYTEGQILGF--NCRFLQRGDENAQARADIRDALKLGRELQVVLRNYRAND   92 (176)
T ss_dssp             CSSCCEEEETTSTT-CCEEEECHHHHHHHTCCHHHHTTS--CGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTC
T ss_pred             CCCcEEEEecCCCC-CcEEEECHHHHHHHCcCHHHHcCC--CcceeeCCCCCHHHHHHHHHHHHcCCceEEEEEEEcCCC
Confidence            35688999986555 899999999999999999999999  766666676777777888888888999999999999999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|+.
T Consensus        93 ~~~~~~   98 (176)
T 4hia_A           93 EPFDNL   98 (176)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            988865

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

Probab=99.40  E-value=1e-11  Score=71.32  Aligned_cols=83  Identities=27%  Similarity=0.562  Sum_probs=67.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++.+|+++|...++ ++|+++|++|+.++|++.++++|+  ....+.++.........+...+..+..+..++...+.+|
T Consensus         6 ~~~~i~~~d~~~~~-g~i~~~N~~~~~l~g~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g   82 (128)
T 3t50_A            6 TLMPMLITNPHLPD-NPIVFANPAFLKLTGYEADEVMGR--NCRFLQGHGTDPAHVRAIKSAIAAEKPIDIDIINYKKSG   82 (128)
T ss_dssp             CSSCEEEECTTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEECTTC
T ss_pred             CcccEEEecCCCCC-CcEEEEcHHHHHHhCcCHHHHcCC--CHhhhcCCccCHHHHHHHHHHHHcCCCceeEEEEEcCCC
Confidence            35789999982111 899999999999999999999998  666666666677777788888888888999999889999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ..+|+.
T Consensus        83 ~~~~~~   88 (128)
T 3t50_A           83 EAFWNR   88 (128)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            887764

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

Probab=99.40  E-value=5.7e-12  Score=81.37  Aligned_cols=82  Identities=20%  Similarity=0.452  Sum_probs=69.7

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +++|+++|....+ ++|+++|++|++++||+.++++|+  ....+.++.........+...+..+..+..++..++++|.
T Consensus        73 ~~~i~~~d~~~~~-g~i~~~N~a~~~l~G~~~~el~g~--~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~~dG~  149 (258)
T 3p7n_A           73 PIASVVSDPRLAD-NPLIAINQAFTDLTGYSEEECVGR--NCRFLAGSGTEPWLTDKIRQGVREHKPVLVEILNYKKDGT  149 (258)
T ss_dssp             SSEEEEECTTSTT-CCEEEECHHHHHHHCCCGGGTTTS--CGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSC
T ss_pred             CccEEEEcCCCCC-CcEEEEhHHHHHHcCCCHHHHCCC--ChhhccCCCCchhHHHHHHHHHHcCCCeEEEEEEEcCCCC
Confidence            5689999982111 789999999999999999999999  7777777777777888888888899999999999999999


Q ss_pred             eeeec
Q psy8548          82 HEEEE   86 (102)
Q Consensus        82 ~~~~~   86 (102)
                      .+|+.
T Consensus       150 ~~~~~  154 (258)
T 3p7n_A          150 PFRNA  154 (258)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            88764

>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=99.38  E-value=7.7e-12  Score=83.37  Aligned_cols=83  Identities=30%  Similarity=0.646  Sum_probs=70.0

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|...++ |+|+++|++|++++||+.++++|+  +...+.++.........+...+..+..+..+++.++++|
T Consensus        20 ~~~~i~~~D~~~~~-g~i~~~N~a~~~l~G~~~~el~G~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG   96 (332)
T 2wkq_A           20 IEKNFVITDPRLPD-NPIIFASDSFLQLTEYSREEILGR--NARFLQGPETDRATVRKIRDAIDNQTEVTVQLINYTKSG   96 (332)
T ss_dssp             CCSEEEEECTTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTC
T ss_pred             CCCcEEEecCCCCC-CCEEEeehHHHHHhCCCHHHHcCC--CchhhcCCCCCHHHHHHHHHHHHcCCeeEEEEEEEcCCC
Confidence            46799999982222 999999999999999999999999  666676666777777888888989999999999999999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|++
T Consensus        97 ~~~~~~  102 (332)
T 2wkq_A           97 KKFWNL  102 (332)
T ss_dssp             CEEEEE
T ss_pred             CEEEEe
Confidence            987764

>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light photoreceptor, signal protein; HET: FMN; 2.75A {Vaucheria frigida} PDB: 3ulf_A*

Probab=99.37  E-value=1.6e-11  Score=73.36  Aligned_cols=82  Identities=32%  Similarity=0.634  Sum_probs=68.0

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +++|+++|...++ ++|+++|++|++++||+.++++|+  +...+.++.........+...+..+..+..++...+++|.
T Consensus        45 ~~~i~~~d~~~~~-g~i~~~N~~~~~l~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~  121 (166)
T 3ue6_A           45 QQNFVITDASLPD-NPIVYASRGFLTLTGYSLDQILGR--NCRFLQGPETDPRAVDKIRNAITKGVDTSVCLLNYRQDGT  121 (166)
T ss_dssp             TSCEEEEETTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSC
T ss_pred             CceEEEEEccCCC-CcEEEECHHHHHHhCcCHHHHcCC--CHhheeCCCCCHHHHHHHHHHHhcCCceEEEEEEEcCCCC
Confidence            5689999982112 899999999999999999999998  6666666666777777888888888889999998899998


Q ss_pred             eeeec
Q psy8548          82 HEEEE   86 (102)
Q Consensus        82 ~~~~~   86 (102)
                      .+|+.
T Consensus       122 ~~~~~  126 (166)
T 3ue6_A          122 TFWNL  126 (166)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            87764

>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=99.36  E-value=2e-11  Score=72.05  Aligned_cols=82  Identities=28%  Similarity=0.570  Sum_probs=65.4

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCC-----------CHHHHHHHHHHHHhCCcEEE
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDT-----------SEEHKTQIEKALESKTELKL   71 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~-----------~~~~~~~i~~~l~~~~~~~~   71 (102)
                      .+|+++|..... ++|+++|+++++++||+.++++|+  ....+.++..           .......+...+..+..+..
T Consensus        36 ~~i~~~d~~d~~-g~i~~~N~a~~~l~G~~~~el~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (149)
T 3d72_A           36 VALILCDLKQKD-TPIVYASEAFLYMTGYSNAEVLGR--NCRFLQSPDGMVKPKSTRKYVDSNTINTMRKAIDRNAEVQV  112 (149)
T ss_dssp             SCEEEEETTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGGSTTSCCCTTCCCSSSCHHHHHHHHHHHHHTCCEEE
T ss_pred             ccEEEEeccCCC-CcEEEECHHHHHHHCcCHHHHcCC--ChhHhCCccccccccccccccChHHHHHHHHHHHCCCceEE
Confidence            578888831112 899999999999999999999999  6665655542           56666777788888888999


Q ss_pred             EEEEEecCCCeeeecc
Q psy8548          72 EVIFYKKNGYHEEEEE   87 (102)
Q Consensus        72 e~~~~~~~G~~~~~~~   87 (102)
                      ++..++++|+.+|+.-
T Consensus       113 e~~~~~~dG~~~~~~~  128 (149)
T 3d72_A          113 EVVNFKKNGQRFVNFL  128 (149)
T ss_dssp             EEEEECTTCCEEEEEE
T ss_pred             EEEEECCCCCEEEEEE
Confidence            9999999999888753

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

Probab=99.36  E-value=8.4e-12  Score=71.32  Aligned_cols=80  Identities=14%  Similarity=0.182  Sum_probs=60.4

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHh-CCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALES-KTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~-~~~~~~e~~~~~~~G   80 (102)
                      +++|++.|.+    ++++++|+++++++||+.++++|+  ....+.++.........+...+.. +..+..++++++++|
T Consensus        13 ~~~i~~~d~~----g~i~~~N~~~~~~~G~~~~el~g~--~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~~e~r~~~~dG   86 (121)
T 2kdk_A           13 TEFITRFAVN----GKFVYVDQRATAILGYLPQELLGT--SCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKFRAKDG   86 (121)
T ss_dssp             SEEEEEECTT----SBEEEECTHHHHHTCCCTTTSBTS--BTTTTBCSSSHHHHHHHHHHHHTSSSCEEEEEEEEECSSS
T ss_pred             ccEEEEECCC----eeEEEEChhHHHHHCCCHHHHcCC--cHHHeeCHHHHHHHHHHHHHHHhCCCCCccEEEEEEEcCC
Confidence            4577888887    899999999999999999999998  544444554444444555555554 344577889999999


Q ss_pred             Ceeeecc
Q psy8548          81 YHEEEEE   87 (102)
Q Consensus        81 ~~~~~~~   87 (102)
                      +.+|++.
T Consensus        87 ~~~~~~~   93 (121)
T 2kdk_A           87 SFVTLKS   93 (121)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEE
Confidence            9998864

>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=99.35  E-value=7.9e-12  Score=71.64  Aligned_cols=80  Identities=11%  Similarity=0.115  Sum_probs=55.3

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc----EEEEEEEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE----LKLEVIFY   76 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~----~~~e~~~~   76 (102)
                      ++++|+++|.+    |+|+++|+++++++||+.++++|+  +...+.++.........+......+..    ...++..+
T Consensus         2 ~~d~i~~~d~~----g~i~~~N~a~~~l~G~~~~el~G~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (119)
T 2vv6_A            2 IPDAMIVIDGH----GIIQLFSTAAERLFGWSELEAIGQ--NVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGK   75 (119)
T ss_dssp             CCCEEEEEETT----SBEEEECHHHHHHHCCCHHHHTTS--BGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEE
T ss_pred             CcceEEEECCC----CeEEEEhHHHHHHhCCCHHHHcCC--CHHHhCCchHHHHHHHHHHHHhcCCCcccCCCceEEEEE
Confidence            36789999987    899999999999999999999998  655554433222222223333333321    23466778


Q ss_pred             ecCCCeeeec
Q psy8548          77 KKNGYHEEEE   86 (102)
Q Consensus        77 ~~~G~~~~~~   86 (102)
                      +++|+.+|++
T Consensus        76 ~~dG~~~~~~   85 (119)
T 2vv6_A           76 RRDGTTFPMH   85 (119)
T ss_dssp             CTTSCEEEEE
T ss_pred             eCCCCEEEEE
Confidence            8999988775

>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=99.35  E-value=8.5e-12  Score=72.62  Aligned_cols=79  Identities=14%  Similarity=0.174  Sum_probs=55.7

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc----EEEEEEEEe
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE----LKLEVIFYK   77 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~----~~~e~~~~~   77 (102)
                      +++|+++|.+    |+|+++|+++++++||+.++++|+  +...+.++.........+......+..    ...++..++
T Consensus        26 ~d~i~~~d~~----g~i~~~N~a~~~l~Gy~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   99 (130)
T 1d06_A           26 PDATVVSATD----GTIVSFNAAAVRQFGYAEEEVIGQ--NLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQR   99 (130)
T ss_dssp             SSEEEEEETT----SBEEEECHHHHHHHCCCHHHHTTS--BGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTSCEEEEEEC
T ss_pred             cCeEEEECCC----CeEEEEcHHHHHHHCCCHHHHcCC--cHHHHCCchhHHHHHHHHHHHHhcCCccccCCeeEEEEEe
Confidence            5789999987    899999999999999999999998  655555443322222233333333321    234667789


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      ++|+.+|++
T Consensus       100 kdG~~~~~~  108 (130)
T 1d06_A          100 KDGSTFPMK  108 (130)
T ss_dssp             TTSCEEEEE
T ss_pred             CCCCEEEEE
Confidence            999988875

>1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain, membrane protein; 2.60A {Homo sapiens} SCOP: d.110.3.6

Probab=99.35  E-value=4.7e-11  Score=65.49  Aligned_cols=82  Identities=41%  Similarity=0.802  Sum_probs=65.8

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCC--cccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCA--CKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~--~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      +++|+++|...++ ++|+++|++++.++|++.++++|+  .  ...+.++.........+...+..+..+..++...+++
T Consensus         1 ~~~i~i~d~~~~~-g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (110)
T 1byw_A            1 SRKFIIANARVEN-CAVIYCNDGFCELCGYSRAEVMQR--PCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKD   77 (110)
T ss_dssp             CCEEEEEETTSSS-CBEEEECHHHHHHHTCCHHHHTTS--BTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTT
T ss_pred             CCCEEEEeccCCC-CcEEEECHHHHHHhCCCHHHHccC--CCccccccCCcCCHHHHHHHHHHHhcCCCceEEEEEEcCC
Confidence            4688999975444 899999999999999999999998  6  4555555556666667777788888888888888899


