Psyllid ID: psy8547

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MVTHPDTNYRQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEEEEEEccccccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccEEEEEEEcEcccccccEEEEEEEccccHcccccccccccccccccccccccccccHcccccHHHcccEEEEEEEcccccccccEEEccccccccccccccc
Coil and Loop (DISEMBL)
mvthpdtnyrqrtpfwclldivpikneKREVVLYLASHkdvtntkmaqmadngegdyedmqelgtpfwclldivpikneKREVVLYLASHkdvtntkmaqmadngegdyedmqel
Flexible Loop (DISEMBL)
mvthpdtnyrqrtpfwcLLDIVPIKNEKREVVLYLashkdvtntkMAQMADNGEGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLashkdvtntkmAQMADNGEGDYEDMQEL
Low Complexity Region (SEG)
MVTHPDTNYRQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL
Disordered region (IsUnstruct)
**********QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT*****************MQELGTPFWCLLDIVPIKNEKREVVLYLASHK************************
Disordered Region (DISOPRED)
********YRQRTPFWCLLDIVPIKNEKREVVLYLASHKDV***********************************KNEKREVVLYL****************************
Disordered Region (DISEMBL)
********YRQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL
Disordered Region (DISPRO)
****PDTNYRQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT*********************PFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVTHPDTNYRQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL
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	115	2.2.26 [Sep-21-2011]
Q9QWS8	1102	Potassium voltage-gated c	yes	N/A	0.391	0.040	0.622	9e-11
P59111	1102	Potassium voltage-gated c	yes	N/A	0.391	0.040	0.622	9e-11
Q96L42	1107	Potassium voltage-gated c	yes	N/A	0.391	0.040	0.622	1e-10
O89047	1087	Potassium voltage-gated c	no	N/A	0.347	0.036	0.634	4e-10
Q9WVJ0	1087	Potassium voltage-gated c	no	N/A	0.347	0.036	0.634	4e-10
Q9ULD8	1083	Potassium voltage-gated c	no	N/A	0.286	0.030	0.705	8e-10
Q9UQ05	1017	Potassium voltage-gated c	no	N/A	0.478	0.054	0.451	8e-07
Q9R1T9	1017	Potassium voltage-gated c	no	N/A	0.356	0.040	0.510	7e-06
Q02280	1174	Potassium voltage-gated c	no	N/A	0.391	0.038	0.4	0.0004
Q920E3	988	Potassium voltage-gated c	no	N/A	0.373	0.043	0.413	0.0007

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

 Score = 65.5 bits (158), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 28/45 (62%), Positives = 37/45 (82%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+   +++ + D
Sbjct: 104 GAPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITSEDKKED 148

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 = 65.5 bits (158), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 28/45 (62%), Positives = 37/45 (82%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+   +++ + D
Sbjct: 104 GAPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITSEDKKED 148

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

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/45 (62%), Positives = 37/45 (82%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G+PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+    ++ + D
Sbjct: 104 GSPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITPEDKKED 148

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

 Score = 63.5 bits (153), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 26/41 (63%), Positives = 31/41 (75%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104
           G PFWCLLD++PIKNEK EV L+L SHKD++ TK     DN
Sbjct: 104 GLPFWCLLDVIPIKNEKGEVALFLVSHKDISETKNRGGPDN 144

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 = 63.5 bits (153), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 26/41 (63%), Positives = 31/41 (75%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104
           G PFWCLLD++PIKNEK EV L+L SHKD++ TK     DN
Sbjct: 104 GLPFWCLLDVIPIKNEKGEVALFLVSHKDISETKNRGGPDN 144

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 = 62.4 bits (150), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 24/34 (70%), Positives = 29/34 (85%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK 97
           G PFWCLLD++PIKNEK EV L+L SHKD++ TK
Sbjct: 104 GLPFWCLLDVIPIKNEKGEVALFLVSHKDISETK 137

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

 Score = 52.4 bits (124), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 36/62 (58%), Gaps = 7/62 (11%)

Query: 54  EGDYEDMQEL------GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA-DNGE 106
           EG  E   E+      G+ FWCLLD++PIKNE  EVVL+L S KD+T +    +    G 
Sbjct: 88  EGHQEHRAEICFYRKDGSAFWCLLDMMPIKNEMGEVVLFLFSFKDITQSGSPGLGPQGGR 147

Query: 107 GD 108
           GD
Sbjct: 148 GD 149

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

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/47 (51%), Positives = 31/47 (65%), Gaps = 6/47 (12%)

Query: 54  EGDYEDMQEL------GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
           EG  E   E+      G+ FWCLLD++PIKNE  EVVL+L S KD++
Sbjct: 88  EGHQEHRAEICFYRKDGSAFWCLLDMMPIKNELGEVVLFLFSFKDIS 134

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|Q02280|KCNAE_DROME Potassium voltage-gated channel protein eag OS=Drosophila melanogaster GN=eag PE=1 SV=2

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 29/45 (64%)

Query: 11  QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEG 55
           Q TP W LL + PI+NE+  VVL+L + +D+T  K    +++ +G
Sbjct: 123 QETPLWLLLQVAPIRNERDLVVLFLLTFRDITALKQPIDSEDTKG 167

Structural component of a potassium channel. Mediates the potassium permeability of membranes; potassium current is regulated by CaMKII and CASK. Has a role in growth of the perineurial glial layer of the larval peripheral nerve.

Drosophila melanogaster (taxid: 7227)

>sp|Q920E3|KCNH5_MOUSE Potassium voltage-gated channel subfamily H member 5 OS=Mus musculus GN=Kcnh5 PE=2 SV=3

 Score = 42.7 bits (99), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/46 (41%), Positives = 28/46 (60%)

Query: 10  RQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEG 55
           + RTP W  + I PI+NE  +VVL+L + KD+T  K     D+ +G
Sbjct: 100 KNRTPVWFYMQIAPIRNEHEKVVLFLCTFKDITLFKQPIEDDSTKG 145

Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits a non-inactivating outward rectifying current (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	115
189240721	900	PREDICTED: similar to AGAP005251-PA [Tri	0.373	0.047	0.790	6e-14
270012947	1034	hypothetical protein TcasGA2_TC004313 [T	0.373	0.041	0.790	8e-14
357608448	1053	hypothetical protein KGM_17508 [Danaus p	0.391	0.042	0.822	1e-13
242006252	770	voltage-gated channel, putative [Pedicul	0.426	0.063	0.725	3e-13
158292882	1196	AGAP005251-PA [Anopheles gambiae str. PE	0.391	0.037	0.777	3e-13
195121032	1324	GI20242 [Drosophila mojavensis] gi|19391	0.391	0.033	0.755	7e-13
328709452	1477	PREDICTED: hypothetical protein LOC10056	0.330	0.025	0.868	7e-13
195584425	632	GD11328 [Drosophila simulans] gi|1941940	0.391	0.071	0.733	1e-12
487736	1284	putative potassium channel subunit [Dros	0.391	0.035	0.733	2e-12
17136946	1284	eag-like K[+] channel [Drosophila melano	0.391	0.035	0.733	2e-12

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

 Score = 81.6 bits (200), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 34/43 (79%), Positives = 41/43 (95%)

Query: 10  RQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 52
           +  TPFWCLLDIVPIKNEKREVVL+LASHKD+TNTKMA+M+++
Sbjct: 102 KNSTPFWCLLDIVPIKNEKREVVLFLASHKDITNTKMAEMSES 144

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 = 81.3 bits (199), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 34/43 (79%), Positives = 41/43 (95%)

Query: 10  RQRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 52
           +  TPFWCLLDIVPIKNEKREVVL+LASHKD+TNTKMA+M+++
Sbjct: 102 KNSTPFWCLLDIVPIKNEKREVVLFLASHKDITNTKMAEMSES 144

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608448|gb|EHJ66015.1| hypothetical protein KGM_17508 [Danaus plexippus]

 Score = 80.1 bits (196), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/45 (82%), Positives = 39/45 (86%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           GTPFWCLLDIVPIKNEKREVVL+LAS KD+TNTKMA M  N E D
Sbjct: 105 GTPFWCLLDIVPIKNEKREVVLFLASFKDITNTKMAAMNTNEEFD 149

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

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 = 79.3 bits (194), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/51 (72%), Positives = 42/51 (82%), Gaps = 2/51 (3%)

Query: 61  QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYED 111
           ++ G PFWCLLDIVPIKNEKREVVL+LASHKDVTNTKM +M  N    YE+
Sbjct: 79  KKTGVPFWCLLDIVPIKNEKREVVLFLASHKDVTNTKMEEM--NPSSTYEN 127

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158292882|ref|XP_314166.4| AGAP005251-PA [Anopheles gambiae str. PEST] gi|157017201|gb|EAA09546.4| AGAP005251-PA [Anopheles gambiae str. PEST]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/45 (77%), Positives = 40/45 (88%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           GTPFWCLLDIVPIKNEKREVVL+LASHKDVT  KM++M+ + E D
Sbjct: 103 GTPFWCLLDIVPIKNEKREVVLFLASHKDVTTAKMSEMSMSDECD 147

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195121032|ref|XP_002005025.1| GI20242 [Drosophila mojavensis] gi|193910093|gb|EDW08960.1| GI20242 [Drosophila mojavensis]

 Score = 77.8 bits (190), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 34/45 (75%), Positives = 38/45 (84%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCL DIVPIKNEKREVVL+LASHKD+T+TKM +M  N E D
Sbjct: 103 GAPFWCLFDIVPIKNEKREVVLFLASHKDITHTKMLEMNVNEECD 147

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328709452|ref|XP_003243964.1| PREDICTED: hypothetical protein LOC100568954 [Acyrthosiphon pisum]

 Score = 77.8 bits (190), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 33/38 (86%), Positives = 38/38 (100%)

Query: 12  RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49
           R+PFWCLLDIVPIKNEKREVVL+LASHKD+T+TKMA+M
Sbjct: 465 RSPFWCLLDIVPIKNEKREVVLFLASHKDITHTKMAEM 502

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195584425|ref|XP_002082007.1| GD11328 [Drosophila simulans] gi|194194016|gb|EDX07592.1| GD11328 [Drosophila simulans]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/45 (73%), Positives = 38/45 (84%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCL DIVPIKNEKR+VVL+LASHKD+T+TKM +M  N E D
Sbjct: 132 GAPFWCLFDIVPIKNEKRDVVLFLASHKDITHTKMLEMNVNEECD 176

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|487736|gb|AAA62472.1| putative potassium channel subunit [Drosophila melanogaster]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/45 (73%), Positives = 38/45 (84%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCL DIVPIKNEKR+VVL+LASHKD+T+TKM +M  N E D
Sbjct: 103 GAPFWCLFDIVPIKNEKRDVVLFLASHKDITHTKMLEMNVNEECD 147

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|17136946|ref|NP_477009.1| eag-like K[+] channel [Drosophila melanogaster] gi|21627052|gb|AAF57772.2| eag-like K[+] channel [Drosophila melanogaster]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/45 (73%), Positives = 38/45 (84%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
           G PFWCL DIVPIKNEKR+VVL+LASHKD+T+TKM +M  N E D
Sbjct: 103 GAPFWCLFDIVPIKNEKRDVVLFLASHKDITHTKMLEMNVNEECD 147

Source: Drosophila melanogaster

Species: melanogaster group

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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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	115
FB|FBgn0011589	1284	Elk "Eag-like K[+] channel" [D	0.391	0.035	0.733	2.5e-12
UNIPROTKB|F8WCG6	195	KCNH8 "Potassium voltage-gated	0.391	0.230	0.622	5.8e-11
UNIPROTKB|I3LM91	85	LOC100626445 "Uncharacterized	0.304	0.411	0.771	7.4e-11
UNIPROTKB|J9P8R4	433	KCNH8 "Uncharacterized protein	0.391	0.103	0.622	3.9e-10
UNIPROTKB|J9NXB3	546	KCNH3 "Uncharacterized protein	0.356	0.075	0.658	4.6e-10
UNIPROTKB|F1P602	1056	KCNH3 "Uncharacterized protein	0.356	0.038	0.658	1.1e-09
MGI|MGI:2445160	1102	Kcnh8 "potassium voltage-gated	0.478	0.049	0.527	1.2e-09
RGD|2549	1102	Kcnh8 "potassium voltage-gated	0.478	0.049	0.527	1.2e-09
UNIPROTKB|Q9QWS8	1102	Kcnh8 "Potassium voltage-gated	0.478	0.049	0.527	1.2e-09
ZFIN|ZDB-GENE-070912-23	914	kcnh3 "potassium voltage-gated	0.408	0.051	0.645	1.2e-09

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

 Score = 179 (68.1 bits), Expect = 2.5e-12, P = 2.5e-12
 Identities = 33/45 (73%), Positives = 38/45 (84%)

Query:    64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
             G PFWCL DIVPIKNEKR+VVL+LASHKD+T+TKM +M  N E D
Sbjct:   103 GAPFWCLFDIVPIKNEKRDVVLFLASHKDITHTKMLEMNVNEECD 147

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 = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 28/45 (62%), Positives = 38/45 (84%)

Query:    54 EGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 98
             +G+    ++ G+PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+
Sbjct:    94 KGEIMFYKKNGSPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKV 138

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

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

UNIPROTKB|I3LM91 LOC100626445 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 27/35 (77%), Positives = 33/35 (94%)

Query:    64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 98
             G+PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+
Sbjct:     7 GSPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKV 41

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

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

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

 Score = 152 (58.6 bits), Expect = 3.9e-10, P = 3.9e-10
 Identities = 28/45 (62%), Positives = 38/45 (84%)

Query:    54 EGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 98
             +G+    ++ G+PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+
Sbjct:    68 KGEIMFYKKNGSPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKV 112

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|J9NXB3 KCNH3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 153 (58.9 bits), Expect = 4.6e-10, P = 4.6e-10
 Identities = 27/41 (65%), Positives = 32/41 (78%)

Query:    64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104
             G PFWCLLD++PIKNEK EV L+L SHKD+T+TK     DN
Sbjct:    44 GLPFWCLLDVIPIKNEKGEVALFLVSHKDITDTKNRGGPDN 84

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

 Score = 153 (58.9 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 27/41 (65%), Positives = 32/41 (78%)

Query:    64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104
             G PFWCLLD++PIKNEK EV L+L SHKD+T+TK     DN
Sbjct:    78 GLPFWCLLDVIPIKNEKGEVALFLVSHKDITDTKNRGGPDN 118

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

MGI|MGI:2445160 Kcnh8 "potassium voltage-gated channel, subfamily H (eag-related), member 8" [Mus musculus (taxid:10090)]

 Score = 153 (58.9 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 29/55 (52%), Positives = 42/55 (76%)

Query:    54 EGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
             +G+    ++ G PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+   +++ + D
Sbjct:    94 KGEIMFYKKNGAPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITSEDKKED 148

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

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=ISO

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=ISO

GO:0005267 "potassium channel activity" evidence=IEA

GO:0006468 "protein phosphorylation" 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:0034220 "ion transmembrane transport" evidence=IEA

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

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0055085 "transmembrane transport" evidence=IEA

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

RGD|2549 Kcnh8 "potassium voltage-gated channel, subfamily H (eag-related), member 8" [Rattus norvegicus (taxid:10116)]

 Score = 153 (58.9 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 29/55 (52%), Positives = 42/55 (76%)

Query:    54 EGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
             +G+    ++ G PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+   +++ + D
Sbjct:    94 KGEIMFYKKNGAPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITSEDKKED 148

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IMP

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

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

GO:0016021 "integral to membrane" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

UNIPROTKB|Q9QWS8 Kcnh8 "Potassium voltage-gated channel subfamily H member 8" [Rattus norvegicus (taxid:10116)]

 Score = 153 (58.9 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 29/55 (52%), Positives = 42/55 (76%)

Query:    54 EGDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGD 108
             +G+    ++ G PFWCLLDIVPIKNEK +VVL+LAS KD+T+TK+   +++ + D
Sbjct:    94 KGEIMFYKKNGAPFWCLLDIVPIKNEKGDVVLFLASFKDITDTKVKITSEDKKED 148

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

GO:0016021 "integral to membrane" evidence=IEA

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

 Score = 152 (58.6 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 31/48 (64%), Positives = 35/48 (72%)

Query:    64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG-EGDYE 110
             GT FWCLLDIVPIKNEK EVVL+L SHKD+T+ K  Q  +   E D E
Sbjct:   104 GTQFWCLLDIVPIKNEKGEVVLFLVSHKDITDNKKDQDEEQSPERDEE 151

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	115
smart00086	43	smart00086, PAC, Motif C-terminal to PAS motifs (l	2e-05
pfam13426	101	pfam13426, PAS_9, PAS domain	9e-05
smart00086	43	smart00086, PAC, Motif C-terminal to PAS motifs (l	2e-04
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	4e-04
PRK13558	665	PRK13558, PRK13558, bacterio-opsin activator; Prov	7e-04
pfam13426	101	pfam13426, PAS_9, PAS domain	8e-04

>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

 Score = 38.3 bits (90), Expect = 2e-05
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
          G+  W L+   PI++E  EV   L   +D+T
Sbjct: 11 GSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41

PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold. Length = 43

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

 Score = 38.1 bits (89), Expect = 9e-05
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
           G PF  L+   P+++E  EVV  +   +D+T
Sbjct: 70  GEPFPVLVSASPVRDEDGEVVGIVGILRDIT 100

Length = 101

>gnl|CDD|197509 smart00086, PAC, Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

 Score = 35.6 bits (83), Expect = 2e-04
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 4/38 (10%)

Query: 9  YRQR----TPFWCLLDIVPIKNEKREVVLYLASHKDVT 42
          YR R    +  W L+   PI++E  EV   L   +D+T
Sbjct: 4  YRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDIT 41

PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold. Length = 43

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 8   NYRQR-TPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL 63
           NYR+  + FW  +DI PI++E   V  Y+    DVT  K A++A   + +   +Q L
Sbjct: 228 NYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELA--LQRERRKLQRL 282

Length = 665

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

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL 115
           G+ FW  +DI PI++E   V  Y+    DVT  K A++A   + +   +Q L
Sbjct: 233 GSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELA--LQRERRKLQRL 282

Length = 665

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

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 10/30 (33%), Positives = 17/30 (56%)

Query: 13  TPFWCLLDIVPIKNEKREVVLYLASHKDVT 42
            PF  L+   P+++E  EVV  +   +D+T
Sbjct: 71  EPFPVLVSASPVRDEDGEVVGIVGILRDIT 100

Length = 101

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
PRK13560	807	hypothetical protein; Provisional	99.49
PRK09776	1092	putative diguanylate cyclase; Provisional	99.46
PRK09776	1092	putative diguanylate cyclase; Provisional	99.27
PRK13560	807	hypothetical protein; Provisional	99.19
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	98.96
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	98.86
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.56
PF13426	104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	98.45
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.34
PF08448	110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	98.19
PRK11359	799	cyclic-di-GMP phosphodiesterase; Provisional	98.16
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	98.13
PRK13559	361	hypothetical protein; Provisional	98.03
PRK13558	665	bacterio-opsin activator; Provisional	98.02
PRK10060	663	RNase II stability modulator; Provisional	98.02
PRK13559	361	hypothetical protein; Provisional	97.97
KOG0501|consensus	971		97.91
smart00086	43	PAC Motif C-terminal to PAS motifs (likely to cont	97.87
PRK13557	540	histidine kinase; Provisional	97.83
KOG0501|consensus	971		97.81
PRK13558	665	bacterio-opsin activator; Provisional	97.76
smart00086	43	PAC Motif C-terminal to PAS motifs (likely to cont	97.76
TIGR02938	494	nifL_nitrog nitrogen fixation negative regulator N	97.69
PRK13557	540	histidine kinase; Provisional	97.58
PRK11091	779	aerobic respiration control sensor protein ArcB; P	97.55
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	97.51
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	97.36
PRK11091	779	aerobic respiration control sensor protein ArcB; P	97.35
TIGR00229	124	sensory_box PAS domain S-box. The PAS domain was p	97.28
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	97.2
PF00989	113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	97.13
PRK11360	607	sensory histidine kinase AtoS; Provisional	96.95
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	96.87
PF08447	91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	96.67
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	96.55
PRK11360	607	sensory histidine kinase AtoS; Provisional	95.96
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	95.7
PF13596	106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	95.47
cd00130	103	PAS PAS domain; PAS motifs appear in archaea, euba	94.92
PF12860	115	PAS_7: PAS fold	94.43
PF08348	118	PAS_6: YheO-like PAS domain; InterPro: IPR013559 T	94.3
PRK10060	663	RNase II stability modulator; Provisional	92.85
PF12860	115	PAS_7: PAS fold	92.57
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	92.48
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	90.39
PRK11073	348	glnL nitrogen regulation protein NR(II); Provision	89.31
TIGR02966	333	phoR_proteo phosphate regulon sensor kinase PhoR.	88.34
PF02743	81	Cache_1: Cache domain; InterPro: IPR004010 Cache i	87.84
COG5002	459	VicK Signal transduction histidine kinase [Signal	87.61
PRK11086	542	sensory histidine kinase DcuS; Provisional	87.05
PF08348	118	PAS_6: YheO-like PAS domain; InterPro: IPR013559 T	86.74
COG5002	459	VicK Signal transduction histidine kinase [Signal	86.51
PRK11086	542	sensory histidine kinase DcuS; Provisional	86.08
PF14827	116	Cache_3: Sensory domain of two-component sensor ki	85.65
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	83.74
COG2202	232	AtoS FOG: PAS/PAC domain [Signal transduction mech	83.31

>PRK13560 hypothetical protein; Provisional

Probab=99.49  E-value=1.5e-13  Score=115.49  Aligned_cols=98  Identities=16%  Similarity=0.211  Sum_probs=84.7

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------------------C--------------
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------------------N--------------   52 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------~--------------   52 (115)
                      ..+ ||+.+|+.+...|++|++|++++++++..|||++|++|+++                    .              
T Consensus       428 ~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~~~~~  507 (807)
T PRK13560        428 IEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKNITQF  507 (807)
T ss_pred             EEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecchhhhc
Confidence            335 99999999999999999999999999999999999988732                    0              


Q ss_pred             ---------CC-------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeee
Q psy8547          53 ---------GE-------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKD   92 (115)
Q Consensus        53 ---------~~-------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~D   92 (115)
                               +.                               ..++..+|||+.+|......|++|++|++.+++++..|
T Consensus       508 G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~~~D  587 (807)
T PRK13560        508 GYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGIVID  587 (807)
T ss_pred             CCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEEEec
Confidence                     00                               01123579999999999999999999999999999999


Q ss_pred             cccchhhchhhcc
Q psy8547          93 VTNTKMAQMADNG  105 (115)
Q Consensus        93 IT~~k~~E~~~~~  105 (115)
                      ||++|++|++++.
T Consensus       588 ITerK~aE~~L~~  600 (807)
T PRK13560        588 ISERKHAEEKIKA  600 (807)
T ss_pred             hHHHHHHHHHHHH
Confidence            9999999998764

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.46  E-value=5.3e-13  Score=116.64  Aligned_cols=108  Identities=16%  Similarity=0.047  Sum_probs=92.7

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------C----------
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------N----------   52 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~----------   52 (115)
                      ..++ || ..|+.....|++|++|++.+++++.+|||++|++++++                       +          
T Consensus       487 r~~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~g~i~~~N~a~  565 (1092)
T PRK09776        487 RIVVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDMAMKVTFMNPVA  565 (1092)
T ss_pred             EEEcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECCCCeEEEEcHHH
Confidence            3445 99 99999999999999999999999999999999877631                       0          


