Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database
ID Alignment Graph Length
Definition
E-value Query 109
pfam13426 101
pfam13426, PAS_9, PAS domain
1e-14 PRK13559 361
PRK13559, PRK13559, hypothetical protein; Provisio
1e-13 PRK13557 540
PRK13557, PRK13557, histidine kinase; Provisional
1e-11 PRK13558 665
PRK13558, PRK13558, bacterio-opsin activator; Prov
4e-08 cd00130 103
cd00130, PAS, PAS domain; PAS motifs appear in arc
1e-05 pfam00989 113
pfam00989, PAS, PAS fold
3e-04 COG2202 232
COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu
0.001 smart00091 67
smart00091, PAS, PAS domain
0.002 TIGR00229 124
TIGR00229, sensory_box, PAS domain S-box
0.004
>gnl|CDD|222120 pfam13426, PAS_9, PAS domain
Back Hide alignment and domain information
Score = 63.5 bits (155), Expect = 1e-14
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAA 70
LV + I+Y +D RL G++R E++ + + L GP + AV ++EAL
Sbjct: 1 ILVLDPD---GRIVYANDAALRLLGYTREELLGKS--IRDLFGPGDDEEAVARLREALRN 55
Query: 71 GVEKHFEILYYKKDGKY 87
G E E+ +KDG+
Sbjct: 56 GGEVEVELELRRKDGEP 72
>gnl|CDD|237427 PRK13559, PRK13559, hypothetical protein; Provisional
Back Show alignment and domain information
Score = 64.8 bits (158), Expect = 1e-13
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 13 VANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGV 72
+ + H I+ + F LTG++ EV+ ++ C+FL G T AV ++ A+AA
Sbjct: 58 ITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN--CRFLQGAATDPIAVAKIRAAIAAER 115
Query: 73 EKHFEILYYKKDG 85
E E+L Y+KDG
Sbjct: 116 EIVVELLNYRKDG 128
>gnl|CDD|237425 PRK13557, PRK13557, histidine kinase; Provisional
Back Show alignment and domain information
Score = 59.3 bits (144), Expect = 1e-11
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 8/81 (9%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I++ + F +TG++ E++ + C+FL GP T + V V++A+A E EIL Y+
Sbjct: 55 IVFANRAFLEMTGYAAEEIIGNN--CRFLQGPETDRATVAEVRDAIAERREIATEILNYR 112
Query: 83 KDGKYSSVGGSYGDITPVSPV 103
KD G S+ + VSPV
Sbjct: 113 KD------GSSFWNALFVSPV 127
>gnl|CDD|237426 PRK13558, PRK13558, bacterio-opsin activator; Provisional
Back Show alignment and domain information
Score = 49.1 bits (117), Expect = 4e-08
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
+IY +D F R+TG+S EV+ ++ C+FL G T++ V ++EA+ E+ Y+
Sbjct: 173 LIYINDAFERITGYSPDEVLGRN--CRFLQGEDTNEERVAELREAIDEERPTSVELRNYR 230
Query: 83 KDGK--YSSVGGSYGDITPVS 101
KDG ++ V DI P+
Sbjct: 231 KDGSTFWNQV-----DIAPIR 246
>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya
Back Show alignment and domain information
Score = 40.3 bits (94), Expect = 1e-05
Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I+Y + +L G+S E++ + + +H + + ++ L+ G E+ +
Sbjct: 14 ILYANPAAEQLLGYSPEELIGKSLL-DLIHPEDREEL-RERLENLLSGGEPVTLEVRLRR 71
Query: 83 KDGKY 87
KDG
Sbjct: 72 KDGSV 76
Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. Length = 103
>gnl|CDD|216228 pfam00989, PAS, PAS fold
Back Show alignment and domain information
Score = 37.0 bits (86), Expect = 3e-04
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 23 IIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82
I+Y + L G SR EV+ + + + ++ A + + L + FE+ +
Sbjct: 23 ILYVNAAAEELLGLSREEVIGKSLL-DLIPEDDDAEVAELLRQALLQGEESRGFEVSFRV 81
Query: 83 KDGKY 87
DG+
Sbjct: 82 PDGRP 86
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. Length = 113
>gnl|CDD|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]
Back Show alignment and domain information
Score = 36.0 bits (81), Expect = 0.001
Identities = 12/66 (18%), Positives = 20/66 (30%)
Query: 22 HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81
I+Y + L G+S E + + + A G E
Sbjct: 133 RILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYRVR 192
Query: 82 KKDGKY 87
+KDG+
Sbjct: 193 RKDGER 198
>gnl|CDD|214512 smart00091, PAS, PAS domain
Back Show alignment and domain information
Score = 33.9 bits (78), Expect = 0.002
Identities = 8/49 (16%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 12 LVANSHLGLC------HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGP 54
++ + G+ I+Y + L G+S E++ + + + +H
Sbjct: 6 ILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKS-LLELIHPE 53
PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. Length = 67
>gnl|CDD|232884 TIGR00229, sensory_box, PAS domain S-box
Back Show alignment and domain information
Score = 33.8 bits (78), Expect = 0.004
Identities = 12/67 (17%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 22 HIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKH-FEILY 80
+I+Y + F + G+S E++ ++ + + + + + ++ L E E
Sbjct: 24 NILYVNPAFEEIFGYSAEELIGRNVL-ELIPEEDREEVR-ERIERRLEGEREPVSEERRV 81
Query: 81 YKKDGKY 87
+KDG
Sbjct: 82 RRKDGSE 88
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 [Regulatory functions, Small molecule interactions]. Length = 124
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
ID Alignment Graph Length
Definition
Probability Query
109
PF13426 104
PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_
99.68 PF00989 113
PAS: PAS fold; InterPro: IPR013767 PAS domains are
99.55 PF08448 110
PAS_4: PAS fold; InterPro: IPR013656 The PAS fold
99.44 PRK13557 540
histidine kinase; Provisional
99.34 PRK13559 361
hypothetical protein; Provisional
99.23 PRK10060 663
RNase II stability modulator; Provisional
99.21 PRK13560 807
hypothetical protein; Provisional
99.09 TIGR02040 442
PpsR-CrtJ transcriptional regulator PpsR. This mod
99.08 PRK11091 779
aerobic respiration control sensor protein ArcB; P
99.08 TIGR02938 494
nifL_nitrog nitrogen fixation negative regulator N
98.99 PRK13558 665
bacterio-opsin activator; Provisional
98.98 PF08447 91
PAS_3: PAS fold; InterPro: IPR013655 The PAS fold
98.93 PRK11073 348
glnL nitrogen regulation protein NR(II); Provision
98.93 cd00130 103
PAS PAS domain; PAS motifs appear in archaea, euba
98.91 TIGR02040 442
PpsR-CrtJ transcriptional regulator PpsR. This mod
98.87 PF14598 111
PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W
98.86 PRK09776 1092
putative diguanylate cyclase; Provisional
98.82 PRK11359 799
cyclic-di-GMP phosphodiesterase; Provisional
98.82 PRK11359 799
cyclic-di-GMP phosphodiesterase; Provisional
98.79 TIGR00229 124
sensory_box PAS domain S-box. The PAS domain was p
98.75 KOG0501|consensus 971
98.72 KOG1229|consensus 775
98.67 TIGR02966 333
phoR_proteo phosphate regulon sensor kinase PhoR.
98.63 PRK09776 1092
putative diguanylate cyclase; Provisional
98.47 PF13188 64
PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
98.34 PF12860 115
PAS_7: PAS fold
98.28 PF13596 106
PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
98.23 PRK10820 520
DNA-binding transcriptional regulator TyrR; Provis
98.18 PF08670 148
MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK
98.05 PRK11360 607
sensory histidine kinase AtoS; Provisional
98.03 TIGR02373 124
photo_yellow photoactive yellow protein. Members o
98.01 PRK13560 807
hypothetical protein; Provisional
97.99 PRK11006 430
phoR phosphate regulon sensor protein; Provisional
97.91 PRK11388 638
DNA-binding transcriptional regulator DhaR; Provis
97.9 KOG3558|consensus 768
97.85 smart00091 67
PAS PAS domain. PAS motifs appear in archaea, euba
97.81 COG3852 363
NtrB Signal transduction histidine kinase, nitroge
97.72 COG2202 232
AtoS FOG: PAS/PAC domain [Signal transduction mech
97.67 COG3829 560
RocR Transcriptional regulator containing PAS, AAA
97.21 KOG3561|consensus 803
97.0 PRK15053 545
dpiB sensor histidine kinase DpiB; Provisional
96.78 COG3283 511
TyrR Transcriptional regulator of aromatic amino a
96.68 TIGR02938 494
nifL_nitrog nitrogen fixation negative regulator N
96.64 PRK11086 542
sensory histidine kinase DcuS; Provisional
96.54 COG5002 459
VicK Signal transduction histidine kinase [Signal
96.16 PRK09959 1197
hybrid sensory histidine kinase in two-component r
95.77 KOG3558|consensus 768
95.67 PF08446 110
PAS_2: PAS fold; InterPro: IPR013654 The PAS fold
95.48 COG5000 712
NtrY Signal transduction histidine kinase involved
95.33 KOG3560|consensus 712
95.16 COG3290 537
CitA Signal transduction histidine kinase regulati
94.46 KOG3560|consensus 712
94.16 KOG3559|consensus 598
92.6 PF06785 401
UPF0242: Uncharacterised protein family (UPF0242);
87.17 PRK10618 894
phosphotransfer intermediate protein in two-compon
86.13 KOG3753|consensus 1114
84.58 KOG3559|consensus 598
80.72
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A
Back Hide alignment and domain information
Probab=99.68 E-value=2.1e-15 Score=79.77 Aligned_cols=82 Identities=22% Similarity=0.238 Sum_probs=68.6
Q ss_pred CccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCE
Q psy6003 8 NRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKY 87 (109)
Q Consensus 8 ~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~ 87 (109)
|++++++| .+|+++++|++|++++|+++++++|++ ...+.++.........+.+++.++..+..+...++++|+.
T Consensus 1 p~~i~i~d---~~g~i~~~N~~~~~~~g~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~ 75 (104)
T PF13426_consen 1 PDGIFILD---PDGRILYVNPAFERLFGYSREELIGKS--ISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGET 75 (104)
T ss_dssp -SEEEEEE---TTSBEEEE-HHHHHHHTS-HHHHTTSB--GGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEE
T ss_pred CEEEEEEC---CcCcEEehhHHHHHHHCcCHHHHcCCC--cccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCE
Confidence 68999999 789999999999999999999999998 5666666666777788888888888899999999999999
Q ss_pred EEEeeec
Q psy6003 88 SSVGGSY 94 (109)
Q Consensus 88 ~~~~~~~ 94 (109)
+|++++.
T Consensus 76 ~~~~~~~ 82 (104)
T PF13426_consen 76 FWVEVSA 82 (104)
T ss_dssp EEEEEEE
T ss_pred EEEEEEE
Confidence 9996554
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []
Back Show alignment and domain information
Probab=99.55 E-value=1.1e-13 Score=74.15 Aligned_cols=88 Identities=20% Similarity=0.298 Sum_probs=64.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCee-EEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEK-HFEILY 80 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~ 80 (109)
.++++++++++++| .+|+|+++|+++++++|++.++++|++ ...+.++.........+...+..++.. ..+...
T Consensus 5 ~i~~~~~~~i~~~d---~~g~I~~~N~a~~~l~g~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (113)
T PF00989_consen 5 AILENSPDGIFVID---EDGRILYVNQAAEELLGYSREELIGKS--LFDLIHPEDRRELRERLRQALSQGESGESFEVRF 79 (113)
T ss_dssp HHHHCSSSEEEEEE---TTSBEEEECHHHHHHHSS-HHHHTTSB--GGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEE
T ss_pred HHHhcCCceEEEEe---CcCeEEEECHHHHHHHccCHHHHcCCc--HHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEE
Confidence 46899999999999 899999999999999999999999999 444444443334556666666665554 344444
Q ss_pred EecCCCEEEEeeec
Q psy6003 81 YKKDGKYSSVGGSY 94 (109)
Q Consensus 81 ~~~~g~~~~~~~~~ 94 (109)
..++|+.+|+.+..