Q ss_pred             CCeeeec
Q psy8548          80 GYHEEEE   86 (102)
Q Consensus        80 G~~~~~~   86 (102)
                      |..+|+.
T Consensus        78 g~~~~~~   84 (110)
T 1byw_A           78 GSCFLCL   84 (110)
T ss_dssp             SCEEEEE
T ss_pred             CCEEEEE
Confidence            9887764

>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A

Probab=99.32  E-value=7.9e-12  Score=71.62  Aligned_cols=79  Identities=16%  Similarity=0.177  Sum_probs=59.3

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCC-HHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTS-EEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~-~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      +.+|+ ++.+    ++|+++|++|++++||+.++++|+  ....+.++... ......+...+..+..+..++..++++|
T Consensus        13 ~~~i~-~~~~----g~i~~~N~a~~~l~G~~~~el~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG   85 (120)
T 3mqq_A           13 PIGLV-LSRD----RVIEDCNDELAAIFRCARADLIGR--SFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGG   85 (120)
T ss_dssp             SSEEE-EEET----TEEEEECHHHHHHTTSCHHHHTTC--BGGGGSSSHHHHHHHHHHHHHHHHHHSCEEEEEEEECTTS
T ss_pred             CceEE-EecC----CEEHHHHHHHHHHhCcCHHHhCCC--chhhccCChhhHHHHHHHHHHHHhcCCcceEEEEEEeCCC
Confidence            45675 4655    899999999999999999999998  65555443222 2344455566677778889999999999


Q ss_pred             Ceeeecc
Q psy8548          81 YHEEEEE   87 (102)
Q Consensus        81 ~~~~~~~   87 (102)
                      +.+|+.-
T Consensus        86 ~~~~~~~   92 (120)
T 3mqq_A           86 ELFWCHV   92 (120)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEE
Confidence            9998753

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

Probab=99.32  E-value=5.5e-12  Score=72.99  Aligned_cols=77  Identities=12%  Similarity=0.018  Sum_probs=56.1

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH-hCCcEEEEEEEEecC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE-SKTELKLEVIFYKKN   79 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~-~~~~~~~e~~~~~~~   79 (102)
                      +++.|+++|.+    |+++|+|+++++++||+.++++|+  ....+.+|.+.....    ..+. .......++++++++
T Consensus         8 ~~d~i~v~d~~----G~i~yvn~~~~~~lGy~~~el~G~--~~~~~ihp~D~~~~~----~~~~~~~~~~~~e~r~~~kd   77 (111)
T 2vlg_A            8 KTDIHAVLASN----GRIIYISANSKLHLGYLQGEMIGS--FLKTFLHEEDQFLVE----SYFYNEHHLMPCTFRFIKKD   77 (111)
T ss_dssp             -CCEEEEECTT----SBEEEECTTHHHHHSCCHHHHTTS--BGGGGBCGGGHHHHH----HHHHCSCCSSCEEEEEECTT
T ss_pred             CCCEEEEEcCC----CeEEEEChHHHHHhCCCHHHHcCC--cHHHeECHhHHHHHH----HHHhccCCCccEEEEEEcCC
Confidence            35678899877    899999999999999999999998  544444444433332    2222 233345678889999


Q ss_pred             CCeeeecc
Q psy8548          80 GYHEEEEE   87 (102)
Q Consensus        80 G~~~~~~~   87 (102)
                      |+.+|++.
T Consensus        78 G~~~wve~   85 (111)
T 2vlg_A           78 HTIVWVEA   85 (111)
T ss_dssp             SCEEEEEE
T ss_pred             CCEEEEEE
Confidence            99999865

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

Probab=99.31  E-value=5.1e-12  Score=74.84  Aligned_cols=80  Identities=13%  Similarity=0.145  Sum_probs=54.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-------CcEEEEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-------TELKLEV   73 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-------~~~~~e~   73 (102)
                      ++++|+++|.+    |+|+++|+++++++||+.++++|+  +...+.++.........+......+       ..+..++
T Consensus        16 ~~d~i~~~D~~----g~I~~~N~aa~~l~G~~~~el~G~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~   89 (129)
T 3mfx_A           16 LTEAMILVNAN----GFIRSCNQRSAELLDCPQVSLKGQ--DWRNFLTEHHQARYDNLLSHDVQLGTNCGQPVQHPAQET   89 (129)
T ss_dssp             CSSEEEEEETT----SBEEEECHHHHHHTTSCHHHHTTS--BGGGGBCTTCCGGGGCTTC----------CCSCEEEEEE
T ss_pred             CCceEEEECCC----CEEEeEhHHHHHHHCcCHHHHcCC--cHHHHcChHhHHHHHHHHHHHHhcCcccccccCCCceEE
Confidence            46799999998    999999999999999999999999  6554444433221111111111111       1345788


Q ss_pred             EEEecCCCeeeec
Q psy8548          74 IFYKKNGYHEEEE   86 (102)
Q Consensus        74 ~~~~~~G~~~~~~   86 (102)
                      ..++++|+.+|++
T Consensus        90 ~~~rkdG~~~~ve  102 (129)
T 3mfx_A           90 TLICASGKAKDVE  102 (129)
T ss_dssp             EEECTTSCEEEEE
T ss_pred             EEEcCCCCEEEEE
Confidence            8899999999886

>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=99.26  E-value=2.3e-11  Score=68.68  Aligned_cols=75  Identities=11%  Similarity=0.173  Sum_probs=56.5

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|.+    |+++++|+++++++||+.++++|+  ....+.+......     +..+..+..+..+....+++|
T Consensus        22 ~~~~i~~~d~~----g~i~~~N~~~~~l~G~~~~el~g~--~~~~~~~~~~~~~-----~~~~~~~~~~~~e~~~~~~~g   90 (118)
T 3olo_A           22 AVEASFCLGDN----WQFLYVNDATCRMTEYSREQLLSM--NLQDIDVDFALHD-----WEEIRQKNNYTFKTRYRSQSG   90 (118)
T ss_dssp             CSSEEEEECTT----SBEEEECHHHHHHHCCCHHHHTTC--BGGGTBTTGGGSC-----HHHHHHHSEEEEEEEEECTTC
T ss_pred             CCceEEEECCC----CcEEEEHHHHHHHHCCCHHHHhCC--ChhhcccccCHHH-----HHHHHhcCcEEEEEEEEccCC
Confidence            35789999987    899999999999999999999998  5544443222111     233445567778888899999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +.+|++
T Consensus        91 ~~~~~~   96 (118)
T 3olo_A           91 RIFLVE   96 (118)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            988875

>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea}

Probab=99.25  E-value=2e-10  Score=64.19  Aligned_cols=80  Identities=20%  Similarity=0.247  Sum_probs=65.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++.+++++|.+    ++++++|++++.++|++.++++|+  ....+.++.........+...+..+..+..+....+.+|
T Consensus        16 ~~~~i~~~d~~----~~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   89 (124)
T 3lyx_A           16 VFDAIVVTDLQ----GFIIDWNKGSETLYGYSKEQAIGQ--PVNMLHVPGDTEHITSEVISAVENQGKWTGEIRMLHKDG   89 (124)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHHCCCHHHHTTS--BGGGGSCTTTHHHHHHHHHHHHHHTSCEEEEEEEECTTS
T ss_pred             cCceEEEECCC----CcEeehhhHHHHHhCCCHHHHcCC--CHHHhcCcchhhHHHHHHHHHHHcCCcccceEEEEccCC
Confidence            35789999987    899999999999999999999998  655555555555566667778888888888999889999


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ..+|+.
T Consensus        90 ~~~~~~   95 (124)
T 3lyx_A           90 HIGWIE   95 (124)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            887764

>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=99.19  E-value=8.4e-10  Score=61.93  Aligned_cols=80  Identities=29%  Similarity=0.606  Sum_probs=64.9

Q ss_pred             CCceEEEEe---CCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEe
Q psy8548           1 MNSNFVLGN---AQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK   77 (102)
Q Consensus         1 ~~~~i~i~d---~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~   77 (102)
                      ++++++++|   .+    +.++++|++++.++|++.++++|+  ....+..+.........+...+..+..+..++...+
T Consensus        15 ~~~~i~~~d~~d~~----~~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (130)
T 2z6d_A           15 LQQTFVVSDATQPH----CPIVYASSGFFTMTGYSSKEIVGR--NCRFLQGPDTDKNEVAKIRDCVKNGKSYCGRLLNYK   88 (130)
T ss_dssp             TTCEEEEEETTSTT----CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEEC
T ss_pred             cccceeeeeccCCC----CcEEEecHHHHHHhCcCHHHHcCC--ChhhccCCCCCchHHHHHHHHHHcCCcceeEEEEEc
Confidence            357889999   65    899999999999999999999998  665566665666666777777888888888888888


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      .+|..+|+.
T Consensus        89 ~~g~~~~~~   97 (130)
T 2z6d_A           89 KDGTPFWNL   97 (130)
T ss_dssp             TTSCEEEEE
T ss_pred             CCCcEEEEE
Confidence            888877654

>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=99.18  E-value=8.8e-10  Score=63.25  Aligned_cols=80  Identities=31%  Similarity=0.672  Sum_probs=65.1

Q ss_pred             CCceEEEEeC---CCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEe
Q psy8548           1 MNSNFVLGNA---QVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK   77 (102)
Q Consensus         1 ~~~~i~i~d~---~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~   77 (102)
                      ++.+++++|.   +    +.++++|++++.++|++.++++|+  +...+..+.........+...+..+..+..++...+
T Consensus        11 ~~~~i~~~d~~~~~----~~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (146)
T 2v0u_A           11 IEKNFVITDPRLPD----NPIIFASDSFLQLTEYSREEILGR--NCRFLQGPETDRATVRKIRDAIDNQTEVTVQLINYT   84 (146)
T ss_dssp             SSSCEEEECTTSTT----CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHTTCCEEEEEEEEC
T ss_pred             CCCcEEEEcCCCCC----ceEEEEcHHHHHHHCcCHHHHcCC--CHHHhcCCcCChHHHHHHHHHHhcCCCcceEEEEEe
Confidence            3568899998   6    899999999999999999999998  666566666666667777788888888888888888


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      .+|..+|+.
T Consensus        85 ~~g~~~~~~   93 (146)
T 2v0u_A           85 KSGKKFWNL   93 (146)
T ss_dssp             TTCCEEEEE
T ss_pred             cCCcEEEEE
Confidence            888766553

>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling protein; HET: FMN; 2.63A {Pseudomonas putida}

Probab=99.17  E-value=4.3e-10  Score=66.89  Aligned_cols=80  Identities=25%  Similarity=0.456  Sum_probs=65.7

Q ss_pred             CCceEEEEeCCCCCCC---CEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEe
Q psy8548           1 MNSNFVLGNAQVPSLY---PIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYK   77 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~---~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~   77 (102)
                      +..+|+++|.+    +   +|+++|++++.++|++.++++|+  ....+..+.........+...+..+..+..++...+
T Consensus        34 ~~~~i~~~d~~----~~~~~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (162)
T 3sw1_A           34 SNDGIVVAEKE----GDDTILIYVNAAFEYLTGYSRDEILYQ--DCRFLQGDDRDQLGRARIRKAMAEGRPCREVLRNYR  107 (162)
T ss_dssp             CSSEEEEEEEE----TTEEEEEEECHHHHHHHTCCHHHHTTS--BGGGGTTTCCCCHHHHHHHHHHHHTCCEEEEEEEEC
T ss_pred             ccCcEEEEeCC----CCccEEEEECHHHHHHHCCCHHHHcCC--CcceecCCCcCHHHHHHHHHHHhcCCCCcceEEEEC
Confidence            35689999987    7   99999999999999999999998  656565555555666677788888888888888888


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      .+|..+|+.
T Consensus       108 ~~g~~~~~~  116 (162)
T 3sw1_A          108 KDGSAFWNE  116 (162)
T ss_dssp             TTCCEEEEE
T ss_pred             CCCCEEEEE
Confidence            899887764

>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=99.15  E-value=8.5e-10  Score=62.87  Aligned_cols=79  Identities=42%  Similarity=0.825  Sum_probs=64.2

Q ss_pred             CceEEEEeC---CCCCCCCEEEecHHHHHhhCCChhhhcCCCCC--cccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEE
Q psy8548           2 NSNFVLGNA---QVPSLYPIVYCSDGFCELSGFARAQIMQKGCA--CKFLYGPDTSEEHKTQIEKALESKTELKLEVIFY   76 (102)
Q Consensus         2 ~~~i~i~d~---~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~--~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~   76 (102)
                      +.+|+++|.   +    ++++++|++++.++|++.++++|+  .  ...+..+.........+...+..+..+..+....
T Consensus        29 ~~~i~~~d~~~~~----g~i~~~N~~~~~l~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (138)
T 2l0w_A           29 SRKFIIANARVEN----CAVIYCNDGFCELCGYSRAEVMQR--PCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEIAFY  102 (138)
T ss_dssp             TSEEEEEESSSTT----CBEEEECSHHHHHHSCCHHHHTTS--BTTCGGGCCTTCCHHHHHHHHHHTTCSSCEEEEEEEE
T ss_pred             CCCEEEEecCCCC----CEEEEeCHHHHHHhCCCHHHHcCC--CCcccccCCcccchhHHHHHHHHHhhcCCceeEEEEE
Confidence            568899998   6    899999999999999999999998  6  4556666666666667777777777788888888