Q ss_pred             ------------CC---------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEE
Q psy8547          53 ------------GE---------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYL   87 (115)
Q Consensus        53 ------------~~---------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i   87 (115)
                                  |.                                 ......+|||..+|...+++|+++++|++.+++
T Consensus       566 ~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v  645 (1092)
T PRK09776        566 EKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLSTLDGENIGSV  645 (1092)
T ss_pred             HHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEEEEeeeeecCCCCEEEEE
Confidence                        00                                 011235799999999999999999999999999


Q ss_pred             EEeeecccchhhchhhccCCCccccccC
Q psy8547          88 ASHKDVTNTKMAQMADNGEGDYEDMQEL  115 (115)
Q Consensus        88 ~~~~DIT~~k~~E~~~~~~~~~~~~~~~  115 (115)
                      ++++|||++|+.|+++++.+.+|.|-.|
T Consensus       646 ~~~~DITe~k~~e~~L~~~a~~D~lTgl  673 (1092)
T PRK09776        646 LVIQDVTESRKMLRQLSYSASHDALTHL  673 (1092)
T ss_pred             EEEEecchHHHHHHHHHhhcCCCcccCC
Confidence            9999999999999999999999987543

>PRK09776 putative diguanylate cyclase; Provisional

Probab=99.27  E-value=1.1e-11  Score=108.30  Aligned_cols=94  Identities=15%  Similarity=0.180  Sum_probs=82.2

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------C--------------C
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------N--------------G   53 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~--------------~   53 (115)
                      ||+.+|+.++++|+++++|.+.+++++.+|||++|++|+.+                       .              |
T Consensus       365 dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G  444 (1092)
T PRK09776        365 DGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYE  444 (1092)
T ss_pred             CCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhC
Confidence            99999999999999999999999999999999999988631                       0              0


Q ss_pred             ---C-----------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeeccc
Q psy8547          54 ---E-----------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   95 (115)
Q Consensus        54 ---~-----------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~   95 (115)
                         +                                   ..++.++||| .+|......|++|++|++..++++..|||+
T Consensus       445 ~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITe  523 (1092)
T PRK09776        445 IPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTE  523 (1092)
T ss_pred             CCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhH
Confidence               0                                   0123468999 999999999999999999999999999999


Q ss_pred             chhhchhhcc
Q psy8547          96 TKMAQMADNG  105 (115)
Q Consensus        96 ~k~~E~~~~~  105 (115)
                      +|++|+++++
T Consensus       524 rk~~e~~L~~  533 (1092)
T PRK09776        524 VRQLNEALFQ  533 (1092)
T ss_pred             HHHHHHHHHH
Confidence            9999988764

>PRK13560 hypothetical protein; Provisional

Probab=99.19  E-value=1.9e-10  Score=96.92  Aligned_cols=95  Identities=12%  Similarity=0.041  Sum_probs=79.3

Q ss_pred             CCCceeEEEE--EEEeeCCCCCEEEEEEEEEeccchhhhhhhc------------------------------CCC--C-
Q psy8547          11 QRTPFWCLLD--IVPIKNEKREVVLYLASHKDVTNTKMAQMAD------------------------------NGE--G-   55 (115)
Q Consensus        11 dG~~fw~~~~--i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------------~~~--e-   55 (115)
                      ||+.+|+.+.  ..|+.|++|.+.+++++.+|||++|.+++++                              ++.  + 
T Consensus       285 dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~~i~~~d~~g~i~~~nn~~~~~  364 (807)
T PRK13560        285 DGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAER  364 (807)
T ss_pred             CCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcccEEEEcCCCCEEEecCHHHHH
Confidence            9999976555  4667899999999999999999999988732                              000  0 


Q ss_pred             ------------------------------------------------------------ceeceecCCceeEEEEEeEE
Q psy8547          56 ------------------------------------------------------------DYEDMQELGTPFWCLLDIVP   75 (115)
Q Consensus        56 ------------------------------------------------------------~~~~yrKdGs~f~~~~~i~p   75 (115)
                                                                                  .....+++|+.+|+.....|
T Consensus       365 ~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~p  444 (807)
T PRK13560        365 MLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEP  444 (807)
T ss_pred             HhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCceEEEEcCCCCeEEEEEEEee
Confidence                                                                        01124689999999999999


Q ss_pred             eeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          76 IKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        76 irde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ++|++|++..+++++.|||++|++|+++++
T Consensus       445 ~~d~~g~~~~~~~~~~DITerk~~E~~L~~  474 (807)
T PRK13560        445 LHDADGNIIGAIALLVDITERKQVEEQLLL  474 (807)
T ss_pred             eECCCCCEEEEEEEeehhhhHHHHHHHHHH
Confidence            999999999999999999999999998875

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=98.96  E-value=2.9e-10  Score=90.00  Aligned_cols=98  Identities=19%  Similarity=0.220  Sum_probs=74.6

Q ss_pred             cc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------CC-----------
Q psy8547           9 YR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------NG-----------   53 (115)
Q Consensus         9 Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~~-----------   53 (115)
                      .+ +|+.+|..+.++|+++++|.+.+++++++|||++|++++.+                       .+           
T Consensus        82 ~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~  161 (494)
T TIGR02938        82 RRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKK  161 (494)
T ss_pred             cCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHH
Confidence            45 99999999999999999999999999999999999877621                       00           


Q ss_pred             -------C-----------C------------------ceece-ecCCc-eeEEEEEeEEeeCCCCCEE---------EE
Q psy8547          54 -------E-----------G------------------DYEDM-QELGT-PFWCLLDIVPIKNEKREVV---------LY   86 (115)
Q Consensus        54 -------~-----------e------------------~~~~y-rKdGs-~f~~~~~i~pirde~G~v~---------~~   86 (115)
                             +           +                  ....+ +++|. .+|......|+.+..|.+.         ++
T Consensus       162 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (494)
T TIGR02938       162 LATDLRVKEPAHTVLDLLREAWREALAENWPQQLAFSNREARFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYL  241 (494)
T ss_pred             hhchhhhhHHHHHHHHHhhHHhhhhhhhcchhhhccccceeeeccCCCceeeEEEecCceEEeecchhhheeccCCCchh
Confidence                   0           0                  00012 33444 7999999999988877653         45


Q ss_pred             EEEeeecccchhhchhhccC
Q psy8547          87 LASHKDVTNTKMAQMADNGE  106 (115)
Q Consensus        87 i~~~~DIT~~k~~E~~~~~~  106 (115)
                      ++++.|||++|++|++++..
T Consensus       242 ~~~~~DITe~k~~ee~l~~~  261 (494)
T TIGR02938       242 LLTIADISNLREEQERARLS  261 (494)
T ss_pred             eehHHHHHHHHHHHHHHHHH
Confidence            66899999999999877643

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.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=98.86  E-value=1.9e-08  Score=85.62  Aligned_cols=95  Identities=15%  Similarity=0.307  Sum_probs=74.6

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------------------------C-------
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------------------------N-------   52 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------------~-------   52 (115)
                      ..++ ||+.+|+.+.+.|+. ..|.. +++++.+|||++++.++..                          +       
T Consensus        92 ~~~~~dG~~~~v~~~~~~~~-~~g~~-~~~~~~~DiT~~~~~~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~  169 (799)
T PRK11359         92 QLEKKDGSKIWTRFALSKVS-AEGKV-YYLALVRDASVEMAQKEQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMF  169 (799)
T ss_pred             EEecCCcCEEEEEEEeeeec-cCCce-EEEEEEeeccchhhhHHHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhh
Confidence            3445 999999999999984 45654 6789999999987765521                          0       


Q ss_pred             --------CC------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          53 --------GE------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        53 --------~~------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                              |.                              ..+...+++|..+|+..+..|+.+++|.+.+++++..|||
T Consensus       170 G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DIT  249 (799)
T PRK11359        170 GYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDIT  249 (799)
T ss_pred             CCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhh
Confidence                    00                              0012357899999999999999999999999999999999


Q ss_pred             cchhhchhh
Q psy8547          95 NTKMAQMAD  103 (115)
Q Consensus        95 ~~k~~E~~~  103 (115)
                      ++|++++..
T Consensus       250 erk~~e~~~  258 (799)
T PRK11359        250 EERQIRQLE  258 (799)
T ss_pred             hHHHHHHHH
Confidence            999887643

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A

Probab=98.56  E-value=1.3e-07  Score=59.96  Aligned_cols=39  Identities=23%  Similarity=0.442  Sum_probs=35.3

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      ....++ ||+.+|+.++++|+++++|++.+++++++|||+
T Consensus        65 e~~~~~~~g~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe  104 (104)
T PF13426_consen   65 EVRLRRKDGETFWVEVSASPIRDEDGEITGIIGIFRDITE  104 (104)
T ss_dssp             EEEEEETTSEEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred             EEEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence            344556 999999999999999999999999999999995

...

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A

Probab=98.45  E-value=4.1e-07  Score=57.57  Aligned_cols=73  Identities=16%  Similarity=0.336  Sum_probs=52.4

Q ss_pred             EeeCCCCCEEEEEEEEEeccchhhhhhhc------------------------CCC---CceeceecCCceeEEEEEeEE
Q psy8547          23 PIKNEKREVVLYLASHKDVTNTKMAQMAD------------------------NGE---GDYEDMQELGTPFWCLLDIVP   75 (115)
Q Consensus        23 Pi~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~---e~~~~yrKdGs~f~~~~~i~p   75 (115)
                      -+.|.+|.++.+=..+..++.....+-..                        ++.   .....++++|+.+|+.++++|
T Consensus         5 ~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~   84 (104)
T PF13426_consen    5 FILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFWVEVSASP   84 (104)
T ss_dssp             EEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEEEEEEEEE
T ss_pred             EEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEEEEEEEEE
Confidence            35677888877666666666544322210                        011   122347899999999999999


Q ss_pred             eeCCCCCEEEEEEEeeeccc
Q psy8547          76 IKNEKREVVLYLASHKDVTN   95 (115)
Q Consensus        76 irde~G~v~~~i~~~~DIT~   95 (115)
                      +++++|++.++++++.|||+
T Consensus        85 i~~~~g~~~~~i~~~~DiTe  104 (104)
T PF13426_consen   85 IRDEDGEITGIIGIFRDITE  104 (104)
T ss_dssp             EEETTSSEEEEEEEEEEEHH
T ss_pred             EECCCCCEEEEEEEEEECCC
Confidence            99999999999999999996

...

>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=98.34  E-value=1.7e-06  Score=55.37  Aligned_cols=36  Identities=31%  Similarity=0.421  Sum_probs=34.8

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~   46 (115)
                      +|...|..++++|++|++|++.+++.+.+|||++|+
T Consensus        75 ~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr  110 (110)
T PF08448_consen   75 DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR  110 (110)
T ss_dssp             TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred             cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence            899999999999999999999999999999999985

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.

>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=98.19  E-value=4.8e-06  Score=53.21  Aligned_cols=38  Identities=32%  Similarity=0.412  Sum_probs=35.8

Q ss_pred             ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchh
Q psy8547          61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~   98 (115)
                      ..+|...|..++++|++|++|++.+++.+..|||++|+
T Consensus        73 ~~~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr  110 (110)
T PF08448_consen   73 LRDGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR  110 (110)
T ss_dssp             CTTSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred             eecCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence            34899999999999999999999999999999999985

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.

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional

Probab=98.16  E-value=1.2e-05  Score=68.55  Aligned_cols=104  Identities=10%  Similarity=0.175  Sum_probs=74.2

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------CC-------------------CCc---
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------NG-------------------EGD---   56 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------~~-------------------~e~---   56 (115)
                      ..+ ||..+|+.+...|+.+++|.+.+++++.+|||++++++++.        .+                   ...   
T Consensus       214 ~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  293 (799)
T PRK11359        214 LLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLEGNILAAMCSSPPFHEMGEIICRNIESVLNESHVSL  293 (799)
T ss_pred             EeCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCceeeE
Confidence            334 99999999999999999999999999999999999876521        00                   000   


Q ss_pred             ----------e----eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc----------------------cchhhc
Q psy8547          57 ----------Y----EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT----------------------NTKMAQ  100 (115)
Q Consensus        57 ----------~----~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT----------------------~~k~~E  100 (115)
                                +    ......|...|.    .|+++.+|.+.+++.+..+..                      ++++.+
T Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~i~~~dG~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  369 (799)
T PRK11359        294 FALRNGMPIHWASSSHGAEYQNAQSWS----ATIRQRDGAPAGTLQIKTSSGAETSAFIERVADISQHLAALALEQEKSR  369 (799)
T ss_pred             EEecCCceeeccCCCCCHHHhhcccee----eeeecCCCcEEEEEEEEECCCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence                      0    001223334443    688889999988888876532                      455566


Q ss_pred             hhhccCCCccccccC
Q psy8547         101 MADNGEGDYEDMQEL  115 (115)
Q Consensus       101 ~~~~~~~~~~~~~~~  115 (115)
                      .++++.+.+|.|..|
T Consensus       370 ~~l~~~~~~D~lTgl  384 (799)
T PRK11359        370 QHIEQLIQFDPLTGL  384 (799)
T ss_pred             HHHHHHhCcCCCCCC
Confidence            778888888887543

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=98.13  E-value=2.9e-05  Score=62.74  Aligned_cols=40  Identities=13%  Similarity=0.126  Sum_probs=35.2

Q ss_pred             eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547          60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM  101 (115)
Q Consensus        60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~  101 (115)
                      .+|||+.+|+.++++|+++..+  ..++++++|||++|+.+.
T Consensus       330 ~~~~G~~~~ve~s~~~i~~~~~--~~~~~v~rDITeR~~~~~  369 (442)
T TIGR02040       330 TGEFGAQTEVEISAAWVDQGER--PLIVLVIRDISRRLTMRD  369 (442)
T ss_pred             EcCCCCEEEEEEEEEEeccCCc--eEEEEEEecchhhccCCC
Confidence            5899999999999999987665  468899999999999865

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).

>PRK13559 hypothetical protein; Provisional

Probab=98.03  E-value=8.6e-06  Score=63.47  Aligned_cols=46  Identities=24%  Similarity=0.539  Sum_probs=41.7

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD  103 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~  103 (115)
                      ..+++||+.||+.++++|++++.|.+..+++++.|||++|++|+..
T Consensus       122 ~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~  167 (361)
T PRK13559        122 LNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE  167 (361)
T ss_pred             EEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH
Confidence            3478999999999999999999999999999999999999876643

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.02  E-value=1e-05  Score=68.44  Aligned_cols=49  Identities=33%  Similarity=0.578  Sum_probs=45.3

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ++.++|||+.+|+.+++.|++++.|.+..++++..|||++|++|+++++
T Consensus       226 ~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~  274 (665)
T PRK13558        226 LRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQR  274 (665)
T ss_pred             EEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHH
Confidence            3457899999999999999999999999999999999999999998774

>PRK10060 RNase II stability modulator; Provisional

Probab=98.02  E-value=1.3e-05  Score=68.50  Aligned_cols=56  Identities=13%  Similarity=0.167  Sum_probs=45.2

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCC-EEEEEEEeeecccchhhchhhccCCCccccccC
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKRE-VVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL  115 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~-v~~~i~~~~DIT~~k~~E~~~~~~~~~~~~~~~  115 (115)
                      ..+|+|+.+|...... +.+..|. ..+++++..|||++|.+|+++++++.+|.|-.|
T Consensus       189 ~~~~~G~~~~~~~~~~-~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL  245 (663)
T PRK10060        189 IKTRKGQRLFLFRNKF-VHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGL  245 (663)
T ss_pred             EEeCCCCEEEEEeeeE-EEcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCC
Confidence            3689999999876644 4544554 567889999999999999999999999998654

>PRK13559 hypothetical protein; Provisional

Probab=97.97  E-value=1.6e-05  Score=62.00  Aligned_cols=44  Identities=30%  Similarity=0.601  Sum_probs=39.6

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..+++ ||+.+|+.++++|+++++|.+.+++++.+|||++|++++
T Consensus       121 ~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~  165 (361)
T PRK13559        121 LLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRA  165 (361)
T ss_pred             EEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHH
Confidence            34556 999999999999999999999999999999999997654

>KOG0501|consensus

Probab=97.91  E-value=1.1e-05  Score=69.27  Aligned_cols=45  Identities=40%  Similarity=0.606  Sum_probs=41.5

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM  101 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~  101 (115)
                      ...|+|+.+|.|..+.|+||||+...|+.|+..|+|||..||.-+
T Consensus        97 illyKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQPid  141 (971)
T KOG0501|consen   97 ILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQPID  141 (971)
T ss_pred             eEeeecCCCceEEEEEeecccCCCceEEEEEeecccchhhcCCCc
Confidence            346999999999999999999999999999999999999988654

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

Probab=97.87  E-value=0.0001  Score=35.81  Aligned_cols=34  Identities=29%  Similarity=0.518  Sum_probs=31.8

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      +|..+|+.....|+.+.+|.+.+++++..|||++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~   43 (43)
T smart00086       10 DGSYIWVLVSASPIRDEDGEVEGILGVVRDITER   43 (43)
T ss_pred             CCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence            9999999999999999999999999999999863

PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.

>PRK13557 histidine kinase; Provisional

Probab=97.83  E-value=1.8e-05  Score=63.96  Aligned_cols=49  Identities=24%  Similarity=0.443  Sum_probs=44.4

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccC
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGE  106 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~  106 (115)
                      ..++|+|+.+|..++++|+++.+|.+++++++..|||+++++|++++..
T Consensus       109 ~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~  157 (540)
T PRK13557        109 LNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQA  157 (540)
T ss_pred             EEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHH
Confidence            3478999999999999999999999999999999999999998876543

>KOG0501|consensus

Probab=97.81  E-value=2e-05  Score=67.67  Aligned_cols=46  Identities=43%  Similarity=0.710  Sum_probs=42.8

Q ss_pred             cceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           4 HPDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         4 ~~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      -+.+.|| +-+|.|..+.|.||+|+...++.|+..|+|||..|++-.
T Consensus        95 fEillyKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQPid  141 (971)
T KOG0501|consen   95 FEILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQPID  141 (971)
T ss_pred             eeeEeeecCCCceEEEEEeecccCCCceEEEEEeecccchhhcCCCc
Confidence            3578899 999999999999999999999999999999999999755

>PRK13558 bacterio-opsin activator; Provisional

Probab=97.76  E-value=6.3e-05  Score=63.66  Aligned_cols=43  Identities=40%  Similarity=0.737  Sum_probs=40.0

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..++ ||+.+|+.+.+.|+++++|.+.+++++.+|||++|++++
T Consensus       227 ~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~  270 (665)
T PRK13558        227 RNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAEL  270 (665)
T ss_pred             EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHH
Confidence            4456 999999999999999999999999999999999999877

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)

Probab=97.76  E-value=0.00022  Score=34.56  Aligned_cols=39  Identities=28%  Similarity=0.453  Sum_probs=34.6

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      ...+++|..+|+.....++.+..|.+..++++..|||++
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~   43 (43)
T smart00086        5 RLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER   43 (43)
T ss_pred             EEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence            346788999999999999999999999999999999863

PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL

Probab=97.69  E-value=2.5e-05  Score=61.89  Aligned_cols=48  Identities=21%  Similarity=0.340  Sum_probs=43.8

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ..++|+|..+|..+.++|+++++|.+..+++++.|||++|++|+++++
T Consensus        80 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~  127 (494)
T TIGR02938        80 LNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVAN  127 (494)
T ss_pred             eccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHH
Confidence            347899999999999999999999999999999999999999987654

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.

>PRK13557 histidine kinase; Provisional

Probab=97.58  E-value=0.00014  Score=58.80  Aligned_cols=44  Identities=30%  Similarity=0.560  Sum_probs=40.1

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..+++ ||+.+|..++++|+++++|.+++++++..|||+++.+++
T Consensus       108 ~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~  152 (540)
T PRK13557        108 ILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAED  152 (540)
T ss_pred             EEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHH
Confidence            34567 999999999999999999999999999999999988765

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=97.55  E-value=0.00012  Score=62.93  Aligned_cols=47  Identities=19%  Similarity=0.002  Sum_probs=43.1

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ..++||+.+|..++.+|+++++|.+.++++++.|||++|++|++++.
T Consensus       232 ~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~  278 (779)
T PRK11091        232 LDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEK  278 (779)
T ss_pred             EEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHH
Confidence            36789999999999999999999999999999999999999987653

>TIGR00229 sensory_box PAS domain S-box

Probab=97.51  E-value=0.00019  Score=42.69  Aligned_cols=43  Identities=21%  Similarity=0.342  Sum_probs=38.7

Q ss_pred             eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547          60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD  103 (115)
Q Consensus        60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~  103 (115)
                      ..++|..+|+.+...|+. +.|.+..+++++.|||++++++.++
T Consensus        82 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~l  124 (124)
T TIGR00229        82 RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEAL  124 (124)
T ss_pred             EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhcC
Confidence            478999999999999999 8899999999999999999988653

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.

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

Probab=97.36  E-value=0.00037  Score=44.47  Aligned_cols=32  Identities=22%  Similarity=0.564  Sum_probs=30.0

Q ss_pred             cCCCceeEEEEEEEeeCCCCCEEEEEEEEEec
Q psy8547          10 RQRTPFWCLLDIVPIKNEKREVVLYLASHKDV   41 (115)
Q Consensus        10 rdG~~fw~~~~i~Pi~de~G~~~~fi~~~~DI   41 (115)
                      ++|+.+|+.+..+|+++.+|++.+++++.+||
T Consensus        82 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI  113 (113)
T PF00989_consen   82 RDGRPRWVEVRASPVRDEDGQIIGILVIFRDI  113 (113)
T ss_dssp             TTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred             cCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence            49999999999999999999999999999997

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 ....

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=97.35  E-value=0.0004  Score=59.86  Aligned_cols=39  Identities=18%  Similarity=0.072  Sum_probs=37.7

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ||+.+|+.++.+|+++++|.+.+++++.+|||++|++++
T Consensus       236 ~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~  274 (779)
T PRK11091        236 DGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQD  274 (779)
T ss_pred             CCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHH
Confidence            999999999999999999999999999999999999875

>TIGR00229 sensory_box PAS domain S-box

Probab=97.28  E-value=0.00054  Score=40.68  Aligned_cols=38  Identities=18%  Similarity=0.368  Sum_probs=35.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      +|..+|+.+...|+. ++|...+++++..|||+++.+++
T Consensus        85 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~  122 (124)
T TIGR00229        85 DGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE  122 (124)
T ss_pred             CCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence            999999999999999 88999999999999999998764

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.