T Consensus 80 ~~~~g~~~~~~~~~ 93 (113)
T PF00989_consen 80 RLRDGRPRWVEVRA 93 (113)
T ss_dssp EETTSCEEEEEEEE
T ss_pred EecCCcEEEEEEEE
Confidence 44689999885443
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 ....
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []
Back Show alignment and domain information
Probab=99.44 E-value=2.3e-12 Score=68.71 Aligned_cols=84 Identities=21% Similarity=0.252 Sum_probs=66.8
Q ss_pred cccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEec
Q psy6003 4 KHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKK 83 (109)
Q Consensus 4 ~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 83 (109)
|++++++++++| .+++++++|+++.+++|++.++++|++ ...+.++.........+.+++.++.....+.....
T Consensus 1 l~~~p~~i~v~D---~~~~i~~~N~~~~~~~~~~~~~~~G~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 74 (110)
T PF08448_consen 1 LDSSPDGIFVID---PDGRIVYANQAAAELFGVSPEELIGRS--LFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR- 74 (110)
T ss_dssp HHHCSSEEEEEE---TTSBEEEE-HHHHHHHTSTHHHHTTSB--HHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-
T ss_pred CCCCCceeEEEC---CCCEEEEEHHHHHHHhCCCHHHHhhcc--chhccccchhhhhHHHHHHhhccCceEEEEEEEee-
Confidence 578999999999 899999999999999999999999999 55566666666677777888888777766554444
Q ss_pred CCCEEEEeee
Q psy6003 84 DGKYSSVGGS 93 (109)
Q Consensus 84 ~g~~~~~~~~ 93 (109)
+|..+|+.+.
T Consensus 75 ~~~~~~~~~~ 84 (110)
T PF08448_consen 75 DGEERWFEVS 84 (110)
T ss_dssp TSCEEEEEEE
T ss_pred cCCcEEEEEE
Confidence 7888887543
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.
>PRK13557 histidine kinase; Provisional
Back Show alignment and domain information
Probab=99.34 E-value=1.6e-11 Score=81.20 Aligned_cols=88 Identities=28% Similarity=0.477 Sum_probs=70.7
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (109)
+++.+++++++.|....+|+++|+|++|++++||+.++++|++ ...+.++.........+...+..+..+..+....+
T Consensus 35 ~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 (540)
T PRK13557 35 AVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNN--CRFLQGPETDRATVAEVRDAIAERREIATEILNYR 112 (540)
T ss_pred HHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCC--hHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEEe
Confidence 4678899999999654578999999999999999999999998 55555555555555667777777777777888888
Q ss_pred cCCCEEEEee
Q psy6003 83 KDGKYSSVGG 92 (109)
Q Consensus 83 ~~g~~~~~~~ 92 (109)
++|+.+|+.+
T Consensus 113 ~~G~~~~~~~ 122 (540)
T PRK13557 113 KDGSSFWNAL 122 (540)
T ss_pred CCCCEEEEEE
Confidence 9999999854
>PRK13559 hypothetical protein; Provisional
Back Show alignment and domain information
Probab=99.23 E-value=2e-10 Score=73.10 Aligned_cols=88 Identities=30% Similarity=0.448 Sum_probs=69.5
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (109)
++++++++++++|.+..++.++++|+++++++||+.++++|++ ...+..+.........+...+..+..+..+...++
T Consensus 48 ~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 125 (361)
T PRK13559 48 AMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN--CRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYR 125 (361)
T ss_pred HHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCC--hhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEEc
Confidence 5789999999999543467899999999999999999999998 55555444444555566667777777778888888
Q ss_pred cCCCEEEEee
Q psy6003 83 KDGKYSSVGG 92 (109)
Q Consensus 83 ~~g~~~~~~~ 92 (109)
++|..+|+..
T Consensus 126 ~dG~~~~~~~ 135 (361)
T PRK13559 126 KDGEPFWNAL 135 (361)
T ss_pred CCCCEEEEEE
Confidence 9999998854
>PRK10060 RNase II stability modulator; Provisional
Back Show alignment and domain information
Probab=99.21 E-value=1.4e-10 Score=79.19 Aligned_cols=84 Identities=12% Similarity=0.140 Sum_probs=67.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (109)
++++++++++++| .+|+++++|+++++++||+.++++|++. ..++.++.........+......+..+..+.+.++
T Consensus 116 v~~~~~~gI~i~D---~~g~I~~~N~a~~~l~Gy~~~eliG~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 191 (663)
T PRK10060 116 VVSEANSVIVILD---SRGNIQRFNRLCEEYTGLKEHDVIGQSV-FKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKT 191 (663)
T ss_pred HHhhCCceEEEEe---CCCCEEEEcHHHHHHHCcCHHHHcCCCH-HHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEEe
Confidence 5788999999999 7899999999999999999999999982 34444444333444555666777888888988899
Q ss_pred cCCCEEEE
Q psy6003 83 KDGKYSSV 90 (109)
Q Consensus 83 ~~g~~~~~ 90 (109)
++|..+|.
T Consensus 192 ~~G~~~~~ 199 (663)
T PRK10060 192 RKGQRLFL 199 (663)
T ss_pred CCCCEEEE
Confidence 99988776
>PRK13560 hypothetical protein; Provisional
Back Show alignment and domain information
Probab=99.09 E-value=1.3e-09 Score=75.35 Aligned_cols=86 Identities=16% Similarity=0.227 Sum_probs=65.5
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
.+++++++++++.| .+|+++++|+++++++||+.++++|++ ...+.++.............+..++....+....
T Consensus 208 ~l~e~~~~~i~~~d---~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 282 (807)
T PRK13560 208 QLLDNIADPAFWKD---EDAKVFGCNDAACLACGFRREEIIGMS--IHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQ 282 (807)
T ss_pred HHHhhCCCeEEEEc---CCCCEEEEhHHHHHHhCCCHHHHcCCc--chhcCCcchhHHHHHHHHHHhccCCceEEEEEEE
Confidence 36789999999999 789999999999999999999999998 4555544433333233344455566666777888
Q ss_pred ecCCCEEEEee
Q psy6003 82 KKDGKYSSVGG 92 (109)
Q Consensus 82 ~~~g~~~~~~~ 92 (109)
+++|..+|+.+
T Consensus 283 ~~dG~~~~~~~ 293 (807)
T PRK13560 283 NKDGRTRPVDV 293 (807)
T ss_pred cCCCCEEEEEE
Confidence 99999987754
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR
Back Show alignment and domain information
Probab=99.08 E-value=1.1e-09 Score=71.67 Aligned_cols=87 Identities=15% Similarity=0.075 Sum_probs=59.4
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCC-hHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFS-RAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILY 80 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~-~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 80 (109)
.++++++++++++| .+|+++++|++|++++||+ .++++|++ ...+...... .....+......+.....+...
T Consensus 256 ~l~e~~~d~I~v~D---~~G~I~~~N~a~~~l~G~~~~~~l~G~~--~~~~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~ 329 (442)
T TIGR02040 256 RLYHEAPDAIVFSD---ADGTIRGANEAFLELTDSSSLEAVRGRT--LDRWLGRGGV-DLRVLLSNVRRTGQVRLYATTL 329 (442)
T ss_pred HHHHhCCceEEEEc---CCCcEEehhHHHHHHhCCCChHHHcCCC--HHHHhCCCcc-cHHHHHHHHhhcCceEEEEEEE
Confidence 36799999999999 7899999999999999997 57899998 3323322221 1111122222334334456667
Q ss_pred EecCCCEEEEeeec
Q psy6003 81 YKKDGKYSSVGGSY 94 (109)
Q Consensus 81 ~~~~g~~~~~~~~~ 94 (109)
.+++|..+|++++.
T Consensus 330 ~~~~G~~~~ve~s~ 343 (442)
T TIGR02040 330 TGEFGAQTEVEISA 343 (442)
T ss_pred EcCCCCEEEEEEEE
Confidence 78999999986443
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).
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Back Show alignment and domain information
Probab=99.08 E-value=9.2e-10 Score=76.26 Aligned_cols=87 Identities=14% Similarity=0.133 Sum_probs=68.2
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
.+++++++++++.| .+|+++++|+++++++|++.++++|++ ...+.++................+..+..+....
T Consensus 159 ~il~~~~~~i~~~D---~~g~i~~~N~a~~~l~G~~~~eliG~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 233 (779)
T PRK11091 159 SFLDASPDLVYYRN---EDGEFSGCNRAMELLTGKSEKQLIGLT--PKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLD 233 (779)
T ss_pred HHHhcCcceEEEEC---CCCcEEeEcHHHHHHhCcCHHHHcCCC--hHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEE
Confidence 36789999999999 789999999999999999999999998 4445444433444444555666777777788888
Q ss_pred ecCCCEEEEeee
Q psy6003 82 KKDGKYSSVGGS 93 (109)
Q Consensus 82 ~~~g~~~~~~~~ 93 (109)
.++|..+|+.+.
T Consensus 234 ~~~G~~~~~~~~ 245 (779)
T PRK11091 234 YPDGRKACFELR 245 (779)
T ss_pred cCCCCEEEEEEE
Confidence 889999888543
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL
Back Show alignment and domain information
Probab=98.99 E-value=1.2e-09 Score=71.49 Aligned_cols=85 Identities=20% Similarity=0.305 Sum_probs=66.2
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
.+++++++++++.| .+++++++|+++++++||++++++|+. ...+..+.........+...+..+..+..+....
T Consensus 8 ~i~~~~~~~i~~~d---~~g~~~~~N~~~~~~~G~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (494)
T TIGR02938 8 QTVDQAPLAISITD---LKANILYANDAFTRITGYTKEEIIGKN--ESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNR 82 (494)
T ss_pred HHHHhCCceEEEEC---CCCcEEEEchhheeecCCCHHHHhCCC--chhhcCCCCCHHHHHHHHHHHHhCCcccceeecc
Confidence 36789999999999 789999999999999999999999987 4444444444444555666666677777777777
Q ss_pred ecCCCEEEEe
Q psy6003 82 KKDGKYSSVG 91 (109)
Q Consensus 82 ~~~g~~~~~~ 91 (109)
+++|+.+|+.
T Consensus 83 ~~~g~~~~~~ 92 (494)
T TIGR02938 83 RKDGELYLAE 92 (494)
T ss_pred CCCccchhhh
Confidence 8889888864
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.
>PRK13558 bacterio-opsin activator; Provisional
Back Show alignment and domain information
Probab=98.98 E-value=9.4e-09 Score=70.25 Aligned_cols=89 Identities=28% Similarity=0.433 Sum_probs=70.0
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (109)
+++++++++++.|....+++++++|+++++++||++++++|++ ...+.++.........+...+..+..+..+.+.++
T Consensus 153 ~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 230 (665)
T PRK13558 153 ALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRN--CRFLQGEDTNEERVAELREAIDEERPTSVELRNYR 230 (665)
T ss_pred HHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCC--HHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEEC
Confidence 4678889999987433478999999999999999999999998 55555555444555566667777777888888889
Q ss_pred cCCCEEEEeee
Q psy6003 83 KDGKYSSVGGS 93 (109)
Q Consensus 83 ~~g~~~~~~~~ 93 (109)
++|..+|+.+.
T Consensus 231 ~dG~~~~~~~~ 241 (665)
T PRK13558 231 KDGSTFWNQVD 241 (665)
T ss_pred CCCCEEEEEEE
Confidence 99999998543
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []
Back Show alignment and domain information
Probab=98.93 E-value=8e-09 Score=53.42 Aligned_cols=70 Identities=27% Similarity=0.354 Sum_probs=50.7
Q ss_pred EEEecHHHHHhhCCChHHHhCCcc--ccccccCCCCcHHHHHHHHH-HHHcCCeeEEEEEEEecCCCEEEEeee
Q psy6003 23 IIYCSDGFCRLTGFSRAEVMQQDA--ICKFLHGPLTSQHAVQVVKE-ALAAGVEKHFEILYYKKDGKYSSVGGS 93 (109)
Q Consensus 23 i~~~N~~~~~~~g~~~~e~~g~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~~g~~~~~~~~ 93 (109)
++++|+++.+++||+++++ +... ....+.++++.......+.. ....+..+..+++.++++|+.+|+++.
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~ 73 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVR 73 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEE
Confidence 5799999999999999998 5431 01223456776777777777 677788899999999999999999654
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.