Q ss_pred             ecCCCeeeec
Q psy8548          77 KKNGYHEEEE   86 (102)
Q Consensus        77 ~~~G~~~~~~   86 (102)
                      +++|..+|+.
T Consensus       103 ~~~g~~~~~~  112 (138)
T 2l0w_A          103 RKDGSCFLCL  112 (138)
T ss_dssp             CTTSCEEEEE
T ss_pred             CCCCCEEEEE
Confidence            8899887754

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

Probab=99.11  E-value=8.3e-10  Score=61.51  Aligned_cols=78  Identities=15%  Similarity=0.244  Sum_probs=54.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEE-EEEecC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEV-IFYKKN   79 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~-~~~~~~   79 (102)
                      ++.+|+++|.+    ++++++|+++++++|++.++++|+  ....+. +.........+...+ .+.....+. ...+.+
T Consensus        12 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   83 (114)
T 3luq_A           12 APAALAMFDRE----MRYLAVSRRWREDYGLGDGDILGM--SHYDIF-PEIGEEWKSVHRRGL-AGEVIRVEEDCFVRAD   83 (114)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHTTCCSSCCTTC--BHHHHC-TTCCHHHHHHHHHHH-TTCCEEEEEEEEEC--
T ss_pred             CCceEEEEcCC----cEEEEECHHHHHHHCCCHHHHcCC--cHHHHC-CccHHHHHHHHHHHh-cCCcceeeeeEEEcCC
Confidence            35789999987    899999999999999999999998  554444 334444444444444 455544443 677888


Q ss_pred             CCeeeec
Q psy8548          80 GYHEEEE   86 (102)
Q Consensus        80 G~~~~~~   86 (102)
                      |..+|+.
T Consensus        84 g~~~~~~   90 (114)
T 3luq_A           84 GRTQWLR   90 (114)
T ss_dssp             CCEEEEE
T ss_pred             CcEEEEE
Confidence            9887764

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

Probab=99.11  E-value=1.1e-10  Score=66.22  Aligned_cols=81  Identities=12%  Similarity=-0.008  Sum_probs=61.7

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCc-ccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCAC-KFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~-~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      +.++|.+|..  . ++++|+|+++++++||+.+++++.  .. ..+.+|.+.......+...+..+..+..++++++++|
T Consensus         3 ~~giw~~d~~--~-~~~~~~n~~~~~l~G~~~~e~~~~--~~~~~~ihpdd~~~~~~~~~~~~~~~~~~~~e~r~~~~dG   77 (115)
T 3h9w_A            3 KAIPWKINWQ--T-MAFEYIGPQIEALLGWPQGSWKSV--EDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDG   77 (115)
T ss_dssp             CCEEEEEETT--T-TEEEEECTHHHHHHCSCGGGCCBH--HHHHHSBCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTS
T ss_pred             ceEEEEEEcC--C-CcEEEEChhHHHHhCCChHHccCH--HHHHHhcCHHHHHHHHHHHHHHHhcCCcccEEEEEEcCCC
Confidence            4678888954  3 789999999999999999998863  21 1233344444555666777777788999999999999


Q ss_pred             Ceeeecc
Q psy8548          81 YHEEEEE   87 (102)
Q Consensus        81 ~~~~~~~   87 (102)
                      +.+|+..
T Consensus        78 ~~~w~~~   84 (115)
T 3h9w_A           78 HYVWIRD   84 (115)
T ss_dssp             CEEEEEE
T ss_pred             CEEEEEE
Confidence            9999864

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

Probab=99.10  E-value=7.3e-10  Score=62.90  Aligned_cols=79  Identities=14%  Similarity=0.222  Sum_probs=58.3

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|.+    ++++++|+++++++|++.++++|+  ....+.++.........+...+..+.. ..++...+.+|
T Consensus         8 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g   80 (126)
T 3mjq_A            8 IEDMILIINRE----GRLLYANTAVPKKLGYTHEELMSM--HILTITSAGKMAEGEKILAELFAGKKE-SLPLSLEKKEG   80 (126)
T ss_dssp             CSSEEEEEETT----SBEEEECTHHHHHHSCCHHHHHHS--BHHHHHCTTCHHHHHHHHHHHHHTCCS-EEEEEEECTTS
T ss_pred             CCceEEEEeCC----CcEEEEcHHHHHHHCCCHHHHcCC--CHHHHcCchhHHHHHHHHHHHHhCCCc-eeEEEEEccCC
Confidence            35789999987    899999999999999999999998  655455544444444444444444443 67777788899


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      ..+|+.
T Consensus        81 ~~~~~~   86 (126)
T 3mjq_A           81 TSIPAK   86 (126)
T ss_dssp             CEEEEE
T ss_pred             CEEEEE
Confidence            887765

>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=99.08  E-value=1.2e-09  Score=62.59  Aligned_cols=76  Identities=17%  Similarity=0.225  Sum_probs=50.2

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhc--CCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIM--QKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~--g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      +++|+++|.+    |+|+++|++|++++||+.++++  |+  ....+.+  ........+ .....+.....+....+++
T Consensus        27 ~~~i~~~d~~----g~i~~~N~a~~~~~G~~~~el~g~g~--~~~~~~~--~~~~~~~~~-~~~~~~~~~~~e~~~~~~d   97 (126)
T 3bwl_A           27 PDMIDVLDAD----GTICEVNQRFCAELGYDESEVLGRSI--WEFDLMF--DAEDVQTQL-SGFSVDERRKFEGLYERRD   97 (126)
T ss_dssp             SSEEEEECTT----CBEEEECHHHHHHHTCCGGGTTTSBG--GGTBTTC--CHHHHHHHH-HTCCTTCEEEEEEEEECTT
T ss_pred             CcEEEEEcCC----CCEEEEcHHHHHHhCCCHHHHhhCCC--chhhccC--CHHHHHHHH-HHHhcCCCcceEEEEEeCC
Confidence            5688999987    8999999999999999999995  45  3332322  212221111 1111233445566777999


Q ss_pred             CCeeeec
Q psy8548          80 GYHEEEE   86 (102)
Q Consensus        80 G~~~~~~   86 (102)
                      |+.+|++
T Consensus        98 G~~~~~~  104 (126)
T 3bwl_A           98 GSTMSVE  104 (126)
T ss_dssp             SCEEEEE
T ss_pred             CCEEEEE
Confidence            9988875

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

Probab=99.08  E-value=8.4e-10  Score=62.34  Aligned_cols=82  Identities=12%  Similarity=0.071  Sum_probs=62.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +.+++++|..    ++++++|++++.++|++.++++|.......+..+.+.......+...+..+..+..++++.+++|.
T Consensus        17 ~~~i~~~d~~----~~~~~~n~~~~~~~G~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~   92 (125)
T 3nja_A           17 GIGSWVLHME----SGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARVRRELDRHVLGDRPFDVEYRIVRPDGQ   92 (125)
T ss_dssp             CCEEEEEETT----TTEEEECHHHHHHHTCCTTTCCCBHHHHHHHBCTTTHHHHHHHHHHHHHSCCCEEEEEEEECTTSC
T ss_pred             CeeEEEEEcC----CCcEEECHHHHHHhCCCcccccccHHHHHhhcChhHHHHHHHHHHHHHhcCCCceEEEEEECCCCC
Confidence            4688999987    899999999999999999998873102222334445555666667777778888899999999999


Q ss_pred             eeeecc
Q psy8548          82 HEEEEE   87 (102)
Q Consensus        82 ~~~~~~   87 (102)
                      .+|+..
T Consensus        93 ~~~~~~   98 (125)
T 3nja_A           93 VRELLE   98 (125)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            888754

>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=99.07  E-value=7.7e-10  Score=63.47  Aligned_cols=77  Identities=13%  Similarity=0.127  Sum_probs=55.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++++|+++|.+    ++|+++|+++++++|++.++++|+  +...+.++.........+...+..+.....++.....+|
T Consensus        21 ~~~~i~~~D~~----g~i~~~N~a~~~l~g~~~~e~~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   94 (118)
T 3fg8_A           21 GGLGFMALDED----LRIIYVNSGCLRHVRRSRDELLGR--VVTEVLPETQGSYFDALCRKVLATGREQQTRVDSLYSPG   94 (118)
T ss_dssp             TTCEEEEECTT----CBEEEECHHHHHHHTCCHHHHTTS--BHHHHCGGGTTSHHHHHHHHHHHHCCCEEEEEECSSSTT
T ss_pred             CCceEEEECCC----CeEEEECHHHHHHhCCCHHHHcCC--cHHHHcCccchHHHHHHHHHHHHcCCceEEEEEEEcCCC
Confidence            46789999987    899999999999999999999998  654444443344455666777778877766433333355


Q ss_pred             Cee
Q psy8548          81 YHE   83 (102)
Q Consensus        81 ~~~   83 (102)
                      .++
T Consensus        95 ~~~   97 (118)
T 3fg8_A           95 MTI   97 (118)
T ss_dssp             CEE
T ss_pred             eEE
Confidence            543

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

Probab=99.04  E-value=2.7e-09  Score=62.92  Aligned_cols=82  Identities=13%  Similarity=0.159  Sum_probs=63.0

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY   81 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~   81 (102)
                      +.++|.+|+.    +.++++|++++.++||+..++.+.......+.+|.+.......+...+..+..+..++++++++|.
T Consensus        19 ~~g~w~~d~~----~~~~~~s~~~~~~~G~~~~~~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~e~r~~~~~G~   94 (142)
T 3mr0_A           19 SAGLWDWNPK----TGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARVLAALKAHLEHRDTYDVEYRVRTRSGD   94 (142)
T ss_dssp             TCEEEEECTT----TCCEEECHHHHHHTTCCGGGSCSEEC---CCBCTTTHHHHHHHHHHHHHHCCCEEEEEEEECTTSC
T ss_pred             CcEEEEEEcC----CCeEEECHHHHHHhCCCccccCCCHHHHHhhcCHHHHHHHHHHHHHHHhCCCceEEEEEEECCCCC
Confidence            4578889987    788999999999999999987653101222345556666777777888888889999999999999


Q ss_pred             eeeecc
Q psy8548          82 HEEEEE   87 (102)
Q Consensus        82 ~~~~~~   87 (102)
                      .+|+..
T Consensus        95 ~~w~~~  100 (142)
T 3mr0_A           95 FRWIQS  100 (142)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            988764

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

Probab=99.00  E-value=3.2e-10  Score=77.36  Aligned_cols=71  Identities=10%  Similarity=0.048  Sum_probs=57.8

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~~   88 (102)
                      |.++|+|++++.++||+.++++|+  ....+.+|++.......+...+..+..+..++++++++|..+|+++.
T Consensus       261 g~~~~vn~~~~~ilGY~~eEl~g~--~~~~~iHpdD~~~~~~~~~~~l~~g~~~~~eyR~~~kdG~~vWv~~~  331 (361)
T 4f3l_A          261 WKFLFLDHRAPPIIGYLPFEVLGT--SGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTH  331 (361)
T ss_dssp             SBEEEECTTSHHHHCCCHHHHTTS--BGGGGBCHHHHHHHHHHHHHHHHHSEEECCCEEEECTTSEEEEEEEE
T ss_pred             ceEEEECChhhhhhCcCHHHHcCC--CHHHeECHHHHHHHHHHHHHHHhCCCcceEEEEEEecCCCEEEEEEE
Confidence            899999999999999999999998  54445555555555566777777777777889999999999999763

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

Probab=98.99  E-value=2.3e-10  Score=64.95  Aligned_cols=79  Identities=14%  Similarity=0.218  Sum_probs=51.7

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHH-HHh-CCcE---EEEEEEE
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKA-LES-KTEL---KLEVIFY   76 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~-l~~-~~~~---~~e~~~~   76 (102)
                      +++|+++|.+  . |+|+++|+++++++||+.++++|+  +...+.++..... ...+... +.. +...   ..++..+
T Consensus         8 ~~~i~~~d~~--~-g~I~~~N~aa~~l~G~~~~el~g~--~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (114)
T 1ll8_A            8 NKAIFTVDAK--T-TEILVANDKACGLLGYSSQDLIGQ--KLTQFFLRSDSDV-VEALSEEHMEADGHAAVVFGTVVDII   81 (114)
T ss_dssp             TCEEEEEETT--T-CBEEEECTTHHHHHTCCTTTTTTS--BGGGGSSCTTTHH-HHHTTSSTTSSSSCSSCCCSSSEEEC
T ss_pred             CceEEEEECC--C-CeEEEehHHHHHHhCCCHHHHcCC--CHHHhcCcchhHH-HHHHHHHhhccCCcceeccCcEEEEE
Confidence            4688999974  2 799999999999999999999998  6555555433322 2222211 111 1111   2345667