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=97.20  E-value=0.0013  Score=41.18  Aligned_cols=35  Identities=17%  Similarity=0.223  Sum_probs=30.9

Q ss_pred             ceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEe
Q psy8547          56 DYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASH   90 (115)
Q Consensus        56 ~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~   90 (115)
                      .++.++|||+..|+.....|++|++|+++.++|+.
T Consensus        57 e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~~~Gv~   91 (91)
T PF08447_consen   57 EYRIRRKDGEYRWIEVRGRPIFDENGKPIRIIGVI   91 (91)
T ss_dssp             EEEEEGTTSTEEEEEEEEEEEETTTS-EEEEEEEE
T ss_pred             EEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEC
Confidence            45678899999999999999999999999999874

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

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

Probab=97.13  E-value=0.00096  Score=42.52  Aligned_cols=70  Identities=14%  Similarity=0.332  Sum_probs=48.0

Q ss_pred             eeCCCCCEEEEEEEEEeccchhhhhhhc------------------------CCC--C--ceeceecCCceeEEEEEeEE
Q psy8547          24 IKNEKREVVLYLASHKDVTNTKMAQMAD------------------------NGE--G--DYEDMQELGTPFWCLLDIVP   75 (115)
Q Consensus        24 i~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~--e--~~~~yrKdGs~f~~~~~i~p   75 (115)
                      +.|.+|+++++-..+.+++.....+..-                        .+.  .  ......++|+.+|+.++.+|
T Consensus        16 ~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~   95 (113)
T PF00989_consen   16 VIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRDGRPRWVEVRASP   95 (113)
T ss_dssp             EEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETTSCEEEEEEEEEE
T ss_pred             EEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecCCcEEEEEEEEEE
Confidence            4678888887666666666554433210                        000  0  01112359999999999999


Q ss_pred             eeCCCCCEEEEEEEeeec
Q psy8547          76 IKNEKREVVLYLASHKDV   93 (115)
Q Consensus        76 irde~G~v~~~i~~~~DI   93 (115)
                      +++.+|++.++++++.||
T Consensus        96 ~~~~~~~~~~~~~~~~DI  113 (113)
T PF00989_consen   96 VRDEDGQIIGILVIFRDI  113 (113)
T ss_dssp             EEETTEEEEEEEEEEEE-
T ss_pred             EEeCCCCEEEEEEEEEeC
Confidence            999999999999999997

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 ....

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=96.95  E-value=0.00063  Score=55.05  Aligned_cols=48  Identities=17%  Similarity=-0.024  Sum_probs=42.3

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCC
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEG  107 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~  107 (115)
                      ..+++|..+ +.++.+|+.+++|++..+++++.|||++|++|+++++..
T Consensus       338 ~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~  385 (607)
T PRK11360        338 FPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE  385 (607)
T ss_pred             EEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHH
Confidence            356778777 899999999999999999999999999999999887643

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=96.87  E-value=0.0017  Score=52.48  Aligned_cols=37  Identities=8%  Similarity=0.008  Sum_probs=32.6

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ||+.+|+.++++|+.+..+  ..++++.+|||++++++.
T Consensus       333 ~G~~~~ve~s~~~i~~~~~--~~~~~v~rDITeR~~~~~  369 (442)
T TIGR02040       333 FGAQTEVEISAAWVDQGER--PLIVLVIRDISRRLTMRD  369 (442)
T ss_pred             CCCEEEEEEEEEEeccCCc--eEEEEEEecchhhccCCC
Confidence            9999999999999998666  457889999999999853

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).

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []

Probab=96.67  E-value=0.0058  Score=38.15  Aligned_cols=27  Identities=15%  Similarity=0.182  Sum_probs=25.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEE
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLAS   37 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~   37 (115)
                      ||+..|+.....|++|++|+++.++++
T Consensus        64 ~G~~~wi~~~~~~~~d~~g~~~~~~Gv   90 (91)
T PF08447_consen   64 DGEYRWIEVRGRPIFDENGKPIRIIGV   90 (91)
T ss_dssp             TSTEEEEEEEEEEEETTTS-EEEEEEE
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEE
Confidence            999999999999999999999999987

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.

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

Probab=96.55  E-value=0.0062  Score=39.79  Aligned_cols=30  Identities=23%  Similarity=0.398  Sum_probs=24.2

Q ss_pred             CceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          13 TPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        13 ~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ...|..+.+.|+++++|+..|.+.++.|||
T Consensus        77 ~~~~~~~~~~P~~~~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   77 GGRWYLVRYRPYRDEDGEYAGAVITFQDIT  106 (106)
T ss_dssp             TTEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred             CCEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            355668899999999999999999999998

>PRK11360 sensory histidine kinase AtoS; Provisional

Probab=95.96  E-value=0.018  Score=46.60  Aligned_cols=38  Identities=24%  Similarity=0.161  Sum_probs=34.8

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      +|..+ +.++.+|++|++|++.+++++++|||+++++++
T Consensus       342 ~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~  379 (607)
T PRK11360        342 DRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQR  379 (607)
T ss_pred             CCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHH
Confidence            77766 899999999999999999999999999988775

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

Probab=95.70  E-value=0.059  Score=29.78  Aligned_cols=31  Identities=29%  Similarity=0.641  Sum_probs=29.1

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEec
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDV   41 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DI   41 (115)
                      +|...|+.+...|+.+..|...+++++..||
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             CCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence            7999999999999999999999999998886

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.

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

Probab=95.47  E-value=0.041  Score=35.85  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=22.9

Q ss_pred             eeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          66 PFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        66 ~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      -.|..+.+.|+++++|++.+.+.++.|||
T Consensus        78 ~~~~~~~~~P~~~~~g~~~G~v~~~~DIT  106 (106)
T PF13596_consen   78 GRWYLVRYRPYRDEDGEYAGAVITFQDIT  106 (106)
T ss_dssp             TEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred             CEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            34556799999999999999999999998

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

Probab=94.92  E-value=0.15  Score=27.98  Aligned_cols=35  Identities=29%  Similarity=0.565  Sum_probs=31.0

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeec
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDV   93 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DI   93 (115)
                      ...++|...|+.+...|+.+..|....++++..||
T Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di  103 (103)
T cd00130          69 LRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI  103 (103)
T ss_pred             EEccCCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence            35677999999999999999999999999998886

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.

>PF12860 PAS_7: PAS fold

Probab=94.43  E-value=0.058  Score=35.53  Aligned_cols=31  Identities=19%  Similarity=0.351  Sum_probs=24.8

Q ss_pred             ceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          14 PFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        14 ~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      --|..+...|.-+  |   +++.++.|||+++++|+
T Consensus        85 gr~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~  115 (115)
T PF12860_consen   85 GRWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE  115 (115)
T ss_pred             CEEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence            3467788888854  5   67899999999999874

>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT)

Probab=94.30  E-value=0.13  Score=35.47  Aligned_cols=84  Identities=15%  Similarity=0.206  Sum_probs=58.5

Q ss_pred             EEEEEEEeeCCCCCEEEEEEEEEe-ccchhhhhhh-------c-CC--C-C---ceeceecCCceeEEEEEeEEeeCCCC
Q psy8547          17 CLLDIVPIKNEKREVVLYLASHKD-VTNTKMAQMA-------D-NG--E-G---DYEDMQELGTPFWCLLDIVPIKNEKR   81 (115)
Q Consensus        17 ~~~~i~Pi~de~G~~~~fi~~~~D-IT~~k~~e~~-------~-~~--~-e---~~~~yrKdGs~f~~~~~i~pirde~G   81 (115)
                      |++.+-=+.+.+..++.   +..- ||.|+.=...       + +.  + .   .|...-|||..+.+  +-..|||++|
T Consensus        20 ~EVVLHDl~~~~~sIv~---I~Ng~vsgR~vGdp~t~~~l~~l~~~~~~~~~~~nY~~~~~~Gk~lrS--sT~~Ird~~g   94 (118)
T PF08348_consen   20 CEVVLHDLSDPEHSIVA---IANGHVSGRKVGDPITDLALELLKEKQYEEDYIINYKTKTKDGKILRS--STFFIRDENG   94 (118)
T ss_pred             eEEEEEECCCCCCEEEE---EECCCccCCccCCchhHHHHHHHhccccCCCccccccccCCCCCEEEE--EEEEEECCCC
Confidence            67777777777776653   4444 7777653221       1 11  1 1   23345689988876  5678999999


Q ss_pred             CEEEEEEEeeecccchhhchhhcc
Q psy8547          82 EVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        82 ~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ++++.+++-.|+|...++..-|+|
T Consensus        95 ~~iG~LCIN~D~s~~~~~~~~L~q  118 (118)
T PF08348_consen   95 KLIGALCINFDISALEQAQNFLDQ  118 (118)
T ss_pred             CEEEEEEEEeccHHHHHHHHHHcC
Confidence            999999999999999988776654

Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.

>PRK10060 RNase II stability modulator; Provisional

Probab=92.85  E-value=0.26  Score=42.46  Aligned_cols=41  Identities=12%  Similarity=0.176  Sum_probs=30.6

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCC-EEEEEEEEEeccchhhhhh
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKRE-VVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~-~~~fi~~~~DIT~~k~~e~   49 (115)
                      +.+ +|+.+|+.... |+.+.+|. ..+++++.+|||+++.+++
T Consensus       189 ~~~~~G~~~~~~~~~-~~~~~~g~~~~~~i~~~~DITe~k~~e~  231 (663)
T PRK10060        189 IKTRKGQRLFLFRNK-FVHSGSGKNEIFLICSGTDITEERRAQE  231 (663)
T ss_pred             EEeCCCCEEEEEeee-EEEcCCCCceEEEEEEEEechHHHHHHH
Confidence            334 99999987664 45555554 4678899999999998776

>PF12860 PAS_7: PAS fold

Probab=92.57  E-value=0.18  Score=33.11  Aligned_cols=34  Identities=21%  Similarity=0.370  Sum_probs=25.2

Q ss_pred             ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547          61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM  101 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~  101 (115)
                      ..||.  |..++.+|.-+  |   .++.++.|||+.+++|+
T Consensus        82 ~~dgr--~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~  115 (115)
T PF12860_consen   82 LPDGR--WLEVRAQPLPD--G---GFVLTFTDVTERRRAEE  115 (115)
T ss_pred             CCCCE--EEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence            34554  55667778743  4   48899999999999985

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

Probab=92.48  E-value=0.055  Score=41.69  Aligned_cols=41  Identities=10%  Similarity=0.017  Sum_probs=32.9

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN  104 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~  104 (115)
                      .+.+||..+|+.++.+|+.  .   ..++..+.|+|++++.+.++.
T Consensus        82 ~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~  122 (348)
T PRK11073         82 TLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQL  122 (348)
T ss_pred             EEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHH
Confidence            3678999999999999998  2   246778999999888766543

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=90.39  E-value=0.37  Score=36.02  Aligned_cols=40  Identities=18%  Similarity=0.140  Sum_probs=33.3

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD  103 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~  103 (115)
                      ...++|..+|..+.++|+.+..     +++++.|||+.++.++..
T Consensus        75 ~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~  114 (333)
T TIGR02966        75 LPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMR  114 (333)
T ss_pred             eecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHH
Confidence            3458999999999999998754     788999999998877643

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).

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

Probab=89.31  E-value=0.55  Score=36.10  Aligned_cols=37  Identities=8%  Similarity=0.021  Sum_probs=29.5

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ   48 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e   48 (115)
                      ..++ ||+.+|+.++.+|+.  .   .+++..++|+|+++..+
T Consensus        81 ~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~  118 (348)
T PRK11073         81 VTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLS  118 (348)
T ss_pred             eEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHH
Confidence            3455 999999999999999  2   34667899999987754

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR

Probab=88.34  E-value=0.74  Score=34.38  Aligned_cols=34  Identities=21%  Similarity=0.192  Sum_probs=29.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      +|..+|+.+.++|+.+..     ++++++|||+.++.++
T Consensus        79 ~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~  112 (333)
T TIGR02966        79 INSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQ  112 (333)
T ss_pred             CCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHH
Confidence            899999999999998854     7789999999887654

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).

>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors

Probab=87.84  E-value=2.7  Score=25.92  Aligned_cols=35  Identities=14%  Similarity=0.147  Sum_probs=27.2

Q ss_pred             cc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547           9 YR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus         9 Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      |. ..+.-|+.....||++++|+++|++++--++..
T Consensus         5 y~~~~~~~~vi~~s~pi~~~~g~~~Gvv~~di~l~~   40 (81)
T PF02743_consen    5 YVDAATGQPVITISVPIYDDDGKIIGVVGIDISLDQ   40 (81)
T ss_dssp             EEETTTTEEEEEEEEEEEETTTEEEEEEEEEEEHHH
T ss_pred             EEeCCCCcEEEEEEEEEECCCCCEEEEEEEEeccce
Confidence            44 446667889999999999999999987555443

The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.

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

Probab=87.61  E-value=1.2  Score=36.85  Aligned_cols=44  Identities=14%  Similarity=0.099  Sum_probs=39.4

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ++..+ .|+.+-..+..+.++-|.|.+.|+|++..|+|++...|+
T Consensus       179 lld~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~  223 (459)
T COG5002         179 LLDSSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVER  223 (459)
T ss_pred             EEeecCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHH
Confidence            44556 788889999999999999999999999999999988777

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=87.05  E-value=1.2  Score=36.13  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=29.1

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      +|..  +.....|+++ +|.+.+++.+++|+|+.++.++
T Consensus       296 ~g~~--~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~  331 (542)
T PRK11086        296 NGRL--LLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQ  331 (542)
T ss_pred             CCEE--EEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHH
Confidence            5544  4556789999 8999999999999999877554

>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT)

Probab=86.74  E-value=2.4  Score=29.14  Aligned_cols=37  Identities=16%  Similarity=0.158  Sum_probs=31.2

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ||+.+.+  +-..|+|++|+++|.+++=.|+|....+..
T Consensus        78 ~Gk~lrS--sT~~Ird~~g~~iG~LCIN~D~s~~~~~~~  114 (118)
T PF08348_consen   78 DGKILRS--STFFIRDENGKLIGALCINFDISALEQAQN  114 (118)
T ss_pred             CCCEEEE--EEEEEECCCCCEEEEEEEEeccHHHHHHHH
Confidence            8877654  456899999999999999999999887654

Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.

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

Probab=86.51  E-value=1.1  Score=37.05  Aligned_cols=44  Identities=14%  Similarity=0.117  Sum_probs=39.1

Q ss_pred             ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547          61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN  104 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~  104 (115)
                      +..|..+-..+.-+-++-+.|-+.+++++..|+|++...|++.|
T Consensus       183 ~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErR  226 (459)
T COG5002         183 SDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERR  226 (459)
T ss_pred             cCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHH
Confidence            44788888899999999999999999999999999988887655

>PRK11086 sensory histidine kinase DcuS; Provisional

Probab=86.08  E-value=1.2  Score=36.19  Aligned_cols=36  Identities=19%  Similarity=0.301  Sum_probs=30.0

Q ss_pred             EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547          68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN  104 (115)
Q Consensus        68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~  104 (115)
                      +......|+.+ +|.+..++.+++|+|+.++.++++.
T Consensus       299 ~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~  334 (542)
T PRK11086        299 LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLD  334 (542)
T ss_pred             EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHH
Confidence            34556789998 8999999999999999988777654

>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B

Probab=85.65  E-value=2.1  Score=28.64  Aligned_cols=30  Identities=17%  Similarity=0.081  Sum_probs=22.9

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEe
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKD   40 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~D   40 (115)
                      .|+.-+..-...||+|++|+++|++.+-..
T Consensus        83 ~~~~~~~~~~~~PV~d~~g~viG~V~VG~~  112 (116)
T PF14827_consen   83 QGTGGPSLRAFAPVYDSDGKVIGVVSVGVS  112 (116)
T ss_dssp             ECTTCEEEEEEEEEE-TTS-EEEEEEEEEE
T ss_pred             ecCCceEEEEEEeeECCCCcEEEEEEEEEE
Confidence            555567788999999999999999987554

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

Probab=83.74  E-value=3.7  Score=25.89  Aligned_cols=41  Identities=27%  Similarity=0.437  Sum_probs=35.1

Q ss_pred             ceecCCce-eEEEEEeEEeeCCCCCEEEEEEEeeecccchhhc
Q psy8547          59 DMQELGTP-FWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ  100 (115)
Q Consensus        59 ~yrKdGs~-f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E  100 (115)
                      ...++|.. +|....+.+..+ .|.+..++....|+++.++++
T Consensus       191 ~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~  232 (232)
T COG2202         191 VRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQAE  232 (232)
T ss_pred             EEecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhcC
Confidence            36799996 999999999886 788999999999999988754

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

Probab=83.31  E-value=4.1  Score=25.72  Aligned_cols=40  Identities=28%  Similarity=0.431  Sum_probs=34.2

Q ss_pred             eecc-CCCc-eeEEEEEEEeeCCCCCEEEEEEEEEeccchhhh
Q psy8547           7 TNYR-QRTP-FWCLLDIVPIKNEKREVVLYLASHKDVTNTKMA   47 (115)
Q Consensus         7 ~~Yr-dG~~-fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~   47 (115)
                      .... +|.. .|....+.|..+ .|.+..+.....|+|+++..
T Consensus       190 ~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~  231 (232)
T COG2202         190 RVRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA  231 (232)
T ss_pred             EEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence            3444 9996 999999999988 89999999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	115
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	3e-12
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	9e-12
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	4e-12
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	9e-12
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	1e-11
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	3e-11
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	4e-11
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	6e-11
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	5e-11
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	1e-10
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	1e-10
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	3e-10
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	3e-10
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	4e-10
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	5e-09
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	1e-08
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	5e-07
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	6e-07
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	6e-07
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	7e-07
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	1e-06
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	2e-06
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	4e-06
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	5e-06

>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 = 57.2 bits (139), Expect = 3e-12
 Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVT 42
            YR+  + F CL+D+VP+KNE   V++++ + + V 
Sbjct: 73  FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVM 108

>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 = 56.0 bits (136), Expect = 9e-12
 Identities = 12/31 (38%), Positives = 22/31 (70%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
           G+ F CL+D+VP+KNE   V++++ + + V 
Sbjct: 78  GSCFLCLVDVVPVKNEDGAVIMFILNFEVVM 108

>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 = 57.6 bits (140), Expect = 4e-12
 Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)

Query: 8   NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT 42
            YR   + F CL+D+VP+KNE   V++++ + + V 
Sbjct: 101 FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVM 136

>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 = 56.9 bits (138), Expect = 9e-12
 Identities = 12/31 (38%), Positives = 22/31 (70%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
           G+ F CL+D+VP+KNE   V++++ + + V 
Sbjct: 106 GSCFLCLVDVVPVKNEDGAVIMFILNFEVVM 136

>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 = 56.0 bits (136), Expect = 1e-11
 Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48
           NY++  TPFW LL + PIK+++   + ++    +V+      
Sbjct: 86  NYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGV 127

>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 = 55.3 bits (134), Expect = 3e-11
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100
           GTPFW LL + PIK+++   + ++    +V+      
Sbjct: 91  GTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGV 127

>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 = 55.3 bits (134), Expect = 4e-11
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48
           NY +    FW L  + P++++K +V  ++    D T      
Sbjct: 82  NYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDA 123

>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 = 54.6 bits (132), Expect = 6e-11
 Identities = 9/37 (24%), Positives = 17/37 (45%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100
           G  FW L  + P++++K +V  ++    D T      
Sbjct: 87  GKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDA 123

>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 = 54.0 bits (131), Expect = 5e-11
 Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 43
           NYR+  TPFW LL + PIK     V  ++    DVT+
Sbjct: 73  NYRKDGTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS 109

>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 = 53.3 bits (129), Expect = 1e-10
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 95
           GTPFW LL + PIK     V  ++    DVT+
Sbjct: 78  GTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS 109

>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 = 52.9 bits (128), Expect = 1e-10
 Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVT 42
           NY +    FW LL + P++++K E+  ++    D +
Sbjct: 77  NYTKSGKKFWNLLHLQPVRDQKGELQYFIGVQLDGS 112

>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 = 52.1 bits (126), Expect = 3e-10
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94
           G  FW LL + P++++K E+  ++    D +
Sbjct: 82  GKKFWNLLHLQPVRDQKGELQYFIGVQLDGS 112

>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 = 53.1 bits (128), Expect = 3e-10
 Identities = 10/47 (21%), Positives = 21/47 (44%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYE 110
           GT FW L  +  +++ K  +V Y+     V+      + +    +Y+
Sbjct: 120 GTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEYK 166

>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 = 53.1 bits (128), Expect = 4e-10
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYE 58
           NYRQ  T FW L  +  +++ K  +V Y+     V+      + +    +Y+
Sbjct: 115 NYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQNIEYK 166

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

 Score = 51.1 bits (122), Expect = 5e-09
 Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 2/100 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQELGTP 66
           NY++  TPF   + + PI ++  E++ +L S  +V + +        E   E ++ L   
Sbjct: 143 NYKKDGTPFRNAVLVAPIYDDDDELLYFLGSQVEVDDDQPNMGMARRERAAEMLKTLSPR 202

Query: 67  FWCLLDIVPIKNEKREVVLYLA-SHKDVTNTKMAQMADNG 105
              +  +V      +EV   L  S K V   +   M    
Sbjct: 203 QLEVTTLVASGLRNKEVAARLGLSEKTVKMHRGLVMEKLN 242

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

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 13/52 (25%), Positives = 25/52 (48%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL 115
           GTPF   + + PI ++  E++ +L S  +V + +        E   E ++ L
Sbjct: 148 GTPFRNAVLVAPIYDDDDELLYFLGSQVEVDDDQPNMGMARRERAAEMLKTL 199

>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 = 44.6 bits (106), Expect = 5e-07
 Identities = 6/34 (17%), Positives = 16/34 (47%), Gaps = 1/34 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKD 40
           N+++    F   L ++P+++E  E    +    +
Sbjct: 116 NFKKNGQRFVNFLTMIPVRDETGEYRYSMGFQCE 149

>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 = 44.3 bits (105), Expect = 6e-07
 Identities = 6/29 (20%), Positives = 13/29 (44%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKD 92
           G  F   L ++P+++E  E    +    +
Sbjct: 121 GQRFVNFLTMIPVRDETGEYRYSMGFQCE 149

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

 Score = 44.1 bits (105), Expect = 6e-07
 Identities = 11/37 (29%), Positives = 18/37 (48%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100
           G  FW  L I P+ N    +  +++S  DVT   + +
Sbjct: 82  GEAFWNRLHISPVHNANGRLQHFVSSQLDVTLELVPR 118

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

 Score = 43.7 bits (104), Expect = 7e-07
 Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48
           NY++    FW  L I P+ N    +  +++S  DVT   + +
Sbjct: 77  NYKKSGEAFWNRLHISPVHNANGRLQHFVSSQLDVTLELVPR 118

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

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 10/37 (27%), Positives = 19/37 (51%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100
           G+ FW  L I P+K++  +   ++   KDV+     +
Sbjct: 110 GSAFWNELSITPVKSDFDQRTYFIGIQKDVSRQVELE 146

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48
           NYR+  + FW  L I P+K++  +   ++   KDV+     +
Sbjct: 105 NYRKDGSAFWNELSITPVKSDFDQRTYFIGIQKDVSRQVELE 146

>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 = 41.7 bits (99), Expect = 4e-06
 Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 2/37 (5%)

Query: 64  GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100
           GT FW  L+I P++ E  +   ++    D+T  K  +
Sbjct: 84  GTMFWNELNIDPMEIE--DKTYFVGIQNDITKQKEYE 118

>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 = 41.4 bits (98), Expect = 5e-06
 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 8   NYRQ-RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48
           NY++  T FW  L+I P++ E  +   ++    D+T  K  +
Sbjct: 79  NYKKDGTMFWNELNIDPMEIE--DKTYFVGIQNDITKQKEYE 118