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Back Show alignment and domain information
Probab=98.93 E-value=1e-08 Score=64.93 Aligned_cols=85 Identities=15% Similarity=0.122 Sum_probs=59.8
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
.++++++++++++| .+++|+++|+++++++|++.++++|++ ...+.+... ............+..+.......
T Consensus 11 ~il~~~~~gi~~~d---~~~~i~~~N~a~~~~~g~~~~~~~g~~--~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 83 (348)
T PRK11073 11 QILNSLINSILLLD---DDLAIHYANPAAQQLLAQSSRKLFGTP--LPELLSYFS--LNIELMRESLQAGQGFTDNEVTL 83 (348)
T ss_pred HHHhcCcCeEEEEC---CCCeEeeEcHHHHHHhCCCHHHHcCCC--HHHHcCcch--hhHHHHHHHHHcCCcccccceEE
Confidence 46899999999999 789999999999999999999999998 444433222 11223344455554444333445
Q ss_pred ecCCCEEEEeee
Q psy6003 82 KKDGKYSSVGGS 93 (109)
Q Consensus 82 ~~~g~~~~~~~~ 93 (109)
..+|+.+|+.++
T Consensus 84 ~~~g~~~~~~~~ 95 (348)
T PRK11073 84 VIDGRSHILSLT 95 (348)
T ss_pred EECCceEEEEEE
Confidence 568888887543
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya
Back Show alignment and domain information
Probab=98.91 E-value=1e-07 Score=47.42 Aligned_cols=80 Identities=20% Similarity=0.213 Sum_probs=56.8
Q ss_pred CccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCE
Q psy6003 8 NRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKY 87 (109)
Q Consensus 8 ~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~ 87 (109)
+++++++| .++.+.++|+++.+++|++.+++.|+. ...+..+.........+......+.....+......+|..
T Consensus 2 ~~~i~~~d---~~~~~~~~n~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (103)
T cd00130 2 PDGVIVLD---LDGRILYANPAAEQLLGYSPEELIGKS--LLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSV 76 (103)
T ss_pred CceEEEEC---CCCcEEEECHHHHHHhCCCHHHHcCcc--HHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCE
Confidence 56788888 789999999999999999999999987 3334444444444444555554445556666666777877
Q ss_pred EEEee
Q psy6003 88 SSVGG 92 (109)
Q Consensus 88 ~~~~~ 92 (109)
.|+.+
T Consensus 77 ~~~~~ 81 (103)
T cd00130 77 IWVLV 81 (103)
T ss_pred EEEEE
Confidence 77643
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.
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR
Back Show alignment and domain information
Probab=98.87 E-value=2.5e-09 Score=69.90 Aligned_cols=86 Identities=9% Similarity=-0.104 Sum_probs=59.8
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCC-eeEEEEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGV-EKHFEILYY 81 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~ 81 (109)
++++++|+++++| .+|+++++|++++.++||+.++++|++ ...+.++.........+......+. .+..+....
T Consensus 1 ~~~~~~d~~~~~d---~~g~i~~~n~~~~~~~g~~~~el~G~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 75 (442)
T TIGR02040 1 LLATAADVTLLLD---AEGVVREVAANPHHPSFEQLSEWEGRR--WEEIVTAESVEKFELRLSEALRTGRGAVRVELNHI 75 (442)
T ss_pred CCcccCcEEEEEC---CCCcEEEEEECCCcccccccccCCCCc--HhHhhCcchHHHHHHHHHHHhccCCCcceEeeccC
Confidence 4688999999999 789999999999999999999999998 5555555443444444444444443 344444444
Q ss_pred ecCCCEEEEeee
Q psy6003 82 KKDGKYSSVGGS 93 (109)
Q Consensus 82 ~~~g~~~~~~~~ 93 (109)
.++|...|+.++
T Consensus 76 ~~~g~~~~~~~~ 87 (442)
T TIGR02040 76 DPSSFELPMRFI 87 (442)
T ss_pred CCCCCccCeEEE
Confidence 555655566443
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).
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A
Back Show alignment and domain information
Probab=98.86 E-value=1.7e-07 Score=50.59 Aligned_cols=72 Identities=21% Similarity=0.165 Sum_probs=57.3
Q ss_pred CCeeEEEecHH-HHHhhCCChHHHhCCccccccccCCCCcHH-HHHHHHHHHHcCCeeEEEEEEEecCCCEEEEee
Q psy6003 19 GLCHIIYCSDG-FCRLTGFSRAEVMQQDAICKFLHGPLTSQH-AVQVVKEALAAGVEKHFEILYYKKDGKYSSVGG 92 (109)
Q Consensus 19 ~~~~i~~~N~~-~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~ 92 (109)
.+|.++++.++ ...++||.++|++|++ ...+.++++... ..+.....+.+|.....-++++.++|...|+..
T Consensus 10 ~dgki~~~d~~~v~~~lgy~~~eLvG~s--~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt 83 (111)
T PF14598_consen 10 LDGKITYVDSRAVSSLLGYLPEELVGRS--IYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT 83 (111)
T ss_dssp TTSBEEEEETTHHHHHHSS-HHHHTTSB--GGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred CCcEEEEEcCccChhhcCCCcHHHcCCc--hHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence 68999999999 6899999999999999 555666666564 556677788888877778999999999999864
>PRK09776 putative diguanylate cyclase; Provisional
Back Show alignment and domain information
Probab=98.82 E-value=3.3e-08 Score=70.66 Aligned_cols=86 Identities=16% Similarity=0.223 Sum_probs=64.0
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC-CeeEEEEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG-VEKHFEILYY 81 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~ 81 (109)
+++++++++++.| .+|+++++|+++++++||+.+++.|++ ...+.++.+.......+....... ..+..+.+..
T Consensus 288 l~e~~~~~i~~~d---~dG~i~~~N~~~~~l~G~~~~el~g~~--~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~ 362 (1092)
T PRK09776 288 AMEYSAIGMALVG---TEGQWLQVNKALCQFLGYSQEELRGLT--FQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYY 362 (1092)
T ss_pred HHHhCCceEEEEc---CCCcEEehhHHHHHHhCCCHHHHccCC--ceeccCcchhHhHHHHHHHHHcCCccceeeeeEEE
Confidence 5788999999999 789999999999999999999999998 444444444444333444333322 3356777888
Q ss_pred ecCCCEEEEeee
Q psy6003 82 KKDGKYSSVGGS 93 (109)
Q Consensus 82 ~~~g~~~~~~~~ 93 (109)
+++|+.+|+...
T Consensus 363 ~~dG~~~~~~~~ 374 (1092)
T PRK09776 363 RRDGEVVWALLA 374 (1092)
T ss_pred cCCCCEEEEEEE
Confidence 999999998543
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Back Show alignment and domain information
Probab=98.82 E-value=3.6e-08 Score=68.47 Aligned_cols=86 Identities=16% Similarity=0.233 Sum_probs=66.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYK 82 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 82 (109)
+++++++++++.| .+|+++++|+++++++||+.++++|+.. ...+.++.........+......+..+..+.+...
T Consensus 141 ~~~~~~~~i~~~d---~~g~i~~~N~~~~~l~G~~~~e~~g~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 216 (799)
T PRK11359 141 AVDHLDRPVIVLD---PERRIVQCNRAFTEMFGYCISEASGMQP-DTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLT 216 (799)
T ss_pred HHhcCCCcEEEEc---CCCcEEEEChhhHhhhCCCHHHHCCCCh-HHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeC
Confidence 4688999999999 7899999999999999999999999972 33444444444444455556666666777778888
Q ss_pred cCCCEEEEee
Q psy6003 83 KDGKYSSVGG 92 (109)
Q Consensus 83 ~~g~~~~~~~ 92 (109)
++|..+|+.+
T Consensus 217 ~dG~~~~~~~ 226 (799)
T PRK11359 217 RTGEKIWIKA 226 (799)
T ss_pred CCCCEEEEEe
Confidence 9999998854
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Back Show alignment and domain information
Probab=98.79 E-value=2.9e-08 Score=68.88 Aligned_cols=86 Identities=15% Similarity=0.128 Sum_probs=61.0
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC----CeeEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG----VEKHFEI 78 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~e~ 78 (109)
.++.+++++++.| .+|+++++|+++++++||++++++|++ ...+.++.........+......+ ..+..+.
T Consensus 17 ~le~~~~~i~~~d---~~g~i~~~N~~~~~l~G~s~eeliG~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 91 (799)
T PRK11359 17 ALEQNMMGAVLIN---ENDEVLFFNPAAEKLWGYKREEVIGNN--IDMLIPRDLRPAHPEYIRHNREGGKARVEGMSREL 91 (799)
T ss_pred HHHhhcCcEEEEc---CCCeEEEEcHHHHHHhCCCHHHHcCCC--HHHhcCccccccchHHHhhhhccCCccccccceee
Confidence 4678899999999 789999999999999999999999998 444544443322222233322222 2234477
Q ss_pred EEEecCCCEEEEeee
Q psy6003 79 LYYKKDGKYSSVGGS 93 (109)
Q Consensus 79 ~~~~~~g~~~~~~~~ 93 (109)
+.++++|..+|+...
T Consensus 92 ~~~~~dG~~~~v~~~ 106 (799)
T PRK11359 92 QLEKKDGSKIWTRFA 106 (799)
T ss_pred EEecCCcCEEEEEEE
Confidence 788899999998544
>TIGR00229 sensory_box PAS domain S-box
Back Show alignment and domain information
Probab=98.75 E-value=2.1e-07 Score=48.24 Aligned_cols=84 Identities=17% Similarity=0.175 Sum_probs=56.4
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC-CeeEEEEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG-VEKHFEILYY 81 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~ 81 (109)
++++++++++++| .++.++++|+++.+++|++.+++.|+. ...+.++.........+....... .....+....
T Consensus 8 ~~~~~~~~~~~~d---~~~~i~~~n~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (124)
T TIGR00229 8 IFESSPDAIIVID---LEGNILYVNPAFEEIFGYSAEELIGRN--VLELIPEEDREEVRERIERLLEGEREPVSEERRVR 82 (124)
T ss_pred HHhhCCceEEEEc---CCCcEEEEchHHHHHhCCChHHhcCcc--hhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeE
Confidence 5678899999999 789999999999999999999999987 333443333333333344444422 2223334444
Q ss_pred ecCCCEEEEe
Q psy6003 82 KKDGKYSSVG 91 (109)
Q Consensus 82 ~~~g~~~~~~ 91 (109)
..+|...|+.
T Consensus 83 ~~~~~~~~~~ 92 (124)
T TIGR00229 83 RKDGSEIWVE 92 (124)
T ss_pred cCCCCEEEEE
Confidence 6678777764
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.
>KOG0501|consensus
Back Show alignment and domain information
Probab=98.72 E-value=5.8e-08 Score=64.84 Aligned_cols=78 Identities=40% Similarity=0.766 Sum_probs=64.6
Q ss_pred CeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEEeeeccccee
Q psy6003 20 LCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVGGSYGDITP 99 (109)
Q Consensus 20 ~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~ 99 (109)
+.-|+|||..||++.||.++|++.++..+.+++++..+....+.+...++..+.-.+|+.+++++..+.|+ ++++.|
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TPvW~---~vqiAP 115 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTPVWL---LVQIAP 115 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCceEE---EEEeec
Confidence 56699999999999999999999988434566777777788888888888888888999999999999999 544444
Q ss_pred c
Q psy6003 100 V 100 (109)
Q Consensus 100 i 100 (109)
|
T Consensus 116 I 116 (971)
T KOG0501|consen 116 I 116 (971)
T ss_pred c
Confidence 3
>KOG1229|consensus
Back Show alignment and domain information
Probab=98.67 E-value=2.3e-09 Score=69.25 Aligned_cols=84 Identities=13% Similarity=0.174 Sum_probs=66.1
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccC-CCCcHHHHHHHHHHHHcCCeeEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHG-PLTSQHAVQVVKEALAAGVEKHFEILY 80 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~e~~~ 80 (109)
..++...+++-|+| ++..+.|+|++|++++||...|++|++ ...+.. ........+.+..++..|+.+.+++..