Q ss_pred             ecCCCeeeec
Q psy8548          77 KKNGYHEEEE   86 (102)
Q Consensus        77 ~~~G~~~~~~   86 (102)
                      +++|+.+|++
T Consensus        82 ~~dG~~~~v~   91 (114)
T 1ll8_A           82 SRSGEKIPVS   91 (114)
T ss_dssp             CTTCCCEEEE
T ss_pred             ecCCCEEEEE
Confidence            8999988765

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

Probab=98.98  E-value=1.4e-09  Score=73.98  Aligned_cols=78  Identities=14%  Similarity=0.096  Sum_probs=60.2

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc-----EEEEEEEEecC
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE-----LKLEVIFYKKN   79 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~-----~~~e~~~~~~~   79 (102)
                      +...+++    |.++|+|+++..++||..++++|+  ....+.+|++.....+.+...+..|..     ...++++++++
T Consensus       157 i~r~~~d----G~~~yvn~~~~~lLGY~peELiG~--s~~~~vHPdD~~~~~~~~~~~l~~G~~~~~~~~s~~yR~~~kd  230 (339)
T 3rty_A          157 AIRHTAT----GIISHVDSAAVSALGYLPQDLIGR--SIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQN  230 (339)
T ss_dssp             EEEEETT----CBEEEECTTHHHHHCCCHHHHTTS--BGGGGBCGGGHHHHHHHHHHHHHHTTSTTCCCBCCCEEEECTT
T ss_pred             EEEECCC----CeEEEcChhhhcccCCCHHHHcCC--cHHHEECHHHHHHHHHHHHHHHHcCCcccccccceEEEEEccC
Confidence            4455565    899999999999999999999999  544555565555566666677766653     35689999999


Q ss_pred             CCeeeecch
Q psy8548          80 GYHEEEEEE   88 (102)
Q Consensus        80 G~~~~~~~~   88 (102)
                      |..+|+++.
T Consensus       231 G~~vWlet~  239 (339)
T 3rty_A          231 GCYVLLETE  239 (339)
T ss_dssp             SCEEEEEEE
T ss_pred             CCEEEEEEE
Confidence            999999764

>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=98.93  E-value=1.2e-08  Score=60.34  Aligned_cols=79  Identities=10%  Similarity=0.052  Sum_probs=58.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccc-ccCCCCCHHHHHHHHHHHHhCCcEEEEEEE-Eec
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKF-LYGPDTSEEHKTQIEKALESKTELKLEVIF-YKK   78 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~-l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~-~~~   78 (102)
                      ++.|++++|.+    ++|+++|++.++++|+++++++|+  ++.. +.+......+...+.+.+..+. +...... .+.
T Consensus        26 l~~Gii~lD~~----g~I~~~N~~~e~~sG~~~~eviGk--~~f~~~~~~~~~~~f~~rf~~~~~~g~-l~~~~~~v~~~   98 (125)
T 1nwz_A           26 LAFGAIQLDGD----GNILQYNAAEGDITGRDPKQVIGK--NFFKDVAPCTDSPEFYGKFKEGVASGN-LNTMFEYTFDY   98 (125)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHHCCCHHHHTTS--BCCCCCCGGGCSTTTHHHHHHHHHHTC-CEEEEEEEECT
T ss_pred             cCceEEEECCC----CEEEEEHHHHHHHhCCCHHHHcCC--chhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEEEcC
Confidence            46789999998    999999999999999999999999  6533 3332334455666777777666 4444443 478


Q ss_pred             CCCeeeec
Q psy8548          79 NGYHEEEE   86 (102)
Q Consensus        79 ~G~~~~~~   86 (102)
                      +|+++++.
T Consensus        99 ~~~p~~v~  106 (125)
T 1nwz_A           99 QMTPTKVK  106 (125)
T ss_dssp             TSCCEEEE
T ss_pred             CCCEEEEE
Confidence            88877664

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

Probab=98.93  E-value=4.8e-10  Score=63.08  Aligned_cols=80  Identities=11%  Similarity=-0.062  Sum_probs=62.7

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCc--ccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCAC--KFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~--~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      +.+++++|..    +.++++|++++.++||+.+++.+.  ..  ..+.++.+.......+...+..+..+..++++.+++
T Consensus        14 ~~~i~~~d~~----~~~~~~n~~~~~~~G~~~~~~~~~--~~~~~~~i~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~~   87 (118)
T 3icy_A           14 PAAIYHLDVS----GQATIRFRPPAFLKTLVSEHAGTT--RLNTLSMIHHDDRHMLSNAYSKLREAKHSLTLVYRIVTPE   87 (118)
T ss_dssp             CCCCEEECTT----SCEEECCCCCGGGGGGEEEETTEE--EEGGGGGBCGGGHHHHHHHHHHHHHSCCEEEEEEEEECTT
T ss_pred             CceEEEEEcC----CCceEEechhHhhcCCCHHHccCC--hhHHHHHcCHHHHHHHHHHHHHHHhcCCCceEEEEEECCC
Confidence            5678888987    899999999999999999998775  32  223344455556666777777888888999999999


Q ss_pred             CCeeeecc
Q psy8548          80 GYHEEEEE   87 (102)
Q Consensus        80 G~~~~~~~   87 (102)
                      |+.+|+..
T Consensus        88 g~~~w~~~   95 (118)
T 3icy_A           88 GKLHWIED   95 (118)
T ss_dssp             CCEEEEEE
T ss_pred             CCEEEEEE
Confidence            99988864

>1mzu_A PPR; photoactive yellow protein, PAS, PYP, signaling protein; HET: HC4; 2.00A {Rhodospirillum centenum} SCOP: d.110.3.1

Probab=98.92  E-value=1.4e-08  Score=60.16  Aligned_cols=79  Identities=10%  Similarity=0.005  Sum_probs=58.3

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccc-ccCCCCCHHHHHHHHHHHHhCCcEEEEEEE-Eec
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKF-LYGPDTSEEHKTQIEKALESKTELKLEVIF-YKK   78 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~-l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~-~~~   78 (102)
                      ++.|++++|.+    ++|+++|++.++++|+++++++|+  ++.. +.+......+...+.+.+..+. +...... .+.
T Consensus        31 l~~GiivlD~d----g~I~~~N~~~e~isG~s~eeviGk--~~f~~~~p~~~~~~f~grf~~~~~~G~-l~~~~~yv~~~  103 (129)
T 1mzu_A           31 LPVGAIQVDGS----GVIHRYNRTESRLSGRIPERVIGR--NFFTEVAPCTNIPAFSGRFMDGVTSGT-LDARFDFVFDF  103 (129)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHHCCCHHHHTTS--BCCCCCCGGGCSTTTHHHHHHHHHTSC-CEEEEEEEEEC
T ss_pred             cCceEEEECCC----CeEEEEHHHHHHHhCCCHHHHcCC--chhhhccchhcccHHHHHHHHHHhcCc-eeEEEEEEEcC
Confidence            46789999998    999999999999999999999999  6533 3332334455666777777665 5544444 478


Q ss_pred             CCCeeeec
Q psy8548          79 NGYHEEEE   86 (102)
Q Consensus        79 ~G~~~~~~   86 (102)
                      +|+++++.
T Consensus       104 ~~~p~~v~  111 (129)
T 1mzu_A          104 QMAPVRVQ  111 (129)
T ss_dssp             SSCEEEEE
T ss_pred             CCCEEEEE
Confidence            88877764

>3a0s_A Sensor protein; PAS-fold, kinase, phosphoprotein, transferase, two-component regulatory system; HET: PG4 PGE; 1.47A {Thermotoga maritima} PDB: 3a0v_A*

Probab=98.90  E-value=6e-08  Score=51.63  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=46.0

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELK   70 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~   70 (102)
                      |+++|+++|.+    ++++++|+++++++|++.++++|+  +...+ +  ........+...+..+..+.
T Consensus         1 ~~~~i~~~d~~----g~i~~~N~~~~~l~g~~~~~~~g~--~~~~~-~--~~~~~~~~~~~~~~~~~~~~   61 (96)
T 3a0s_A            1 METAIITLSKD----GRITEWNKKAEQLFGLKKENVLGR--RLKDL-P--DFEEIGSVAESVFENKEPVF   61 (96)
T ss_dssp             CCCEEEEEETT----SBEEEECHHHHHHHCCCHHHHTTS--BGGGS-T--TCHHHHHHHHHHHHHTCCEE
T ss_pred             CCceEEEEcCC----CCEeehhHHHHHHhCCCHHHhcCC--CHHHC-c--chHHHHHHHHHHhccCCeEE
Confidence            67899999987    899999999999999999999998  65544 2  23344445555566565553

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

Probab=98.90  E-value=6.6e-09  Score=70.02  Aligned_cols=71  Identities=13%  Similarity=0.101  Sum_probs=56.3

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc---EEEEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE---LKLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~---~~~e~~~~~~~G~~~~~~~~   88 (102)
                      |.++|+|+++..++||..++++|+  ....+.++++.....+.....+..+..   ...++++++++|.++|+++.
T Consensus       184 G~~~yvs~~~~~lLGY~peELig~--s~~~~vHPdD~~~~~~~~~~~l~~~~~~~f~s~~yR~~~kdG~~vwvet~  257 (317)
T 4dj3_A          184 CVFLEVDERAVPLLGYLPQDLIGT--SILTYLHPEDRPLMVAIHQKVLKYAGHPPFEHSPVRFCTQNGEYVILDSS  257 (317)
T ss_dssp             SBEEEECTTHHHHHSCCHHHHTTS--BGGGGBCTTTTTHHHHHHHHHHHTTTSCCEECCCEEEECTTSCEEEEEEE
T ss_pred             CeEEEEChHHhhhcCcChHHHcCC--CHHHeECHHHHHHHHHHHHHHHHcCCCccccceEEEEEccCCCEEEEEEE
Confidence            899999999999999999999999  544455555555666666666765543   35789999999999999875

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

Probab=98.86  E-value=2.7e-09  Score=73.48  Aligned_cols=78  Identities=9%  Similarity=0.091  Sum_probs=56.5

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCC-cEEEEEEEEecCCCee
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKT-ELKLEVIFYKKNGYHE   83 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~-~~~~e~~~~~~~G~~~   83 (102)
                      ++..+.+    |.++|+|++++.++||+.++++|+  ....+.+|++.......+...+..+. .+..++++++++|.++
T Consensus       281 i~~~~~d----g~~~~vn~~~~~ilGY~~eEl~g~--~~~~~iHpdD~~~~~~~~~~~l~~~~~~~~~eyR~~~kdG~~v  354 (387)
T 4f3l_B          281 VSRHAID----GKFVFVDQRATAILAYLPQELLGT--SCYEYFHQDDIGHLAECHRQVLQTREKITTNCYKFKIKDGSFI  354 (387)
T ss_dssp             EEEECTT----SBEEEECTHHHHHHCCCHHHHTTS--BGGGTBCHHHHHHHHHHHHHHTTCSSCEECCCEEEECTTSCEE
T ss_pred             EEEECCC----CEEEEECCCcccccCCCHHHHcCC--cHHHeeCHHHHHHHHHHHHHHHhcCCCeeeEEEEEEccCCCEE
Confidence            3444555    899999999999999999999998  44334444444444445555554444 3557999999999999


Q ss_pred             eecch
Q psy8548          84 EEEEE   88 (102)
Q Consensus        84 ~~~~~   88 (102)
                      |+++.
T Consensus       355 Wv~~~  359 (387)
T 4f3l_B          355 TLRSR  359 (387)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99753

>3b33_A Sensor protein; structural genomics, PAS domain, nitrogen regulation protein APC91440.4, PSI-2; HET: MSE; 1.83A {Vibrio parahaemolyticus rimd 2210633}

Probab=98.86  E-value=1.1e-08  Score=57.59  Aligned_cols=76  Identities=14%  Similarity=0.135  Sum_probs=51.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcE-EEEEEEEecC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTEL-KLEVIFYKKN   79 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~-~~e~~~~~~~   79 (102)
                      ++++|+++|.+    ++|+++|+++++++|++.++++|+  +...+.++...  ....+...+..+... ..+.... ++
T Consensus        16 ~~~~i~~~D~~----g~I~~~N~aa~~l~g~~~~~~~g~--~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-~~   86 (115)
T 3b33_A           16 MVTATLILDDG----LAIRYANPAAELLFSQSAKRIVEQ--SLSQLIQHASL--DLALLTQPLQSGQSITDSDVTFV-VD   86 (115)
T ss_dssp             CSSEEEEECTT----CBEEEECHHHHHHTTSCHHHHTTC--BHHHHCSEEEC--CTHHHHHHHHHCCCEEEEEEEEE-ET
T ss_pred             cCceEEEECCC----CcEEEECHHHHHHhCCCHHHHhCC--CHHHHhCccch--hhHHHHHHHHcCCcccCCceEEe-cC
Confidence            46799999988    899999999999999999999998  54433322111  112334455555543 3455554 67