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	99.67
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	99.07
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	99.02
1n9l_A	109	PHOT-LOV1, putative blue light receptor; phototrop	98.95
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	98.88
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.87
3mr0_A	142	Sensory box histidine kinase/response regulator; P	98.85
3ewk_A	227	Sensor protein; PAS domain, alpha/beta fold, kinas	98.8
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	98.77
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	98.77
2gj3_A	120	Nitrogen fixation regulatory protein; PAS domain,	98.76
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	98.75
3h9w_A	115	Diguanylate cyclase with PAS/PAC sensor; alpha-bet	98.74
4hia_A	176	LOV protein; PAS, HTH, signaling protein; HET: FMN	98.74
2pr5_A	132	Blue-light photoreceptor; light-oxygen-voltage, LO	98.71
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	98.7
3t50_A	128	Blue-light-activated histidine kinase; PAS superfa	98.7
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	98.67
3ue6_A	166	Aureochrome1; PAS/LOV domain, FMN-binding blue-lig	98.64
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.64
3mr0_A	142	Sensory box histidine kinase/response regulator; P	98.55
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	98.54
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	98.54
3f1p_A	117	Endothelial PAS domain-containing protein 1; PAS d	98.53
3nja_A	125	Probable ggdef family protein; structural genomics	98.51
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	98.5
3nja_A	125	Probable ggdef family protein; structural genomics	98.5
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	98.5
4eet_B	115	Phototropin-2; LOV, blue light photoreceptor, sign	98.47
4eho_A	635	Bacteriophytochrome, PAS/PAC sensor; photoreceptor	98.47
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	98.43
2z6d_A	130	Phototropin-2; PAS-fold, LOV-fold, alternative spl	98.43
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	98.43
3f1p_B	121	ARYL hydrocarbon receptor nuclear translocator; PA	98.41
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.41
2vv6_A	119	FIXL, sensor protein FIXL; signaling protein, tran	98.39
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	98.38
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	98.38
2wkq_A	332	NPH1-1, RAS-related C3 botulinum toxin substrate 1	98.37
3sw1_A	162	Sensory box protein; light-oxygen-voltage, LOV, PA	98.37
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	98.35
3mqq_A	120	Transcriptional regulator, LUXR family; PAS domain	98.34
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	98.33
3k3c_A	158	Protein RV1364C/MT1410; sensor, PAS, signal transd	98.33
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	98.32
2v0u_A	146	NPH1-1, LOV2; kinase, transferase, ATP-binding, se	98.29
3lyx_A	124	Sensory BOX/ggdef domain protein; structural genom	98.28
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.27
1byw_A	110	Protein (human ERG potassium channel); PAS domain,	98.23
3kx0_X	185	Uncharacterized protein RV1364C/MT1410; PAS domain	98.12
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	98.1
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	98.08
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	98.07
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.06
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.04
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	98.03
3mxq_A	152	Sensor protein; PSI2, MCSG, structural genomics, p	98.02
3icy_A	118	Sensor protein; sensory box histidine kinase/respo	98.01
3eeh_A	125	Putative light and redox sensing histidine kinase;	97.97
2l0w_A	138	Potassium voltage-gated channel, subfamily H (EAG	97.97
3luq_A	114	Sensor protein; PAS, histidine, kinase, PSI, MCSG,	97.96
3eeh_A	125	Putative light and redox sensing histidine kinase;	97.89
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	97.87
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	97.84
3vol_A	233	Aerotaxis transducer AER2; heme, oxygen sensor pro	97.82
4f3l_A	361	Mclock, circadian locomoter output cycles protein	97.8
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	97.75
2kdk_A	121	ARYL hydrocarbon receptor nuclear translocator-LI	97.67
3d72_A	149	Vivid PAS protein VVD; circadian, photoreceptor, b	97.66
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	97.65
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.64
1d06_A	130	Nitrogen fixation regulatory protein FIXL; oxygen	97.62
3mjq_A	126	Uncharacterized protein; NESG, structural genomics	97.57
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	97.55
4f3l_A	361	Mclock, circadian locomoter output cycles protein	97.49
1v9y_A	167	Heme PAS sensor protein; signaling protein; HET: H	97.47
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	97.31
2r78_A	117	Sensor protein; sensory box sensor histidine kinas	97.25
4hi4_A	121	Aerotaxis transducer AER2; PAS domain, diatomic GA	97.17
3rty_A	339	Period circadian protein; PAS domain, signalling,	97.09
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	96.89
3cax_A	369	Uncharacterized protein PF0695; structural genomic	96.88
3olo_A	118	Two-component sensor histidine kinase; structural	96.87
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	96.8
3olo_A	118	Two-component sensor histidine kinase; structural	96.78
3cax_A	369	Uncharacterized protein PF0695; structural genomic	96.68
2qkp_A	151	Uncharacterized protein; structural genomics, unkn	96.66
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	96.64
3bwl_A	126	Sensor protein; structural genomics, APC87707.1, P	96.63
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	96.49
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	96.46
1ll8_A	114	PAS kinase; PAS domain, ligand binding, ligand scr	96.42
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	96.19
3mfx_A	129	Sensory BOX/ggdef family protein; alpha-beta prote	96.12
3b33_A	115	Sensor protein; structural genomics, PAS domain, n	96.06
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	95.88
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	95.66
3fc7_A	125	HTR-like protein, sensor protein; APC87712.1, HTR-	95.64
3a0r_A	349	Sensor protein; four helix bundle, PAS fold, kinas	95.32
3a0s_A	96	Sensor protein; PAS-fold, kinase, phosphoprotein,	94.55
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	93.69
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	93.55
2w0n_A	118	Sensor protein DCUS; signal transduction, two-comp	92.69
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	91.25
2ykf_A	305	Pdtas, probable sensor histidine kinase pdtas; tra	90.09
2vlg_A	111	Sporulation kinase A; histidine kinase, two-compon	90.43
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	90.37
4dj3_A	317	Period circadian protein homolog 3; PAS domain, ci	89.21
3rty_A	339	Period circadian protein; PAS domain, signalling,	89.06
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	88.95
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	88.08
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	87.4
1p0z_A	131	Sensor kinase CITA; transferase; HET: FLC MO7; 1.6	86.54
3fg8_A	118	Uncharacterized protein RHA05790; PAS domain, stru	85.29
4dj2_A	320	Period circadian protein homolog 1; PAS domains, c	82.15
3by8_A	142	Sensor protein DCUS; histidine kinase sensor domai	81.87
3gdi_A	309	Period circadian protein homolog 2; tandem PAS dom	81.07

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

Probab=99.67  E-value=8e-16  Score=111.17  Aligned_cols=88  Identities=25%  Similarity=0.464  Sum_probs=74.3

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------------------------C-----
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------------------------N-----   52 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------------~-----   52 (115)
                      +..+.+ ||+.+|+.++++|++|++|++.+++++.+|||++|++++.+                          |     
T Consensus        63 e~~~~~~dG~~~~~~~~~~p~~d~~g~~~~~~~~~~DIT~~k~~e~~l~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~  142 (227)
T 3ewk_A           63 EFCNRRKDGTRYWVDSTIVPLMDNAGKPRQYISIRRDITAQKEAEAQLARLKQAMDANSEMILLTDRAGRIIYANPALCR  142 (227)
T ss_dssp             EEEEECSSSCEEEEEEEEEEEECSSSCEEEEEEEEEECTTTTHHHHHHHHHHHHHHTCCSEEEEECTTSCEEEECHHHHH
T ss_pred             EEEEEcCCCCEEeeeeEEEEEEcCCCCEEEEEEEEEehhhHHHHHHHHHHHHHHHhcCcCeEEEEcCCCcEEEEchHHHH
Confidence            344556 99999999999999999999999999999999999988732                          0     


Q ss_pred             ----------C--------C---------------------CceeceecCCc------eeEEEEEeEEeeCCCCCEEEEE
Q psy8547          53 ----------G--------E---------------------GDYEDMQELGT------PFWCLLDIVPIKNEKREVVLYL   87 (115)
Q Consensus        53 ----------~--------~---------------------e~~~~yrKdGs------~f~~~~~i~pirde~G~v~~~i   87 (115)
                                |        .                     .....++|||+      .||++++++|++|++|.+++|+
T Consensus       143 ~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~k~G~~~~dg~~~~~~~~~~pi~d~~g~~~~~v  222 (227)
T 3ewk_A          143 FSGMAEGELLGQSPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRRRTGPAPHDAEDYWAEISTTPIHTDGNGLVGYV  222 (227)
T ss_dssp             HHTCCTHHHHSSCGGGGBCTTSCHHHHHHHHHHHHHTCCEECCEEEEEECCSSSSCEEEEEEEEEEEEEECSSSCEEEEE
T ss_pred             HhCCCHHHHcCCChhhccCCCCCHHHHHHHHHHHHcCCceeEEEEEECCCCCcCcccceEEEEEEEEEEECCCCCEEEEE
Confidence                      0        0                     01234788887      8999999999999999999999


Q ss_pred             EEeee
Q psy8547          88 ASHKD   92 (115)
Q Consensus        88 ~~~~D   92 (115)
                      +++.|
T Consensus       223 ~i~~D  227 (227)
T 3ewk_A          223 QIQHD  227 (227)
T ss_dssp             EEEEC
T ss_pred             EEecC
Confidence            99987

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

Probab=99.07  E-value=2.7e-11  Score=82.51  Aligned_cols=56  Identities=16%  Similarity=0.230  Sum_probs=51.9

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCCCcccccc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQE  114 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~~~~~~~~  114 (115)
                      ..++|||+.+|+.++++|+++++|.+.++++++.|||++|++|++ .++|.+|.|..
T Consensus        86 ~~~~~dG~~~~~~~~~~pi~~~~g~~~~~~~~~~DITe~k~~e~~-~~~a~~d~Ltg  141 (176)
T 4hia_A           86 RNYRANDEPFDNLLFLHPVGGRPDAPDYFLGSQFELGRSGNSEEA-AAAGHAGALTG  141 (176)
T ss_dssp             EEECTTCCEEEEEEEEEEESSBTTBCSEEEEEEEEESSSGGGHHH-HHHHHHHHHHH
T ss_pred             EEEcCCCCEEEEEEEEEEeeCCCCCeEEEEEEEEECcHhhHHHHH-HHHhhhhHHhh
Confidence            347899999999999999999999999999999999999999999 88999998753

>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=99.02  E-value=5.4e-10  Score=71.64  Aligned_cols=39  Identities=41%  Similarity=0.710  Sum_probs=36.5

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      +..+|| ||+.||++++++|++|++|++.+|+++++|||+
T Consensus        70 e~~~~~kdG~~~~~~~~~~pi~d~~G~~~~~v~~~~DITe  109 (109)
T 1n9l_A           70 RLLNYRKDGTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC
T ss_pred             EEEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCCC
Confidence            456888 999999999999999999999999999999995

>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=98.95  E-value=1.5e-09  Score=69.53  Aligned_cols=39  Identities=36%  Similarity=0.663  Sum_probs=36.6

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeeccc
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   95 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~   95 (115)
                      ...++|||+.||++++++|++|++|++.+|++++.|||+
T Consensus        71 ~~~~~kdG~~~~~~~~~~pi~d~~G~~~~~v~~~~DITe  109 (109)
T 1n9l_A           71 LLNYRKDGTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC
T ss_pred             EEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCCC
Confidence            346899999999999999999999999999999999995

>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=98.88  E-value=2.1e-09  Score=70.28  Aligned_cols=46  Identities=24%  Similarity=0.419  Sum_probs=41.8

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ..++|||+.||+.++++|++++.  +.++++++.|||++|++|++|++
T Consensus        78 ~~~~kdG~~~~~~~~~~~~~~~~--~~~~~~~~~DITe~k~~e~~l~~  123 (132)
T 2pr5_A           78 QNYKKDGTMFWNELNIDPMEIED--KTYFVGIQNDITKQKEYEKLLED  123 (132)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETT--EEEEEEEEEECHHHHHHHHHHHH
T ss_pred             EEEecCCCeeeeEEEEEeccCCC--eeEEEEEEEeCcHHHHHHHHHHH
Confidence            34789999999999999999876  88999999999999999998865

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

Probab=98.87  E-value=5.3e-09  Score=66.45  Aligned_cols=45  Identities=13%  Similarity=0.217  Sum_probs=39.9

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM  101 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~  101 (115)
                      ++..+|||+.+|+.....|++|++|+++.++++..|||++|.+|+
T Consensus        70 ~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~G~~~Dit~~k~~~~  114 (115)
T 3h9w_A           70 YRALHRDGHYVWIRDVVHVVRDDSGEVEALIGFMFDISLEHHHHH  114 (115)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECGGGGC---
T ss_pred             EEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEeccCccccccc
Confidence            456789999999999999999999999999999999999999986

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

Probab=98.85  E-value=3.8e-09  Score=70.25  Aligned_cols=49  Identities=20%  Similarity=0.060  Sum_probs=45.7

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ++..++||+..|+.....|++|++|.+..++++..|||++|++|++|+.
T Consensus        86 ~r~~~~~G~~~w~~~~~~~~~d~~g~~~~~~G~~~DITerk~~E~~L~~  134 (142)
T 3mr0_A           86 YRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDALRV  134 (142)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHH
T ss_pred             EEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEcCchHHHHHHHHHH
Confidence            4567899999999999999999999999999999999999999998874

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

Probab=98.80  E-value=7.7e-09  Score=74.20  Aligned_cols=48  Identities=23%  Similarity=0.375  Sum_probs=45.0

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ..++|||+.+|+.++++|++|++|++.+++++..|||++|++|++++.
T Consensus        65 ~~~~~dG~~~~~~~~~~p~~d~~g~~~~~~~~~~DIT~~k~~e~~l~~  112 (227)
T 3ewk_A           65 CNRRKDGTRYWVDSTIVPLMDNAGKPRQYISIRRDITAQKEAEAQLAR  112 (227)
T ss_dssp             EEECSSSCEEEEEEEEEEEECSSSCEEEEEEEEEECTTTTHHHHHHHH
T ss_pred             EEEcCCCCEEeeeeEEEEEEcCCCCEEEEEEEEEehhhHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999998765

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

Probab=98.77  E-value=1.4e-08  Score=65.30  Aligned_cols=39  Identities=31%  Similarity=0.574  Sum_probs=36.0

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK   45 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k   45 (115)
                      .+.+ ||+.+|+.++++|++|++|.+.+++++++|||++|
T Consensus        81 ~~~~~dG~~~~~~~~~~pi~~~~g~~~~~v~~~~DITe~k  120 (120)
T 2gj3_A           81 VNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH  120 (120)
T ss_dssp             EEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCSCC
T ss_pred             EEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEeccCcccC
Confidence            3455 99999999999999999999999999999999976

>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=98.77  E-value=1.1e-08  Score=65.54  Aligned_cols=47  Identities=17%  Similarity=0.118  Sum_probs=30.1

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccC
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGE  106 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~  106 (115)
                      ..++|||+.||+.++++|+.+..  ...++++++|||++|++|++|+++
T Consensus        73 ~~~~~dG~~~~~~~~~~~~~~~~--~~~~~~~~~DITerk~~e~~l~~l  119 (119)
T 2vv6_A           73 TGKRRDGTTFPMHLSIGEMQSGG--EPYFTGFVRDLTEHQQTQARLQEL  119 (119)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETT--EEEEEEEEEECC------------
T ss_pred             EEEeCCCCEEEEEEEEEEEEECC--eEEEEEEEEEcHHHHHHHHHHHhC
Confidence            34789999999999999998743  356899999999999999998763

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

Probab=98.76  E-value=1.5e-08  Score=65.03  Aligned_cols=40  Identities=25%  Similarity=0.443  Sum_probs=37.5

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccch
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK   97 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k   97 (115)
                      ..++|||+.+|+.++++|++|++|++.++++++.|||++|
T Consensus        81 ~~~~~dG~~~~~~~~~~pi~~~~g~~~~~v~~~~DITe~k  120 (120)
T 2gj3_A           81 VNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH  120 (120)
T ss_dssp             EEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCSCC
T ss_pred             EEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEeccCcccC
Confidence            3478999999999999999999999999999999999986

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

Probab=98.75  E-value=1.5e-08  Score=64.44  Aligned_cols=48  Identities=23%  Similarity=0.392  Sum_probs=38.9

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ...+++|..+|+.++++|++++.|.+.++++++.|||++|++|++.+.
T Consensus        76 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~e~~~~~  123 (128)
T 3t50_A           76 INYKKSGEAFWNRLHISPVHNANGRLQHFVSSQLDVTLELVPRGSLEH  123 (128)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHC-------
T ss_pred             EEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEcchhhhhhhhhhh
Confidence            346899999999999999999999999999999999999999997664

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

Probab=98.74  E-value=2.4e-08  Score=63.36  Aligned_cols=39  Identities=10%  Similarity=0.123  Sum_probs=35.7

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ||+..|+.....|++|++|++++++++..|||++|.+|+
T Consensus        76 dG~~~w~~~~~~~~~d~~G~~~~~~G~~~Dit~~k~~~~  114 (115)
T 3h9w_A           76 DGHYVWIRDVVHVVRDDSGEVEALIGFMFDISLEHHHHH  114 (115)
T ss_dssp             TSCEEEEEEEEEEEECTTSCEEEEEEEEEECGGGGC---
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEEEeccCccccccc
Confidence            999999999999999999999999999999999999874

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

Probab=98.74  E-value=9.8e-09  Score=69.60  Aligned_cols=45  Identities=24%  Similarity=0.327  Sum_probs=41.1

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      ...++ ||+.+|+.++++|+++++|.+.+++++.+|||++|++|+.
T Consensus        85 ~~~~~~dG~~~~~~~~~~pi~~~~g~~~~~~~~~~DITe~k~~e~~  130 (176)
T 4hia_A           85 LRNYRANDEPFDNLLFLHPVGGRPDAPDYFLGSQFELGRSGNSEEA  130 (176)
T ss_dssp             EEEECTTCCEEEEEEEEEEESSBTTBCSEEEEEEEEESSSGGGHHH
T ss_pred             EEEEcCCCCEEEEEEEEEEeeCCCCCeEEEEEEEEECcHhhHHHHH
Confidence            44556 9999999999999999999999999999999999998874

>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=98.71  E-value=2e-08  Score=65.46  Aligned_cols=43  Identities=28%  Similarity=0.482  Sum_probs=38.2

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      ..+++ ||+.||+.++++|+++++  +.+++++++|||++|++|+.
T Consensus        77 ~~~~~kdG~~~~~~~~~~~~~~~~--~~~~~~~~~DITe~k~~e~~  120 (132)
T 2pr5_A           77 IQNYKKDGTMFWNELNIDPMEIED--KTYFVGIQNDITKQKEYEKL  120 (132)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEETT--EEEEEEEEEECHHHHHHHHH
T ss_pred             EEEEecCCCeeeeEEEEEeccCCC--eeEEEEEEEeCcHHHHHHHH
Confidence            34566 999999999999999976  88999999999999998874

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

Probab=98.70  E-value=7.1e-09  Score=75.44  Aligned_cols=55  Identities=22%  Similarity=0.364  Sum_probs=38.9

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCCCccccc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQ  113 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~~~~~~~  113 (115)
                      .++|||+.+|+.++++|++|++|.+.++++++.|||++|+.+......+..+.|.
T Consensus       143 ~~~~dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITerk~~~~e~~~~~~~~~l~  197 (258)
T 3p7n_A          143 NYKKDGTPFRNAVLVAPIYDDDDELLYFLGSQVEVDDDQPNMGMARRERAAEMLK  197 (258)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCSEEEEEEEEEC-------CHHHHHHHHHHHT
T ss_pred             EEcCCCCEEEEeeEEEEEEcCCCCEEEEEEEeeecchhhhhhhHHHHHHHHHHHh
Confidence            4789999999999999999999999999999999999955554443333344433

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

Probab=98.70  E-value=2.7e-08  Score=63.30  Aligned_cols=44  Identities=27%  Similarity=0.509  Sum_probs=37.5

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      ...+ +|..+|+.++++|+++++|.+.+++++++|||++|.+++.
T Consensus        76 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~e~~  120 (128)
T 3t50_A           76 INYKKSGEAFWNRLHISPVHNANGRLQHFVSSQLDVTLELVPRGS  120 (128)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHC----
T ss_pred             EEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEcchhhhhhhh
Confidence            3445 9999999999999999999999999999999999998875

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

Probab=98.67  E-value=2.2e-08  Score=66.43  Aligned_cols=47  Identities=19%  Similarity=0.457  Sum_probs=42.9

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      .++++|+.+|+.++++|+++++|.+.++++++.|||++|+++.....
T Consensus       115 ~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~~~~~e~  161 (166)
T 3ue6_A          115 NYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLVNEQ  161 (166)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEECCBCCHHHHHHHHHHH
T ss_pred             EEcCCCCEEEEEEEEEeeeCCCCCEEEEEEEEEechHHHHHHHHHhh
Confidence            46899999999999999999999999999999999999999876443

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

Probab=98.64  E-value=4.4e-08  Score=64.91  Aligned_cols=44  Identities=25%  Similarity=0.526  Sum_probs=40.2

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      ..++ ||+.+|+.++++|+++++|.+.+++++++|||++|+++.+
T Consensus       114 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DITe~k~~~~~  158 (166)
T 3ue6_A          114 LNYRQDGTTFWNLFFVAGLRDSKGNIVNYVGVQSKVSEDYAKLLV  158 (166)
T ss_dssp             EEECTTSCEEEEEEEEEEEECTTSCEEEEEEECCBCCHHHHHHHH
T ss_pred             EEEcCCCCEEEEEEEEEeeeCCCCCEEEEEEEEEechHHHHHHHH
Confidence            3455 9999999999999999999999999999999999998764

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A

Probab=98.64  E-value=5.2e-08  Score=61.81  Aligned_cols=44  Identities=11%  Similarity=0.118  Sum_probs=39.3

Q ss_pred             ceeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchhh
Q psy8547          56 DYEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMA   99 (115)
Q Consensus        56 ~~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~~   99 (115)
                      .++.++|||+.+|+.++.+|++|+ .|++..++++..|||++|++
T Consensus        73 e~r~~~~dG~~~w~~~~~~~~~d~~~g~~~~iv~~~~DITer~~~  117 (117)
T 3f1p_A           73 QYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN  117 (117)
T ss_dssp             CEEEECTTSSEEEEEEEEEEEEETTTTEEEEEEEEEEECSCCBC-
T ss_pred             EEEEEecCCCEEEEEEeeEEEECCCCCCceEEEEEeeeccccccC
Confidence            345678999999999999999998 89999999999999999874

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

Probab=98.55  E-value=1.3e-07  Score=62.70  Aligned_cols=41  Identities=20%  Similarity=0.020  Sum_probs=39.4

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD   51 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~   51 (115)
                      ||+..|+.....|++|++|.++.++++..|||++|++|+++
T Consensus        92 ~G~~~w~~~~~~~~~d~~g~~~~~~G~~~DITerk~~E~~L  132 (142)
T 3mr0_A           92 SGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKRDEDAL  132 (142)
T ss_dssp             TSCEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHH
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEEEEcCchHHHHHHHH
Confidence            99999999999999999999999999999999999998864

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*

Probab=98.54  E-value=1.9e-07  Score=57.40  Aligned_cols=39  Identities=26%  Similarity=0.612  Sum_probs=35.6

