Query psy6003
Match_columns 109
No_of_seqs 128 out of 1003
Neff 11.1
Searched_HMMs 46136
Date Sat Aug 17 00:07:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6003.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6003hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13426 PAS_9: PAS domain; PD 99.7 2.1E-15 4.5E-20 79.8 10.6 82 8-94 1-82 (104)
2 PF00989 PAS: PAS fold; Inter 99.6 1.1E-13 2.4E-18 74.2 9.1 88 2-94 5-93 (113)
3 PF08448 PAS_4: PAS fold; Int 99.4 2.3E-12 4.9E-17 68.7 8.7 84 4-93 1-84 (110)
4 PRK13557 histidine kinase; Pro 99.3 1.6E-11 3.6E-16 81.2 9.7 88 3-92 35-122 (540)
5 PRK13559 hypothetical protein; 99.2 2E-10 4.2E-15 73.1 10.0 88 3-92 48-135 (361)
6 PRK10060 RNase II stability mo 99.2 1.4E-10 3E-15 79.2 8.7 84 3-90 116-199 (663)
7 PRK13560 hypothetical protein; 99.1 1.3E-09 2.7E-14 75.4 9.3 86 2-92 208-293 (807)
8 TIGR02040 PpsR-CrtJ transcript 99.1 1.1E-09 2.3E-14 71.7 8.2 87 2-94 256-343 (442)
9 PRK11091 aerobic respiration c 99.1 9.2E-10 2E-14 76.3 8.2 87 2-93 159-245 (779)
10 TIGR02938 nifL_nitrog nitrogen 99.0 1.2E-09 2.6E-14 71.5 5.8 85 2-91 8-92 (494)
11 PRK13558 bacterio-opsin activa 99.0 9.4E-09 2E-13 70.2 10.0 89 3-93 153-241 (665)
12 PF08447 PAS_3: PAS fold; Int 98.9 8E-09 1.7E-13 53.4 6.6 70 23-93 1-73 (91)
13 PRK11073 glnL nitrogen regulat 98.9 1E-08 2.2E-13 64.9 8.2 85 2-93 11-95 (348)
14 cd00130 PAS PAS domain; PAS mo 98.9 1E-07 2.2E-12 47.4 10.1 80 8-92 2-81 (103)
15 TIGR02040 PpsR-CrtJ transcript 98.9 2.5E-09 5.5E-14 69.9 3.9 86 3-93 1-87 (442)
16 PF14598 PAS_11: PAS domain; P 98.9 1.7E-07 3.7E-12 50.6 10.3 72 19-92 10-83 (111)
17 PRK09776 putative diguanylate 98.8 3.3E-08 7.1E-13 70.7 8.5 86 3-93 288-374 (1092)
18 PRK11359 cyclic-di-GMP phospho 98.8 3.6E-08 7.7E-13 68.5 8.3 86 3-92 141-226 (799)
19 PRK11359 cyclic-di-GMP phospho 98.8 2.9E-08 6.4E-13 68.9 7.3 86 3-93 17-106 (799)
20 TIGR00229 sensory_box PAS doma 98.8 2.1E-07 4.6E-12 48.2 8.4 84 3-91 8-92 (124)
21 KOG0501|consensus 98.7 5.8E-08 1.3E-12 64.8 6.6 78 20-100 39-116 (971)
22 KOG1229|consensus 98.7 2.3E-09 5E-14 69.2 -0.9 84 2-90 161-245 (775)
23 TIGR02966 phoR_proteo phosphat 98.6 1.8E-07 3.8E-12 58.6 6.7 41 2-45 10-50 (333)
24 PRK09776 putative diguanylate 98.5 1.4E-06 3.1E-11 62.5 8.5 86 3-93 541-630 (1092)
25 PF13188 PAS_8: PAS domain; PD 98.3 1.3E-06 2.9E-11 42.3 4.2 37 2-45 5-41 (64)
26 PF12860 PAS_7: PAS fold 98.3 2.8E-05 6.1E-10 41.9 8.9 39 4-45 1-40 (115)
27 PF13596 PAS_10: PAS domain; P 98.2 4.3E-06 9.3E-11 44.5 5.0 78 2-87 3-80 (106)
28 PRK10820 DNA-binding transcrip 98.2 5.6E-06 1.2E-10 55.6 5.8 46 2-52 84-129 (520)
29 PF08670 MEKHLA: MEKHLA domain 98.1 8.2E-05 1.8E-09 42.1 7.8 83 6-91 39-121 (148)
30 PRK11360 sensory histidine kin 98.0 4.7E-05 1E-09 51.2 7.9 79 3-88 267-346 (607)
31 TIGR02373 photo_yellow photoac 98.0 0.0002 4.4E-09 39.1 8.5 63 4-71 22-85 (124)
32 PRK13560 hypothetical protein; 98.0 3E-05 6.4E-10 54.1 6.6 85 3-92 337-440 (807)
33 PRK11006 phoR phosphate regulo 97.9 7.7E-06 1.7E-10 53.5 2.4 40 3-45 103-142 (430)
34 PRK11388 DNA-binding transcrip 97.9 8.8E-05 1.9E-09 51.1 7.4 40 3-45 208-247 (638)
35 KOG3558|consensus 97.8 2.4E-05 5.3E-10 53.3 4.0 71 19-91 282-352 (768)