Q ss_pred             CCeeee
Q psy8548          80 GYHEEE   85 (102)
Q Consensus        80 G~~~~~   85 (102)
                      |+.+|+
T Consensus        87 g~~~~~   92 (115)
T 3b33_A           87 GRPLML   92 (115)
T ss_dssp             TEEEEE
T ss_pred             CCEEEE
Confidence            876664

>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=98.84  E-value=1.1e-08  Score=57.09  Aligned_cols=80  Identities=14%  Similarity=0.098  Sum_probs=56.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccc--ccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecC
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKF--LYGPDTSEEHKTQIEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~--l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      +.+++++|..  . ++++++|++++.++|++.++++|+  ...+  +..+......... ...+..+..+..+++..+++
T Consensus        21 ~~~i~~~d~~--~-~~i~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~~~~~   94 (125)
T 3eeh_A           21 NDILWEFTAD--L-SEVLVINSAYEDIWGRSVAKLREN--PHDFLNGIHPEDRELMKDT-MQSLMDGESADVECRVNATE   94 (125)
T ss_dssp             CCEEEEEETT--S-SCEEEECTHHHHHHSSCHHHHHHC--GGGGGGGBCHHHHHHHHHH-HHHHHTTCCEEEEEEECGGG
T ss_pred             CceEEEEEcC--C-CcEEEecHHHHHHHCCCHHHHccC--cHHHHHhcCHHHHHHHHHH-HHHHHcCCCccEEEEEEcCC
Confidence            5688888875  3 799999999999999999999987  4211  2222222223233 33356777788898888999


Q ss_pred             CCeeeecc
Q psy8548          80 GYHEEEEE   87 (102)
Q Consensus        80 G~~~~~~~   87 (102)
                      |+.+|+..
T Consensus        95 g~~~~~~~  102 (125)
T 3eeh_A           95 EYQRWVWI  102 (125)
T ss_dssp             TTCEEEEE
T ss_pred             CCEEEEEE
Confidence            98887753

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

Probab=98.84  E-value=1.8e-08  Score=67.64  Aligned_cols=71  Identities=11%  Similarity=0.126  Sum_probs=55.3

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-CcEE-EEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TELK-LEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~~~-~e~~~~~~~G~~~~~~~~   88 (102)
                      |.++|+|+++..++||..++++|+  ....+.++++.....+.....+..+ ..+. .++++++++|..+|+++.
T Consensus       175 G~~~yvd~~~~~lLGY~peELig~--s~~~~iHpdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwvet~  247 (309)
T 3gdi_A          175 CLFQAVDERAVPLLGYLPQDLIET--PVLVQLHPSDRPLMLAIHKKILQAGGQPFDYSPIRFRTRNGEYITLDTS  247 (309)
T ss_dssp             CBEEEECTTHHHHHSCCHHHHTTS--BHHHHBCTTSHHHHHHHHHHHHHTTTCCEEEEEEEEECTTSCEEEEEEE
T ss_pred             CeEEEECcccccccCcCHHHHcCC--CHHHhCCHHHHHHHHHHHHHHHhcCCceeeceEEEEEccCCCEEEEEEE
Confidence            899999999999999999999998  5444555555555555556666644 3455 589999999999999874

>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=98.80  E-value=2.2e-08  Score=59.25  Aligned_cols=79  Identities=19%  Similarity=0.221  Sum_probs=51.1

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc----EEEEEEEEe
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE----LKLEVIFYK   77 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~----~~~e~~~~~   77 (102)
                      +.+|+++|.+    +.++++|++++.++|++.++++|+  ....+.++.........+......+..    +..+....+
T Consensus        50 ~~~i~~~d~~----g~i~~~N~~~~~l~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (167)
T 1v9y_A           50 MMGAVLINEN----DEVMFFNPAAEKLWGYKREEVIGN--NIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEK  123 (167)
T ss_dssp             SSEEEEECTT----SBEEEECHHHHHHHSCCGGGTTTS--BGGGGSCGGGTTTHHHHHHHHHC----------CEEEEEC
T ss_pred             CCCEEEECCC----CcEEEECHHHHHHhCCCHHHHcCC--ChhhccCccccchHHHHHHHHhhcCCCcccccceEEEEEc
Confidence            5688899987    899999999999999999999998  555444433322222333333333322    344666777


Q ss_pred             cCCCeeeec
Q psy8548          78 KNGYHEEEE   86 (102)
Q Consensus        78 ~~G~~~~~~   86 (102)
                      .+|..+|+.
T Consensus       124 ~~g~~~~~~  132 (167)
T 1v9y_A          124 KDGSKIWTR  132 (167)
T ss_dssp             TTSCEEEEE
T ss_pred             CCCcEEEEE
Confidence            788776653

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

Probab=98.79  E-value=1.1e-08  Score=69.13  Aligned_cols=71  Identities=11%  Similarity=0.144  Sum_probs=54.0

Q ss_pred             CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHh-CCcE-EEEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALES-KTEL-KLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~-~~~~-~~e~~~~~~~G~~~~~~~~   88 (102)
                      |+++|+|+++..++||..++++|+  ....+.++++.....+.+...+.. +... ..++++++++|.++|+++.
T Consensus       186 G~~~yvd~~~~~lLGY~peELig~--s~~~~vHPdD~~~~~~~~~~~l~~~g~~~~~~~yR~~~kdG~~vwvet~  258 (320)
T 4dj2_A          186 CLFQDVDERAAPLLGYLPQDLLGA--PVLLFLHPEDRPLMLAIHKKILQLAGQPFDHSPIRFCARNGEYVTMDTS  258 (320)
T ss_dssp             CBEEEECTTHHHHHSCCHHHHTTS--BGGGGBCGGGHHHHHHHHHHHTTSSSCCEECCCEEEECSSSCEEEEECE
T ss_pred             ceEEEcCcceeccCCcChHHHcCC--cHHHhCCHHHHHHHHHHHHHHHhcCCCcccceEEEEEccCCCEEEEEEE
Confidence            899999999999999999999999  544455555544555555555553 4445 3689999999999999875

>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=98.72  E-value=2.6e-08  Score=56.41  Aligned_cols=41  Identities=7%  Similarity=0.015  Sum_probs=35.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLY   47 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~   47 (102)
                      ++++|+++|.+    |+|+++|+++++++|++.++++|+  +...+.
T Consensus        28 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~   68 (125)
T 3fc7_A           28 SPDGIVHLTTN----GTILSVNPSMAGRLGADPDTLVGQ--QLSAVM   68 (125)
T ss_dssp             SCCEEEEEETT----SBEEEECHHHHHHHTSCHHHHTTS--BGGGSS
T ss_pred             CCCeEEEEcCC----CeEEEECHHHHHHhCCCHHHHcCc--cHHHhC
Confidence            46789999988    899999999999999999999998  544443

>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=98.71  E-value=1.8e-08  Score=61.21  Aligned_cols=61  Identities=18%  Similarity=0.204  Sum_probs=47.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE   68 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~   68 (102)
                      ++++|+++|.+    ++|+++|+++++++|++.++++|+  ....+.+. ......+.++..+..+.+
T Consensus        31 ~~~gi~v~D~~----g~I~~~N~a~~~~~G~~~~eviG~--~~~~~~p~-~~~~~~~~l~~vl~~G~~   91 (152)
T 3mxq_A           31 LSFALCIVRND----YVIVKVNEYFESRVIFDGETMQGK--NILELFPE-SADYLKRKIDTALVIESS   91 (152)
T ss_dssp             HCCEEEEEETT----SBEEEECHHHHHTSSSCHHHHTTS--BHHHHSGG-GHHHHHHHHHHHHHHTSC
T ss_pred             CCCCEEEEcCC----CEEEEECHHHHHHHCcCHHHHCCC--CHHHhcCC-hHHHHHHHHHHHHhcCCc
Confidence            36799999998    999999999999999999999999  66555555 444455566777766543

>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=98.65  E-value=5.1e-08  Score=57.76  Aligned_cols=63  Identities=6%  Similarity=0.066  Sum_probs=45.6

Q ss_pred             CCceEEEEe-CCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEE
Q psy8548           1 MNSNFVLGN-AQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKL   71 (102)
Q Consensus         1 ~~~~i~i~d-~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~   71 (102)
                      ++.+|+++| .+    ++++++|++++.++|++  +++|+  +...+.++.........+...+..+.....
T Consensus        26 ~~~~i~~~d~~~----~~i~~~N~~~~~~~g~~--~~~G~--~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   89 (158)
T 3k3c_A           26 IPAILVGLEGPD----HRFVAVNAAYRGFSPLL--DTVGQ--PAREVYPELEGQQIYEMLDRVYQTGEPQSG   89 (158)
T ss_dssp             CSSEEEEEETTT----TEEEEECHHHHHHCTTC--CSTTS--BHHHHSGGGGGTTHHHHHHHHHHHCCCEEE
T ss_pred             CCceEEEEECCC----cEeHHHHHHHHHHcCCc--hhcCC--cHHHhCCchhHHHHHHHHHHHHHhCCcccc
Confidence            356889999 77    89999999999999999  88998  544444443333345566667767766443

>3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis}

Probab=98.62  E-value=1.2e-07  Score=58.22  Aligned_cols=64  Identities=6%  Similarity=0.066  Sum_probs=46.0

Q ss_pred             CCceEEEEe-CCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEE
Q psy8548           1 MNSNFVLGN-AQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLE   72 (102)
Q Consensus         1 ~~~~i~i~d-~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e   72 (102)
                      ++.+|+++| .+    ++++++|++|++++|++  +++|+  +...+.++.........+...+..+.....+
T Consensus        46 ~~~~i~~~d~~~----g~i~~~N~a~~~l~G~~--~~~G~--~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  110 (185)
T 3kx0_X           46 IPAILVGLEGPD----HRFVAVNAAYRGFSPLL--DTVGQ--PAREVYPELEGQQIYEMLDRVYQTGEPQSGS  110 (185)
T ss_dssp             CSSEEEEEETTT----TEEEEECHHHHHHCCCC--SCTTS--BHHHHCTTSCSSSSHHHHHHHHHHCCCEEEE
T ss_pred             CCceEEEEECCC----cEEEEEcHHHHHHcCCc--cccCC--cHHHHCCchhhhhHHHHHHHHHHcCCccccc
Confidence            357899999 77    89999999999999999  89998  6544444444333444556666667665543

>4hi4_A Aerotaxis transducer AER2; PAS domain, diatomic GAS sensor, signaling protein; HET: HEM GOL; 2.30A {Pseudomonas aeruginosa}

Probab=98.47  E-value=1.2e-06  Score=50.04  Aligned_cols=41  Identities=17%  Similarity=0.421  Sum_probs=35.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhC------------CChhhhcCCCCCccccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSG------------FARAQIMQKGCACKFLY   47 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G------------~~~~ei~g~~~~~~~l~   47 (102)
                      |.++|+++|.+    ++|+++|+++++++|            ++.++++|+  +...+.
T Consensus        14 ~~~gviv~D~~----g~I~~~N~a~~~llg~~~~~i~~~~~g~~~~~~~G~--~~~~~~   66 (121)
T 4hi4_A           14 VSANVMIADND----LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGA--NIDVFH   66 (121)
T ss_dssp             SSSEEEEEETT----CBEEEECHHHHHHHHHTHHHHHHHCTTCCGGGCTTC--BGGGGC
T ss_pred             CCccEEEEcCC----CeEEEecHHHHHHHHHHHHHHHHhcCCCChHHhcCC--CHHHhc
Confidence            56899999998    999999999999995            899999998  655444

>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS, HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A {Pseudomonas aeruginosa}

Probab=98.34  E-value=2.2e-06  Score=54.94  Aligned_cols=42  Identities=14%  Similarity=0.354  Sum_probs=36.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhh------------CCChhhhcCCCCCcccccC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELS------------GFARAQIMQKGCACKFLYG   48 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~------------G~~~~ei~g~~~~~~~l~~   48 (102)
                      +..+|+++|++    |+|+|+|++|++++            ||+.++++|+  +...+.+
T Consensus        31 ~~~~vii~D~~----g~I~~~N~a~~~ll~~~~~~~~~~l~G~~~~eliG~--~~~~~~~   84 (233)
T 3vol_A           31 VSANVMIADND----LNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGA--NIDVFHK   84 (233)
T ss_dssp             SSSEEEEEETT----SBEEEECHHHHHHHHHTHHHHHTTCTTCCTTSCTTC--BGGGGSS
T ss_pred             CCCcEEEECCC----CcEEEecHHHHHHHHHHHHHHHhhcCCCCHHHHcCC--CHHHHcC
Confidence            46789999998    99999999999998            8999999999  6665543