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK   45 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k   45 (115)
                      ...+ ||+.+|+.++++|+++++|.+.+++++.+|||+++
T Consensus        76 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DITer~  115 (115)
T 4eet_B           76 INYTKSGKKFWNLLHLQPVRDQKGELQYFIGVQLDGSDHV  115 (115)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECSCCC
T ss_pred             EEecCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeecccC
Confidence            3445 99999999999999999999999999999999874

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B

Probab=98.54  E-value=1.1e-07  Score=60.73  Aligned_cols=43  Identities=12%  Similarity=0.220  Sum_probs=37.0

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchhh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMA   99 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~~   99 (115)
                      ++.++|||+.+|+..+.+|++|+ .|++..++++..|||++|+.
T Consensus        78 ~r~~~~dG~~~w~~~~~~~~~~~~~g~~~~iv~~~~DIT~~kqe  121 (121)
T 3f1p_B           78 FRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE  121 (121)
T ss_dssp             EEEECTTSCEEEEEEEEEEECCTTCCCCCEEEEEEEECCCC---
T ss_pred             EEEEecCCCEEEEEEEEEEEECCCCCceeEEEEEeEEcccccCC
Confidence            45578999999999999999998 88999999999999999873

>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.7 PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A 4h6j_A

Probab=98.53  E-value=1.5e-07  Score=59.57  Aligned_cols=37  Identities=8%  Similarity=0.011  Sum_probs=34.6

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMA   47 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~~   47 (115)
                      ||+.+|++++.+|++|+ +|.+.+++++.+|||++|++
T Consensus        80 dG~~~w~~~~~~~~~d~~~g~~~~iv~~~~DITer~~~  117 (117)
T 3f1p_A           80 HGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN  117 (117)
T ss_dssp             TSSEEEEEEEEEEEEETTTTEEEEEEEEEEECSCCBC-
T ss_pred             CCCEEEEEEeeEEEECCCCCCceEEEEEeeeccccccC
Confidence            99999999999999998 89999999999999999863

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

Probab=98.51  E-value=2.8e-07  Score=57.45  Aligned_cols=41  Identities=15%  Similarity=-0.044  Sum_probs=35.8

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchh
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~   98 (115)
                      +..+++|+.+|+.++..|+++++|.+..++++..|||++|+
T Consensus        85 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~g~~~DITe~k~  125 (125)
T 3nja_A           85 RIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ  125 (125)
T ss_dssp             EEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC---
T ss_pred             EEECCCCCEEEEEEeeEEEECCCCCEEEEEEEEEecccccC
Confidence            44679999999999999999999999999999999999985

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

Probab=98.50  E-value=2.9e-07  Score=57.36  Aligned_cols=36  Identities=14%  Similarity=-0.068  Sum_probs=32.6

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~   46 (115)
                      ||+..|+.+...|+++++|.+.+++++..|||++|+
T Consensus        90 ~g~~~~~~~~~~~~~~~~g~~~~~~g~~~DITe~k~  125 (125)
T 3nja_A           90 DGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ  125 (125)
T ss_dssp             TSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC---
T ss_pred             CCCEEEEEEeeEEEECCCCCEEEEEEEEEecccccC
Confidence            999999999999999999999999999999999984

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

Probab=98.50  E-value=1.6e-07  Score=62.02  Aligned_cols=48  Identities=21%  Similarity=0.389  Sum_probs=44.6

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccC
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGE  106 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~  106 (115)
                      .++++|..+|+.+++.|+.+++|.+.++++++.|||++|++|+++++.
T Consensus       105 ~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DiTe~k~~e~~l~~~  152 (162)
T 3sw1_A          105 NYRKDGSAFWNELSITPVKSDFDQRTYFIGIQKDVSRQVELERELAEL  152 (162)
T ss_dssp             EECTTCCEEEEEEEEEEEECSSSSCEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             EECCCCCEEEEEEEEEEeecCCCCEEEEEEEEEeCcHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999999988754

>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein, flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB: 4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*

Probab=98.47  E-value=4e-07  Score=55.92  Aligned_cols=40  Identities=23%  Similarity=0.556  Sum_probs=37.1

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccch
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK   97 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k   97 (115)
                      ...+++|+.+|+.++++|+++++|.+.++++++.|||+++
T Consensus        76 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DITer~  115 (115)
T 4eet_B           76 INYTKSGKKFWNLLHLQPVRDQKGELQYFIGVQLDGSDHV  115 (115)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECSCCC
T ss_pred             EEecCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeecccC
Confidence            3468999999999999999999999999999999999874

>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=98.43  E-value=5.4e-07  Score=55.30  Aligned_cols=42  Identities=29%  Similarity=0.673  Sum_probs=35.8

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..+ +|+.+|+.+.+.|+++++|.+.+++++.+|||+++++++
T Consensus        86 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~~e~  128 (130)
T 2z6d_A           86 NYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGVN  128 (130)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCTTC----
T ss_pred             EEcCCCcEEEEEEEEEEEECCCCCeeEEEEEEecchHHHHhhc
Confidence            345 999999999999999999999999999999999998774

>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=98.43  E-value=5e-07  Score=55.43  Aligned_cols=44  Identities=25%  Similarity=0.588  Sum_probs=37.1

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchh
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA  102 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~  102 (115)
                      ..+++|+.+|+.+++.|+.++.|.+..+++++.|||++|++|+.
T Consensus        86 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~~e~e  129 (130)
T 2z6d_A           86 NYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTEGVND  129 (130)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCTTC-----
T ss_pred             EEcCCCcEEEEEEEEEEEECCCCCeeEEEEEEecchHHHHhhcc
Confidence            46789999999999999999999999999999999999998863

>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=98.43  E-value=3.3e-07  Score=68.79  Aligned_cols=47  Identities=19%  Similarity=0.442  Sum_probs=43.3

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN  104 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~  104 (115)
                      +.++|||+.+|+.++++|++|+.|++.++++++.|||++|+.|++.+
T Consensus        90 ~~~~~dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITe~k~~e~~~~  136 (332)
T 2wkq_A           90 INYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAERE  136 (332)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHHHHH
T ss_pred             EEEcCCCCEEEEeeEEEEeEcCCCCEEEEEEEeccCchhhhhhhhcc
Confidence            45789999999999999999999999999999999999999887653

>3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} SCOP: d.110.3.0 PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 4h6j_B 2b02_A* 2k7s_A 2a24_B

Probab=98.41  E-value=3.3e-07  Score=58.44  Aligned_cols=36  Identities=14%  Similarity=0.313  Sum_probs=33.0

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~   46 (115)
                      ||+.+|++++.+|++|+ +|.+.+++++.+|||++|+
T Consensus        84 dG~~~w~~~~~~~~~~~~~g~~~~iv~~~~DIT~~kq  120 (121)
T 3f1p_B           84 NQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQ  120 (121)
T ss_dssp             TSCEEEEEEEEEEECCTTCCCCCEEEEEEEECCCC--
T ss_pred             CCCEEEEEEEEEEEECCCCCceeEEEEEeEEcccccC
Confidence            99999999999999998 8999999999999999986

>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=98.41  E-value=2.6e-07  Score=61.25  Aligned_cols=42  Identities=14%  Similarity=0.052  Sum_probs=39.8

Q ss_pred             CceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        64 Gs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      |..+|+.++++|+++++|.+.++++++.|||++|++|++++.
T Consensus       103 g~~~~~~~~~~pi~~~~g~~~g~~~~~~DITe~k~~e~~l~~  144 (158)
T 3k3c_A          103 VEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQAAEA  144 (158)
T ss_dssp             EEEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHHHH
T ss_pred             cceEEEEEEEEEeECCCCCEEEEEEEEEehhHHHHHHHHHHH
Confidence            788999999999999999999999999999999999998864

>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=98.39  E-value=5.9e-07  Score=57.23  Aligned_cols=42  Identities=21%  Similarity=0.222  Sum_probs=28.7

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      ...+ ||+.||+.++++|+.+..+  .+|+++++|||++|++|+.
T Consensus        73 ~~~~~dG~~~~~~~~~~~~~~~~~--~~~~~~~~DITerk~~e~~  115 (119)
T 2vv6_A           73 TGKRRDGTTFPMHLSIGEMQSGGE--PYFTGFVRDLTEHQQTQAR  115 (119)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETTE--EEEEEEEEECC--------
T ss_pred             EEEeCCCCEEEEEEEEEEEEECCe--EEEEEEEEEcHHHHHHHHH
Confidence            3446 9999999999999997433  5689999999999998864

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

Probab=98.38  E-value=4.3e-07  Score=65.90  Aligned_cols=42  Identities=26%  Similarity=0.498  Sum_probs=33.8

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhh
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   46 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~   46 (115)
                      ....++ ||+.+|+.++++|++|++|.+.+++++++|||++|.
T Consensus       140 e~~~~~~dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITerk~  182 (258)
T 3p7n_A          140 EILNYKKDGTPFRNAVLVAPIYDDDDELLYFLGSQVEVDDDQP  182 (258)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEECTTSCSEEEEEEEEEC-----
T ss_pred             EEEEEcCCCCEEEEeeEEEEEEcCCCCEEEEEEEeeecchhhh
Confidence            344556 999999999999999999999999999999999943

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

Probab=98.38  E-value=8.9e-07  Score=54.01  Aligned_cols=36  Identities=28%  Similarity=0.290  Sum_probs=33.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~   46 (115)
                      +|..+|+.+++.|+++++|.+.+++++.+|||++|+
T Consensus        88 ~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~  123 (124)
T 3lyx_A           88 DGHIGWIESMCVPIYGENYQMVGALGINRDITKRKK  123 (124)
T ss_dssp             TSCEEEEEEEEEEEECSTTCEEEEEEEEEECSCC--
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEEEecchhhhc
Confidence            999999999999999999999999999999999875

>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=98.37  E-value=5.6e-07  Score=67.53  Aligned_cols=44  Identities=23%  Similarity=0.474  Sum_probs=40.2

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ...++ ||+.+|+.++++|++|++|.+.+++++.+|||++++.++
T Consensus        89 ~~~~~~dG~~~~~~~~~~pi~d~~g~~~~~v~~~~DITe~k~~e~  133 (332)
T 2wkq_A           89 LINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAA  133 (332)
T ss_dssp             EEEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHH
T ss_pred             EEEEcCCCCEEEEeeEEEEeEcCCCCEEEEEEEeccCchhhhhhh
Confidence            34556 999999999999999999999999999999999988776

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

Probab=98.37  E-value=6.2e-07  Score=59.17  Aligned_cols=45  Identities=27%  Similarity=0.508  Sum_probs=40.8

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD   51 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~   51 (115)
                      ..++ +|+.+|+.+.+.|+.+++|.+.+++++.+|||+++++++.+
T Consensus       104 ~~~~~~g~~~~~~~~~~~i~~~~g~~~~~~~~~~DiTe~k~~e~~l  149 (162)
T 3sw1_A          104 RNYRKDGSAFWNELSITPVKSDFDQRTYFIGIQKDVSRQVELEREL  149 (162)
T ss_dssp             EEECTTCCEEEEEEEEEEEECSSSSCEEEEEEEEECHHHHHHHHHH
T ss_pred             EEECCCCCEEEEEEEEEEeecCCCCEEEEEEEEEeCcHHHHHHHHH
Confidence            3445 99999999999999999999999999999999999988753

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

Probab=98.35  E-value=2.6e-07  Score=58.82  Aligned_cols=40  Identities=15%  Similarity=0.293  Sum_probs=31.3

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhh
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMA   47 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~   47 (115)
                      ...+ ||+.+|+.++..|+ +.+|...+++++++|||++|+.
T Consensus        79 ~~~~~dG~~~~~~~~~~~~-~~~~~~~~~v~~~~DITerk~~  119 (120)
T 3mqq_A           79 IMKRAGGELFWCHVTGRAL-DRTAPLAAGVWTFEDLSATRRV  119 (120)
T ss_dssp             EEECTTSCEEEEEEEEEES-STTSTTSSEEEEEEESCC----
T ss_pred             EEEeCCCCEEEEEEEEEEC-CCCCCceeEEEEEEcccHhhcc
Confidence            3445 99999999999999 6677777899999999999975

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

Probab=98.34  E-value=3e-07  Score=58.58  Aligned_cols=41  Identities=15%  Similarity=0.276  Sum_probs=32.6

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhh
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMA   99 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~   99 (115)
                      ..++|||+.+|+.++..|+ +..|.+..+++++.|||++|+.
T Consensus        79 ~~~~~dG~~~~~~~~~~~~-~~~~~~~~~v~~~~DITerk~~  119 (120)
T 3mqq_A           79 IMKRAGGELFWCHVTGRAL-DRTAPLAAGVWTFEDLSATRRV  119 (120)
T ss_dssp             EEECTTSCEEEEEEEEEES-STTSTTSSEEEEEEESCC----
T ss_pred             EEEeCCCCEEEEEEEEEEC-CCCCCceeEEEEEEcccHhhcc
Confidence            4578999999999999999 5666677899999999999975

>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=98.33  E-value=3.1e-07  Score=57.89  Aligned_cols=46  Identities=20%  Similarity=0.445  Sum_probs=40.7

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD  103 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~  103 (115)
                      ...+++|..+|+.++..|++++.|.+.++++++.|||++|+.++..
T Consensus        81 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~~~~~~  126 (146)
T 2v0u_A           81 INYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAER  126 (146)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHHHH
T ss_pred             EEEecCCcEEEEEEEEEEeECCCCCEEEEEEEEeechHHHHHHHHH
Confidence            3468999999999999999999999999999999999999855433

>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=98.33  E-value=5.9e-07  Score=59.49  Aligned_cols=40  Identities=15%  Similarity=0.053  Sum_probs=37.5

Q ss_pred             CCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc
Q psy8547          12 RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD   51 (115)
Q Consensus        12 G~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~   51 (115)
                      |...|+.++++|+++++|.+.+++++.+|||++|++++.+
T Consensus       103 g~~~~~~~~~~pi~~~~g~~~g~~~~~~DITe~k~~e~~l  142 (158)
T 3k3c_A          103 VEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQAA  142 (158)
T ss_dssp             EEEEEEEEEEEEEECTTSCEEEEEEEEEECHHHHHHHHHH
T ss_pred             cceEEEEEEEEEeECCCCCEEEEEEEEEehhHHHHHHHHH
Confidence            7789999999999999999999999999999999998753

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

Probab=98.32  E-value=1.4e-06  Score=52.00  Aligned_cols=37  Identities=35%  Similarity=0.740  Sum_probs=34.2

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      .++ +|+.+|+.+++.|+++++|.+.+++++.+|||++
T Consensus        73 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DiTe~  110 (110)
T 1byw_A           73 FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTCCEEEEEEEEEEEEEC
T ss_pred             EEcCCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccCC
Confidence            345 9999999999999999999999999999999975

>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=98.29  E-value=1.7e-06  Score=54.40  Aligned_cols=42  Identities=24%  Similarity=0.533  Sum_probs=37.9

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..+ +|..+|+.+...|+++++|.+.+++++.+|||+++..+.
T Consensus        82 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~~~~  124 (146)
T 2v0u_A           82 NYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAA  124 (146)
T ss_dssp             EECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEEESSCCCHHH
T ss_pred             EEecCCcEEEEEEEEEEeECCCCCEEEEEEEEeechHHHHHHH
Confidence            345 999999999999999999999999999999999998443

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

Probab=98.28  E-value=2.2e-06  Score=52.25  Aligned_cols=40  Identities=28%  Similarity=0.302  Sum_probs=36.1

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchh
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~   98 (115)
                      ..+++|..+|+.+++.|+.++.|.+.++++++.|||++|+
T Consensus        84 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~~~  123 (124)
T 3lyx_A           84 MLHKDGHIGWIESMCVPIYGENYQMVGALGINRDITKRKK  123 (124)
T ss_dssp             EECTTSCEEEEEEEEEEEECSTTCEEEEEEEEEECSCC--
T ss_pred             EEccCCCEEEEEEEEEEEECCCCCEEEEEEEEecchhhhc
Confidence            4679999999999999999999999999999999999875

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

Probab=98.27  E-value=1e-06  Score=60.97  Aligned_cols=39  Identities=15%  Similarity=0.046  Sum_probs=36.2

Q ss_pred             CceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchh
Q psy8547          64 GTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA  102 (115)
Q Consensus        64 Gs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~  102 (115)
                      |..+|+.++++|+++++|.+..+++++.|||++|++|++
T Consensus       123 g~~~~~~~~~~pi~~~~g~~~g~~~~~~DITerk~~e~~  161 (185)
T 3kx0_X          123 VEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQA  161 (185)
T ss_dssp             -CCEEEEEEEEEEECTTSCEEEEEEEEEECHHHHTTCC-
T ss_pred             CccEEEEEEEEEEECCCCCEEEEEEEEEeCCHHHHHHHH
Confidence            888999999999999999999999999999999999998

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

Probab=98.23  E-value=2.6e-06  Score=50.82  Aligned_cols=38  Identities=32%  Similarity=0.645  Sum_probs=35.6

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      .++++|+.+|+.++++|++++.|.+..+++++.|||++
T Consensus        73 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DiTe~  110 (110)
T 1byw_A           73 FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTCCEEEEEEEEEEEEEC
T ss_pred             EEcCCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccCC
Confidence            46899999999999999999999999999999999975

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

Probab=98.12  E-value=3.5e-06  Score=58.26  Aligned_cols=39  Identities=15%  Similarity=0.057  Sum_probs=35.9

Q ss_pred             CCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547          12 RTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus        12 G~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      |...|+.++++|++|++|.+.+++++.+|||++|+++++
T Consensus       123 g~~~~~~~~~~pi~~~~g~~~g~~~~~~DITerk~~e~~  161 (185)
T 3kx0_X          123 VEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQA  161 (185)
T ss_dssp             -CCEEEEEEEEEEECTTSCEEEEEEEEEECHHHHTTCC-
T ss_pred             CccEEEEEEEEEEECCCCCEEEEEEEEEeCCHHHHHHHH
Confidence            888999999999999999999999999999999999876

>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=98.10  E-value=2.6e-06  Score=55.75  Aligned_cols=48  Identities=15%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCC
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEG  107 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~  107 (115)
                      ...+++|..+|+.+++.|+ +..|.+. +++++.|||+++++|++++++|
T Consensus       120 ~~~~~~g~~~~~~~~~~~~-~~~g~~~-~~~~~~DiT~~~~~e~~l~~la  167 (167)
T 1v9y_A          120 QLEKKDGSKIWTRFALSKV-SAEGKVY-YLALVRDASVEMAQKEQTRQLI  167 (167)
T ss_dssp             EEECTTSCEEEEEEEEEEE-EETTEEE-EEEEEEC---------------
T ss_pred             EEEcCCCcEEEEEEEEEEE-ecCCCEE-EEEEEecCcHHHHHHHHHHhhC
Confidence            3467899999999999999 5677775 9999999999999999998764

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

Probab=98.08  E-value=9.1e-06  Score=49.68  Aligned_cols=32  Identities=16%  Similarity=0.202  Sum_probs=30.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      +|+.+|+.++++|+++++|.+.+++++.+|||
T Consensus        83 ~g~~~~~~~~~~p~~~~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           83 DGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             -CCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             CCcEEEEEEEEEEeECCCCCEEEEEEEEeeCC
Confidence            99999999999999999999999999999998

>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=98.07  E-value=8.4e-06  Score=50.75  Aligned_cols=37  Identities=35%  Similarity=0.740  Sum_probs=34.1

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      .++ +|+.+|+.+++.|+++++|.+.+++++++|||++
T Consensus       101 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~  138 (138)
T 2l0w_A          101 FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  138 (138)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEEEEEC
T ss_pred             EECCCCCEEEEEEEEEEEeCCCCCEEEEEEEEEeccCC
Confidence            345 9999999999999999999999999999999974

>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=98.06  E-value=5.6e-06  Score=57.67  Aligned_cols=38  Identities=21%  Similarity=0.274  Sum_probs=31.0

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ   48 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e   48 (115)
                      +|..+|..++++|++|++|++.+++.+.+|||+++.+.
T Consensus       114 ~~~~~~~~~ti~Pl~d~~G~v~gv~~ii~DVTe~~~a~  151 (152)
T 3mxq_A          114 EEEQMYQNLEVIPIHSEDGTIEHVCLCVYDVTIQASQQ  151 (152)
T ss_dssp             --CCEEEEEEEEEEECTTSCEEEEEEEEEEEECC----
T ss_pred             CCcEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHhcc
Confidence            56788999999999999999999999999999998764

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

Probab=98.04  E-value=1.3e-05  Score=49.51  Aligned_cols=38  Identities=13%  Similarity=0.024  Sum_probs=35.3

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ++..+++|+..|+.....|+++++|.+..++++..|||
T Consensus        81 ~r~~~~~g~~~w~~~~~~~~~~~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           81 YRIVTPEGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT  118 (118)
T ss_dssp             EEEECTTCCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            34568999999999999999999999999999999998

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

Probab=98.03  E-value=9.2e-06  Score=50.66  Aligned_cols=50  Identities=18%  Similarity=-0.033  Sum_probs=28.8

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCCCcc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYE  110 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~~~~  110 (115)
                      ..+++|..+|+.++..|+...  ....+++++.|||++|++|++++...-|+
T Consensus        75 ~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~DITe~k~a~~~~~~~~~~~  124 (126)
T 3mjq_A           75 LEKKEGTSIPAKARIWQGKWH--NEPCLFAIIKDLSKEERASSPPFLEHHHH  124 (126)
T ss_dssp             EECTTSCEEEEEEEEEEEESS--SSEEEEEEEEECC----------------
T ss_pred             EEccCCCEEEEEEEEEeeeEC--CceEEEEEEEechHHHHhhcccchhhccc
Confidence            467999999999999988753  35678999999999999999988876665

>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=98.02  E-value=7e-06  Score=57.17  Aligned_cols=39  Identities=21%  Similarity=0.212  Sum_probs=31.2

Q ss_pred             cCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhc
Q psy8547          62 ELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ  100 (115)
Q Consensus        62 KdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E  100 (115)
                      ++|..+|.+++++|++|++|+|.+++.+..|||+++.+.
T Consensus       113 ~~~~~~~~~~ti~Pl~d~~G~v~gv~~ii~DVTe~~~a~  151 (152)
T 3mxq_A          113 GEEEQMYQNLEVIPIHSEDGTIEHVCLCVYDVTIQASQQ  151 (152)
T ss_dssp             ---CCEEEEEEEEEEECTTSCEEEEEEEEEEEECC----
T ss_pred             CCCcEEEEEEEEEEEECCCCCEEEEEEEEEECCHHHhcc
Confidence            577888999999999999999999999999999998764

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

Probab=98.01  E-value=1.6e-05  Score=49.09  Aligned_cols=32  Identities=9%  Similarity=-0.062  Sum_probs=31.4

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ||+..|+.....|+++++|.+++++++..|||
T Consensus        87 ~g~~~w~~~~~~~~~~~~g~~~~~~g~~~DIT  118 (118)
T 3icy_A           87 EGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT  118 (118)
T ss_dssp             TCCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             CCCEEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence            99999999999999999999999999999998

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}

Probab=97.97  E-value=2e-05  Score=48.13  Aligned_cols=32  Identities=25%  Similarity=0.385  Sum_probs=31.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ||+.+|+.+...|+++++|.+.+++++.+|||
T Consensus        94 ~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  125 (125)
T 3eeh_A           94 EEYQRWVWIQGEPITNDAGETVRVAGFARDIT  125 (125)
T ss_dssp             GTTCEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             CCCEEEEEEecEEEECCCCCEEEEEEEEEecC
Confidence            99999999999999999999999999999998