T Consensus 161 aaLD~c~eAiEI~~---ddhViQYVNpAfE~mmG~hkgEliGke--~adlpkkdknradlldtintcikkgke~qG~~~a 235 (775)
T KOG1229|consen 161 AALDECDEAIEICD---DDHVIQYVNPAFENMMGCHKGELIGKE--EADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA 235 (775)
T ss_pred HHHhhhhhhheecc---chhHHHHhcHHHHhhhcchhhhhcCCc--hhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence 35677888899998 788899999999999999999999998 444433 223345567778888999999998888
Q ss_pred EecCCCEEEE
Q psy6003 81 YKKDGKYSSV 90 (109)
Q Consensus 81 ~~~~g~~~~~ 90 (109)
+++.|..+..
T Consensus 236 RRksgdS~dq 245 (775)
T KOG1229|consen 236 RRKSGDSCDQ 245 (775)
T ss_pred hhccCCcccc
Confidence 8888875533
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR
Back Show alignment and domain information
Probab=98.63 E-value=1.8e-07 Score=58.56 Aligned_cols=41 Identities=17% Similarity=0.251 Sum_probs=38.5
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
.++++++++++++| .+|+++++|+++++++|+++++..|++
T Consensus 10 ~~~~~~~~~i~~~d---~~g~i~~~N~~~~~~~g~~~~~~~g~~ 50 (333)
T TIGR02966 10 AAAQALPDAVVVLD---EEGQIEWCNPAAERLLGLRWPDDLGQR 50 (333)
T ss_pred HHHHhCcCcEEEEC---CCCcEEEEcHHHHHHhCCChHHHcCCc
Confidence 36899999999999 789999999999999999999999988
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).
>PRK09776 putative diguanylate cyclase; Provisional
Back Show alignment and domain information
Probab=98.47 E-value=1.4e-06 Score=62.50 Aligned_cols=86 Identities=8% Similarity=0.082 Sum_probs=59.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCC-C-CcHHHHHHHHHHHHcCCe--eEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGP-L-TSQHAVQVVKEALAAGVE--KHFEI 78 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~--~~~e~ 78 (109)
++++++++++..| .+|+++++|+++++++||+.++++|++ ...+... . ........+......... ...+.
T Consensus 541 ~l~~~~~~i~~~D---~~g~i~~~N~a~~~l~G~~~~e~iG~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 615 (1092)
T PRK09776 541 TLDSIGEAVVCTD---MAMKVTFMNPVAEKMTGWTQEEALGVP--LLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDV 615 (1092)
T ss_pred HHhccccEEEEEC---CCCeEEEEcHHHHHHhCCCHHHHcCCC--HHHHcccccCCcchhhHHHHHHHhcCCCccccceE
Confidence 5688999999999 789999999999999999999999998 3333221 1 111222223333333332 34566
Q ss_pred EEEecCCCEEEEeee
Q psy6003 79 LYYKKDGKYSSVGGS 93 (109)
Q Consensus 79 ~~~~~~g~~~~~~~~ 93 (109)
...+++|..+|+..+
T Consensus 616 ~~~~~~G~~~~~~~~ 630 (1092)
T PRK09776 616 VLHCRSGGSYDVHYS 630 (1092)
T ss_pred EEEeCCCcEEEEEEE
Confidence 677889998888543
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A
Back Show alignment and domain information
Probab=98.34 E-value=1.3e-06 Score=42.26 Aligned_cols=37 Identities=27% Similarity=0.478 Sum_probs=30.0
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
+++++++++++++| . ++++++|+++++++||+ ..|+.
T Consensus 5 ~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~ 41 (64)
T PF13188_consen 5 SLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGED 41 (64)
T ss_dssp HHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCC
T ss_pred HHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCC
Confidence 47899999999998 3 48999999999999998 55665
>PF12860 PAS_7: PAS fold
Back Show alignment and domain information
Probab=98.28 E-value=2.8e-05 Score=41.95 Aligned_cols=39 Identities=10% Similarity=0.152 Sum_probs=35.9
Q ss_pred cccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHH-hCCc
Q psy6003 4 KHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEV-MQQD 45 (109)
Q Consensus 4 ~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~-~g~~ 45 (109)
++++++++++.| .+++++++|+.|.++++++.+.+ .|.+
T Consensus 1 Ld~l~~Gv~v~D---~~~rl~~~N~~~~~l~~~~~~~~~~G~~ 40 (115)
T PF12860_consen 1 LDSLPQGVAVFD---SDGRLVFWNQRFRELFGLPPEMLRPGAS 40 (115)
T ss_pred CCCcCceEEEEc---CCCeEEeEcHHHHHHhCCCHHHhcCCCC
Confidence 589999999999 79999999999999999999987 6766
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D
Back Show alignment and domain information
Probab=98.23 E-value=4.3e-06 Score=44.54 Aligned_cols=78 Identities=19% Similarity=0.338 Sum_probs=47.0
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
+++++++.+++.+| .++++.+.|+++.++++..+.+ +|++ ...+.++.. ........+.+..++....+...
T Consensus 3 ~il~s~~~~i~~vD---~~~~I~~~n~~a~~~f~~~~~~-iGr~--l~~~~~~~~-~~~l~~~i~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 3 NILDSMPIGIIFVD---RNLRIRYFNPAAARLFNLSPSD-IGRP--LFDIHPPLS-YPNLKKIIEQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHSSSEEEEEE---TTSBEEEE-SCGC-SS---GGG-TTSB--CCCSS-HHH-HHHHHHHHHHHHTTSBSEEEEEE-
T ss_pred HHHhcCCCCEEEEc---CCCeEEEeChhHhhhcCCChHH-CCCC--HHHcCCccc-hHHHHHHHHHHHcCCCceEEEEe-
Confidence 46889999999999 8999999999999999987655 7998 454544322 22333344455556544344333
Q ss_pred ecCCCE
Q psy6003 82 KKDGKY 87 (109)
Q Consensus 82 ~~~g~~ 87 (109)
..+|..
T Consensus 75 ~~~~~~ 80 (106)
T PF13596_consen 75 PNGGRW 80 (106)
T ss_dssp EETTEE
T ss_pred cCCCEE
Confidence 244543
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Back Show alignment and domain information
Probab=98.18 E-value=5.6e-06 Score=55.63 Aligned_cols=46 Identities=15% Similarity=0.154 Sum_probs=40.9
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCcccccccc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLH 52 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~ 52 (109)
.++++++++++++| .+|+|+++|+++.+++|++.+++.|++ ...+.
T Consensus 84 aIL~sm~eGVi~vD---~~G~I~~iN~aA~~Llg~~~eel~Gk~--i~eli 129 (520)
T PRK10820 84 ALLEALPEPVLSID---MKGKVELANPASCQLFGQSEEKLRNHT--AAQLI 129 (520)
T ss_pred HHHHhCCCcEEEEC---CCCeeeHhHHHHHHHHCcCHHHHCCCc--HHHHc
Confidence 46899999999999 899999999999999999999999998 44443
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins
Back Show alignment and domain information
Probab=98.05 E-value=8.2e-05 Score=42.06 Aligned_cols=83 Identities=10% Similarity=0.131 Sum_probs=61.5
Q ss_pred cCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCC
Q psy6003 6 HTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDG 85 (109)
Q Consensus 6 ~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g 85 (109)
+.+++|+-.+.+ .+-.++|.|++..++++++-+++.+.+ .+.-..+..+......+.++.++|-.....-....+.|
T Consensus 39 ~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lP--sr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRiss~G 115 (148)
T PF08670_consen 39 HAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLP--SRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRISSTG 115 (148)
T ss_pred cCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCc--HhhccChhhHHHHHHHHHHHHHhCCccCCCeEEEcCCC
Confidence 377788777655 578899999999999999999999998 66555555555555666666666654444445667888
Q ss_pred CEEEEe
Q psy6003 86 KYSSVG 91 (109)
Q Consensus 86 ~~~~~~ 91 (109)
++++++
T Consensus 116 rrf~ie 121 (148)
T PF08670_consen 116 RRFRIE 121 (148)
T ss_pred CeEEEe
Confidence 888775
>PRK11360 sensory histidine kinase AtoS; Provisional
Back Show alignment and domain information
Probab=98.03 E-value=4.7e-05 Score=51.23 Aligned_cols=79 Identities=18% Similarity=0.218 Sum_probs=54.3
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCee-EEEEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEK-HFEILYY 81 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~ 81 (109)
++++++++++++| .+++++++|+++++++|+++++.+|++ ...+.++.. .....+.+....+... ..+....
T Consensus 267 i~~~~~~~i~~~d---~~g~i~~~N~~~~~l~g~~~~~~~g~~--~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 339 (607)
T PRK11360 267 ILESIADGVIAID---RQGKITTMNPAAEVITGLQRHELVGKP--YSELFPPNT--PFASPLLDTLEHGTEHVDLEISFP 339 (607)
T ss_pred HHHhccCeEEEEc---CCCCEEEECHHHHHHhCCChHHhcCCc--HHHHcCCch--hHHHHHHHHHhcCCCccceEEEEE
Confidence 5678999999999 789999999999999999999999998 444544322 2223344444444333 3344455
Q ss_pred ecCCCEE
Q psy6003 82 KKDGKYS 88 (109)
Q Consensus 82 ~~~g~~~ 88 (109)
.++|...
T Consensus 340 ~~~~~~~ 346 (607)
T PRK11360 340 GRDRTIE 346 (607)
T ss_pred cCCCcEE
Confidence 5566544
>TIGR02373 photo_yellow photoactive yellow protein
Back Show alignment and domain information
Probab=98.01 E-value=0.0002 Score=39.10 Aligned_cols=63 Identities=17% Similarity=0.088 Sum_probs=47.0
Q ss_pred cccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcH-HHHHHHHHHHHcC
Q psy6003 4 KHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQ-HAVQVVKEALAAG 71 (109)
Q Consensus 4 ~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 71 (109)
++..|-+++.+| .+|.|+..|.+-.++.|++++.++|++. ..-..|.... .+..++.+..+.+
T Consensus 22 lD~lpFGvI~lD---~~G~V~~YN~aE~~~sg~~p~~vlGr~F--F~eVAPC~~~~~f~gRF~~g~~~g 85 (124)
T TIGR02373 22 FDALPFGAIQLD---GSGVILRYNAAEGRITGRDPERVIGRNF--FKEVAPCTDIPEFSGRFMEGVASG 85 (124)
T ss_pred hhcCCcceEEEC---CCCEEEEEecchhhhcCCChhhhhchhh--hhhcccccCCHHHHHHHHhhhhcC
Confidence 578899999999 8999999999999999999999999983 2223344433 3445555544433
Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
>PRK13560 hypothetical protein; Provisional
Back Show alignment and domain information
Probab=97.99 E-value=3e-05 Score=54.11 Aligned_cols=85 Identities=15% Similarity=0.158 Sum_probs=55.0
Q ss_pred ccccCCccEEEEecCCCCeeEEEe-cHHHHHhhCCChHHHhCCccccccccCCCCcHHH-----------------HHHH
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYC-SDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHA-----------------VQVV 64 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~-N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~-----------------~~~~ 64 (109)
+++++++++++.| .+|+++++ |+++++++||+.++++|++ ...+.++...... ....
T Consensus 337 l~~~~~~~i~~~d---~~g~i~~~nn~~~~~~~G~~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 411 (807)
T PRK13560 337 IIEAAPIAAIGLD---ADGNICFVNNNAAERMLGWSAAEVMGKP--LPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPM 411 (807)
T ss_pred HHHhCcccEEEEc---CCCCEEEecCHHHHHHhCCCHHHHcCCC--ccccChhhhhhhhhchhhhcCCcCCcchhhhhhH
Confidence 5789999999999 78889887 6788889999999999987 3322221111100 0011
Q ss_pred HHHHHcCCeeE-EEEEEEecCCCEEEEee
Q psy6003 65 KEALAAGVEKH-FEILYYKKDGKYSSVGG 92 (109)
Q Consensus 65 ~~~~~~~~~~~-~e~~~~~~~g~~~~~~~ 92 (109)
...+..+..+. .+....+++|...|+..