>2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein struct initiative; 1.75A {Streptococcus mutans}

Probab=98.21  E-value=2.6e-06  Score=51.42  Aligned_cols=67  Identities=10%  Similarity=0.109  Sum_probs=46.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHH---HHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDG---FCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIF   75 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~---~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~   75 (102)
                      |+.+|+++|.+    ++|+|+|++   +++++| ..++++|+  +...+.++. .......+...++.+.....++..
T Consensus        28 ~~~gI~~vD~~----g~I~~~N~a~~~~~~i~g-~~~~~iGr--~v~~~~~~~-~~~~v~~i~~~l~~g~~~~~~~~~   97 (151)
T 2qkp_A           28 LPLEITFVNKD----DIFQYYNDSVPAAEMVFK-RTPSQVGR--NVELCHPPK-VLDKVKKVFELLRNGQRDKVNMWF   97 (151)
T ss_dssp             SSSEEEEEETT----SBEEEECCCSCGGGCSSC-CCGGGTTS--BGGGSSCHH-HHHHHHHHHHHHHTTSBSEEEEEE
T ss_pred             CCCceEEEcCC----CeEEEEeCCCchhhhhcC-CCHHHcCC--CHHHhCCHH-HHHHHHHHHHHHHcCCccEEEEEE
Confidence            57899999998    999999999   999999 55789999  655443321 122234455566667655555544

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=98.05  E-value=8.1e-06  Score=49.95  Aligned_cols=42  Identities=10%  Similarity=0.143  Sum_probs=36.2

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG   48 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~   48 (102)
                      |+++|+++|.+    |+|+++|+++++++|++.++++|+  +...+.+
T Consensus        89 ~~~gvi~~D~~----g~I~~~N~aa~~llg~~~~~~~g~--~~~~~~~  130 (190)
T 2jhe_A           89 LPEPVLSVDMK----SKVDMANPASCQLFGQKLDRLRNH--TAAQLIN  130 (190)
T ss_dssp             CSSCEEEECTT----CBEEEECHHHHHHHTSCHHHHTTS--BGGGTST
T ss_pred             CCCcEEEEcCC----CCEEEEcHHHHHHhCCCHHHhcCc--cHHHHhC
Confidence            56899999998    999999999999999999999998  6554443

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

Probab=98.04  E-value=5.8e-06  Score=56.27  Aligned_cols=53  Identities=11%  Similarity=0.141  Sum_probs=39.9

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHH
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQI   59 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i   59 (102)
                      ++..+++++.+    |+|+|+|++++.++||+.++++|+  ....+.+|.+.......+
T Consensus        95 ~~~~i~v~~~~----G~i~yvs~~~~~~lGy~~~el~g~--~~~~~ihp~D~~~~~~~l  147 (361)
T 4f3l_A           95 LDGFFLAIMTD----GSIIYVSESVTSLLEHLPSDLVDQ--SIFNFIPEGEHSEVYKIL  147 (361)
T ss_dssp             TTEEEEEEETT----SBEEEECTTHHHHHCCCHHHHTTS--BGGGGSCGGGHHHHHHHH
T ss_pred             cCceEEEEcCC----ccEEEEechhhhhcCCCHHHhcCC--cHHHhcCHHHHHHHHHHh
Confidence            35667888887    999999999999999999999999  544455554444443333

>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase, phosphoprotein, transfe two-component regulatory system; 3.80A {Thermotoga maritima}

Probab=98.02  E-value=1.1e-05  Score=53.66  Aligned_cols=40  Identities=13%  Similarity=0.150  Sum_probs=35.3

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFL   46 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l   46 (102)
                      ++++|+++|.+    |+|+++|+++++++||+.++++|+  +...+
T Consensus        17 ~~~~i~~~d~~----g~i~~~N~a~~~l~G~~~~e~~G~--~~~~~   56 (349)
T 3a0r_A           17 LETAIITLSKD----GRITEWNKKAEQLFGLKKENVLGR--RLKDL   56 (349)
T ss_dssp             SSSEEEEEESS----SBCSCBCHHHHHHHSCCSTTTTTC--BSTTS
T ss_pred             hcCeEEEECCC----CCEEeeHHHHHHHhCCCHHHHcCc--CHHHC
Confidence            46789999998    899999999999999999999998  65544

>2w0n_A Sensor protein DCUS; signal transduction, two-component regulatory system, PAS, kinase, membrane, transferase, solid state cell inner membrane; NMR {Escherichia coli}

Probab=97.96  E-value=3.9e-06  Score=46.51  Aligned_cols=40  Identities=10%  Similarity=0.120  Sum_probs=33.8

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCC---ChhhhcCCCCCcccc
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGF---ARAQIMQKGCACKFL   46 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~---~~~ei~g~~~~~~~l   46 (102)
                      ++++|+++|.+    ++|+++|++++.++|+   +.++++|+  +...+
T Consensus        24 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~~~~g~--~~~~~   66 (118)
T 2w0n_A           24 IKEGVVAVDDR----GEVTLINDAAQELLNYRKSQDDEKLST--LSHSW   66 (118)
T ss_dssp             CCCCCEEEBTT----TBCCCBCHHHHHHHCSCTTTTTSSCCC--TTCCC
T ss_pred             ccccEEEECCC----CcEeehhHHHHHHhCCCccChhhhhcc--Ccccc
Confidence            46789999987    8999999999999997   78899988  54433

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

Probab=97.73  E-value=4.8e-05  Score=52.29  Aligned_cols=49  Identities=6%  Similarity=0.171  Sum_probs=36.5

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHH
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEH   55 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~   55 (102)
                      +..+++++.+  . |+|+|+|++++.++||+.++++|+  ....+.+|++...+
T Consensus        96 ~gfi~v~~~~--~-G~i~yvs~~~~~~lG~~~~el~g~--~~~~~ihp~D~~~~  144 (387)
T 4f3l_B           96 DGFLFVVGCD--R-GKILFVSESVFKILNYSQNDLIGQ--SLFDYLHPKDIAKV  144 (387)
T ss_dssp             CSEEEEEETT--T-CBEEEECTTHHHHHSCCHHHHTTS--BGGGGBCGGGHHHH
T ss_pred             CCEEEEEecC--C-eEEEEEchhhHHHcCCCHHHHCCC--cHHHhcCCCCHHHH
Confidence            4566777764  2 899999999999999999999998  54444444443333

>3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein struct initiative; 2.43A {Pyrococcus furiosus dsm 3638}

Probab=97.62  E-value=8.8e-05  Score=50.67  Aligned_cols=61  Identities=11%  Similarity=0.152  Sum_probs=43.7

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELK   70 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~   70 (102)
                      |+++|+++|.+    |+|+++|++ ++++ ++.++++|+  ++..+.++. .......+...+..+....
T Consensus       248 l~dgIivvD~~----g~I~~~N~a-e~i~-~~~~e~iGr--~v~~~~p~~-~~~~~~~l~~~l~~g~~~~  308 (369)
T 3cax_A          248 LPVDVTFIDKD----DRVRFFSPG-ERIF-TRTPSVLGR--PVQLCHPPK-SVYVVNKILKAFKEGRKKE  308 (369)
T ss_dssp             SSSEEEEECTT----SBEEEECCS-SCSS-CCCGGGTTC--BTTTSSCGG-GHHHHHHHHHHHHHTSCSC
T ss_pred             CCCcEEEECCC----CcEEEEcCH-HHcc-CChHHHcCC--cHHHHCChh-hHHHHHHHHHHHHcCCceE
Confidence            57899999998    999999999 9999 889999999  655454432 2233344555666665433

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

Probab=97.39  E-value=0.0001  Score=50.07  Aligned_cols=39  Identities=8%  Similarity=0.140  Sum_probs=31.0

Q ss_pred             EEEEe-CCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCC
Q psy8548           5 FVLGN-AQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGP   49 (102)
Q Consensus         5 i~i~d-~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~   49 (102)
                      +++.+ .+    |+|+|+|+++..++||+.++++|+  ....+.++
T Consensus         6 ~~vv~~~~----G~i~yvS~~~~~~LGy~~~el~G~--s~~d~ihp   45 (339)
T 3rty_A            6 CCVISMHD----GIVLYTTPSITDVLGYPRDMWLGR--SFIDFVHL   45 (339)
T ss_dssp             EEEEETTT----CBEEEECTTHHHHHCCCTTSSTTS--BGGGGBCH
T ss_pred             EEEEECCC----cEEEEEChHHHHHcCCCHHHHCCC--cHHHhcCH
Confidence            34666 45    999999999999999999999999  54444443

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

Probab=97.17  E-value=0.00042  Score=41.00  Aligned_cols=70  Identities=10%  Similarity=0.100  Sum_probs=51.9

Q ss_pred             CCEEEecHHHHHhhCCCh--hhhcCCCCCcccccCCCCCH--HHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548          16 YPIVYCSDGFCELSGFAR--AQIMQKGCACKFLYGPDTSE--EHKTQIEKALESKTELKLEVIFYKKNGYHEEEEEE   88 (102)
Q Consensus        16 ~~i~~~N~~~~~i~G~~~--~ei~g~~~~~~~l~~~~~~~--~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~~   88 (102)
                      |.|++|.++..+ .++..  ++++|+  .+..+.++.+..  ...+.....+..|.....-++++.++|..+|+.+.
T Consensus        17 GKf~~vDq~~~r-~~~~~g~qdLlGr--siy~f~H~~D~~~s~l~~h~~~vl~~Gq~~S~~YRfr~k~g~~V~~qT~   90 (132)
T 1oj5_A           17 GKIISIDTSSLR-AAGRTGWEDLVRK--CIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTR   90 (132)
T ss_dssp             CCEEEEECHHHH-TTCCSCHHHHHHH--HHHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEEEEEEE
T ss_pred             CcEEEEeccccc-ccccccHHHHHHH--HHHHHhCcccchHHHHHHHHHHHHHcCCccccceEEEecCCcEEEEEEE
Confidence            899999998875 55666  899998  444344444422  55556666677777777889999999999999874

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

Probab=96.98  E-value=0.00094  Score=44.92  Aligned_cols=48  Identities=13%  Similarity=-0.038  Sum_probs=34.4

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHH
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEH   55 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~   55 (102)
                      .-+++++.+  + |+|+|+|+++..++||+.++++|+  ....+.++.+...+
T Consensus        37 gF~~vvs~~--~-G~i~yvS~~~~~~Lg~~~~el~g~--s~~d~ihp~D~~~f   84 (317)
T 4dj3_A           37 TFAAVFSFL--S-GRLVHISEQAALILNSKRGFLKSV--HFVDLLAPQDVRAF   84 (317)
T ss_dssp             EEEEEEETT--T-CBEEEECTTHHHHTTCCHHHHHTS--BGGGGBCGGGHHHH
T ss_pred             CEEEEEEcC--C-cEEEEECCHHHHHcCCCHHHHcCC--chhhhcChhhHHHH
Confidence            344566653  3 899999999999999999999998  43334344343333

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

Probab=96.85  E-value=0.00067  Score=45.46  Aligned_cols=48  Identities=13%  Similarity=0.039  Sum_probs=27.3

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHH
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEH   55 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~   55 (102)
                      ..+++++.+  + |+|+|+++++..++||+.++++|+  ....+.++.+...+
T Consensus        26 gF~~vvs~~--~-G~i~yvS~s~~~~Lg~~~~el~g~--s~~d~iHp~D~~~~   73 (309)
T 3gdi_A           26 MFAVAVSLV--S-GKILYISNQVASIFHCKKDAFSDA--KFVEFLAPHDVSVF   73 (309)
T ss_dssp             EEEEEECTT--T-CBEEEECTTTTTTC-------CCS--BGGGGBCTTTHHHH
T ss_pred             CEEEEEECC--C-ceEEEECCHHHHHcCCCHHHHcCC--chhhccCHhHHHHH
Confidence            344566653  3 899999999999999999999998  44334444443333

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

Probab=96.77  E-value=0.00077  Score=45.39  Aligned_cols=34  Identities=21%  Similarity=-0.018  Sum_probs=28.4

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCC
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKG   40 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~   40 (102)
                      .++++...  + |+|+|+++++..++||+.++++|++
T Consensus        38 F~~vvs~~--~-G~i~yvS~sv~~~Lg~~~~~l~g~s   71 (320)
T 4dj2_A           38 FSVAVSFL--T-GRIVYISEQAGVLLRCKRDVFRGAR   71 (320)
T ss_dssp             EEEEEETT--T-CBEEEECTHHHHHHTSCSTTTTTSB
T ss_pred             EEEEEECC--C-ceEEEECcHHHHHhCcCHHHHcCCc
Confidence            34566653  3 8999999999999999999999983