>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=97.97  E-value=1.6e-05  Score=49.45  Aligned_cols=38  Identities=32%  Similarity=0.645  Sum_probs=35.5

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      .++++|+.+|+.+++.|+.++.|.+..+++++.|||++
T Consensus       101 ~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit~~  138 (138)
T 2l0w_A          101 FYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  138 (138)
T ss_dssp             EECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEEEEEC
T ss_pred             EECCCCCEEEEEEEEEEEeCCCCCEEEEEEEEEeccCC
Confidence            46899999999999999999999999999999999975

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

Probab=97.96  E-value=2e-05  Score=48.12  Aligned_cols=37  Identities=16%  Similarity=0.160  Sum_probs=32.7

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ...+++|..+|+.++++|+++++|.+.++++++.|||
T Consensus        78 ~~~~~~g~~~~~~~~~~p~~~~~g~~~~~~~~~~DIT  114 (114)
T 3luq_A           78 CFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT  114 (114)
T ss_dssp             EEEC--CCEEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEEcCCCcEEEEEEEEEEeECCCCCEEEEEEEEeeCC
Confidence            3467999999999999999999999999999999998

>3eeh_A Putative light and redox sensing histidine kinase; structural genomic MCSG, protein structure initiative, midwest center for STRU genomics; HET: PG5; 1.95A {Haloarcula marismortui}

Probab=97.89  E-value=3.1e-05  Score=47.29  Aligned_cols=37  Identities=22%  Similarity=0.237  Sum_probs=34.4

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      +..+++|+.+|+.++..|+.++.|.+..++++..|||
T Consensus        89 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT  125 (125)
T 3eeh_A           89 RVNATEEYQRWVWIQGEPITNDAGETVRVAGFARDIT  125 (125)
T ss_dssp             EECGGGTTCEEEEEEEEEEECTTSCEEEEEEEEEECC
T ss_pred             EEEcCCCCEEEEEEecEEEECCCCCEEEEEEEEEecC
Confidence            3467999999999999999999999999999999998

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

Probab=97.87  E-value=3.4e-05  Score=48.45  Aligned_cols=41  Identities=12%  Similarity=0.055  Sum_probs=35.4

Q ss_pred             eeceecCCceeEEEEEeEEeeCCC-CCEEEEEEEeeecccch
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEK-REVVLYLASHKDVTNTK   97 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~-G~v~~~i~~~~DIT~~k   97 (115)
                      ++..+|||+.+|+.++.+|++|+. |.+.+++++..||++.+
T Consensus        79 ~r~~~~dG~~~~~~~~~~~~~d~~~~~~~~~v~~~~~i~~~~  120 (121)
T 2kdk_A           79 YKFRAKDGSFVTLKSQWFSFTNPDTKELEYIVSVNTLVLGHS  120 (121)
T ss_dssp             EEEECSSSCEEEEEEEEEEEECCSSSCEEEEEEEEECCSSCC
T ss_pred             EEEEEcCCCEEEEEEEEEEEECCCCCeeeEEEEEEEeccccC
Confidence            345689999999999999999986 56788999999999875

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

Probab=97.84  E-value=1.9e-05  Score=57.75  Aligned_cols=45  Identities=22%  Similarity=0.186  Sum_probs=38.6

Q ss_pred             eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccC
Q psy8547          60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGE  106 (115)
Q Consensus        60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~  106 (115)
                      ++++|.  |..++++||+|++|++.+++.++.|||+++++|+++++.
T Consensus       104 ~~~~g~--~~~~~~~Pi~d~~G~~~g~v~~~~DITe~~~~e~ei~~l  148 (233)
T 3vol_A          104 LNLGGR--RFSLDVVPVFNDANERLGSAVQWTDRTEEHRAEQEVSQL  148 (233)
T ss_dssp             EEETTE--EEEEEEEEEECTTCCEEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             EEECCE--EEEEEEEEEECCCCCEEEEEEEEehhhHHHHHHHHHHHH
Confidence            455664  568999999999999999999999999999999876643

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

Probab=97.82  E-value=2.3e-05  Score=57.22  Aligned_cols=38  Identities=24%  Similarity=0.228  Sum_probs=34.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      +|.  |+.++++||+|++|++.+++++++|||+++++++.
T Consensus       107 ~g~--~~~~~~~Pi~d~~G~~~g~v~~~~DITe~~~~e~e  144 (233)
T 3vol_A          107 GGR--RFSLDVVPVFNDANERLGSAVQWTDRTEEHRAEQE  144 (233)
T ss_dssp             TTE--EEEEEEEEEECTTCCEEEEEEEEEECHHHHHHHHH
T ss_pred             CCE--EEEEEEEEEECCCCCEEEEEEEEehhhHHHHHHHH
Confidence            664  67899999999999999999999999999998873

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

Probab=97.80  E-value=3.4e-05  Score=60.11  Aligned_cols=45  Identities=9%  Similarity=0.106  Sum_probs=41.0

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchhhch
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMAQM  101 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~~E~  101 (115)
                      ++.++|||+..|+..+..|++|+ .|++..++++..|||+++.+++
T Consensus       316 yR~~~kdG~~vWv~~~~~~v~~~~~g~~~~iv~~~~dITe~~~~~~  361 (361)
T 4f3l_A          316 YRFLTKGQQWIWLQTHYYITYHQWNSRPEFIVCTHTVVSYAEVRAE  361 (361)
T ss_dssp             EEEECTTSEEEEEEEEEEEEECTTTCCEEEEEEEEEECCHHHHHHC
T ss_pred             EEEEecCCCEEEEEEEEEEEEcCCCCCeeEEEEEEEECChhHhhcC
Confidence            45678999999999999999998 8999999999999999988763

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*

Probab=97.75  E-value=4.2e-05  Score=49.71  Aligned_cols=34  Identities=18%  Similarity=0.424  Sum_probs=30.7

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEe
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKD   40 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~D   40 (115)
                      ..++ ||+.+|+.++++|+++++|++.+++++++|
T Consensus       115 ~~~~~dG~~~~~~~~~~~i~~~~g~~~~~v~~~~D  149 (149)
T 3d72_A          115 VNFKKNGQRFVNFLTMIPVRDETGEYRYSMGFQCE  149 (149)
T ss_dssp             EEECTTCCEEEEEEEEEEEECTTSSEEEEEEECCC
T ss_pred             EEECCCCCEEEEEEEEEEEEcCCCCEEEEEEEEeC
Confidence            3445 999999999999999999999999999876

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

Probab=97.67  E-value=0.0001  Score=46.13  Aligned_cols=35  Identities=9%  Similarity=0.003  Sum_probs=31.1

Q ss_pred             CCCceeEEEEEEEeeCCC-CCEEEEEEEEEeccchh
Q psy8547          11 QRTPFWCLLDIVPIKNEK-REVVLYLASHKDVTNTK   45 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~-G~~~~fi~~~~DIT~~k   45 (115)
                      ||+.+|+.++++|++|+. |.+.+++++..|||+.+
T Consensus        85 dG~~~~~~~~~~~~~d~~~~~~~~~v~~~~~i~~~~  120 (121)
T 2kdk_A           85 DGSFVTLKSQWFSFTNPDTKELEYIVSVNTLVLGHS  120 (121)
T ss_dssp             SSCEEEEEEEEEEEECCSSSCEEEEEEEEECCSSCC
T ss_pred             CCCEEEEEEEEEEEECCCCCeeeEEEEEEEeccccC
Confidence            999999999999999986 56777889999999865

>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* 3rh8_B*

Probab=97.66  E-value=8.5e-05  Score=48.21  Aligned_cols=34  Identities=18%  Similarity=0.412  Sum_probs=31.7

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeee
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKD   92 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~D   92 (115)
                      .++|||+.+|+.++++|+++++|++.++++++.|
T Consensus       116 ~~~~dG~~~~~~~~~~~i~~~~g~~~~~v~~~~D  149 (149)
T 3d72_A          116 NFKKNGQRFVNFLTMIPVRDETGEYRYSMGFQCE  149 (149)
T ss_dssp             EECTTCCEEEEEEEEEEEECTTSSEEEEEEECCC
T ss_pred             EECCCCCEEEEEEEEEEEEcCCCCEEEEEEEEeC
Confidence            4689999999999999999999999999999876

>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=97.65  E-value=8.6e-05  Score=47.70  Aligned_cols=35  Identities=14%  Similarity=0.207  Sum_probs=29.7

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..++|||+.||+.++++|++++.  ...++++++|||
T Consensus        96 ~~~~kdG~~~~~~~~~~~~~~~~--~~~~~~~~~DIT  130 (130)
T 1d06_A           96 SGQRKDGSTFPMKLAVGEMRSGG--ERFFTGFIRDLT  130 (130)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETT--EEEEEEEEEECC
T ss_pred             EEEeCCCCEEEEEEEEEEEEECC--eEEEEEEEEECc
Confidence            34799999999999999998743  346899999998

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

Probab=97.64  E-value=6.6e-05  Score=59.15  Aligned_cols=42  Identities=14%  Similarity=0.074  Sum_probs=35.5

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~   98 (115)
                      ++.++|||+..|+..+.++++|. .|++..++++..|||++|+
T Consensus       344 yR~~~kdG~~vWv~~~~~~~~~~~~g~~~~ivg~~~dIT~Rk~  386 (387)
T 4f3l_B          344 YKFKIKDGSFITLRSRWFSFMNPWTKEVEYIVSTNTVVLANVL  386 (387)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEETTTTEEEEEEEEEEECC----
T ss_pred             EEEEccCCCEEEEEEEEEEEECCCCCCEEEEEEEEEEcchhhc
Confidence            45678999999999999999998 8999999999999999985

>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=97.62  E-value=0.00011  Score=47.11  Aligned_cols=34  Identities=15%  Similarity=0.215  Sum_probs=28.3

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ...+ ||+.||+.++++|++++.  ..+++++.+|||
T Consensus        96 ~~~~kdG~~~~~~~~~~~~~~~~--~~~~~~~~~DIT  130 (130)
T 1d06_A           96 SGQRKDGSTFPMKLAVGEMRSGG--ERFFTGFIRDLT  130 (130)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETT--EEEEEEEEEECC
T ss_pred             EEEeCCCCEEEEEEEEEEEEECC--eEEEEEEEEECc
Confidence            3456 999999999999998743  356899999998

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

Probab=97.57  E-value=0.00014  Score=45.03  Aligned_cols=38  Identities=18%  Similarity=0.022  Sum_probs=26.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      +|+.+|+.+.+.|+...  ...+++++.+|||++|++++.
T Consensus        79 ~g~~~~~~~~~~~~~~~--~~~~~~~~~~DITe~k~a~~~  116 (126)
T 3mjq_A           79 EGTSIPAKARIWQGKWH--NEPCLFAIIKDLSKEERASSP  116 (126)
T ss_dssp             TSCEEEEEEEEEEEESS--SSEEEEEEEEECC--------
T ss_pred             CCCEEEEEEEEEeeeEC--CceEEEEEEEechHHHHhhcc
Confidence            99999999999988763  356789999999999998875

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

Probab=97.55  E-value=0.00014  Score=46.64  Aligned_cols=32  Identities=22%  Similarity=0.212  Sum_probs=26.9

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      +|.  |+.++++||+|++|++.+++.+++|||++
T Consensus        90 ~~~--~~~~~~~pi~~~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           90 GGR--RFSLDVVPVFNDANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             TTE--EEEEEEEEEECTTSCEEEEEEEEEECC--
T ss_pred             CCE--EEEEEEEEEECCCCCEEEEEEEEEEecCC
Confidence            565  44789999999999999999999999974

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

Probab=97.49  E-value=0.00018  Score=55.93  Aligned_cols=38  Identities=8%  Similarity=0.127  Sum_probs=36.3

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMAQ   48 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~~e   48 (115)
                      ||+..|+.....|++|+ +|++.+++++.+|||+++..+
T Consensus       322 dG~~vWv~~~~~~v~~~~~g~~~~iv~~~~dITe~~~~~  360 (361)
T 4f3l_A          322 GQQWIWLQTHYYITYHQWNSRPEFIVCTHTVVSYAEVRA  360 (361)
T ss_dssp             TSEEEEEEEEEEEEECTTTCCEEEEEEEEEECCHHHHHH
T ss_pred             CCCEEEEEEEEEEEEcCCCCCeeEEEEEEEECChhHhhc
Confidence            99999999999999998 899999999999999998865

>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L*

Probab=97.47  E-value=0.00012  Score=47.55  Aligned_cols=38  Identities=16%  Similarity=0.332  Sum_probs=25.1

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA   50 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~   50 (115)
                      +|..+|+.+.+.|+ +++|.+. ++++++|||+++++++.
T Consensus       125 ~g~~~~~~~~~~~~-~~~g~~~-~~~~~~DiT~~~~~e~~  162 (167)
T 1v9y_A          125 DGSKIWTRFALSKV-SAEGKVY-YLALVRDASVEMAQKEQ  162 (167)
T ss_dssp             TSCEEEEEEEEEEE-EETTEEE-EEEEEEC----------
T ss_pred             CCcEEEEEEEEEEE-ecCCCEE-EEEEEecCcHHHHHHHH
Confidence            99999999999999 5677765 99999999999988764

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

Probab=97.31  E-value=0.00033  Score=55.12  Aligned_cols=36  Identities=11%  Similarity=0.039  Sum_probs=31.2

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~   46 (115)
                      ||+..|+.....|++|+ +|++.+++++.+|||++|+
T Consensus       350 dG~~vWv~~~~~~~~~~~~g~~~~ivg~~~dIT~Rk~  386 (387)
T 4f3l_B          350 DGSFITLRSRWFSFMNPWTKEVEYIVSTNTVVLANVL  386 (387)
T ss_dssp             TSCEEEEEEEEEEEEETTTTEEEEEEEEEEECC----
T ss_pred             CCCEEEEEEEEEEEECCCCCCEEEEEEEEEEcchhhc
Confidence            99999999999999998 8999999999999999985

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

Probab=97.25  E-value=0.00032  Score=44.55  Aligned_cols=32  Identities=16%  Similarity=0.120  Sum_probs=25.7

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..++|||+.+|+.++++|+.  +|.   ++++++|||
T Consensus        86 ~~~~kdG~~~~v~~~~~~~~--~g~---~~~i~~DIT  117 (117)
T 2r78_A           86 TVWTRNGDQLTVELSAHLLP--DGK---ILGIARDVS  117 (117)
T ss_dssp             EEECTTSCEEEEEEEEEECT--TSC---EEEEEEC--
T ss_pred             EEEecCCCEEEEEEEEEEec--CCe---EEEEEEeCC
Confidence            34789999999999999996  565   678999998

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

Probab=97.17  E-value=0.00077  Score=43.07  Aligned_cols=35  Identities=23%  Similarity=0.247  Sum_probs=27.8

Q ss_pred             eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      .+.+|..  ..++++||+|++|++.+++++++|||+.
T Consensus        87 ~~~~~~~--~~~~~~pi~~~~g~~~g~v~~~~DiTee  121 (121)
T 4hi4_A           87 LNLGGRR--FSLDVVPVFNDANARLGSAVQWTDRTEE  121 (121)
T ss_dssp             EEETTEE--EEEEEEEEECTTSCEEEEEEEEEECC--
T ss_pred             EEECCEE--EEEEEEEEECCCCCEEEEEEEEEEecCC
Confidence            3445553  4789999999999999999999999974

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

Probab=97.09  E-value=0.0041  Score=48.53  Aligned_cols=88  Identities=14%  Similarity=0.160  Sum_probs=65.5

Q ss_pred             CCCceeEEEEEEEeeCC---------CCCEEEEEEEEEeccchhhh--h-----hh--------c---------------
Q psy8547          11 QRTPFWCLLDIVPIKNE---------KREVVLYLASHKDVTNTKMA--Q-----MA--------D---------------   51 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de---------~G~~~~fi~~~~DIT~~k~~--e-----~~--------~---------------   51 (115)
                      .+.+||+.++..|+.++         .|..++++++..+++.....  +     ..        +               
T Consensus        99 ~~~p~~l~~~~~~~~~e~~~~~~~~~~g~~~~lv~~a~~i~s~~~~p~e~~~~~~~~fi~r~~~dG~~~yvn~~~~~lLG  178 (339)
T 3rty_A           99 SYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALG  178 (339)
T ss_dssp             CEEEEEEEEEEEECCCC----------CCCEEEEEEEEECCCSCSSTTBBCCSSCCEEEEEEETTCBEEEECTTHHHHHC
T ss_pred             cceeEEEEEEEeccccccccccccccCCceEEEEEEcccCCccccccchhhccCCceEEEEECCCCeEEEcChhhhcccC
Confidence            55678888888898887         78888899999999864332  1     00        0               


Q ss_pred             --------------------------------CCCC--------ceeceecCCceeEEEEEeEEeeCCC-CCEEEEEEEe
Q psy8547          52 --------------------------------NGEG--------DYEDMQELGTPFWCLLDIVPIKNEK-REVVLYLASH   90 (115)
Q Consensus        52 --------------------------------~~~e--------~~~~yrKdGs~f~~~~~i~pirde~-G~v~~~i~~~   90 (115)
                                                      +|+.        .++.++|||+..|+..+.++++|.. |++...+++.
T Consensus       179 Y~peELiG~s~~~~vHPdD~~~~~~~~~~~l~~G~~~~~~~~s~~yR~~~kdG~~vWlet~~~~~~np~s~~~~~II~~h  258 (339)
T 3rty_A          179 YLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHH  258 (339)
T ss_dssp             CCHHHHTTSBGGGGBCGGGHHHHHHHHHHHHHHTTSTTCCCBCCCEEEECTTSCEEEEEEEEEEEECTTTCSEEEEEEEE
T ss_pred             CCHHHHcCCcHHHEECHHHHHHHHHHHHHHHHcCCcccccccceEEEEEccCCCEEEEEEEEEEEECCCCCCeeEEEEEE
Confidence                                            1121        2556789999999999999999975 5788889999


Q ss_pred             eecccchh
Q psy8547          91 KDVTNTKM   98 (115)
Q Consensus        91 ~DIT~~k~   98 (115)
                      ..|+.+..
T Consensus       259 ~vi~~p~~  266 (339)
T 3rty_A          259 RVFQGPKQ  266 (339)
T ss_dssp             EEEECCSS
T ss_pred             EECCCCCC
Confidence            98887754

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

Probab=96.89  E-value=0.003  Score=43.37  Aligned_cols=36  Identities=6%  Similarity=0.037  Sum_probs=32.1

Q ss_pred             ceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          14 PFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        14 ~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      ..++.++.+||+|++|+++|.+.+++|||+.+..+.
T Consensus       103 ~~~v~v~~~Pi~d~~G~~~G~vev~~Dit~l~~le~  138 (151)
T 2qkp_A          103 GKFVYVTYAAVRDQAGDFQGVLEYVQDIKPFFELDS  138 (151)
T ss_dssp             TEEEEEEEEEEECTTCCEEEEEEEEEECGGGGGGGG
T ss_pred             CeEEEEEEEEEECCCCCEEEEEEEEEECHHHHhhhh
Confidence            456789999999999999999999999999888764

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

Probab=96.88  E-value=0.0014  Score=51.23  Aligned_cols=37  Identities=24%  Similarity=0.275  Sum_probs=33.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~   49 (115)
                      +|  .|+.++.+||+|++|+++|++.+++|||+.+..+.
T Consensus       316 ~g--~~v~v~~~PI~d~~G~~~G~v~v~~DITe~~~le~  352 (369)
T 3cax_A          316 RE--KYVYIKYVPLFNEKGEYIGTLEMTMDIAPYKKIEG  352 (369)
T ss_dssp             TT--EEEEEEEEEEECTTSCEEEEEEEEEECHHHHTCCS
T ss_pred             CC--EEEEEEEEEEECCCCCEEEEEEEEEcCHHHHHHHH
Confidence            66  57899999999999999999999999999988754

>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=96.87  E-value=0.0015  Score=39.86  Aligned_cols=30  Identities=7%  Similarity=0.148  Sum_probs=25.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ||+.+|+.++++|+.++.+  .+++++.+|||
T Consensus        89 ~g~~~~~~~~~~~~~~~~~--~~~~~~~~DIT  118 (118)
T 3olo_A           89 SGRIFLVEMSLTFLEDQER--RFSCVFVREKS  118 (118)
T ss_dssp             TCCEEEEEEEEEEEEETTE--EEEEEEEEEC-
T ss_pred             CCCEEEEEEEEEEEEECCc--cEEEEEEEeCC
Confidence            9999999999999998643  46779999997

>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=96.80  E-value=0.0016  Score=40.78  Aligned_cols=34  Identities=18%  Similarity=0.224  Sum_probs=26.7

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..+|||+.+|+.++..|+.+ .|.. .+++++.|||
T Consensus        93 ~~~~dG~~~~~~~~~~~~~~-~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           93 YERRDGSTMSVEVHLLRFNL-EGED-RFLAISRDIT  126 (126)
T ss_dssp             EECTTSCEEEEEEEEEEEEE-TTEE-EEEEEEEEC-
T ss_pred             EEeCCCCEEEEEEEeEEEec-CCcE-EEEEEEEeCC
Confidence            35899999999999999854 4443 5789999998

>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=96.78  E-value=0.0018  Score=39.51  Aligned_cols=34  Identities=9%  Similarity=0.157  Sum_probs=28.0

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..+|+|+.+|+.++++|+.++.+  ..+++++.|||
T Consensus        85 ~~~~~g~~~~~~~~~~~~~~~~~--~~~~~~~~DIT  118 (118)
T 3olo_A           85 YRSQSGRIFLVEMSLTFLEDQER--RFSCVFVREKS  118 (118)
T ss_dssp             EECTTCCEEEEEEEEEEEEETTE--EEEEEEEEEC-
T ss_pred             EEccCCCEEEEEEEEEEEEECCc--cEEEEEEEeCC
Confidence            46899999999999999987543  46789999997

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

Probab=96.68  E-value=0.0027  Score=49.58  Aligned_cols=40  Identities=23%  Similarity=0.203  Sum_probs=35.0

Q ss_pred             ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchh
Q psy8547          61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA  102 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~  102 (115)
                      +++|  .++.++.+||+|++|++++++.++.|||+.++.|..
T Consensus       314 ~~~g--~~v~v~~~PI~d~~G~~~G~v~v~~DITe~~~le~~  353 (369)
T 3cax_A          314 RLRE--KYVYIKYVPLFNEKGEYIGTLEMTMDIAPYKKIEGE  353 (369)
T ss_dssp             EETT--EEEEEEEEEEECTTSCEEEEEEEEEECHHHHTCCSC
T ss_pred             eeCC--EEEEEEEEEEECCCCCEEEEEEEEEcCHHHHHHHHH
Confidence            4556  477889999999999999999999999999988765

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

Probab=96.66  E-value=0.0053  Score=42.09  Aligned_cols=82  Identities=13%  Similarity=0.071  Sum_probs=53.1