T Consensus 412 ~~~~~~~~~~~~~e~~~~~~~g~~~~~~~ 440 (807)
T PRK13560 412 AKTIKGGKIFDGQEVLIEREDDGPADCSA 440 (807)
T ss_pred HHHHhcCCcccCceEEEEcCCCCeEEEEE
Confidence 22344444443 35666778888888743
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Back Show alignment and domain information
Probab=97.91 E-value=7.7e-06 Score=53.54 Aligned_cols=40 Identities=18% Similarity=0.215 Sum_probs=37.9
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
++++++++++++| .+|+++++|+++++++|++.++..|++
T Consensus 103 ~~~~~~~~i~~~d---~~g~i~~~N~~a~~l~g~~~~~~~g~~ 142 (430)
T PRK11006 103 GAESLPDAVVLTT---EEGNIFWCNGLAQQLLGFRWPEDNGQN 142 (430)
T ss_pred HHHhCCCeEEEEc---CCCceeHHHHHHHHHhCCCChHhCCCc
Confidence 5789999999999 789999999999999999999999998
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Back Show alignment and domain information
Probab=97.90 E-value=8.8e-05 Score=51.15 Aligned_cols=40 Identities=8% Similarity=0.099 Sum_probs=37.3
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
++++.+++++++| .+|+|+++|+++++++|++.++++|++
T Consensus 208 il~~~~~gVl~vD---~~G~I~~~N~aa~~llg~s~~~l~G~~ 247 (638)
T PRK11388 208 LLESMDDGVIAWD---EQGNLQFLNAQAARLLRLDATASQGRA 247 (638)
T ss_pred HHhccCCcEEEEC---CCCeEehhhHHHHHHhCcCHHHHCCCc
Confidence 5678899999999 899999999999999999999999998
>KOG3558|consensus
Back Show alignment and domain information
Probab=97.85 E-value=2.4e-05 Score=53.33 Aligned_cols=71 Identities=20% Similarity=0.259 Sum_probs=57.4
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEEe
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVG 91 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~ 91 (109)
.+-+|.||...+..++||++++++|++ +..+.+..+.....+-..+.+.+|+...+.++...++|...|+.
T Consensus 282 ~DmkityCedRisdlm~y~PeeLvGrS--~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQ 352 (768)
T KOG3558|consen 282 LDMKITYCEDRISDLMDYEPEELVGRS--CYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQ 352 (768)
T ss_pred cceeEEEEchhHHHHhcCCHHHhhchh--HHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEE
Confidence 477899999999999999999999999 45555555555565666677788888888888888888888885
>smart00091 PAS PAS domain
Back Show alignment and domain information
Probab=97.81 E-value=0.00014 Score=32.88 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=35.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
+++..++++++++ ..+.+.++|+.+.+++|++..++.|..
T Consensus 6 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 (67)
T smart00091 6 ILESLPDGIFVLD---LDGRILYANPAAEELLGYSPEELIGKS 45 (67)
T ss_pred HHhhCCceEEEEc---CCCeEEEECHHHHHHhCCCHHHHcCCc
Confidence 4677888999998 688899999999999999999988876
PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Back Show alignment and domain information
Probab=97.72 E-value=0.00014 Score=45.79 Aligned_cols=82 Identities=12% Similarity=0.026 Sum_probs=55.3
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
.++++....++++| .++.|.|+|++++.+++.+...+.|.+ ...+.+... ....-+.+....+..+.......
T Consensus 11 ~~Ln~~~~pVl~vd---~~~~i~yaN~aAe~~~~~Sa~~L~~~~--l~~l~~~gs--~ll~ll~q~~~~~~~~~~~~v~l 83 (363)
T COG3852 11 AILNNLINPVLLVD---DELAIHYANPAAEQLLAVSARRLAGTR--LSELLPFGS--LLLSLLDQVLERGQPVTEYEVTL 83 (363)
T ss_pred hHHhccCCceEEEc---CCCcEEecCHHHHHHHHHHHHHHhcCC--hHHHcCCCc--HHHHHHHHHHHhcCCcccceeee
Confidence 46789999999999 899999999999999999999999988 444443222 23334455555555543322222
Q ss_pred ecCCCEEEE
Q psy6003 82 KKDGKYSSV 90 (109)
Q Consensus 82 ~~~g~~~~~ 90 (109)
..+|....+
T Consensus 84 ~~~g~~~~v 92 (363)
T COG3852 84 VILGRSHIV 92 (363)
T ss_pred eecCccceE
Confidence 245655444
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Back Show alignment and domain information
Probab=97.67 E-value=0.00089 Score=37.64 Aligned_cols=83 Identities=19% Similarity=0.185 Sum_probs=53.1
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHH--HHcCCeeEEEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEA--LAAGVEKHFEILY 80 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~e~~~ 80 (109)
++++.+++++..| .++.+.++|+++.+++|++..+..+.. ...+................ .........+...
T Consensus 117 ~~~~~~~~~~~~d---~~~~~~~~n~~~~~~~g~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 191 (232)
T COG2202 117 LLEASPDGIWVLD---EDGRILYANPAAEELLGYSPEEELGRG--LSDLIHPEDEERRELELARALAEGRGGPLEIEYRV 191 (232)
T ss_pred HHhhCCceEEEEe---CCCCEEEeCHHHHHHhCCChHHhcCCC--hhheEecCCCchhhHHHHHHhhccCCCCcceEEEE
Confidence 5678889999999 789999999999999999988877765 23232222211101111112 2223335566677
Q ss_pred EecCCCE-EEE
Q psy6003 81 YKKDGKY-SSV 90 (109)
Q Consensus 81 ~~~~g~~-~~~ 90 (109)
..++|.. .+.
T Consensus 192 ~~~~g~~~~~~ 202 (232)
T COG2202 192 RRKDGERVRWI 202 (232)
T ss_pred EecCCCEEEEE
Confidence 7788885 555
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Back Show alignment and domain information
Probab=97.21 E-value=0.00058 Score=45.97 Aligned_cols=41 Identities=24% Similarity=0.446 Sum_probs=38.8
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
.+++.+.++++++| .+|.++++|++..+++|.+.++++|++
T Consensus 121 ~il~~~~~~l~vvD---~~G~~i~~N~~~~~~~gl~~e~~~gk~ 161 (560)
T COG3829 121 AILDSIDDGLLVVD---EDGIIIYYNKAYAKLLGLSPEEVLGKH 161 (560)
T ss_pred HHHhhccCceEEEc---CCCcEEEEcHHHHHHhCCCHHHHcCCc
Confidence 36789999999999 899999999999999999999999998
>KOG3561|consensus
Back Show alignment and domain information
Probab=97.00 E-value=0.00044 Score=48.59 Aligned_cols=46 Identities=22% Similarity=0.395 Sum_probs=39.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCcccccccc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLH 52 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~ 52 (109)
++|+++..++++. .+|+|+||+.+...++||..+++.|++. ..+++
T Consensus 100 mLeAlDGF~fvV~---cdG~IvyVSeSVT~~L~y~QsDL~~qSl-y~ilh 145 (803)
T KOG3561|consen 100 ILEALDGFLFVVN---CDGRIVYVSESVTSVLGYLQSDLMGQSL-YDILH 145 (803)
T ss_pred HHHHhcCeEEEEe---cCceEEEEecchHHhhCcCHHHHhcchH-HHhcC
Confidence 4677888888888 7899999999999999999999999993 44443
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Back Show alignment and domain information
Probab=96.78 E-value=0.0013 Score=44.36 Aligned_cols=40 Identities=10% Similarity=0.100 Sum_probs=35.6
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCCh--HHHhCCc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSR--AEVMQQD 45 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~--~e~~g~~ 45 (109)
+++++.++++++| .+|+++++|+++++++|++. ++.+|++
T Consensus 227 il~~~~egii~~D---~~g~I~~~N~~a~~ll~~~~~~~~~~g~~ 268 (545)
T PRK15053 227 LFSSVYEGLIAVD---PHGYITAINRNARKMLGLSSPGRQWLGKP 268 (545)
T ss_pred HHHHhCceEEEEC---CCCeEEeecHHHHHHhCCCCcchhhcCCc
Confidence 5788899999999 89999999999999999865 4688887
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Back Show alignment and domain information
Probab=96.68 E-value=0.0029 Score=41.14 Aligned_cols=41 Identities=12% Similarity=0.134 Sum_probs=38.0
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
++++++++.++-+| ..|.+..+|+++++++|.+.+++.|..
T Consensus 84 aLL~al~~pVlsvd---~kg~v~~aNpAa~~l~~~~~~~~~g~~ 124 (511)
T COG3283 84 ALLEALPEPVLSVD---MKGKVDMANPAACQLFGRKEDRLRGHT 124 (511)
T ss_pred HHHHhCCCceEEec---ccCceeecCHHHHHHhCCChhhhcCcc
Confidence 35789999999999 789999999999999999999999988
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL
Back Show alignment and domain information
Probab=96.64 E-value=0.0029 Score=41.81 Aligned_cols=41 Identities=10% Similarity=0.139 Sum_probs=35.1
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
.+++++++++++.| .+++++++|+++++++|+...+..+..
T Consensus 134 ~~~~~~~~~i~~~d---~~~~i~~~N~~~~~~~g~~~~~~~~~~ 174 (494)
T TIGR02938 134 SVVDAAPVAFVLLD---PTGRVILDNQEYKKLATDLRVKEPAHT 174 (494)
T ss_pred HHHhcccceEEEEc---CCCCEEEechhHHHhhchhhhhHHHHH
Confidence 35788999999999 789999999999999998887765554
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.
>PRK11086 sensory histidine kinase DcuS; Provisional
Back Show alignment and domain information
Probab=96.54 E-value=0.0027 Score=42.67 Aligned_cols=41 Identities=10% Similarity=0.229 Sum_probs=33.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCCh---HHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSR---AEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~---~e~~g~~ 45 (109)
.++++++++++++| .+|+++++|+++++++|++. .+..|+.
T Consensus 225 ~il~~~~~gIi~~D---~~g~I~~~N~~a~~llg~~~~~~~~~~~~~ 268 (542)
T PRK11086 225 AMLQSIKEGVIAVD---DRGEVTLINDEAKRLFNYKKGLEDDPLGTD 268 (542)
T ss_pred HHHHHhcCcEEEEC---CCCeEEEEhHHHHHHhCCCcCCcccccCCc
Confidence 35789999999999 89999999999999997753 3445554
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Back Show alignment and domain information
Probab=96.16 E-value=0.0057 Score=39.56 Aligned_cols=47 Identities=11% Similarity=0.216 Sum_probs=40.4
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCcccccccc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLH 52 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~ 52 (109)
+++..+.|+++.+| +.|.++.+|..+.+++|.+.++++|++. .+++.
T Consensus 115 SvlayMtDGViATd---RrG~iI~iN~~A~k~L~~~~E~~~~~~i-~elL~ 161 (459)
T COG5002 115 SVLAYMTDGVIATD---RRGKIILINKPALKMLGVSKEDALGRSI-LELLK 161 (459)
T ss_pred HHHHHHcCceEeec---CCCcEEEeccHHHHHhCcCHHHHhcccH-HHHhC
Confidence 35667889999999 8999999999999999999999999983 44443
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Back Show alignment and domain information
Probab=95.77 E-value=0.043 Score=40.80 Aligned_cols=36 Identities=14% Similarity=0.045 Sum_probs=31.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHH
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAE 40 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e 40 (109)
.++++++++++++| .+|+++++|+++++++|++...
T Consensus 580 ~i~~~~~~~i~~~d---~~g~i~~~N~~~~~~~g~~~~~ 615 (1197)
T PRK09959 580 ALSDSLPNPTYVVN---WQGNVISHNSAFEHYFTADYYK 615 (1197)
T ss_pred HHHhhCCCcEEEEc---CCCcEEEehHHHHHHhCccccc
Confidence 35789999999999 8999999999999999986544
>KOG3558|consensus
Back Show alignment and domain information
Probab=95.67 E-value=0.015 Score=40.47 Aligned_cols=58 Identities=10% Similarity=0.123 Sum_probs=47.7
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHH
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVK 65 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~ 65 (109)
+++++..-+++++ .+|.++|++......+|.+.-|+.|.+ ...+.++.+.+.+.+++.