>2ykf_A Pdtas, probable sensor histidine kinase pdtas; transferase, two-component system, GAF domain, PAS domain; 2.00A {Mycobacterium tuberculosis} PDB: 2ykh_A

Probab=95.23  E-value=0.00073  Score=45.06  Aligned_cols=34  Identities=9%  Similarity=0.088  Sum_probs=29.0

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhC---CChhhhcCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSG---FARAQIMQK   39 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G---~~~~ei~g~   39 (102)
                      |+++|+++|.+    |+|+++|++++++++   ++ ++++|+
T Consensus       179 ~~dGIivvD~~----G~Ii~~N~aA~~ll~~lG~~-~~~iGk  215 (305)
T 2ykf_A          179 AGDGFIRLDVD----GVVSYASPNALSAYHRMGLT-TELEGV  215 (305)
Confidence            56799999998    999999999999975   44 678888

>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=91.56  E-value=0.16  Score=34.45  Aligned_cols=50  Identities=12%  Similarity=0.121  Sum_probs=35.1

Q ss_pred             EEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH
Q psy8548           6 VLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE   64 (102)
Q Consensus         6 ~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~   64 (102)
                      ++++..  + ++|+.+|.++..++|++.++++|+  +...+.++    .....+...+.
T Consensus        46 l~~~~~--~-~~i~~~S~N~~~~lg~~~~~llG~--~l~~ll~~----~~~~~l~~~l~   95 (337)
T 2ool_A           46 FVVSET--D-LRIASVSANVEDLLRQPPASLLNV--PIAHYLTA----ASAARLTHALH   95 (337)
T ss_dssp             EEECTT--T-CBEEEEETTHHHHHSSCGGGGTTC--BGGGGBCH----HHHHHHHHHHC
T ss_pred             EEEECC--C-CEEEEEehhHHHHHCcCHHHHcCC--CHHHHcCH----HHHHHHHHHHh
Confidence            345543  4 799999999999999999999998  65544442    33344555443

>4e04_A Bacteriophytochrome (light-regulated signal trans histidine kinase), PHYB1; bacteriophytochrome chromophore binding domain; HET: LBV; 1.79A {Rhodopseudomonas palustris}

Probab=83.92  E-value=7.2  Score=26.32  Aligned_cols=50  Identities=24%  Similarity=0.347  Sum_probs=35.8

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE   64 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~   64 (102)
                      .++++.   + ++|+.++.+...++|.+.++++|+  +...+.+    ......+...+.
T Consensus        32 Ll~~~~---~-~~I~~~S~N~~~~lg~~~~~~lG~--~l~~ll~----~~~~~~l~~~l~   81 (327)
T 4e04_A           32 LLALAA---D-MTIVAGSDNLPELTGLAIGALIGR--SAADVFD----SETHNRLTIALA   81 (327)
T ss_dssp             EEEECT---T-CBEEEEETTHHHHHSCCHHHHTTC--BHHHHBC----HHHHHHHHHHHH
T ss_pred             EEEEcC---C-CeEEEEcccHHHHhCCChHhhcCC--CHHHHcC----HHHHHHHHHHhh
Confidence            345563   3 899999999999999999999998  6554443    344445555554

---

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	102
d1bywa_	110	d.110.3.6 (A:) Erg potassium channel, N-terminal d	1e-08
d1n9la_	109	d.110.3.6 (A:) Putative blue light receptor, phot-	5e-08
d1jnua_	104	d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d	4e-06

>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 110

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]

 Score = 46.2 bits (108), Expect = 1e-08
 Identities = 24/54 (44%), Positives = 38/54 (70%), Gaps = 1/54 (1%)

Query: 2  NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEH 55
          +  F++ NA+V +   ++YC+DGFCEL G++RA++MQ+ C C FL+GP T    
Sbjct: 1  SRKFIIANARVEN-CAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRA 53

>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Length = 109

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]

 Score = 44.8 bits (105), Expect = 5e-08
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 1  MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIE 60
          +   FV+ +A +P   P+VY S+GF  ++G+   +++  G  C+FL G  T  +   +I 
Sbjct: 2  LRHTFVVADATLPD-CPLVYASEGFYAMTGYGPDEVL--GHNCRFLQGEGTDPKEVQKIR 58

Query: 61 KALESKTELKLEVIFYKKN 79
           A++      + ++ Y+K+
Sbjct: 59 DAIKKGEACSVRLLNYRKD 77

>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]} Length = 104

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]

 Score = 39.9 bits (92), Expect = 4e-06
 Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 3/79 (3%)

Query: 4  NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKAL 63
          +FV+ + ++P   PI++ SD F EL+ + R +++  G  C+FL G  T  +    I  A+
Sbjct: 2  SFVITDPRLPD-NPIIFASDRFLELTEYTREEVL--GNNCRFLQGRGTDRKAVQLIRDAV 58

Query: 64 ESKTELKLEVIFYKKNGYH 82
          + + ++ ++V+ Y K G  
Sbjct: 59 KEQRDVTVQVLNYTKGGRA 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	102
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.81
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	99.72
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.67
d1mzua_	110	PYP domain of sensor histidine kinase Ppr {Rhodosp	99.46
d1nwza_	125	Photoactive yellow protein, PYP {Ectothiorhodospir	99.45
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	99.43
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	99.43
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	99.4
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	99.36
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	99.34
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	98.98
d2oola2	114	Sensor protein PhyB2 {Rhodopseudomonas palustris [	97.38
d2veaa3	127	Phytochrome-like protein Cph1 {Synechocystis sp. p	94.91
d2o9ca2	127	Bacteriophytochrome BphP {Deinococcus radiodurans	92.84
d3c2wa3	113	Bacteriophytochrome BphP {Pseudomonas aeruginosa [	85.45

>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=99.81  E-value=4.6e-19  Score=101.08  Aligned_cols=84  Identities=25%  Similarity=0.576  Sum_probs=75.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      |+++|+|+|+..|+ ++|+|+|++|++++||++++++|+  +...+..+.........++..+..+..+..++..+++||
T Consensus         2 i~~~~vi~Da~~pd-g~Ii~vN~a~~~~~Gy~~~El~G~--~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG   78 (109)
T d1n9la_           2 LRHTFVVADATLPD-CPLVYASEGFYAMTGYGPDEVLGH--NCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDG   78 (109)
T ss_dssp             CSCEEEEEETTSTT-CCEEEECHHHHHHHCCCHHHHTTS--CGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTS
T ss_pred             ccceEEEEeCCCCC-CeEEEEcHHHHHHHCcCHHHHcCC--cceeeecccCCHHHhhhhhhHhhcCCceeeeEEEEecCC
Confidence            57899999986666 899999999999999999999999  777787777778888899999999999999999999999


Q ss_pred             Ceeeecc
Q psy8548          81 YHEEEEE   87 (102)
Q Consensus        81 ~~~~~~~   87 (102)
                      +.+|++-
T Consensus        79 ~~~w~~~   85 (109)
T d1n9la_          79 TPFWNLL   85 (109)
T ss_dssp             CEEEEEE
T ss_pred             eEEEEEE
Confidence            9999863

>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=99.72  E-value=8.7e-17  Score=90.45  Aligned_cols=81  Identities=27%  Similarity=0.566  Sum_probs=73.0

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      .|+|+|+..|+ ++|+|+|++|++++||+.++++|+  +...+..+.......+.+...+..+..+..+++.++++|+.+
T Consensus         2 ~fvi~d~~~pd-~~I~y~N~a~~~~~G~s~~e~~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~   78 (104)
T d1jnua_           2 SFVITDPRLPD-NPIIFASDRFLELTEYTREEVLGN--NCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAF   78 (104)
T ss_dssp             EEEEECTTSTT-CCEEEECHHHHHHHTCCHHHHTTS--CGGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEE
T ss_pred             eEEEEcCCCCC-CEEEEEcHHHHHHHCcCHHHHCCc--cceeccccccchHHHhhhhhhhhcCceeEeEEEEEecccceE
Confidence            68899987777 899999999999999999999999  767777777888888899999999999999999999999999


Q ss_pred             eecc
Q psy8548          84 EEEE   87 (102)
Q Consensus        84 ~~~~   87 (102)
                      |+..
T Consensus        79 ~~~~   82 (104)
T d1jnua_          79 WNLF   82 (104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9763

>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=99.67  E-value=1.3e-15  Score=86.34  Aligned_cols=84  Identities=42%  Similarity=0.812  Sum_probs=70.4

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH   82 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~   82 (102)
                      ..++|+|++.++ +.|+|+|++|++|+||+.++++|+.....++.++.........+...+..+..+..+++.++++|+.
T Consensus         2 ~~f~i~~~~~~d-~~I~~~N~a~~~l~G~~~~eiiG~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~~~g~~   80 (110)
T d1bywa_           2 RKFIIANARVEN-CAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSC   80 (110)
T ss_dssp             CEEEEEETTSSS-CBEEEECHHHHHHHTCCHHHHTTSBTTCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCE
T ss_pred             ceEEEEcCCCCC-CEEEEEcHHHHHHhCCCHHHhcccCcccccceeeheecccccccchhhcccccccceeeeeecccce
Confidence            468899987767 8999999999999999999999983112234556667788888899999999999999999999999


Q ss_pred             eeecc
Q psy8548          83 EEEEE   87 (102)
Q Consensus        83 ~~~~~   87 (102)
                      +|+..
T Consensus        81 ~w~~~   85 (110)
T d1bywa_          81 FLCLV   85 (110)
T ss_dssp             EEEEE
T ss_pred             eeeee
Confidence            99764

>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=99.46  E-value=3.2e-13  Score=76.76  Aligned_cols=80  Identities=8%  Similarity=-0.080  Sum_probs=60.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCc-ccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCAC-KFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKN   79 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~-~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~   79 (102)
                      ++.+|+++|.+    |+|+++|+++++|+||++++++|+  +. ..+.++.....+...+.+.+..+..........+++
T Consensus        12 ~p~gvi~~D~~----G~I~~~N~aa~~~~G~~~eellG~--~~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~l~~~   85 (110)
T d1mzua_          12 LPVGAIQVDGS----GVIHRYNRTESRLSGRIPERVIGR--NFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQ   85 (110)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHHCCCHHHHTTS--BCCCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEEEECS
T ss_pred             CCcEEEEEcCC----CCEEEeHHHHHHHHcCCHHHHcCC--CHHHhcCChhhhHHHHHHHHHHHhccccCcceEEEEecC
Confidence            46799999987    999999999999999999999999  54 445444444555566777777776544333445789


Q ss_pred             CCeeeec
Q psy8548          80 GYHEEEE   86 (102)
Q Consensus        80 G~~~~~~   86 (102)
                      |++++++
T Consensus        86 G~~~~v~   92 (110)
T d1mzua_          86 MAPVRVQ   92 (110)
T ss_dssp             SCEEEEE
T ss_pred             CceEEEE
Confidence            9988775

>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=99.45  E-value=3.5e-13  Score=78.07  Aligned_cols=81  Identities=10%  Similarity=0.002  Sum_probs=63.4

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG   80 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G   80 (102)
                      ++.+|+++|.+    |+|+++|+++++++||+.++++|++ ...++.++.........+.+.+..+.....+....+++|
T Consensus        26 ~p~gi~~lD~~----G~i~~~N~a~~~l~G~~~~e~iG~~-~~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G  100 (125)
T d1nwza_          26 LAFGAIQLDGD----GNILQYNAAEGDITGRDPKQVIGKN-FFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQM  100 (125)
T ss_dssp             CSSEEEEEETT----CBEEEECHHHHHHHCCCHHHHTTSB-CCCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEEECTTS
T ss_pred             CCccEEEEeCC----CCEEEEcHHHHHhhccchHhhcCCC-HHHccCchhhhhheeeeceeeeecCCcceEEEEEeccCC
Confidence            46799999998    9999999999999999999999993 234454444444555667777778877676666778899


Q ss_pred             Ceeeec
Q psy8548          81 YHEEEE   86 (102)
Q Consensus        81 ~~~~~~   86 (102)
                      +++|++
T Consensus       101 ~~~~v~  106 (125)
T d1nwza_         101 TPTKVK  106 (125)
T ss_dssp             CCEEEE
T ss_pred             cEEEEE
Confidence            988875

>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=99.43  E-value=7e-13  Score=76.40  Aligned_cols=80  Identities=14%  Similarity=0.179  Sum_probs=61.1