36 smart00091 PAS PAS domain. PAS 97.8 0.00014 3E-09 32.9 5.3 40 3-45 6-45 (67)
37 COG3852 NtrB Signal transducti 97.7 0.00014 2.9E-09 45.8 5.4 82 2-90 11-92 (363)
38 COG2202 AtoS FOG: PAS/PAC doma 97.7 0.00089 1.9E-08 37.6 8.2 83 3-90 117-202 (232)
39 COG3829 RocR Transcriptional r 97.2 0.00058 1.3E-08 46.0 3.9 41 2-45 121-161 (560)
40 KOG3561|consensus 97.0 0.00044 9.5E-09 48.6 2.0 46 3-52 100-145 (803)
41 PRK15053 dpiB sensor histidine 96.8 0.0013 2.9E-08 44.4 2.9 40 3-45 227-268 (545)
42 COG3283 TyrR Transcriptional r 96.7 0.0029 6.2E-08 41.1 3.6 41 2-45 84-124 (511)
43 TIGR02938 nifL_nitrog nitrogen 96.6 0.0029 6.2E-08 41.8 3.6 41 2-45 134-174 (494)
44 PRK11086 sensory histidine kin 96.5 0.0027 5.9E-08 42.7 3.1 41 2-45 225-268 (542)
45 COG5002 VicK Signal transducti 96.2 0.0057 1.2E-07 39.6 2.8 47 2-52 115-161 (459)
46 PRK09959 hybrid sensory histid 95.8 0.043 9.3E-07 40.8 6.1 36 2-40 580-615 (1197)
47 KOG3558|consensus 95.7 0.015 3.2E-07 40.5 3.3 58 3-65 124-181 (768)
48 PF08446 PAS_2: PAS fold; Int 95.5 0.056 1.2E-06 29.1 4.5 42 10-55 17-61 (110)
49 COG5000 NtrY Signal transducti 95.3 0.074 1.6E-06 37.0 5.6 41 2-45 374-414 (712)
50 KOG3560|consensus 95.2 0.12 2.5E-06 35.5 6.0 71 19-91 291-361 (712)
51 COG3290 CitA Signal transducti 94.5 0.035 7.7E-07 37.7 2.4 40 3-45 220-261 (537)
52 KOG3560|consensus 94.2 0.063 1.4E-06 36.7 3.0 57 3-64 116-172 (712)
53 KOG3559|consensus 92.6 0.19 4.1E-06 33.3 3.3 32 11-45 228-259 (598)
54 PF06785 UPF0242: Uncharacteri 87.2 0.76 1.7E-05 29.8 2.7 72 9-88 298-369 (401)
55 PRK10618 phosphotransfer inter 86.1 0.99 2.1E-05 33.3 3.1 34 2-37 347-380 (894)
56 KOG3753|consensus 84.6 5 0.00011 29.7 5.8 70 19-90 339-411 (1114)
57 KOG3559|consensus 80.7 0.84 1.8E-05 30.5 1.0 46 4-53 85-130 (598)
58 COG2461 Uncharacterized conser 74.0 8.6 0.00019 25.8 4.0 67 3-77 295-361 (409)
59 PRK14538 putative bifunctional 69.1 7.5 0.00016 28.8 3.3 38 3-45 107-144 (838)
60 PRK13719 conjugal transfer tra 68.6 5.3 0.00011 24.5 2.1 32 3-37 24-55 (217)
61 COG3887 Predicted signaling pr 66.4 6.7 0.00015 27.8 2.5 30 3-35 80-109 (655)
62 KOG3753|consensus 54.7 16 0.00034 27.4 2.8 27 19-45 200-226 (1114)
63 PF15660 Imm49: Immunity prote 54.0 14 0.00031 17.9 1.8 24 8-31 31-54 (84)
64 PF07310 PAS_5: PAS domain; I 52.0 41 0.00089 18.7 8.7 67 20-91 50-116 (137)
65 PRK10841 hybrid sensory kinase 50.0 26 0.00057 26.3 3.4 35 3-39 339-373 (924)
66 COG3829 RocR Transcriptional r 39.5 24 0.00053 24.9 1.8 41 2-45 5-45 (560)
67 COG4296 Uncharacterized protei 37.9 61 0.0013 18.5 2.9 22 75-96 121-142 (156)
68 COG4251 Bacteriophytochrome (l 33.9 43 0.00093 24.4 2.3 27 19-45 38-64 (750)
69 KOG3561|consensus 32.7 40 0.00087 25.1 2.1 70 19-90 380-450 (803)
70 PF09292 Neil1-DNA_bind: Endon 31.6 53 0.0012 14.1 1.9 11 80-90 20-30 (39)
71 COG3617 Prophage antirepressor 27.6 1.3E+02 0.0028 18.0 3.3 28 10-40 18-45 (176)
72 KOG3439|consensus 27.2 22 0.00048 19.4 0.1 7 23-29 77-83 (116)
73 smart00153 VHP Villin headpiec 25.1 72 0.0016 13.5 1.8 19 27-45 4-22 (36)
74 COG3284 AcoR Transcriptional a 23.3 1.4E+02 0.0031 21.7 3.3 39 4-45 228-267 (606)
75 PF02209 VHP: Villin headpiece 22.6 83 0.0018 13.3 1.5 19 27-45 4-22 (36)
76 PF14584 DUF4446: Protein of u 20.6 1.3E+02 0.0028 17.4 2.4 24 3-26 104-127 (151)
77 PF08646 Rep_fac-A_C: Replicat 20.6 81 0.0018 17.7 1.6 23 21-43 67-89 (146)
No 1
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.68 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
No 2
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. 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 ....
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
No 3
>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 []. 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.
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
No 4
>PRK13557 histidine kinase; Provisional
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
No 5
>PRK13559 hypothetical protein; Provisional
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
No 6
>PRK10060 RNase II stability modulator; Provisional
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
No 7
>PRK13560 hypothetical protein; Provisional
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
No 8
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. 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).
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
No 9
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
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
No 10
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. 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.
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
No 11
>PRK13558 bacterio-opsin activator; Provisional
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
No 12
>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 []. 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.
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
No 13
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
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
No 14
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. 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.
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
No 15
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. 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).
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
No 16
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.86 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
No 17
>PRK09776 putative diguanylate cyclase; Provisional
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
No 18
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
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
No 19
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
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
No 20
>TIGR00229 sensory_box PAS domain S-box. 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.
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
No 21
>KOG0501|consensus
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
No 22
>KOG1229|consensus
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
No 23
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. 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).