T Consensus 124 iLqsLDGFVm~l~---~dG~~lYiSEtVS~yLGLSQvELTG~S--vFDfiHP~DheE~~eqL~ 181 (768)
T KOG3558|consen 124 ILQSLDGFVMALT---QDGDFLYISETVSIYLGLSQVELTGSS--VFDFIHPCDHEEIAEQLG 181 (768)
T ss_pred HHhhccceEEEEc---cCCCEEEEechhHhhhCccceeeecch--hhhccCccCHHHHHHHhc
Confidence 4567777788888 789999999999999999999999999 666777777666666553
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []
Back Show alignment and domain information
Probab=95.48 E-value=0.056 Score=29.12 Aligned_cols=42 Identities=19% Similarity=0.284 Sum_probs=32.3
Q ss_pred cEEEEecCCCCeeEEEecHHHHHhhCCC---hHHHhCCccccccccCCC
Q psy6003 10 SFLVANSHLGLCHIIYCSDGFCRLTGFS---RAEVMQQDAICKFLHGPL 55 (109)
Q Consensus 10 ~i~i~d~~~~~~~i~~~N~~~~~~~g~~---~~e~~g~~~~~~~~~~~~ 55 (109)
.++.+|. .+++|+.++.+...++|.+ .++++|++ ...+.+..
T Consensus 17 ~LLa~d~--~~~~I~~~S~N~~~~lg~~~~~~~~llG~~--l~~ll~~~ 61 (110)
T PF08446_consen 17 ALLALDP--DDLRIVQASENIAELLGIPPELPEELLGRP--LSELLGAE 61 (110)
T ss_dssp EEEEEET--TTTBEEEEETTHHHHHSS----HHHHTTCB--HHHHSCCC
T ss_pred EEEEEEC--CCCEEEEEcCCHHHHhCCccccchhhcccC--HHHHhCHH
Confidence 3456664 4789999999999999999 99999999 55555433
The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Back Show alignment and domain information
Probab=95.33 E-value=0.074 Score=36.98 Aligned_cols=41 Identities=7% Similarity=0.007 Sum_probs=37.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
++++...-+++..| .+|++..+|++.++++|.+-++++|.+
T Consensus 374 ~VLsgvtaGVi~~d---~~g~i~t~N~~ae~~l~~~~~~~~G~~ 414 (712)
T COG5000 374 AVLSGLTAGVIGFD---NRGCITTVNPSAEQILGKPFDQLLGQS 414 (712)
T ss_pred HHHhcCceeEEEEc---CCCeeEeecchHHHHhcCChhHhhcch
Confidence 46778888999999 899999999999999999999999987
>KOG3560|consensus
Back Show alignment and domain information
Probab=95.16 E-value=0.12 Score=35.48 Aligned_cols=71 Identities=13% Similarity=0.067 Sum_probs=50.8
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEEe
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVG 91 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~ 91 (109)
.++..+.+.+....++||...|+.|.+. .. +.+.++..-..+.-.+.+.+|+....-++..+++|+..|+.
T Consensus 291 lDfa~vs~Dak~k~~lgy~eaEL~~m~g-Y~-lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvq 361 (712)
T KOG3560|consen 291 LDFALVSMDAKVKATLGYCEAELHGMPG-YN-LVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQ 361 (712)
T ss_pred cccceeccchhhhhhhccchhhccCCCc-cc-eeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEee
Confidence 3667788888899999999999998762 34 33333333334455566777777766777889999988874
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Back Show alignment and domain information
Probab=94.46 E-value=0.035 Score=37.73 Aligned_cols=40 Identities=8% Similarity=0.174 Sum_probs=35.5
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChH--HHhCCc
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRA--EVMQQD 45 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~--e~~g~~ 45 (109)
+|++..++++.+| +.|.+..+|.++++++|+... +.+|++
T Consensus 220 ~l~si~EGviAvd---~~G~It~~N~~A~~ll~~~~~~~~~ig~~ 261 (537)
T COG3290 220 MLQSIKEGVIAVD---KKGVITLINQAAQKLLGLRQPSGDPIGRS 261 (537)
T ss_pred HHHHhhceEEEEC---CCCeEeehhHHHHHHhcccCcCccccccc
Confidence 5788999999999 789999999999999998776 578887
>KOG3560|consensus
Back Show alignment and domain information
Probab=94.16 E-value=0.063 Score=36.69 Aligned_cols=57 Identities=25% Similarity=0.218 Sum_probs=43.5
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHH
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVV 64 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~ 64 (109)
+++++..-++++. .+|.|.|++...+..+||...+++-++ ...+.+.++++.+.+++
T Consensus 116 lLqsLnGF~lVvt---~eg~ifyAS~tIedYLGFhQSDV~HQs--VYdlIHseDR~dfqrQL 172 (712)
T KOG3560|consen 116 LLQSLNGFALVVT---AEGEIFYASATIEDYLGFHQSDVMHQS--VYDLIHSEDRQDFQRQL 172 (712)
T ss_pred HHHhcCCeEEEEe---cCceEEEehhhHHhhhcccccchhhhh--HHHHhhhhhHHHHHHHH
Confidence 4567777778887 789999999999999999999999888 34444445555555544
>KOG3559|consensus
Back Show alignment and domain information
Probab=92.60 E-value=0.19 Score=33.35 Aligned_cols=32 Identities=16% Similarity=0.353 Sum_probs=27.2
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
+++.. .+-.+++......+++||.+.+++++.
T Consensus 228 mfras---lDlkliF~D~rv~qltgYepqdliekt 259 (598)
T KOG3559|consen 228 MFRAS---LDLKLIFLDSRVHQLTGYEPQDLIEKT 259 (598)
T ss_pred EEEee---cceEEEeehhhHHHhhCCCchhhhhHH
Confidence 34444 467899999999999999999999998
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function
Back Show alignment and domain information
Probab=87.17 E-value=0.76 Score=29.76 Aligned_cols=72 Identities=13% Similarity=0.200 Sum_probs=44.0
Q ss_pred ccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEE
Q psy6003 9 RSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYS 88 (109)
Q Consensus 9 ~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~ 88 (109)
.++++-.+ .+.+.+++|.-|...+||+.++++... .+++.... ......+. . .......+.+..++|+|...
T Consensus 298 gmlfVYs~--k~qRllFAN~~fk~wtGy~~edFl~~~--~dIV~eGl--~qW~~dL~-~-~s~~E~~grlviKTK~~g~i 369 (401)
T PF06785_consen 298 GMLFVYSP--KSQRLLFANSQFKTWTGYSSEDFLKDF--SDIVQEGL--AQWETDLQ-L-LSRQERSGRLVIKTKNGGNI 369 (401)
T ss_pred ceEEEecc--hhhHHHHhHHHHHHHhccCHHHHHhcc--hHHHHhhH--HHHHHHHH-h-hhhhhhhceEEEEecCCCce
Confidence 44555554 578899999999999999999987764 34333211 11212222 1 12333456677788877643
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Back Show alignment and domain information
Probab=86.13 E-value=0.99 Score=33.26 Aligned_cols=34 Identities=9% Similarity=-0.063 Sum_probs=29.3
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCC
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFS 37 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~ 37 (109)
.+++++++++++.|. .+++++.+|+++.+++++.
T Consensus 347 ~Ii~~lp~Gilv~D~--~~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 347 EIVSNLPLGLLVYDF--ESNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHhCCceEEEEEC--CCCeEEEEhHHHHHHhCcc
Confidence 357899999999996 5789999999999999863
>KOG3753|consensus
Back Show alignment and domain information
Probab=84.58 E-value=5 Score=29.73 Aligned_cols=70 Identities=17% Similarity=0.310 Sum_probs=48.0
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC-Ce--eEEEEEEEecCCCEEEE
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG-VE--KHFEILYYKKDGKYSSV 90 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~e~~~~~~~g~~~~~ 90 (109)
..+.+..+..+...++||=+.+++|++ ...+.++.+...+...-...++.+ +. ....+++...+|...-+
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~s--il~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~l 411 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTS--ILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRL 411 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccc--hhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEE
Confidence 567888999999999999999999999 444555555555554444555443 22 23457777788875533
>KOG3559|consensus
Back Show alignment and domain information
Probab=80.72 E-value=0.84 Score=30.47 Aligned_cols=46 Identities=20% Similarity=0.285 Sum_probs=36.8
Q ss_pred cccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccC
Q psy6003 4 KHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHG 53 (109)
Q Consensus 4 ~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~ 53 (109)
++.++.-+++++ ++|.|.|++....--+|.+.-|+-|.. +.+.+++
T Consensus 85 LqtLDGF~fvva---~dGkimYISETaSvhLGLSQVElTGNs-i~eYIH~ 130 (598)
T KOG3559|consen 85 LQTLDGFIFVVA---PDGKIMYISETASVHLGLSQVELTGNS-IYEYIHP 130 (598)
T ss_pred HHhhcceEEEEe---CCCCEEEEecceeeeecceeeEeecch-hhhhhcc
Confidence 455667788999 789999999999989999999999987 2444443
Homologous Structure Domains
Structure Domains Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
E-value Query 109
d1bywa_ 110
d.110.3.6 (A:) Erg potassium channel, N-terminal d
2e-09 d1jnua_ 104
d.110.3.6 (A:) Photoreceptor phy3 flavin-binding d
8e-09 d1n9la_ 109
d.110.3.6 (A:) Putative blue light receptor, phot-
2e-08
>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 110
Back Hide information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Erg potassium channel, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]
Score = 48.9 bits (115), Expect = 2e-09
Identities = 28/52 (53%), Positives = 38/52 (73%)
Query: 8 NRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQH 59
+R F++AN+ + C +IYC+DGFC L G+SRAEVMQ+ C FLHGP T +
Sbjct: 1 SRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPCTQRR 52
>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]} Length = 104
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]
Score = 47.2 bits (111), Expect = 8e-09
Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 5/92 (5%)
Query: 9 RSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEAL 68
+SF++ + L II+ SD F LT ++R EV+ + C+FL G T + AVQ++++A+
Sbjct: 1 KSFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNN--CRFLQGRGTDRKAVQLIRDAV 58
Query: 69 AAGVEKHFEILYYKKDGKYSSVGGSYGDITPV 100
+ ++L Y K G+ + +
Sbjct: 59 KEQRDVTVQVLNYTKGGRAFWN---LFHLQVM 87
>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]} Length = 109
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Putative blue light receptor, phot-lov1 domain
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]
Score = 46.0 bits (108), Expect = 2e-08
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 8 NRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEA 67
+F+VA++ L C ++Y S+GF +TG+ EV+ + C+FL G T VQ +++A
Sbjct: 3 RHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHN--CRFLQGEGTDPKEVQKIRDA 60
Query: 68 LAAGVEKHFEILYYKKDGKY 87
+ G +L Y+KDG
Sbjct: 61 IKKGEACSVRLLNYRKDGTP 80
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
Probability Query 109
d1n9la_ 109
Putative blue light receptor, phot-lov1 domain {Gr
99.84 d1jnua_ 104
Photoreceptor phy3 flavin-binding domain, lov2 {Ma
99.78 d1mzua_ 110
PYP domain of sensor histidine kinase Ppr {Rhodosp
99.73 d1bywa_ 110
Erg potassium channel, N-terminal domain {Human (H
99.71 d1ew0a_ 130
Histidine kinase FixL heme domain {Rhizobium melil
99.68 d1nwza_ 125
Photoactive yellow protein, PYP {Ectothiorhodospir
99.68 d1v9ya_ 113
Direct oxygen sensor protein, DOS {Escherichia col
99.65 d1xj3a1 106
Histidine kinase FixL heme domain {Bradyrhizobium
99.57 d1p97a_ 114
Hypoxia-inducible factor Hif2a, C-terminal domain
99.5 d1ll8a_ 114
N-terminal PAS domain of Pas kinase {Human (Homo s
99.47 d1oj5a_ 109
PAS domain of steroid receptor coactivator 1A, NCo
99.24 d2oola2 114
Sensor protein PhyB2 {Rhodopseudomonas palustris [
98.09 d2o9ca2 127
Bacteriophytochrome BphP {Deinococcus radiodurans
96.15 d2veaa3 127
Phytochrome-like protein Cph1 {Synechocystis sp. p
95.66 d3c2wa3 113
Bacteriophytochrome BphP {Pseudomonas aeruginosa [
84.9
>d1n9la_ d.110.3.6 (A:) Putative blue light receptor, phot-lov1 domain {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}
Back Hide information, alignment and structure
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=99.84 E-value=6.6e-20 Score=96.62 Aligned_cols=85 Identities=32% Similarity=0.590 Sum_probs=73.8
Q ss_pred CCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCC
Q psy6003 7 TNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGK 86 (109)
Q Consensus 7 ~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~ 86 (109)
..++++++|...++|+|+|+|++|++++||+++|++|++ ...+.++.........+.+.+.+++.+..++..+++||+
T Consensus 2 i~~~~vi~Da~~pdg~Ii~vN~a~~~~~Gy~~~El~G~~--~~~l~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~kdG~ 79 (109)
T d1n9la_ 2 LRHTFVVADATLPDCPLVYASEGFYAMTGYGPDEVLGHN--CRFLQGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGT 79 (109)
T ss_dssp CSCEEEEEETTSTTCCEEEECHHHHHHHCCCHHHHTTSC--GGGGCCTTCCHHHHHHHHHHHHHTCCEEEEEEEECTTSC
T ss_pred ccceEEEEeCCCCCCeEEEEcHHHHHHHCcCHHHHcCCc--ceeeecccCCHHHhhhhhhHhhcCCceeeeEEEEecCCe
Confidence 568899999655689999999999999999999999998 566776766677778888889999999999999999999
Q ss_pred EEEEeee
Q psy6003 87 YSSVGGS 93 (109)
Q Consensus 87 ~~~~~~~ 93 (109)
.+|++++
T Consensus 80 ~~w~~~~ 86 (109)
T d1n9la_ 80 PFWNLLT 86 (109)
T ss_dssp EEEEEEE
T ss_pred EEEEEEE
Confidence 9999544
>d1jnua_ d.110.3.6 (A:) Photoreceptor phy3 flavin-binding domain, lov2 {Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Flavin-binding PAS domain
domain: Photoreceptor phy3 flavin-binding domain, lov2
species: Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818]
Probab=99.78 E-value=5.8e-18 Score=88.22 Aligned_cols=82 Identities=32% Similarity=0.522 Sum_probs=71.7
Q ss_pred cEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEE
Q psy6003 10 SFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSS 89 (109)
Q Consensus 10 ~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 89 (109)
.++++|+..++++|+|+|++|++++||+.++++|++ ...+..+.........+...+..++.+..+.+.++++|+.+|
T Consensus 2 ~fvi~d~~~pd~~I~y~N~a~~~~~G~s~~e~~G~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 79 (104)
T d1jnua_ 2 SFVITDPRLPDNPIIFASDRFLELTEYTREEVLGNN--CRFLQGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFW 79 (104)
T ss_dssp EEEEECTTSTTCCEEEECHHHHHHHTCCHHHHTTSC--GGGGCCTTSCHHHHHHHHHHHHHTCCEEEEEEEECTTSCEEE
T ss_pred eEEEEcCCCCCCEEEEEcHHHHHHHCcCHHHHCCcc--ceeccccccchHHHhhhhhhhhcCceeEeEEEEEecccceEE
Confidence 467888766689999999999999999999999998 566777777778888888889999999999999999999999
Q ss_pred Eeee
Q psy6003 90 VGGS 93 (109)
Q Consensus 90 ~~~~ 93 (109)
++++
T Consensus 80 ~~~~ 83 (104)
T d1jnua_ 80 NLFH 83 (104)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9543
>d1mzua_ d.110.3.1 (A:) PYP domain of sensor histidine kinase Ppr {Rhodospirillum centenum [TaxId: 34018]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: PYP domain of sensor histidine kinase Ppr
species: Rhodospirillum centenum [TaxId: 34018]
Probab=99.73 E-value=6e-17 Score=85.29 Aligned_cols=89 Identities=9% Similarity=-0.079 Sum_probs=68.7
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
++++++|++++++| .+|+|+++|+++++++||+++|++|++. ...+.++.........+.+.+.++..........