Q ss_pred             EeeCCCCCEEEEEEE---EEeccchhhhhhhc-----------------------CCCCc-eece-ecCCceeEEEEEeE
Q psy8547          23 PIKNEKREVVLYLAS---HKDVTNTKMAQMAD-----------------------NGEGD-YEDM-QELGTPFWCLLDIV   74 (115)
Q Consensus        23 Pi~de~G~~~~fi~~---~~DIT~~k~~e~~~-----------------------~~~e~-~~~y-rKdGs~f~~~~~i~   74 (115)
                      -+-|++|.+++|-..   ...++.+ ..+..-                       +++.. ...+ .+.|.-.++.++..
T Consensus        33 ~~vD~~g~I~~~N~a~~~~~~i~g~-~~~~iGr~v~~~~~~~~~~~v~~i~~~l~~g~~~~~~~~~~~~~~~~~v~v~~~  111 (151)
T 2qkp_A           33 TFVNKDDIFQYYNDSVPAAEMVFKR-TPSQVGRNVELCHPPKVLDKVKKVFELLRNGQRDKVNMWFQSERLGKFVYVTYA  111 (151)
T ss_dssp             EEEETTSBEEEECCCSCGGGCSSCC-CGGGTTSBGGGSSCHHHHHHHHHHHHHHHTTSBSEEEEEEEETTTTEEEEEEEE
T ss_pred             EEEcCCCeEEEEeCCCchhhhhcCC-CHHHcCCCHHHhCCHHHHHHHHHHHHHHHcCCccEEEEEEecCCCCeEEEEEEE
Confidence            357889999888776   5677762 212100                       12211 1122 22321345688999


Q ss_pred             EeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          75 PIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        75 pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ||+|++|++++.+.++.|||+.+..|...++
T Consensus       112 Pi~d~~G~~~G~vev~~Dit~l~~le~~r~~  142 (151)
T 2qkp_A          112 AVRDQAGDFQGVLEYVQDIKPFFELDSEFNR  142 (151)
T ss_dssp             EEECTTCCEEEEEEEEEECGGGGGGGGC---
T ss_pred             EEECCCCCEEEEEEEEEECHHHHhhhhhhhc
Confidence            9999999999999999999999888876554

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

Probab=96.64  E-value=0.0017  Score=40.31  Aligned_cols=34  Identities=12%  Similarity=0.085  Sum_probs=29.0

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..+|||+.||+.++++|++++.+.  .+++++.|++
T Consensus        80 ~~~~dG~~~~v~~~~~~~~~~~~~--~~v~~~~~~~  113 (114)
T 1ll8_A           80 IISRSGEKIPVSVWMKRMRQERRL--CCVVVLEPVE  113 (114)
T ss_dssp             ECCTTCCCEEEECCEECCBSSSSB--EEEEEEEECC
T ss_pred             EEecCCCEEEEEEEEEeeccCCcc--EEEEEEeecC
Confidence            368999999999999999986653  6889999886

>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=96.63  E-value=0.0028  Score=39.63  Aligned_cols=30  Identities=17%  Similarity=0.256  Sum_probs=24.1

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ||+.+|+.++..|+.+ +|.. .++++.+|||
T Consensus        97 dG~~~~~~~~~~~~~~-~~~~-~~~~~~~DIT  126 (126)
T 3bwl_A           97 DGSTMSVEVHLLRFNL-EGED-RFLAISRDIT  126 (126)
T ss_dssp             TSCEEEEEEEEEEEEE-TTEE-EEEEEEEEC-
T ss_pred             CCCEEEEEEEeEEEec-CCcE-EEEEEEEeCC
Confidence            9999999999999854 4544 5789999998

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

Probab=96.49  E-value=0.005  Score=40.80  Aligned_cols=33  Identities=15%  Similarity=0.126  Sum_probs=26.5

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..+|||+.||++++++|+.++.+   .|+++++|..
T Consensus        91 ~~rkdG~~~~velsis~i~~~~~---~~v~~~~~~~  123 (129)
T 3mfx_A           91 LICASGKAKDVELSISYIPGHEP---MFVMVMHDLE  123 (129)
T ss_dssp             EECTTSCEEEEEEEEEEECSSSC---EEEEEEEEC-
T ss_pred             EEcCCCCEEEEEEEEEEecCCCc---EEEEEEechh
Confidence            46899999999999999994333   4888888874

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

Probab=96.46  E-value=0.0038  Score=38.46  Aligned_cols=31  Identities=16%  Similarity=0.386  Sum_probs=27.4

Q ss_pred             cCCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          10 RQRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        10 rdG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ++|+.+|+.++++|+++ +|. .+++.+++||+
T Consensus        85 ~~g~~~~~~~~~~pi~~-~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           85 VDGRPLMLEVTVSPITW-QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             ETTEEEEEEEEEEEEEE-TTE-EEEEEEEEEC-
T ss_pred             cCCCEEEEEEEEEEeec-CCc-eEEEEEEEeCC
Confidence            39999999999999999 887 68999999985

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

Probab=96.42  E-value=0.0033  Score=39.01  Aligned_cols=33  Identities=9%  Similarity=0.004  Sum_probs=27.6

Q ss_pred             ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547           8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus         8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ..+ ||+.||+.++++|+.++.+.  +|+++++|++
T Consensus        80 ~~~~dG~~~~v~~~~~~~~~~~~~--~~v~~~~~~~  113 (114)
T 1ll8_A           80 IISRSGEKIPVSVWMKRMRQERRL--CCVVVLEPVE  113 (114)
T ss_dssp             ECCTTCCCEEEECCEECCBSSSSB--EEEEEEEECC
T ss_pred             EEecCCCEEEEEEEEEeeccCCcc--EEEEEEeecC
Confidence            345 99999999999999987653  6889999986

>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=96.19  E-value=0.0022  Score=39.63  Aligned_cols=31  Identities=13%  Similarity=0.216  Sum_probs=27.3

Q ss_pred             CCC-ceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRT-PFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~-~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      +|. ..|+.++++|+.++ |...+++++++|||
T Consensus        94 ~~~~~~~~~~~~~p~~~~-~~~~~~~~~~~DIT  125 (125)
T 3fc7_A           94 DAVGGRHYHNQYIPVDSH-RKSDTFQLVSRDIT  125 (125)
T ss_dssp             EEETTEEEEEEEEESSTT-TTTTEEEEEEEECC
T ss_pred             cCCCcEEEEEEEEeEecC-CCeEEEEEEEecCC
Confidence            777 89999999999876 66678999999998

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

Probab=96.12  E-value=0.01  Score=39.24  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=25.7

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      ....+ ||+.||++++++|+.++++   .|+++.+|...
T Consensus        89 ~~~~rkdG~~~~velsis~i~~~~~---~~v~~~~~~~~  124 (129)
T 3mfx_A           89 TTLICASGKAKDVELSISYIPGHEP---MFVMVMHDLEH  124 (129)
T ss_dssp             EEEECTTSCEEEEEEEEEEECSSSC---EEEEEEEEC--
T ss_pred             EEEEcCCCCEEEEEEEEEEecCCCc---EEEEEEechhh
Confidence            34445 9999999999999994332   48888888754

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

Probab=96.06  E-value=0.0091  Score=36.66  Aligned_cols=31  Identities=19%  Similarity=0.416  Sum_probs=27.5

Q ss_pred             cCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          62 ELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        62 KdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ++|+.+|+.++++|+.+ .|. .+++.++.||+
T Consensus        85 ~~g~~~~~~~~~~pi~~-~g~-~~~l~~~~Di~  115 (115)
T 3b33_A           85 VDGRPLMLEVTVSPITW-QRQ-LMLLVEMRKID  115 (115)
T ss_dssp             ETTEEEEEEEEEEEEEE-TTE-EEEEEEEEEC-
T ss_pred             cCCCEEEEEEEEEEeec-CCc-eEEEEEEEeCC
Confidence            79999999999999999 886 68999999985

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

Probab=95.88  E-value=0.0048  Score=45.88  Aligned_cols=41  Identities=15%  Similarity=0.146  Sum_probs=35.0

Q ss_pred             ceeEEEEEeEEeeCCCCCE-EEEEEEeeecccchhhchhhcc
Q psy8547          65 TPFWCLLDIVPIKNEKREV-VLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        65 s~f~~~~~i~pirde~G~v-~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      ...|..++++|+++..|.+ .++++++.|||++|++|+++++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~DiTe~~~~e~~~~~  125 (349)
T 3a0r_A           84 GERYFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEEERKR  125 (349)
T ss_dssp             TTBCCEEEEEEECCTTTTSSCEEEEEEECCSTTTTTTTTTTH
T ss_pred             CceEEEEEEEEEEcCCCceeeEEEEEEEechHHHHHHHHHHH
Confidence            4457789999999998875 5899999999999999987764

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

Probab=95.66  E-value=0.021  Score=32.44  Aligned_cols=30  Identities=13%  Similarity=0.191  Sum_probs=25.6

Q ss_pred             CCCceeEEEEEEEeeCCCCC-EEEEEEEEEe
Q psy8547          11 QRTPFWCLLDIVPIKNEKRE-VVLYLASHKD   40 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~-~~~fi~~~~D   40 (115)
                      +|...|+.++++|+++++|. +.+++++++|
T Consensus        66 ~~~~~~~~~~~~p~~~~~~~~~~g~v~~~~D   96 (96)
T 3a0s_A           66 KFGERYFNIRFSPFRNAKTQLLEGVIITIDD   96 (96)
T ss_dssp             EETTEEEEEEEEEEECTTTCCEEEEEEEEEC
T ss_pred             cCCcEEEEEEEEEeEcCCCCeeeEEEEEecC
Confidence            67778999999999998765 6789998876

>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=95.64  E-value=0.0056  Score=37.68  Aligned_cols=34  Identities=15%  Similarity=0.180  Sum_probs=28.8

Q ss_pred             eecCCc-eeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          60 MQELGT-PFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        60 yrKdGs-~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..++|. .+|+.++++|+.++ |.+..+++++.|||
T Consensus        91 ~~~~~~~~~~~~~~~~p~~~~-~~~~~~~~~~~DIT  125 (125)
T 3fc7_A           91 RSEDAVGGRHYHNQYIPVDSH-RKSDTFQLVSRDIT  125 (125)
T ss_dssp             EEEEEETTEEEEEEEEESSTT-TTTTEEEEEEEECC
T ss_pred             EeEcCCCcEEEEEEEEeEecC-CCeEEEEEEEecCC
Confidence            456777 89999999999875 66778999999998

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

Probab=95.32  E-value=0.012  Score=43.63  Aligned_cols=38  Identities=16%  Similarity=0.134  Sum_probs=32.2

Q ss_pred             CCceeEEEEEEEeeCCCCCE-EEEEEEEEeccchhhhhh
Q psy8547          12 RTPFWCLLDIVPIKNEKREV-VLYLASHKDVTNTKMAQM   49 (115)
Q Consensus        12 G~~fw~~~~i~Pi~de~G~~-~~fi~~~~DIT~~k~~e~   49 (115)
                      +...|+.+.++|++++.|.. .+++++.+|||+++++++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~DiTe~~~~e~  121 (349)
T 3a0r_A           83 FGERYFNIRFSPFRNAKTQLLEGVIITIDDVTELYKYEE  121 (349)
T ss_dssp             BTTBCCEEEEEEECCTTTTSSCEEEEEEECCSTTTTTTT
T ss_pred             cCceEEEEEEEEEEcCCCceeeEEEEEEEechHHHHHHH
Confidence            34457889999999999886 589999999999988766

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

Probab=94.55  E-value=0.063  Score=30.31  Aligned_cols=32  Identities=13%  Similarity=0.066  Sum_probs=25.9

Q ss_pred             ecCCceeEEEEEeEEeeCCCCC-EEEEEEEeee
Q psy8547          61 QELGTPFWCLLDIVPIKNEKRE-VVLYLASHKD   92 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~-v~~~i~~~~D   92 (115)
                      .++|...|+.++++|++++.|. +..+++++.|
T Consensus        64 ~~~~~~~~~~~~~~p~~~~~~~~~~g~v~~~~D   96 (96)
T 3a0s_A           64 FYKFGERYFNIRFSPFRNAKTQLLEGVIITIDD   96 (96)
T ss_dssp             EEEETTEEEEEEEEEEECTTTCCEEEEEEEEEC
T ss_pred             EEcCCcEEEEEEEEEeEcCCCCeeeEEEEEecC
Confidence            3466778999999999998665 6788888876

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

Probab=93.69  E-value=0.0094  Score=36.02  Aligned_cols=29  Identities=17%  Similarity=0.379  Sum_probs=25.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      +|  .|+.++++|+++ +|.+.+++++++|||
T Consensus        90 ~~--~~~~~~~~p~~~-~g~~~g~v~~~~DiT  118 (118)
T 2w0n_A           90 KD--RLLLINTVPVRS-NGVIIGAISTFRDKT  118 (118)
T ss_dssp             SS--CEECCCEECCCC-SSCCCCEEECCCCCC
T ss_pred             CC--EEEEEeeceeee-CCEEEEEEEEEEeCC
Confidence            55  578889999998 899999999999998

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

Probab=93.55  E-value=0.05  Score=35.02  Aligned_cols=25  Identities=8%  Similarity=0.181  Sum_probs=17.9

Q ss_pred             eeceecCCceeEEEEEeEEeeCCCC
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNEKR   81 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde~G   81 (115)
                      ++.++|||+.+|+..+++++++..+
T Consensus        71 ~r~~~kdG~~~wve~~~~~v~~~~~   95 (111)
T 2vlg_A           71 FRFIKKDHTIVWVEAAVEIVTTRAE   95 (111)
T ss_dssp             EEEECTTSCEEEEEEEEEEC-----
T ss_pred             EEEEcCCCCEEEEEEEEEEEecccC
Confidence            4456899999999999999999765

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

Probab=92.69  E-value=0.029  Score=33.76  Aligned_cols=32  Identities=16%  Similarity=0.309  Sum_probs=26.4

Q ss_pred             eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      .+.+|  .|+.+++.|+.+ .|++..+++++.|||
T Consensus        87 ~~~~~--~~~~~~~~p~~~-~g~~~g~v~~~~DiT  118 (118)
T 2w0n_A           87 ITIKD--RLLLINTVPVRS-NGVIIGAISTFRDKT  118 (118)
T ss_dssp             EESSS--CEECCCEECCCC-SSCCCCEEECCCCCC
T ss_pred             EEECC--EEEEEeeceeee-CCEEEEEEEEEEeCC
Confidence            34556  577889999998 888889999999998

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

Probab=91.25  E-value=0.029  Score=42.76  Aligned_cols=37  Identities=24%  Similarity=0.088  Sum_probs=31.3

Q ss_pred             EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547          68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG  105 (115)
Q Consensus        68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~  105 (115)
                      +..++..|+++ +|++.+++.+++|||+.++.|++|+.
T Consensus       259 ~l~v~~~Pi~~-~g~~~G~Vvv~rDITE~~~lE~eL~~  295 (305)
T 2ykf_A          259 TVLLRTLPLVV-AGRNVGAAILIRDVTEVKRRDRALIS  295 (305)
Confidence            45667789987 57888999999999999999998753

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

Probab=90.09  E-value=0.047  Score=41.55  Aligned_cols=36  Identities=25%  Similarity=0.091  Sum_probs=31.2

Q ss_pred             eeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc
Q psy8547          15 FWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD   51 (115)
Q Consensus        15 fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~   51 (115)
                      .++.++.+|+++ +|++.+++.+++|||+.++.++.+
T Consensus       258 ~~l~v~~~Pi~~-~g~~~G~Vvv~rDITE~~~lE~eL  293 (305)
T 2ykf_A          258 ATVLLRTLPLVV-AGRNVGAAILIRDVTEVKRRDRAL  293 (305)
Confidence            567888999997 588999999999999999988754

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

Probab=90.43  E-value=0.19  Score=32.17  Aligned_cols=20  Identities=10%  Similarity=0.243  Sum_probs=13.9

Q ss_pred             CCCceeEEEEEEEeeCCCCC
Q psy8547          11 QRTPFWCLLDIVPIKNEKRE   30 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~   30 (115)
                      ||+.+|++++++|+++..+.
T Consensus        77 dG~~~wve~~~~~v~~~~~~   96 (111)
T 2vlg_A           77 DHTIVWVEAAVEIVTTRAER   96 (111)
T ss_dssp             TSCEEEEEEEEEEC------
T ss_pred             CCCEEEEEEEEEEEecccCC
Confidence            99999999999999998664

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

Probab=90.37  E-value=0.019  Score=39.04  Aligned_cols=33  Identities=9%  Similarity=0.160  Sum_probs=26.2

Q ss_pred             CCCceeEEEEEEEeeCCCCC----EEEEEEEEEeccchh
Q psy8547          11 QRTPFWCLLDIVPIKNEKRE----VVLYLASHKDVTNTK   45 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~----~~~fi~~~~DIT~~k   45 (115)
                      +|..  +.+.++|+++++|.    +.+++.+++|||+.+
T Consensus       153 ~g~~--~~~~~~pi~~~~~~~~~~~~g~v~~~~DiTe~~  189 (190)
T 2jhe_A          153 NGQN--FLMEITPVYLQDENDQHVLTGAVVMLRSTIRMG  189 (190)
T ss_dssp             TTEE--EEEEEEEETTTTEEEEEEEE-HHHHHHHHTTTC
T ss_pred             CCeE--EEEEEEEEEecCCCCcceEEeEEEEEeccchhc
Confidence            6754  56788999987776    889999999999876

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

Probab=89.21  E-value=0.89  Score=34.90  Aligned_cols=42  Identities=17%  Similarity=0.032  Sum_probs=32.8

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~   98 (115)
                      ++.++|||+..|+....++++|. .+++-.+++...=++....
T Consensus       242 yR~~~kdG~~vwvet~~~~~~np~s~~~e~II~~h~v~~~p~~  284 (317)
T 4dj3_A          242 VRFCTQNGEYVILDSSWSSFVNPWSRKVSFIIGRHKVRTSPLN  284 (317)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECSSSCCEEEEEEEEEECCCCSS
T ss_pred             EEEEccCCCEEEEEEEEEEEECCCCCcccEEEEEEEeccCCCC
Confidence            45678999999999999999997 4667777777775555443

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

Probab=89.06  E-value=0.82  Score=35.38  Aligned_cols=37  Identities=11%  Similarity=0.076  Sum_probs=31.2

Q ss_pred             CCCceeEEEEEEEeeCCC-CCEEEEEEEEEeccchhhh
Q psy8547          11 QRTPFWCLLDIVPIKNEK-REVVLYLASHKDVTNTKMA   47 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~-G~~~~fi~~~~DIT~~k~~   47 (115)
                      ||+..|++.+.+|++|+. |++-++|++.+.|+.+...
T Consensus       230 dG~~vWlet~~~~~~np~s~~~~~II~~h~vi~~p~~~  267 (339)
T 3rty_A          230 NGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQC  267 (339)
T ss_dssp             TSCEEEEEEEEEEEECTTTCSEEEEEEEEEEEECCSSS
T ss_pred             CCCEEEEEEEEEEEECCCCCCeeEEEEEEEECCCCCCC
Confidence            999999999999999986 4566777888888887653

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

Probab=88.95  E-value=0.83  Score=35.10  Aligned_cols=42  Identities=17%  Similarity=-0.001  Sum_probs=35.9

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~   98 (115)
                      ++.++|||+..|+....++++|. .+++-++++...-++....
T Consensus       243 yR~~~kdG~~vwvet~~~~~~np~s~~~e~II~~h~v~~gp~~  285 (320)
T 4dj2_A          243 IRFCARNGEYVTMDTSWAGFVHPWSRKVAFVLGRHKVRTAPLN  285 (320)
T ss_dssp             EEEECSSSCEEEEECEEEEEECTTTCSEEEEEEEEEESSCCSS
T ss_pred             EEEEccCCCEEEEEEEEEEEECCCCCCccEEEEEEEEccCCCC
Confidence            55678999999999999999986 6788899999988887654

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

Probab=88.08  E-value=1  Score=34.34  Aligned_cols=42  Identities=12%  Similarity=-0.011  Sum_probs=35.6

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~   98 (115)
                      ++.++|||+..|+....++++|. .+++-.+++...-++....
T Consensus       232 yR~~~kdG~~vwvet~~~~~~np~s~~~e~ii~~h~v~~gp~~  274 (309)
T 3gdi_A          232 IRFRTRNGEYITLDTSWSSFINPWSRKISFIIGRHKVRVGPLN  274 (309)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCSS
T ss_pred             EEEEccCCCEEEEEEEEEEEECCCCCcccEEEEEEEEccCCCC
Confidence            55678999999999999999986 6778899999998887643

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

Probab=87.40  E-value=0.056  Score=36.62  Aligned_cols=36  Identities=11%  Similarity=0.128  Sum_probs=27.0

Q ss_pred             ecCCceeEEEEEeEEeeCCCCC----EEEEEEEeeecccchh
Q psy8547          61 QELGTPFWCLLDIVPIKNEKRE----VVLYLASHKDVTNTKM   98 (115)
Q Consensus        61 rKdGs~f~~~~~i~pirde~G~----v~~~i~~~~DIT~~k~   98 (115)
                      +.+|..  ..++++|+++++|.    +.+++.++.|||+.++
T Consensus       151 ~~~g~~--~~~~~~pi~~~~~~~~~~~~g~v~~~~DiTe~~~  190 (190)
T 2jhe_A          151 VINGQN--FLMEITPVYLQDENDQHVLTGAVVMLRSTIRMGR  190 (190)
T ss_dssp             EETTEE--EEEEEEEETTTTEEEEEEEE-HHHHHHHHTTTCC
T ss_pred             EECCeE--EEEEEEEEEecCCCCcceEEeEEEEEeccchhcC
Confidence            346654  45789999986666    8889999999998763

>1p0z_A Sensor kinase CITA; transferase; HET: FLC MO7; 1.60A {Klebsiella pneumoniae} SCOP: d.110.6.1 PDB: 2v9a_A 2j80_A*

Probab=86.54  E-value=1.5  Score=28.56  Aligned_cols=33  Identities=12%  Similarity=0.095  Sum_probs=25.3

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      .|+.-.......||++++|+++|++.+--++..
T Consensus        95 ~g~~g~~~~~~~PV~~~~g~viGvv~vg~~l~~  127 (131)
T 1p0z_A           95 KGSLGSSLRGKSPIQDATGKVIGIVSVGYTIEQ  127 (131)
T ss_dssp             EETTEEEEEEEEEEECTTCCEEEEEEEEEEGGG
T ss_pred             EccceeeEEEEEeEECCCCCEEEEEEEEEEhHH
Confidence            444445556667999999999999999887654

>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=85.29  E-value=0.75  Score=28.36  Aligned_cols=24  Identities=13%  Similarity=0.088  Sum_probs=19.4

Q ss_pred             eEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          67 FWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        67 f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      .|..+++.|+.+  |    +++++.|||++
T Consensus        95 ~~~~~~~~p~~~--g----~v~~~~DITer  118 (118)
T 3fg8_A           95 MTIEVTAAADSG--A----LVVHFRDVTAE  118 (118)
T ss_dssp             CEEEEEEEEETT--E----EEEEEEECSCC
T ss_pred             eEEEEEEEEcCC--c----EEEEEEeccCC
Confidence            677888899864  3    78899999985

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

Probab=82.15  E-value=2.4  Score=32.44  Aligned_cols=37  Identities=16%  Similarity=0.012  Sum_probs=31.7