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
No 24
>PRK09776 putative diguanylate cyclase; Provisional
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
No 25
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
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
No 26
>PF12860 PAS_7: PAS fold
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
No 27
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
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
No 28
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
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
No 29
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=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
No 30
>PRK11360 sensory histidine kinase AtoS; Provisional
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
No 31
>TIGR02373 photo_yellow photoactive yellow protein. 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.
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
No 32
>PRK13560 hypothetical protein; Provisional
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
No 33
>PRK11006 phoR phosphate regulon sensor protein; Provisional
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
No 34
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
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
No 35
>KOG3558|consensus
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
No 36
>smart00091 PAS PAS domain. 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).
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
No 37
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
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
No 38
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
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
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
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
No 40
>KOG3561|consensus
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
No 41
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
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
No 42
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
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
No 43
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. 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.
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
No 44
>PRK11086 sensory histidine kinase DcuS; Provisional
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
No 45
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
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
No 46
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
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
No 47
>KOG3558|consensus
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
No 48
>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 []. 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 ....
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
No 49
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
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
No 50
>KOG3560|consensus
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
No 51
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
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
No 52
>KOG3560|consensus
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
No 53
>KOG3559|consensus
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
No 54
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
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
No 55
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
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
No 56
>KOG3753|consensus
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
No 57
>KOG3559|consensus
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
No 58
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=73.98 E-value=8.6 Score=25.78 Aligned_cols=67 Identities=16% Similarity=0.194 Sum_probs=43.4
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEE
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFE 77 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 77 (109)
+|++.|--+-.+| .++++.+.|+. .+++-+++.. +|++ .. .-+|.........+.+.+.+|..-..+
T Consensus 295 if~~lP~Ditfvd---k~diV~ffs~~-~rif~rt~sv-iGr~--v~-~chpPksv~iv~ki~~~fksG~kd~~e 361 (409)
T COG2461 295 IFKHLPVDITFVD---KNDIVRFFSGG-ERIFPRTPSV-IGRR--VQ-LCHPPKSVHIVEKILKDFKSGEKDFAE 361 (409)
T ss_pred HHhhCCCceEEec---ccceEEecCCc-ceecccChHh-hCCc--cc-CCCCCchHHHHHHHHHHhhcCCcchHH
Confidence 4667774444566 68899999997 8888887776 7887 33 334444455566666666665543333
No 59
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=69.05 E-value=7.5 Score=28.78 Aligned_cols=38 Identities=3% Similarity=-0.064 Sum_probs=30.0
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 107 ~l~~~p~gi~~~~~--~~~~i~W~N~~~~~~~~--~~-~~g~~ 144 (838)
T PRK14538 107 VLNELPIGIVLIDI--SSKEIQWLNPYANFILK--NP-EINTP 144 (838)
T ss_pred HHHhCCceEEEEeC--CCCEEEEECHHHHHHhC--cc-ccCCc
Confidence 35678899988883 26899999999999877 22 78887
No 60
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=68.55 E-value=5.3 Score=24.48 Aligned_cols=32 Identities=9% Similarity=-0.035 Sum_probs=26.7
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCC
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFS 37 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~ 37 (109)
+.+..+..+++=+ .+|.++++|.+|.+.+..+
T Consensus 24 ~i~~~~~P~CiR~---~~g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 24 FIDDYSYPACIRN---ESGKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHcCCCCeEEEC---CCCCeeecchHHHHHHHhc
Confidence 4567788889988 8999999999999988543
No 61
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=66.36 E-value=6.7 Score=27.81 Aligned_cols=30 Identities=3% Similarity=-0.010 Sum_probs=26.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhC
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTG 35 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g 35 (109)
++.++|-|+++.+ .++.+.|+||-...+++
T Consensus 80 al~nmPiGii~~~---e~~~veW~Npf~~~if~ 109 (655)
T COG3887 80 ALTNMPIGIILFN---ETNKVEWVNPFASKIFN 109 (655)
T ss_pred HHHhCCceEEEEc---CCCceEEecHHHHHhcC
Confidence 4678999999999 88999999998888774
No 62
>KOG3753|consensus
Probab=54.71 E-value=16 Score=27.40 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=25.4
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
.+|+++|+...+..++||.++-+.+..