T Consensus 7 A~ld~~p~gvi~~D---~~G~I~~~N~aa~~~~G~~~eellG~~~-~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~l 82 (110)
T d1mzua_ 7 AEFDALPVGAIQVD---GSGVIHRYNRTESRLSGRIPERVIGRNF-FTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVF 82 (110)
T ss_dssp TTGGGCSSEEEEEE---TTCBEEEECHHHHHHHCCCHHHHTTSBC-CCCCCGGGCSTTTHHHHHHHHHTSCCEEEEEEEE
T ss_pred HHHhCCCcEEEEEc---CCCCEEEeHHHHHHHHcCCHHHHcCCCH-HHhcCChhhhHHHHHHHHHHHhccccCcceEEEE
Confidence 57899999999999 8999999999999999999999999982 3555555555555666777777776543333335
Q ss_pred ecCCCEEEEeeec
Q psy6003 82 KKDGKYSSVGGSY 94 (109)
Q Consensus 82 ~~~g~~~~~~~~~ 94 (109)
+++|..+++++..
T Consensus 83 ~~~G~~~~v~v~~ 95 (110)
T d1mzua_ 83 DFQMAPVRVQIRM 95 (110)
T ss_dssp ECSSCEEEEEEEE
T ss_pred ecCCceEEEEEEE
Confidence 6799988886544
>d1bywa_ d.110.3.6 (A:) Erg potassium channel, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
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=99.71 E-value=3.5e-16 Score=82.08 Aligned_cols=83 Identities=43% Similarity=0.797 Sum_probs=68.4
Q ss_pred cEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccc-cccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEE
Q psy6003 10 SFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICK-FLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYS 88 (109)
Q Consensus 10 ~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~ 88 (109)
.+++.|....+..|+|+|++|++++||+.+|++|+++ .. .+.++.........+...+.+++.+..++..++++|+.+
T Consensus 3 ~f~i~~~~~~d~~I~~~N~a~~~l~G~~~~eiiG~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~~~~~~~g~~~ 81 (110)
T d1bywa_ 3 KFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPC-TCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCF 81 (110)
T ss_dssp EEEEEETTSSSCBEEEECHHHHHHHTCCHHHHTTSBT-TCGGGCCTTCCHHHHHHHHHHHHTTCCEEEEEEEECTTSCEE
T ss_pred eEEEEcCCCCCCEEEEEcHHHHHHhCCCHHHhcccCc-ccccceeeheecccccccchhhcccccccceeeeeeccccee
Confidence 4677887667889999999999999999999999983 23 234556666777888888899999999999999999999
Q ss_pred EEeee
Q psy6003 89 SVGGS 93 (109)
Q Consensus 89 ~~~~~ 93 (109)
|++++
T Consensus 82 w~~~~ 86 (110)
T d1bywa_ 82 LCLVD 86 (110)
T ss_dssp EEEEE
T ss_pred eeeee
Confidence 99543
>d1ew0a_ d.110.3.2 (A:) Histidine kinase FixL heme domain {Rhizobium meliloti [TaxId: 382]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Rhizobium meliloti [TaxId: 382]
Probab=99.68 E-value=3.9e-16 Score=83.93 Aligned_cols=88 Identities=15% Similarity=0.132 Sum_probs=68.9
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCe----eEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVE----KHFE 77 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~e 77 (109)
+++++++++++++| .+|+|+++|+++++++||++++++|++ ...+.++.........+...+..+.. ...+
T Consensus 20 ~i~~~~~~~i~~~d---~~g~i~~~N~~~~~l~Gy~~~el~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 94 (130)
T d1ew0a_ 20 SILDTVPDATVVSA---TDGTIVSFNAAAVRQFGYAEEEVIGQN--LRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRV 94 (130)
T ss_dssp HHHTTCSSEEEEEE---TTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTTGGGHHHHHHHHHHHCCCSSTTSCEE
T ss_pred HHHHcCCCeEEEEe---CCccEEEEHHHHHHhhcCCHHHhcCCc--cccccccchhHHHHHHHHHHHHhCCCccccceee
Confidence 36899999999999 789999999999999999999999998 56566555555544445555544432 4567
Q ss_pred EEEEecCCCEEEEeeec
Q psy6003 78 ILYYKKDGKYSSVGGSY 94 (109)
Q Consensus 78 ~~~~~~~g~~~~~~~~~ 94 (109)
+...++||..+|++++.
T Consensus 95 ~~~~~~dG~~~~v~~~~ 111 (130)
T d1ew0a_ 95 VSGQRKDGSTFPMKLAV 111 (130)
T ss_dssp EEEECTTSCEEEEEEEE
T ss_pred EEEEcCCCCEEEEEEEE
Confidence 78889999999997654
>d1nwza_ d.110.3.1 (A:) Photoactive yellow protein, PYP {Ectothiorhodospira halophila [TaxId: 1053]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PYP-like
domain: Photoactive yellow protein, PYP
species: Ectothiorhodospira halophila [TaxId: 1053]
Probab=99.68 E-value=2.7e-16 Score=84.44 Aligned_cols=89 Identities=13% Similarity=0.011 Sum_probs=70.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYY 81 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 81 (109)
+++++++++++++| .+|+|+++|+++++++||++++++|++. ..++.++.........+.+.+.++.....+....
T Consensus 21 ~~ld~~p~gi~~lD---~~G~i~~~N~a~~~l~G~~~~e~iG~~~-~~~~~p~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 96 (125)
T d1nwza_ 21 GQLDGLAFGAIQLD---GDGNILQYNAAEGDITGRDPKQVIGKNF-FKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTF 96 (125)
T ss_dssp HHHTTCSSEEEEEE---TTCBEEEECHHHHHHHCCCHHHHTTSBC-CCCCCGGGCSTTTHHHHHHHHHHTCCEEEEEEEE
T ss_pred HHHhCCCccEEEEe---CCCCEEEEcHHHHHhhccchHhhcCCCH-HHccCchhhhhheeeeceeeeecCCcceEEEEEe
Confidence 36789999999999 7899999999999999999999999982 4555554555555566777777777666665667
Q ss_pred ecCCCEEEEeeec
Q psy6003 82 KKDGKYSSVGGSY 94 (109)
Q Consensus 82 ~~~g~~~~~~~~~ 94 (109)
+++|+++|+++..
T Consensus 97 ~~~G~~~~v~v~l 109 (125)
T d1nwza_ 97 DYQMTPTKVKVHM 109 (125)
T ss_dssp CTTSCCEEEEEEE
T ss_pred ccCCcEEEEEEEE
Confidence 8899999986543
>d1v9ya_ d.110.3.2 (A:) Direct oxygen sensor protein, DOS {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Direct oxygen sensor protein, DOS
species: Escherichia coli [TaxId: 562]
Probab=99.65 E-value=6e-16 Score=81.11 Aligned_cols=88 Identities=14% Similarity=0.083 Sum_probs=61.6
Q ss_pred cccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHH----cCCeeEEE
Q psy6003 2 TLKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALA----AGVEKHFE 77 (109)
Q Consensus 2 ~~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~e 77 (109)
+++++++++++++| .+|+|+++|+++++++||+++|++|++ ...+.+................ .......+
T Consensus 5 ~~~e~~~d~i~~~d---~~g~i~~~N~~~~~l~Gy~~~e~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 79 (113)
T d1v9ya_ 5 PALEQNMMGAVLIN---ENDEVMFFNPAAEKLWGYKREEVIGNN--IDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRE 79 (113)
T ss_dssp HHHHTCSSEEEEEC---TTSBEEEECHHHHHHHSCCGGGTTTSB--GGGGSCGGGTTTHHHHHHHHHC----------CE
T ss_pred HHHHcCcCcEEEEe---CCCCEEEEchhHhhhhccchhhhcCcc--eeccccccccccccccccccccccccccccccee
Confidence 46899999999999 789999999999999999999999998 4444443333332222222222 22234456
Q ss_pred EEEEecCCCEEEEeeec
Q psy6003 78 ILYYKKDGKYSSVGGSY 94 (109)
Q Consensus 78 ~~~~~~~g~~~~~~~~~ 94 (109)
...++++|+.+|++++.