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCc----EEEEEEEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTE----LKLEVIFY   76 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~----~~~e~~~~   76 (102)
                      ++++|+++|.+    |+|+++|+++++|+||+.++++|+  +...+.++.........+...+..+..    ...++...
T Consensus        25 ~~~~i~~~d~~----g~i~~~N~~~~~l~Gy~~~el~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   98 (130)
T d1ew0a_          25 VPDATVVSATD----GTIVSFNAAAVRQFGYAEEEVIGQ--NLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQ   98 (130)
T ss_dssp             CSSEEEEEETT----SBEEEECHHHHHHHCCCHHHHTTS--BGGGGSCTTTGGGHHHHHHHHHHHCCCSSTTSCEEEEEE
T ss_pred             CCCeEEEEeCC----ccEEEEHHHHHHhhcCCHHHhcCC--ccccccccchhHHHHHHHHHHHHhCCCccccceeeEEEE
Confidence            46799999988    899999999999999999999999  665555554444444444444544432    56788889


Q ss_pred             ecCCCeeeec
Q psy8548          77 KKNGYHEEEE   86 (102)
Q Consensus        77 ~~~G~~~~~~   86 (102)
                      +++|..+|++
T Consensus        99 ~~dG~~~~v~  108 (130)
T d1ew0a_          99 RKDGSTFPMK  108 (130)
T ss_dssp             CTTSCEEEEE
T ss_pred             cCCCCEEEEE
Confidence            9999999875

>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=99.43  E-value=5.2e-13  Score=74.02  Aligned_cols=78  Identities=12%  Similarity=0.108  Sum_probs=57.9

Q ss_pred             ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC----CcEEEEEEEEec
Q psy8548           3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK----TELKLEVIFYKK   78 (102)
Q Consensus         3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~----~~~~~e~~~~~~   78 (102)
                      ++|+++|.+    |+|+++|+++++|+||+.++++|+  +...+.++.........+...+...    .....++..+++
T Consensus         1 dgi~~~D~~----G~I~~~N~a~~~l~Gy~~~el~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~   74 (106)
T d1xj3a1           1 DAMIVIDGH----GIIQLFSTAAERLFGWSELEAIGQ--NVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRR   74 (106)
T ss_dssp             CCEEEEETT----SBEEEECHHHHHHHCCCHHHHTTS--BGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECT
T ss_pred             CEEEEECCC----CcEEEEcHHHHHHhhhchHhhcCC--Ccccccccccccchhhhhhhhhhhcccccccccceeeeeec
Confidence            589999998    999999999999999999999999  6555555544433333333333322    234568888999


Q ss_pred             CCCeeeec
Q psy8548          79 NGYHEEEE   86 (102)
Q Consensus        79 ~G~~~~~~   86 (102)
                      +|+.+|++
T Consensus        75 dg~~~~v~   82 (106)
T d1xj3a1          75 DGTTFPMH   82 (106)
T ss_dssp             TSCEEEEE
T ss_pred             cceEEEEE
Confidence            99998885

>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=99.40  E-value=2.9e-13  Score=76.74  Aligned_cols=82  Identities=18%  Similarity=0.248  Sum_probs=63.6

Q ss_pred             CCceEEEE--eCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEec
Q psy8548           1 MNSNFVLG--NAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKK   78 (102)
Q Consensus         1 ~~~~i~i~--d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~   78 (102)
                      |++..+++  +++    |+++|+|++++.++||+.++++|+  ....+..+.+.....+.+...+..+..+..+++++++
T Consensus         3 ~d~~~fi~r~~~d----G~i~~~N~~~~~~~G~~~~el~g~--~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~k   76 (114)
T d1p97a_           3 MDSKTFLSRHSMD----MKFTYCDDRITELIGYHPEELLGR--SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAK   76 (114)
T ss_dssp             CCCEEEEEEECTT----TSCSEECTTHHHHTSSCHHHHTTS--CHHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECT
T ss_pred             cCcCEEEEEECCC----CcEEEECHHHHHHcCCCccccccc--cccccccccccccceeeeeecccccceeecceeeeee
Confidence            56777775  565    899999999999999999999998  5444444555555555555666666778889999999


Q ss_pred             CCCeeeecch
Q psy8548          79 NGYHEEEEEE   88 (102)
Q Consensus        79 ~G~~~~~~~~   88 (102)
                      +|+.+|+...
T Consensus        77 dG~~~wv~~~   86 (114)
T d1p97a_          77 HGGYVWLETQ   86 (114)
T ss_dssp             TSCEEEEEEE
T ss_pred             cCcceEEEEE
Confidence            9999999753

>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=99.36  E-value=1.5e-13  Score=78.13  Aligned_cols=81  Identities=15%  Similarity=0.221  Sum_probs=59.1

Q ss_pred             CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCC----cEEEEEEEE
Q psy8548           1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKT----ELKLEVIFY   76 (102)
Q Consensus         1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~----~~~~e~~~~   76 (102)
                      +|++|+++|..  . |+|+++|+++++++||++++++|+  +...+.++.........+...+..+.    .+..++...
T Consensus         7 ~n~AI~~id~~--~-G~I~~~N~a~~~l~Gy~~~el~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~   81 (114)
T d1ll8a_           7 FNKAIFTVDAK--T-TEILVANDKACGLLGYSSQDLIGQ--KLTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVVDII   81 (114)
T ss_dssp             TTCEEEEEETT--T-CBEEEECTTHHHHHTCCTTTTTTS--BGGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSEEEC
T ss_pred             cCcEEEEEECC--C-CEEEEECHHHHHhhcCCHHHHcCC--CeeeecCcccHHHHHHHHHHHHhcCCCccceeeEEEEEE
Confidence            68899999964  3 899999999999999999999999  66666666555544333333333222    122367778


Q ss_pred             ecCCCeeeec
Q psy8548          77 KKNGYHEEEE   86 (102)
Q Consensus        77 ~~~G~~~~~~   86 (102)
                      +++|+.+|++
T Consensus        82 ~~~G~~~pve   91 (114)
T d1ll8a_          82 SRSGEKIPVS   91 (114)
T ss_dssp             CTTCCCEEEE
T ss_pred             ccCCcEEEEE
Confidence            9999999886

>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=99.34  E-value=2.3e-12  Score=72.20  Aligned_cols=80  Identities=19%  Similarity=0.193  Sum_probs=54.2

Q ss_pred             CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH----hCCcEEEEEEEEe
Q psy8548           2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE----SKTELKLEVIFYK   77 (102)
Q Consensus         2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~----~~~~~~~e~~~~~   77 (102)
                      .++|+++|.+    ++|+++|+++++++||+.++++|+  +...+.+..........+...+.    .......+...++
T Consensus        11 ~d~i~~~d~~----g~i~~~N~~~~~l~Gy~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~   84 (113)
T d1v9ya_          11 MMGAVLINEN----DEVMFFNPAAEKLWGYKREEVIGN--NIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEK   84 (113)
T ss_dssp             SSEEEEECTT----SBEEEECHHHHHHHSCCGGGTTTS--BGGGGSCGGGTTTHHHHHHHHHC----------CEEEEEC
T ss_pred             cCcEEEEeCC----CCEEEEchhHhhhhccchhhhcCc--ceecccccccccccccccccccccccccccccceeeeecc
Confidence            4689999987    899999999999999999999998  55544443333222222222222    2223456778889


Q ss_pred             cCCCeeeecc
Q psy8548          78 KNGYHEEEEE   87 (102)
Q Consensus        78 ~~G~~~~~~~   87 (102)
                      ++|+.+|++-
T Consensus        85 ~dG~~~~v~~   94 (113)
T d1v9ya_          85 KDGSKIWTRF   94 (113)
T ss_dssp             TTSCEEEEEE
T ss_pred             ccceeEEEEE
Confidence            9999999864

>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=98.98  E-value=1.9e-10  Score=65.00  Aligned_cols=78  Identities=9%  Similarity=0.075  Sum_probs=57.1

Q ss_pred             EEEeCCCCCCCCEEEecHHHHHhhCCCh-hhhcCCCCCcccccCCCCCH-HHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548           6 VLGNAQVPSLYPIVYCSDGFCELSGFAR-AQIMQKGCACKFLYGPDTSE-EHKTQIEKALESKTELKLEVIFYKKNGYHE   83 (102)
Q Consensus         6 ~i~d~~~~~~~~i~~~N~~~~~i~G~~~-~ei~g~~~~~~~l~~~~~~~-~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~   83 (102)
                      .-.|++    |+++++|++.++++||.. ++++|++ ...++++.+.+. .........+..+.....+++++++||.++
T Consensus         6 trh~~~----g~~~~vd~~~~~~~gy~~~eelig~s-~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~v   80 (109)
T d1oj5a_           6 TKQDTT----GKIISIDTSSLRAAGRTGWEDLVRKC-IYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML   80 (109)
T ss_dssp             EEECTT----CCEEEEECHHHHTTCCSCHHHHHHHH-HHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE
T ss_pred             EEECCC----ceEEEECHHHhhHhhcCCHHHHcCCc-HHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEE
Confidence            344565    999999999999999984 8999993 344444433322 222334555677888888999999999999


Q ss_pred             eecch
Q psy8548          84 EEEEE   88 (102)
Q Consensus        84 ~~~~~   88 (102)
                      |+++.
T Consensus        81 Wv~t~   85 (109)
T d1oj5a_          81 SAHTR   85 (109)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            99874

>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=97.38  E-value=7.8e-05  Score=41.36  Aligned_cols=52  Identities=12%  Similarity=0.120  Sum_probs=36.9

Q ss_pred             eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH
Q psy8548           4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE   64 (102)
Q Consensus         4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~   64 (102)
                      .++++|..  + ++|++++++...++|++.++++|+  ....+.++    .....+++.+.
T Consensus        19 ~Llvld~~--d-~~I~~vS~N~~~lLG~~~~~llG~--~l~dll~~----~~~~~i~~~l~   70 (114)
T d2oola2          19 YLFVVSET--D-LRIASVSANVEDLLRQPPASLLNV--PIAHYLTA----ASAARLTHALH   70 (114)
T ss_dssp             EEEEECTT--T-CBEEEEETTHHHHHSSCGGGGTTC--BGGGGBCH----HHHHHHHHHHC
T ss_pred             EEEEEECC--C-CEEEEEcCCHHHHhCCChHHHcCC--CHHHhCCH----HHHHHHHHHHh
Confidence            34566643  3 899999999999999999999999  54444433    33445555554

>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=94.91  E-value=0.0089  Score=33.57  Aligned_cols=40  Identities=10%  Similarity=0.139  Sum_probs=31.5

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCC
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGP   49 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~   49 (102)
                      ++.+|..  + +.|+.++.....++|++.++++|+  +...+.++
T Consensus        29 LLald~~--~-~~I~~aS~N~~~~lG~~~~~lLG~--~l~~ll~~   68 (127)
T d2veaa3          29 VVVLQEP--D-LTISQISANCTGILGRSPEDLLGR--TLGEVFDS   68 (127)
T ss_dssp             EEEEETT--T-TEEEEEETTHHHHTSCCTTTSSTT--TTTTTSBC
T ss_pred             EEEEECC--C-CEEEEEcCCHHHHhCcChHHHcCC--CHHHHCCH
Confidence            4566653  3 899999999999999999999999  65544443

>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=92.84  E-value=0.061  Score=29.94  Aligned_cols=39  Identities=10%  Similarity=0.054  Sum_probs=31.3

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG   48 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~   48 (102)
                      ++++|..  + +.|++++.+...++|++.++++|+  +...+.+
T Consensus        38 LLald~~--~-~~I~~~S~N~~~~lG~~~~~llG~--~l~~ll~   76 (127)
T d2o9ca2          38 LLTADGH--S-GEVLQMSLNAATFLGQEPTVLRGQ--TLAALLP   76 (127)
T ss_dssp             EEEEETT--T-CBEEEEETTHHHHHSSCHHHHTTC--BHHHHCT
T ss_pred             EEEEECC--C-CEEEEECCCHHHHhCCChHHHcCC--CHHHHCC
Confidence            4566753  3 899999999999999999999999  6555543

>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=85.45  E-value=1  Score=24.07  Aligned_cols=54  Identities=19%  Similarity=0.129  Sum_probs=33.2

Q ss_pred             EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcE
Q psy8548           5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTEL   69 (102)
Q Consensus         5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~   69 (102)
                      .+++|++    +.|+.++.+...++|++.+ .+|+  ....+..    ......++..+.....+
T Consensus        25 LLald~~----~~I~~~S~N~~~~lg~~~~-~L~~--~~~~~~~----~~~~~~l~~~~~~~~~~   78 (113)
T d3c2wa3          25 LVTLRAD----GMVLAASENIQALLGFVAS-PGSY--LTQEQVG----PEVLRMLEEGLTGNGPW   78 (113)
T ss_dssp             EEEECTT----SBEEEEETTHHHHTSSCCC-TTCB--CCHHHHH----HHHHHHHHHHHSCSSCC
T ss_pred             EEEEcCC----CeEEEEcCCHHHHhCCChh-Hhcc--cHHHHhC----HHHHHHHHhhhhcCCCc
Confidence            3466654    8999999999999999854 4565  3322221    23444555555444433