T Consensus 200 ~dG~iLyis~q~a~ilg~krDv~s~a~ 226 (1114)
T KOG3753|consen 200 LDGRILYISEQAALILGCKRDVLSSAK 226 (1114)
T ss_pred cCCcEEEeechhhhhccCchhhhccch
Confidence 689999999999999999999998887
No 63
>PF15660 Imm49: Immunity protein 49
Probab=53.98 E-value=14 Score=17.86 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=16.0
Q ss_pred CccEEEEecCCCCeeEEEecHHHH
Q psy6003 8 NRSFLVANSHLGLCHIIYCSDGFC 31 (109)
Q Consensus 8 ~~~i~i~d~~~~~~~i~~~N~~~~ 31 (109)
.+.+++...-+...+++|.||.|.
T Consensus 31 adrlmvttsvgeearlvyfnpdfa 54 (84)
T PF15660_consen 31 ADRLMVTTSVGEEARLVYFNPDFA 54 (84)
T ss_pred cceEEEEeccCceeEEEEeCCCcC
Confidence 344555554446678999999765
No 64
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=51.98 E-value=41 Score=18.73 Aligned_cols=67 Identities=10% Similarity=0.028 Sum_probs=44.4
Q ss_pred CeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcCCeeEEEEEEEecCCCEEEEe
Q psy6003 20 LCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAGVEKHFEILYYKKDGKYSSVG 91 (109)
Q Consensus 20 ~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~ 91 (109)
+.++..+-...++++|+.. .|+. ...+..+.........+..+................+|....++
T Consensus 50 ~~r~RLaGt~i~~~~G~d~---tG~~--~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e 116 (137)
T PF07310_consen 50 DFRYRLAGTRIVELFGRDL---TGRR--LSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYE 116 (137)
T ss_pred ceEEEEecHHHHHHhCCCC---CCCC--HHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEE
Confidence 4566777778888888743 5777 44455555555666677777777777766666666677665443
No 65
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=49.98 E-value=26 Score=26.33 Aligned_cols=35 Identities=3% Similarity=-0.090 Sum_probs=28.7
Q ss_pred ccccCCccEEEEecCCCCeeEEEecHHHHHhhCCChH
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFSRA 39 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~ 39 (109)
++++++.++++.+. .++.++++|+.+..++|+...
T Consensus 339 iv~~~p~gi~i~~~--~~g~~~~~N~~a~~~~~l~~~ 373 (924)
T PRK10841 339 IVASAPVGICILRT--SDGTNILSNELAHNYLNMLTH 373 (924)
T ss_pred HHHhCCccEEEEEc--CCCcEEEehHHHHHHhccCCh
Confidence 56789999999875 579999999999998886443
No 66
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=39.47 E-value=24 Score=24.91 Aligned_cols=41 Identities=7% Similarity=-0.126 Sum_probs=34.8
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 5 ~~l~~~~~~~~vi~---~~~~~~~~~~~a~~~~~~~~~~~i~~~ 45 (560)
T COG3829 5 GILKSILDGPVVID---KNTGIDVANALALAKRQKNAEAVIGRP 45 (560)
T ss_pred hhhhhcccceEEEE---cCCceeeechHHHHhhhcceEEEeccc
Confidence 35788899999998 788999999999988888887788876
No 67
>COG4296 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.92 E-value=61 Score=18.46 Aligned_cols=22 Identities=18% Similarity=0.039 Sum_probs=16.6
Q ss_pred EEEEEEEecCCCEEEEeeeccc
Q psy6003 75 HFEILYYKKDGKYSSVGGSYGD 96 (109)
Q Consensus 75 ~~e~~~~~~~g~~~~~~~~~~~ 96 (109)