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMA   47 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~~   47 (115)
                      ||+..|++...++++|. .+++-++|+...-++...+.
T Consensus       249 dG~~vwvet~~~~~~np~s~~~e~II~~h~v~~gp~~~  286 (320)
T 4dj2_A          249 NGEYVTMDTSWAGFVHPWSRKVAFVLGRHKVRTAPLNE  286 (320)
T ss_dssp             SSCEEEEECEEEEEECTTTCSEEEEEEEEEESSCCSSC
T ss_pred             CCCEEEEEEEEEEEECCCCCCccEEEEEEEEccCCCCC
Confidence            99999999999999997 57777888888888877654

>3by8_A Sensor protein DCUS; histidine kinase sensor domain, inner membrane, membrane, phosphoprotein, transferase, transmembrane; 1.45A {Escherichia coli} SCOP: d.110.6.1 PDB: 1ojg_A

Probab=81.87  E-value=2.3  Score=28.19  Aligned_cols=35  Identities=14%  Similarity=0.104  Sum_probs=25.8

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchh
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTK   45 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k   45 (115)
                      .|+.-...-...||++++|+++|++.+-.++....
T Consensus       100 ~~~~g~~~~~~~PV~~~~g~viGvv~vg~~~~~~~  134 (142)
T 3by8_A          100 RGFLAQALRVFTPIYDENHKQIGVVAIGLELSRVT  134 (142)
T ss_dssp             CSSSSCEEEEEEEEECTTSCEEEEEEEEEEHHHHH
T ss_pred             cCccEEEEEEEEeEEcCCCCEEEEEEEeEEHHHHH
Confidence            34444455566799998999999999988776543

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

Probab=81.07  E-value=3.1  Score=31.68  Aligned_cols=37  Identities=11%  Similarity=0.007  Sum_probs=31.8

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKMA   47 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~~   47 (115)
                      ||+..|++...++++|. .+++-++|++..-++...+.
T Consensus       238 dG~~vwvet~~~~~~np~s~~~e~ii~~h~v~~gp~~~  275 (309)
T 3gdi_A          238 NGEYITLDTSWSSFINPWSRKISFIIGRHKVRVGPLNE  275 (309)
T ss_dssp             TSCEEEEEEEEEEEECTTTCCEEEEEEEEEEEECCSSS
T ss_pred             CCCEEEEEEEEEEEECCCCCcccEEEEEEEEccCCCCC
Confidence            99999999999999997 56777888998888877654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	115
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.15
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	99.06
d1bywa_	110	Erg potassium channel, N-terminal domain {Human (H	99.05
d1n9la_	109	Putative blue light receptor, phot-lov1 domain {Gr	98.99
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.72
d1jnua_	104	Photoreceptor phy3 flavin-binding domain, lov2 {Ma	98.63
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.59
d1p97a_	114	Hypoxia-inducible factor Hif2a, C-terminal domain	98.44
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	98.15
d1xj3a1	106	Histidine kinase FixL heme domain {Bradyrhizobium	98.11
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	97.66
d1ew0a_	130	Histidine kinase FixL heme domain {Rhizobium melil	97.66
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	97.59
d1v9ya_	113	Direct oxygen sensor protein, DOS {Escherichia col	97.5
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	96.41
d1ll8a_	114	N-terminal PAS domain of Pas kinase {Human (Homo s	96.19
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	94.41
d1oj5a_	109	PAS domain of steroid receptor coactivator 1A, NCo	92.22
d1p0za_	131	Sensor kinase CitA {Klebsiella pneumoniae [TaxId:	82.53
d3by8a1	133	Fumarate sensor DcuS {Escherichia coli [TaxId: 562	80.38

>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=99.15  E-value=2.7e-11  Score=77.41  Aligned_cols=42  Identities=31%  Similarity=0.608  Sum_probs=38.4

Q ss_pred             ccceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547           3 THPDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus         3 ~~~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      ..+..++| +|+.||+.++++||+|++|++++|+++++|||+|
T Consensus        68 ~~e~~~~~~~g~~~w~~~~~~pi~d~~G~v~~~i~~~~DITer  110 (110)
T d1bywa_          68 KVEIAFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEECTTCCEEEEEEEEEEEEEC
T ss_pred             cceeeeeecccceeeeeeeEEEEECCCCCEEEEEEEEEECCCC
Confidence            34566778 9999999999999999999999999999999986

>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=99.06  E-value=1.4e-10  Score=74.32  Aligned_cols=39  Identities=41%  Similarity=0.710  Sum_probs=36.1

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      +..++| ||+.||+.++++||+|++|++.+|+++++|||+
T Consensus        70 e~~~~~kdG~~~w~~~~~~pi~d~~G~v~~~v~~~~DITa  109 (109)
T d1n9la_          70 RLLNYRKDGTPFWNLLTVTPIKTPDGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEECTTSCEEEEEEEEEECCC
T ss_pred             eEEEEecCCeEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence            456677 999999999999999999999999999999995

>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=99.05  E-value=1.4e-10  Score=74.03  Aligned_cols=39  Identities=31%  Similarity=0.629  Sum_probs=37.1

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      ..++|+|+.||+.++++||+|++|++++|++++.|||+|
T Consensus        72 ~~~~~~g~~~w~~~~~~pi~d~~G~v~~~i~~~~DITer  110 (110)
T d1bywa_          72 AFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEK  110 (110)
T ss_dssp             EEECTTSCEEEEEEEEEEEECTTCCEEEEEEEEEEEEEC
T ss_pred             eeeecccceeeeeeeEEEEECCCCCEEEEEEEEEECCCC
Confidence            457999999999999999999999999999999999986

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

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.99  E-value=4e-10  Score=72.04  Aligned_cols=69  Identities=26%  Similarity=0.397  Sum_probs=51.7

Q ss_pred             CCCCEEEEEEEEEeccchhhhhhhc------------------------CCC---CceeceecCCceeEEEEEeEEeeCC
Q psy8547          27 EKREVVLYLASHKDVTNTKMAQMAD------------------------NGE---GDYEDMQELGTPFWCLLDIVPIKNE   79 (115)
Q Consensus        27 e~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~---e~~~~yrKdGs~f~~~~~i~pirde   79 (115)
                      ++|.++++-..+..++--...|-.-                        ++.   ..+..+||||+.||+.++++||+|+
T Consensus        14 pdg~Ii~vN~a~~~~~Gy~~~El~G~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~~~w~~~~~~pi~d~   93 (109)
T d1n9la_          14 PDCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPIKTP   93 (109)
T ss_dssp             TTCCEEEECHHHHHHHCCCHHHHTTSCGGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEEEEEEEEEEECT
T ss_pred             CCCeEEEEcHHHHHHHCcCHHHHcCCcceeeecccCCHHHhhhhhhHhhcCCceeeeEEEEecCCeEEEEEEEEEEEECC
Confidence            4688887666666666554433210                        111   1234579999999999999999999


Q ss_pred             CCCEEEEEEEeeeccc
Q psy8547          80 KREVVLYLASHKDVTN   95 (115)
Q Consensus        80 ~G~v~~~i~~~~DIT~   95 (115)
                      +|++.+|+++++|||.
T Consensus        94 ~G~v~~~v~~~~DITa  109 (109)
T d1n9la_          94 DGRVSKFVGVQVDVTS  109 (109)
T ss_dssp             TSCEEEEEEEEEECCC
T ss_pred             CCCEEEEEEEEEECCC
Confidence            9999999999999994

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

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=98.72  E-value=6.7e-09  Score=65.12  Aligned_cols=37  Identities=19%  Similarity=0.543  Sum_probs=34.0

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEec
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDV   41 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DI   41 (115)
                      +..+++ ||+.||++++++||+|++|++++|+++.+||
T Consensus        67 e~~~~~~dg~~~~~~~~~~pi~d~~G~v~~~i~i~~DI  104 (104)
T d1jnua_          67 QVLNYTKGGRAFWNLFHLQVMRDENGDVQYFIGVQQEM  104 (104)
T ss_dssp             EEEEECTTSCEEEEEEEEEEECTTTSSCCEEEEEEEEC
T ss_pred             EEEEEecccceEEEEEEEEEEECCCCCEEEEEEEEEcC
Confidence            445666 9999999999999999999999999999997

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

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]

Probab=98.63  E-value=1.8e-08  Score=63.12  Aligned_cols=67  Identities=10%  Similarity=0.311  Sum_probs=50.5

Q ss_pred             CCCCEEEEEEEEEeccchhhhhhhc------------------------CCC---CceeceecCCceeEEEEEeEEeeCC
Q psy8547          27 EKREVVLYLASHKDVTNTKMAQMAD------------------------NGE---GDYEDMQELGTPFWCLLDIVPIKNE   79 (115)
Q Consensus        27 e~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~---e~~~~yrKdGs~f~~~~~i~pirde   79 (115)
                      ++|.++++--.+..+|.....|-.-                        .++   .....++|||+.||+.++++|++|+
T Consensus        11 pd~~I~y~N~a~~~~~G~s~~e~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~pi~d~   90 (104)
T d1jnua_          11 PDNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVMRDE   90 (104)
T ss_dssp             TTCCEEEECHHHHHHHTCCHHHHTTSCGGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEEEEEEEEEECTT
T ss_pred             CCCEEEEEcHHHHHHHCcCHHHHCCccceeccccccchHHHhhhhhhhhcCceeEeEEEEEecccceEEEEEEEEEEECC
Confidence            4677877666666676665544321                        011   1234589999999999999999999


Q ss_pred             CCCEEEEEEEeeec
Q psy8547          80 KREVVLYLASHKDV   93 (115)
Q Consensus        80 ~G~v~~~i~~~~DI   93 (115)
                      +|++++|+++.+||
T Consensus        91 ~G~v~~~i~i~~DI  104 (104)
T d1jnua_          91 NGDVQYFIGVQQEM  104 (104)
T ss_dssp             TSSCCEEEEEEEEC
T ss_pred             CCCEEEEEEEEEcC
Confidence            99999999999997

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=4.1e-08  Score=62.19  Aligned_cols=42  Identities=12%  Similarity=0.119  Sum_probs=38.7

Q ss_pred             eeceecCCceeEEEEEeEEeeCC-CCCEEEEEEEeeecccchh
Q psy8547          57 YEDMQELGTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   98 (115)
Q Consensus        57 ~~~yrKdGs~f~~~~~i~pirde-~G~v~~~i~~~~DIT~~k~   98 (115)
                      ++.++|||+.+|+.++.+|++|+ +|++.+++++.+|||++|+
T Consensus        71 ~~~~~kdG~~~wv~~~~~~~~~~~~~~~~~ii~~~~dite~k~  113 (114)
T d1p97a_          71 YRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK  113 (114)
T ss_dssp             EEEECTTSCEEEEEEEEEEEECTTTCSEEEEEEEEEEEEEEEC
T ss_pred             eeeeeecCcceEEEEEEEEEEeCCCCCEEEEEEEEEECChhhc
Confidence            45579999999999999999997 6899999999999999986

>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=1.5e-07  Score=59.42  Aligned_cols=36  Identities=8%  Similarity=0.014  Sum_probs=34.3

Q ss_pred             CCCceeEEEEEEEeeCC-CCCEEEEEEEEEeccchhh
Q psy8547          11 QRTPFWCLLDIVPIKNE-KREVVLYLASHKDVTNTKM   46 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de-~G~~~~fi~~~~DIT~~k~   46 (115)
                      ||+.+|+.+..+|++|+ +|++.+++++.+|||++|+
T Consensus        77 dG~~~wv~~~~~~~~~~~~~~~~~ii~~~~dite~k~  113 (114)
T d1p97a_          77 HGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK  113 (114)
T ss_dssp             TSCEEEEEEEEEEEECTTTCSEEEEEEEEEEEEEEEC
T ss_pred             cCcceEEEEEEEEEEeCCCCCEEEEEEEEEECChhhc
Confidence            99999999999999997 6899999999999999986

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=98.15  E-value=9.5e-07  Score=53.83  Aligned_cols=38  Identities=21%  Similarity=0.187  Sum_probs=31.5

Q ss_pred             ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547           5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus         5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      ....++ ||+.||++++++|+++++|.  +|+++.+|||+.
T Consensus        68 e~~~~~~dg~~~~v~~~~~~~~~~~~~--~~~~~~~DITE~  106 (106)
T d1xj3a1          68 IVTGKRRDGTTFPMHLSIGEMQSGGEP--YFTGFVRDLTEH  106 (106)
T ss_dssp             EEEEECTTSCEEEEEEEEEEEEETTEE--EEEEEEEECHHH
T ss_pred             eeeeeeccceEEEEEEEEEEEEECCeE--EEEEEEEeCCCC
Confidence            345556 99999999999999996654  588999999973

>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]

Probab=98.11  E-value=1.2e-06  Score=53.36  Aligned_cols=71  Identities=11%  Similarity=0.098  Sum_probs=49.5

Q ss_pred             eeCCCCCEEEEEEEEEeccchhhhhhhc--------------------------CC-----CCceeceecCCceeEEEEE
Q psy8547          24 IKNEKREVVLYLASHKDVTNTKMAQMAD--------------------------NG-----EGDYEDMQELGTPFWCLLD   72 (115)
Q Consensus        24 i~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------------~~-----~e~~~~yrKdGs~f~~~~~   72 (115)
                      +.|++|+++++-..+..++.-...|-.-                          .+     ......++|||+.||+.++
T Consensus         5 ~~D~~G~I~~~N~a~~~l~Gy~~~el~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~v~~~   84 (106)
T d1xj3a1           5 VIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLS   84 (106)
T ss_dssp             EEETTSBEEEECHHHHHHHCCCHHHHTTSBGGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTTSCEEEEEEE
T ss_pred             EECCCCcEEEEcHHHHHHhhhchHhhcCCCcccccccccccchhhhhhhhhhhcccccccccceeeeeeccceEEEEEEE
Confidence            5688888887666666666554433210                          00     0113447999999999999


Q ss_pred             eEEeeCCCCCEEEEEEEeeecccc
Q psy8547          73 IVPIKNEKREVVLYLASHKDVTNT   96 (115)
Q Consensus        73 i~pirde~G~v~~~i~~~~DIT~~   96 (115)
                      ++|++++++  ..++++++|||+.
T Consensus        85 ~~~~~~~~~--~~~~~~~~DITE~  106 (106)
T d1xj3a1          85 IGEMQSGGE--PYFTGFVRDLTEH  106 (106)
T ss_dssp             EEEEEETTE--EEEEEEEEECHHH
T ss_pred             EEEEEECCe--EEEEEEEEeCCCC
Confidence            999998665  4589999999973

>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=97.66  E-value=2.4e-05  Score=49.47  Aligned_cols=35  Identities=14%  Similarity=0.251  Sum_probs=30.1

Q ss_pred             eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..++|||+.||+.++++|++++++.  .++++.+|||
T Consensus        96 ~~~~~dG~~~~v~~~~~~i~~~~~~--~~~~i~rDIT  130 (130)
T d1ew0a_          96 SGQRKDGSTFPMKLAVGEMRSGGER--FFTGFIRDLT  130 (130)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETTEE--EEEEEEEECC
T ss_pred             EEEcCCCCEEEEEEEEEEEEECCeE--EEEEEEEECC
Confidence            3478999999999999999986653  4889999998

>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=97.66  E-value=2.8e-05  Score=49.16  Aligned_cols=35  Identities=14%  Similarity=0.203  Sum_probs=29.2

Q ss_pred             eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547           6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus         6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ...++ ||+.||++++++|++++++  .+|+++.+|||
T Consensus        95 ~~~~~~dG~~~~v~~~~~~i~~~~~--~~~~~i~rDIT  130 (130)
T d1ew0a_          95 VSGQRKDGSTFPMKLAVGEMRSGGE--RFFTGFIRDLT  130 (130)
T ss_dssp             EEEECTTSCEEEEEEEEEEEEETTE--EEEEEEEEECC
T ss_pred             EEEEcCCCCEEEEEEEEEEEEECCe--EEEEEEEEECC
Confidence            34455 9999999999999998655  34889999998

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=97.59  E-value=3.1e-05  Score=47.33  Aligned_cols=68  Identities=19%  Similarity=0.360  Sum_probs=46.2

Q ss_pred             EeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------C-C-------CCceeceecCCceeEEEE
Q psy8547          23 PIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------N-G-------EGDYEDMQELGTPFWCLL   71 (115)
Q Consensus        23 Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~-~-------~e~~~~yrKdGs~f~~~~   71 (115)
                      -+.|++|.++++=..+..++-....|..-                       . .       ......++|||+.||+++
T Consensus        15 ~~~d~~g~i~~~N~~~~~l~Gy~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~   94 (113)
T d1v9ya_          15 VLINENDEVMFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRF   94 (113)
T ss_dssp             EEECTTSBEEEECHHHHHHHSCCGGGTTTSBGGGGSCGGGTTTHHHHHHHHHC----------CEEEEECTTSCEEEEEE
T ss_pred             EEEeCCCCEEEEchhHhhhhccchhhhcCcceecccccccccccccccccccccccccccccceeeeeccccceeEEEEE
Confidence            35688899887766666666554433210                       0 0       011234789999999999


Q ss_pred             EeEEeeCCCCCEEEEEEEeee
Q psy8547          72 DIVPIKNEKREVVLYLASHKD   92 (115)
Q Consensus        72 ~i~pirde~G~v~~~i~~~~D   92 (115)
                      +++|++++.|.  .|+++++|
T Consensus        95 ~~~~i~~~~~~--~~~~v~rD  113 (113)
T d1v9ya_          95 ALSKVSAEGKV--YYLALVRD  113 (113)
T ss_dssp             EEEEEEETTEE--EEEEEEEC
T ss_pred             EEEEEEECCeE--EEEEEEEC
Confidence            99999987664  47888877

>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]

Probab=97.50  E-value=5.3e-05  Score=46.22  Aligned_cols=32  Identities=19%  Similarity=0.386  Sum_probs=26.2

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEe
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKD   40 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~D   40 (115)
                      ...+ ||+.+|++++++|++++.|.  +|+++.+|
T Consensus        81 ~~~~~dG~~~~v~~~~~~i~~~~~~--~~~~v~rD  113 (113)
T d1v9ya_          81 QLEKKDGSKIWTRFALSKVSAEGKV--YYLALVRD  113 (113)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETTEE--EEEEEEEC
T ss_pred             eeccccceeEEEEEEEEEEEECCeE--EEEEEEEC
Confidence            3345 99999999999999997663  48888887

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.0013  Score=40.70  Aligned_cols=34  Identities=12%  Similarity=0.085  Sum_probs=29.1

Q ss_pred             ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547          59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT   94 (115)
Q Consensus        59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT   94 (115)
                      ..+|+|+.||++++++++..+.+.  .++++..||+
T Consensus        80 ~~~~~G~~~pvevs~~~i~~~~~~--~~l~vi~dV~  113 (114)
T d1ll8a_          80 IISRSGEKIPVSVWMKRMRQERRL--CCVVVLEPVE  113 (114)
T ss_dssp             ECCTTCCCEEEECCEECCBSSSSB--EEEEEEEECC
T ss_pred             EEccCCcEEEEEEEEEEEEECCeE--EEEEEEEECc
Confidence            478999999999999999976653  4789999994

>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.19  E-value=0.0023  Score=39.53  Aligned_cols=34  Identities=9%  Similarity=0.004  Sum_probs=27.8

Q ss_pred             eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547           7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT   42 (115)
Q Consensus         7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT   42 (115)
                      ...+ ||+.||++++++++..+.+.  .++++.+||+
T Consensus        79 ~~~~~~G~~~pvevs~~~i~~~~~~--~~l~vi~dV~  113 (114)
T d1ll8a_          79 DIISRSGEKIPVSVWMKRMRQERRL--CCVVVLEPVE  113 (114)
T ss_dssp             EECCTTCCCEEEECCEECCBSSSSB--EEEEEEEECC
T ss_pred             EEEccCCcEEEEEEEEEEEEECCeE--EEEEEEEECc
Confidence            3345 99999999999999986553  3789999994

>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=94.41  E-value=0.018  Score=35.73  Aligned_cols=35  Identities=11%  Similarity=0.090  Sum_probs=24.8

Q ss_pred             ceeceecCCceeEEEEEeEEeeCCCCCEEEEE-EEe
Q psy8547          56 DYEDMQELGTPFWCLLDIVPIKNEKREVVLYL-ASH   90 (115)
Q Consensus        56 ~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i-~~~   90 (115)
                      .++..+|||+..|+..+..+++|+.|....|| ++.
T Consensus        69 ~yR~~~kdG~~vWv~t~~~~~~~~~~~~~~~Ii~~h  104 (109)
T d1oj5a_          69 SYRFILNDGTMLSAHTRCKLCYPQSPDMQPFIMGIH  104 (109)
T ss_dssp             CEEEECTTSCEEEEEEEEEEECC----CCCEEEEEE
T ss_pred             hhhhhhccCcEEEEEEEEEEEECCCCCcccEEEEEE
Confidence            46778999999999999999999866544444 443

>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=92.22  E-value=0.076  Score=32.69  Aligned_cols=26  Identities=4%  Similarity=-0.060  Sum_probs=19.5

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEE
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLA   36 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~   36 (115)
                      ||+..|+..+..+++|+.|....||.
T Consensus        76 dG~~vWv~t~~~~~~~~~~~~~~~Ii  101 (109)
T d1oj5a_          76 DGTMLSAHTRCKLCYPQSPDMQPFIM  101 (109)
T ss_dssp             TSCEEEEEEEEEEECC----CCCEEE
T ss_pred             cCcEEEEEEEEEEEECCCCCcccEEE
Confidence            99999999999999998777666663

>d1p0za_ d.110.6.1 (A:) Sensor kinase CitA {Klebsiella pneumoniae [TaxId: 573]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: Sensory domain-like
family: Sensory domain of two-component sensor kinase
domain: Sensor kinase CitA
species: Klebsiella pneumoniae [TaxId: 573]

Probab=82.53  E-value=1.4  Score=27.41  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=22.8

Q ss_pred             EEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547          17 CLLDIVPIKNEKREVVLYLASHKDVTN   43 (115)
Q Consensus        17 ~~~~i~Pi~de~G~~~~fi~~~~DIT~   43 (115)
                      ..-..+||+|++|+++|++.+--++.+
T Consensus       101 ~~~~~~PI~~~~G~viGvV~Vg~~l~~  127 (131)
T d1p0za_         101 SLRGKSPIQDATGKVIGIVSVGYTIEQ  127 (131)
T ss_dssp             EEEEEEEEECTTCCEEEEEEEEEEGGG
T ss_pred             EEEEEEEEECCCCcEEEEEEEEEEhHH
Confidence            456788999999999999998877654

>d3by8a1 d.110.6.1 (A:46-178) Fumarate sensor DcuS {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: Sensory domain-like
family: Sensory domain of two-component sensor kinase
domain: Fumarate sensor DcuS
species: Escherichia coli [TaxId: 562]

Probab=80.38  E-value=1.2  Score=28.03  Aligned_cols=34  Identities=15%  Similarity=0.106  Sum_probs=26.9

Q ss_pred             CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547          11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT   44 (115)
Q Consensus        11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~   44 (115)
                      .|+.=.-....+||++++|+++|++.+--+++.-
T Consensus        94 ~gt~g~~~~~~~Pv~~~~G~viGvV~Vg~~~~~i  127 (133)
T d3by8a1          94 RGFLAQALRVFTPIYDENHKQIGVVAIGLELSRV  127 (133)
T ss_dssp             CSSSSCEEEEEEEEECTTSCEEEEEEEEEEHHHH
T ss_pred             EecCceEEEEEEeeECCCCcEEEEEEEEEEHHHH
Confidence            4444456777899999999999999998877653