T Consensus 80 ~~~~~~dG~~~~v~~~~ 96 (113)
T d1v9ya_ 80 LQLEKKDGSKIWTRFAL 96 (113)
T ss_dssp EEEECTTSCEEEEEEEE
T ss_pred eeeccccceeEEEEEEE
Confidence 77789999999996554
>d1xj3a1 d.110.3.2 (A:154-259) Histidine kinase FixL heme domain {Bradyrhizobium japonicum [TaxId: 375]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Heme-binding PAS domain
domain: Histidine kinase FixL heme domain
species: Bradyrhizobium japonicum [TaxId: 375]
Probab=99.57 E-value=2.4e-14 Score=74.00 Aligned_cols=81 Identities=17% Similarity=0.137 Sum_probs=59.4
Q ss_pred ccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC----CeeEEEEEEEecC
Q psy6003 9 RSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG----VEKHFEILYYKKD 84 (109)
Q Consensus 9 ~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~e~~~~~~~ 84 (109)
|+++++| .+|+|+++|+++++++||+.+|++|++ ...+.++................. .....+...++++
T Consensus 1 dgi~~~D---~~G~I~~~N~a~~~l~Gy~~~el~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~d 75 (106)
T d1xj3a1 1 DAMIVID---GHGIIQLFSTAAERLFGWSELEAIGQN--VNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRD 75 (106)
T ss_dssp CCEEEEE---TTSBEEEECHHHHHHHCCCHHHHTTSB--GGGGSCTTHHHHHHHHHHHHHHHCCCSSTTTCEEEEEECTT
T ss_pred CEEEEEC---CCCcEEEEcHHHHHHhhhchHhhcCCC--cccccccccccchhhhhhhhhhhcccccccccceeeeeecc
Confidence 6899999 789999999999999999999999998 455555544444333333333322 2245678888999
Q ss_pred CCEEEEeeec
Q psy6003 85 GKYSSVGGSY 94 (109)
Q Consensus 85 g~~~~~~~~~ 94 (109)
|..+|++++.
T Consensus 76 g~~~~v~~~~ 85 (106)
T d1xj3a1 76 GTTFPMHLSI 85 (106)
T ss_dssp SCEEEEEEEE
T ss_pred ceEEEEEEEE
Confidence 9999996544
>d1p97a_ d.110.3.7 (A:) Hypoxia-inducible factor Hif2a, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: Hypoxia-inducible factor Hif2a, C-terminal domain
domain: Hypoxia-inducible factor Hif2a, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]
Probab=99.50 E-value=3.9e-14 Score=74.45 Aligned_cols=78 Identities=15% Similarity=0.195 Sum_probs=61.3
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEE
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSV 90 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~ 90 (109)
+...+ .+|+++|+|+++++++||+.++++|++ ...+.++.+.....+.....+..+..+..+++.+++||+.+|+
T Consensus 9 i~r~~---~dG~i~~~N~~~~~~~G~~~~el~g~~--~~~~~~~ed~~~~~~~~~~~~~~~~~~~~e~~~~~kdG~~~wv 83 (114)
T d1p97a_ 9 LSRHS---MDMKFTYCDDRITELIGYHPEELLGRS--AYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWL 83 (114)
T ss_dssp EEEEC---TTTSCSEECTTHHHHTSSCHHHHTTSC--HHHHSCSSSHHHHHHHHHHHTTTSEEEEEEEEEECTTSCEEEE
T ss_pred EEEEC---CCCcEEEECHHHHHHcCCCcccccccc--ccccccccccccceeeeeecccccceeecceeeeeecCcceEE
Confidence 33456 789999999999999999999999998 4445555555555566666666667778899999999999999
Q ss_pred eee
Q psy6003 91 GGS 93 (109)
Q Consensus 91 ~~~ 93 (109)
++.
T Consensus 84 ~~~ 86 (114)
T d1p97a_ 84 ETQ 86 (114)
T ss_dssp EEE
T ss_pred EEE
Confidence 643
>d1ll8a_ d.110.3.5 (A:) N-terminal PAS domain of Pas kinase {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: N-terminal PAS domain of Pas kinase
domain: N-terminal PAS domain of Pas kinase
species: Human (Homo sapiens) [TaxId: 9606]
Probab=99.47 E-value=1.7e-14 Score=75.98 Aligned_cols=89 Identities=15% Similarity=0.172 Sum_probs=63.8
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCe----eEEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVE----KHFEI 78 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~e~ 78 (109)
+-+.+.++++++|. .+|+|+++|+++++++||+.++++|++ ...+.++.........+...+..+.. ...+.
T Consensus 3 ~~~~~n~AI~~id~--~~G~I~~~N~a~~~l~Gy~~~el~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 78 (114)
T d1ll8a_ 3 MDPEFNKAIFTVDA--KTTEILVANDKACGLLGYSSQDLIGQK--LTQFFLRSDSDVVEALSEEHMEADGHAAVVFGTVV 78 (114)
T ss_dssp SSTTTTCEEEEEET--TTCBEEEECTTHHHHHTCCTTTTTTSB--GGGGSSCTTTHHHHHTTSSTTSSSSCSSCCCSSSE
T ss_pred cchhcCcEEEEEEC--CCCEEEEECHHHHHhhcCCHHHHcCCC--eeeecCcccHHHHHHHHHHHHhcCCCccceeeEEE
Confidence 45678899999994 369999999999999999999999999 45565555554443333333333221 22356
Q ss_pred EEEecCCCEEEEeeecc
Q psy6003 79 LYYKKDGKYSSVGGSYG 95 (109)
Q Consensus 79 ~~~~~~g~~~~~~~~~~ 95 (109)
..++++|+.+|++++..
T Consensus 79 ~~~~~~G~~~pvevs~~ 95 (114)
T d1ll8a_ 79 DIISRSGEKIPVSVWMK 95 (114)
T ss_dssp EECCTTCCCEEEECCEE
T ss_pred EEEccCCcEEEEEEEEE
Confidence 77889999999976543
>d1oj5a_ d.110.3.8 (A:) PAS domain of steroid receptor coactivator 1A, NCo-A1 {Mouse (Mus musculus) [TaxId: 10090]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: PAS domain of steroid receptor coactivator 1A, NCo-A1
domain: PAS domain of steroid receptor coactivator 1A, NCo-A1
species: Mouse (Mus musculus) [TaxId: 10090]
Probab=99.24 E-value=2.8e-12 Score=66.96 Aligned_cols=77 Identities=16% Similarity=0.146 Sum_probs=58.2
Q ss_pred EEEecCCCCeeEEEecHHHHHhhCCCh-HHHhCCccccccccCCCCc-H-HHHHHHHHHHHcCCeeEEEEEEEecCCCEE
Q psy6003 12 LVANSHLGLCHIIYCSDGFCRLTGFSR-AEVMQQDAICKFLHGPLTS-Q-HAVQVVKEALAAGVEKHFEILYYKKDGKYS 88 (109)
Q Consensus 12 ~i~d~~~~~~~i~~~N~~~~~~~g~~~-~e~~g~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~ 88 (109)
...| .+|+++++|++..+++||.+ +|++|++ ...+.++++. . .........+..+.....+++.+++||...
T Consensus 6 trh~---~~g~~~~vd~~~~~~~gy~~~eelig~s--~~~f~HPeD~~~~~~~~~~~~~~~~g~~~~~~yR~~~kdG~~v 80 (109)
T d1oj5a_ 6 TKQD---TTGKIISIDTSSLRAAGRTGWEDLVRKC--IYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTML 80 (109)
T ss_dssp EEEC---TTCCEEEEECHHHHTTCCSCHHHHHHHH--HHHHTSCBTTBCCHHHHHHHHHHHHSEEECCCEEEECTTSCEE
T ss_pred EEEC---CCceEEEECHHHhhHhhcCCHHHHcCCc--HHHeECcccchHHHhhHHHHHHHhhcccchhhhhhhhccCcEE
Confidence 4456 68999999999999999985 8999999 4444444443 2 222334556677888888899999999999
Q ss_pred EEeee
Q psy6003 89 SVGGS 93 (109)
Q Consensus 89 ~~~~~ 93 (109)
|++..
T Consensus 81 Wv~t~ 85 (109)
T d1oj5a_ 81 SAHTR 85 (109)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 99654
>d2oola2 d.110.3.9 (A:26-139) Sensor protein PhyB2 {Rhodopseudomonas palustris [TaxId: 1076]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Sensor protein PhyB2
species: Rhodopseudomonas palustris [TaxId: 1076]
Probab=98.09 E-value=2.5e-06 Score=44.06 Aligned_cols=40 Identities=13% Similarity=0.027 Sum_probs=32.0
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCC
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGP 54 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~ 54 (109)
++.+|. .+++|++++++...++|+++++++|++ ...+.++
T Consensus 20 Llvld~--~d~~I~~vS~N~~~lLG~~~~~llG~~--l~dll~~ 59 (114)
T d2oola2 20 LFVVSE--TDLRIASVSANVEDLLRQPPASLLNVP--IAHYLTA 59 (114)
T ss_dssp EEEECT--TTCBEEEEETTHHHHHSSCGGGGTTCB--GGGGBCH
T ss_pred EEEEEC--CCCEEEEEcCCHHHHhCCChHHHcCCC--HHHhCCH
Confidence 455553 479999999999999999999999999 4444443
>d2o9ca2 d.110.3.9 (A:4-130) Bacteriophytochrome BphP {Deinococcus radiodurans [TaxId: 1299]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Deinococcus radiodurans [TaxId: 1299]
Probab=96.15 E-value=0.017 Score=29.92 Aligned_cols=39 Identities=15% Similarity=0.059 Sum_probs=31.7
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccC
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHG 53 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~ 53 (109)
++.+|. .++.|+.++.....++|++.++++|++ ...+.+
T Consensus 38 LLald~--~~~~I~~~S~N~~~~lG~~~~~llG~~--l~~ll~ 76 (127)
T d2o9ca2 38 LLTADG--HSGEVLQMSLNAATFLGQEPTVLRGQT--LAALLP 76 (127)
T ss_dssp EEEEET--TTCBEEEEETTHHHHHSSCHHHHTTCB--HHHHCT
T ss_pred EEEEEC--CCCEEEEECCCHHHHhCCChHHHcCCC--HHHHCC
Confidence 455563 479999999999999999999999999 454544
>d2veaa3 d.110.3.9 (A:4-130) Phytochrome-like protein Cph1 {Synechocystis sp. pcc 6803 [TaxId: 1148]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Phytochrome-like protein Cph1
species: Synechocystis sp. pcc 6803 [TaxId: 1148]
Probab=95.66 E-value=0.0055 Score=31.84 Aligned_cols=41 Identities=12% Similarity=0.073 Sum_probs=32.1
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCC
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPL 55 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~ 55 (109)
++.+|. .+++|..++.....++|.++++++|++ ...+.++.
T Consensus 29 LLald~--~~~~I~~aS~N~~~~lG~~~~~lLG~~--l~~ll~~~ 69 (127)
T d2veaa3 29 VVVLQE--PDLTISQISANCTGILGRSPEDLLGRT--LGEVFDSF 69 (127)
T ss_dssp EEEEET--TTTEEEEEETTHHHHTSCCTTTSSTTT--TTTTSBCC
T ss_pred EEEEEC--CCCEEEEEcCCHHHHhCcChHHHcCCC--HHHHCCHH
Confidence 455553 478999999999999999999999998 44444433
>d3c2wa3 d.110.3.9 (A:5-117) Bacteriophytochrome BphP {Pseudomonas aeruginosa [TaxId: 287]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Profilin-like
superfamily: PYP-like sensor domain (PAS domain)
family: BphP N-terminal domain-like
domain: Bacteriophytochrome BphP
species: Pseudomonas aeruginosa [TaxId: 287]
Probab=84.90 E-value=1.3 Score=21.86 Aligned_cols=70 Identities=11% Similarity=0.058 Sum_probs=40.3
Q ss_pred EEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEE
Q psy6003 11 FLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSV 90 (109)
Q Consensus 11 i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~ 90 (109)
++.+| .++.|+.++.....++|++++ .+|+. ...+.. ......+.+.+........... .+.+|..+++
T Consensus 25 LLald---~~~~I~~~S~N~~~~lg~~~~-~L~~~--~~~~~~----~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~d~ 93 (113)
T d3c2wa3 25 LVTLR---ADGMVLAASENIQALLGFVAS-PGSYL--TQEQVG----PEVLRMLEEGLTGNGPWSNSVE-TRIGEHLFDV 93 (113)
T ss_dssp EEEEC---TTSBEEEEETTHHHHTSSCCC-TTCBC--CHHHHH----HHHHHHHHHHHSCSSCCCCEEE-ECCSSSCEEE
T ss_pred EEEEc---CCCeEEEEcCCHHHHhCCChh-Hhccc--HHHHhC----HHHHHHHHhhhhcCCCceeEEE-eccCCeEEEE
Confidence 45666 578999999999999999865 45665 222221 2333444555444443333332 2345666665
Q ss_pred e
Q psy6003 91 G 91 (109)
Q Consensus 91 ~ 91 (109)
-
T Consensus 94 ~ 94 (113)
T d3c2wa3 94 I 94 (113)
T ss_dssp E
T ss_pred E
Confidence 3