.++..++..||..+|.++.+.+
T Consensus 121 dGe~efyy~DGdLF~GH~Ilis 142 (156)
T COG4296 121 DGEAEFYYSDGDLFAGHVILIS 142 (156)
T ss_pred CCcEEEEecCCCeEeeeEEEEE
Confidence 3567788899999998766543
No 68
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=33.88 E-value=43 Score=24.43 Aligned_cols=27 Identities=7% Similarity=0.196 Sum_probs=24.9
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCc
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~ 45 (109)
.++.++.++.....++|..++++.|++
T Consensus 38 ~~~~Vlq~S~N~~~~LG~~~e~l~~~t 64 (750)
T COG4251 38 ADLMVLQASENCANILGREPEDLLGRT 64 (750)
T ss_pred CCchhhhhhhhHHHHhCCChhhhhcCC
Confidence 578899999999999999999999998
No 69
>KOG3561|consensus
Probab=32.71 E-value=40 Score=25.14 Aligned_cols=70 Identities=11% Similarity=0.132 Sum_probs=42.3
Q ss_pred CCeeEEEecHHHHHhhCCChHHHhCCccccccccCCCCcHHHHHHHHHHHHcC-CeeEEEEEEEecCCCEEEE
Q psy6003 19 GLCHIIYCSDGFCRLTGFSRAEVMQQDAICKFLHGPLTSQHAVQVVKEALAAG-VEKHFEILYYKKDGKYSSV 90 (109)
Q Consensus 19 ~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~~~~g~~~~~ 90 (109)
.+|.++++......+.||...++.|+. .....+..+.......+....... .....-++.+.++|...|.
T Consensus 380 ~~g~~~~~dqr~~~i~~~~~~~~~g~s--s~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~~ 450 (803)
T KOG3561|consen 380 SDGSFTFVDQRASAILGYQPQELLGRS--SYESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIPN 450 (803)
T ss_pred cCCceeccccccccccccCchhhcCcc--cccccCccccchhhchHHHHHHhcccccccccccccCCCCcccc
Confidence 478899999999999999999999998 443444443333333333222211 1223334556667765544
No 70
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=31.63 E-value=53 Score=14.13 Aligned_cols=11 Identities=9% Similarity=0.184 Sum_probs=6.9
Q ss_pred EEecCCCEEEE
Q psy6003 80 YYKKDGKYSSV 90 (109)
Q Consensus 80 ~~~~~g~~~~~ 90 (109)
++..+|+.+|+
T Consensus 20 l~D~~gRTiWF 30 (39)
T PF09292_consen 20 LRDRNGRTIWF 30 (39)
T ss_dssp EE-TTS-EEEE
T ss_pred ccccCCCEEEe
Confidence 45678888898
No 71
>COG3617 Prophage antirepressor [Transcription]
Probab=27.60 E-value=1.3e+02 Score=17.97 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=20.9
Q ss_pred cEEEEecCCCCeeEEEecHHHHHhhCCChHH
Q psy6003 10 SFLVANSHLGLCHIIYCSDGFCRLTGFSRAE 40 (109)
Q Consensus 10 ~i~i~d~~~~~~~i~~~N~~~~~~~g~~~~e 40 (109)
.+-++. .+|.+-++-...++++||+...
T Consensus 18 ~vRvv~---~d~epwFva~Dva~~Lg~~n~~ 45 (176)
T COG3617 18 AVRVVL---DDGEPWFVAADVARALGYTNPS 45 (176)
T ss_pred eEEEEE---eCCceeEeHHHHHHHHCCCCHH
Confidence 444444 4678888889999999997754
No 72
>KOG3439|consensus
Probab=27.24 E-value=22 Score=19.38 Aligned_cols=7 Identities=14% Similarity=0.719 Sum_probs=2.8
Q ss_pred EEEecHH
Q psy6003 23 IIYCSDG 29 (109)
Q Consensus 23 i~~~N~~ 29 (109)
++|+|.+
T Consensus 77 flYVN~s 83 (116)
T KOG3439|consen 77 FLYVNNS 83 (116)
T ss_pred EEEEcCc
Confidence 3344433
No 73
>smart00153 VHP Villin headpiece domain.
Probab=25.06 E-value=72 Score=13.50 Aligned_cols=19 Identities=21% Similarity=0.429 Sum_probs=14.4
Q ss_pred cHHHHHhhCCChHHHhCCc
Q psy6003 27 SDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 27 N~~~~~~~g~~~~e~~g~~ 45 (109)
+..|..++|.++++.-..+
T Consensus 4 deeF~~vfgmsr~eF~~LP 22 (36)
T smart00153 4 DEDFEEVFGMTREEFYKLP 22 (36)
T ss_pred HHHHHHHHCCCHHHHHhCc
Confidence 4568899999998875544
No 74
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=23.26 E-value=1.4e+02 Score=21.71 Aligned_cols=39 Identities=10% Similarity=0.177 Sum_probs=31.3
Q ss_pred cccCCccEEEEecCCCCeeEEEecHHHHHhhCCC-hHHHhCCc
Q psy6003 4 KHHTNRSFLVANSHLGLCHIIYCSDGFCRLTGFS-RAEVMQQD 45 (109)
Q Consensus 4 ~~~~~~~i~i~d~~~~~~~i~~~N~~~~~~~g~~-~~e~~g~~ 45 (109)
.+..+.+.++.| .+++++..|++..++++.+ ...+.|.+
T Consensus 228 ~d~~~~~~lavd---~~grvl~at~aA~~~La~~~~~~l~g~p 267 (606)
T COG3284 228 LDSQSEALLAVD---QDGRVLGATRAARQLLALTDRQRLIGQP 267 (606)
T ss_pred cCcccceeeeec---CcchhhhccHHHHHhhccchhhHhhcCC
Confidence 455677888888 7899999999999999988 44556665
No 75
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=22.63 E-value=83 Score=13.35 Aligned_cols=19 Identities=26% Similarity=0.482 Sum_probs=12.9
Q ss_pred cHHHHHhhCCChHHHhCCc
Q psy6003 27 SDGFCRLTGFSRAEVMQQD 45 (109)
Q Consensus 27 N~~~~~~~g~~~~e~~g~~ 45 (109)
+..|.+++|.++++....+
T Consensus 4 d~dF~~vFgm~~~eF~~lP 22 (36)
T PF02209_consen 4 DEDFEKVFGMSREEFYKLP 22 (36)
T ss_dssp HHHHHHHHSS-HHHHHHS-
T ss_pred HHHHHHHHCCCHHHHHHCh
Confidence 3568899999998875544
No 76
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=20.65 E-value=1.3e+02 Score=17.42 Aligned_cols=24 Identities=17% Similarity=0.187 Sum_probs=13.2
Q ss_pred ccccCCccEEEEecCCCCeeEEEe
Q psy6003 3 LKHHTNRSFLVANSHLGLCHIIYC 26 (109)
Q Consensus 3 ~~~~~~~~i~i~d~~~~~~~i~~~ 26 (109)
+++.-.+|+++.....+++..+|+
T Consensus 104 lLD~~~nGvVltsI~~Re~s~~Ya 127 (151)
T PF14584_consen 104 LLDDNNNGVVLTSIHSREESRTYA 127 (151)
T ss_pred EEeCCCCEEEEEeeecCCCcEEEE
Confidence 355566666666554455555554
No 77
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=20.57 E-value=81 Score=17.72 Aligned_cols=23 Identities=17% Similarity=0.238 Sum_probs=17.5
Q ss_pred eeEEEecHHHHHhhCCChHHHhC
Q psy6003 21 CHIIYCSDGFCRLTGFSRAEVMQ 43 (109)
Q Consensus 21 ~~i~~~N~~~~~~~g~~~~e~~g 43 (109)
-.++..+..+.+++|.+.+++..
T Consensus 67 ~~~~~F~~~a~~l~G~~a~el~~ 89 (146)
T PF08646_consen 67 IWVTLFDEEAEQLLGMSADELKE 89 (146)
T ss_dssp EEEEEEHHHHHHHHCCHHCCCHH
T ss_pred EEEEEEhHHHHHHhCCCHHHHHH
Confidence 44667788899999998877543
Done!