Query 022961
Match_columns 289
No_of_seqs 256 out of 3109
Neff 10.7
Searched_HMMs 46136
Date Fri Mar 29 07:26:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022961hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13560 hypothetical protein; 99.8 3.4E-19 7.4E-24 167.2 20.2 181 6-287 193-376 (807)
2 TIGR02040 PpsR-CrtJ transcript 99.8 1.9E-19 4.1E-24 157.5 15.6 166 15-288 130-297 (442)
3 TIGR02938 nifL_nitrog nitrogen 99.8 2.3E-18 4.9E-23 152.7 14.4 170 18-287 4-173 (494)
4 PRK09776 putative diguanylate 99.8 5.4E-18 1.2E-22 164.0 17.7 180 6-287 399-579 (1092)
5 PF13426 PAS_9: PAS domain; PD 99.8 2.1E-17 4.6E-22 114.9 13.6 104 28-135 1-104 (104)
6 TIGR02040 PpsR-CrtJ transcript 99.7 1.1E-17 2.3E-22 146.4 9.9 175 24-287 2-177 (442)
7 PRK09776 putative diguanylate 99.7 7.5E-17 1.6E-21 156.1 15.8 170 15-284 280-450 (1092)
8 PRK13560 hypothetical protein; 99.7 6.9E-16 1.5E-20 145.0 17.3 177 10-288 60-248 (807)
9 PF08448 PAS_4: PAS fold; Int 99.7 7.4E-16 1.6E-20 108.2 12.1 110 24-138 1-110 (110)
10 PRK11359 cyclic-di-GMP phospho 99.7 1.3E-15 2.9E-20 143.0 16.7 166 17-288 11-180 (799)
11 PF00989 PAS: PAS fold; Inter 99.7 1.3E-15 2.9E-20 107.5 12.5 112 18-133 1-113 (113)
12 PRK11091 aerobic respiration c 99.6 5E-14 1.1E-18 131.8 13.7 125 15-143 152-276 (779)
13 PRK13559 hypothetical protein; 99.5 2.2E-13 4.8E-18 116.3 15.6 126 16-142 41-166 (361)
14 PRK13557 histidine kinase; Pro 99.5 2.1E-13 4.4E-18 122.6 15.0 128 15-143 27-154 (540)
15 PRK10060 RNase II stability mo 99.5 3.7E-13 8E-18 123.2 15.7 137 15-156 108-252 (663)
16 PRK13558 bacterio-opsin activa 99.4 3.4E-12 7.5E-17 117.5 15.6 125 19-144 149-273 (665)
17 TIGR00229 sensory_box PAS doma 99.4 3.2E-11 7E-16 83.8 12.9 120 18-142 3-123 (124)
18 PF08447 PAS_3: PAS fold; Int 99.3 3.4E-11 7.5E-16 81.4 8.9 86 43-130 1-91 (91)
19 PRK11359 cyclic-di-GMP phospho 99.2 1.3E-10 2.9E-15 109.4 13.2 123 16-142 134-257 (799)
20 cd00130 PAS PAS domain; PAS mo 99.1 9E-09 2E-13 68.1 13.4 103 27-133 1-103 (103)
21 PRK11360 sensory histidine kin 99.0 6.7E-09 1.5E-13 94.5 13.6 122 15-143 259-381 (607)
22 PF12860 PAS_7: PAS fold 99.0 3.1E-09 6.7E-14 75.2 8.4 105 24-141 1-115 (115)
23 TIGR02966 phoR_proteo phosphat 99.0 5.1E-09 1.1E-13 88.1 11.2 111 15-142 3-113 (333)
24 PRK11073 glnL nitrogen regulat 98.9 7.5E-09 1.6E-13 87.9 10.8 114 19-143 8-121 (348)
25 PF13596 PAS_10: PAS domain; P 98.9 1.4E-08 2.9E-13 70.7 9.5 106 20-134 1-106 (106)
26 PF14598 PAS_11: PAS domain; P 98.9 8.6E-08 1.9E-12 66.9 12.5 100 33-135 7-108 (111)
27 KOG0501 K+-channel KCNQ [Inorg 98.8 4.6E-08 1E-12 83.9 9.0 122 17-139 13-139 (971)
28 COG5002 VicK Signal transducti 98.7 1.3E-07 2.9E-12 76.6 10.5 118 15-143 108-225 (459)
29 PF00989 PAS: PAS fold; Inter 98.6 4.1E-08 8.9E-13 68.8 4.8 43 243-288 3-45 (113)
30 COG3829 RocR Transcriptional r 98.6 4.6E-07 1E-11 78.1 11.0 157 21-287 4-160 (560)
31 PRK11006 phoR phosphate regulo 98.6 1.2E-07 2.6E-12 83.0 7.8 110 15-143 95-204 (430)
32 TIGR02938 nifL_nitrog nitrogen 98.6 4.2E-08 9E-13 87.2 3.9 128 7-143 120-258 (494)
33 PRK10820 DNA-binding transcrip 98.5 7.2E-07 1.6E-11 79.5 10.3 110 15-138 77-190 (520)
34 PF13426 PAS_9: PAS domain; PD 98.5 1.3E-07 2.9E-12 65.0 3.7 34 251-287 1-34 (104)
35 PF13188 PAS_8: PAS domain; PD 98.4 5.9E-07 1.3E-11 56.1 5.0 42 18-66 1-42 (64)
36 COG2202 AtoS FOG: PAS/PAC doma 98.3 2.6E-05 5.7E-10 59.3 13.6 119 16-139 110-231 (232)
37 PRK11086 sensory histidine kin 98.3 5.9E-06 1.3E-10 74.5 10.8 112 16-143 219-333 (542)
38 PRK10060 RNase II stability mo 98.2 1.9E-06 4E-11 79.5 5.4 43 243-288 113-155 (663)
39 COG3829 RocR Transcriptional r 98.2 6.9E-06 1.5E-10 71.0 7.6 116 15-143 114-229 (560)
40 PRK11388 DNA-binding transcrip 98.1 4E-05 8.6E-10 70.5 12.2 42 244-288 206-247 (638)
41 PF13188 PAS_8: PAS domain; PD 98.1 4.7E-06 1E-10 52.0 4.0 34 243-280 3-36 (64)
42 KOG1229 3'5'-cyclic nucleotide 98.1 2.5E-06 5.4E-11 71.2 3.1 106 19-128 158-264 (775)
43 PRK13557 histidine kinase; Pro 97.9 1.5E-05 3.2E-10 71.9 5.3 46 243-288 32-77 (540)
44 PF08448 PAS_4: PAS fold; Int 97.9 1.5E-05 3.2E-10 55.3 4.0 39 247-288 1-39 (110)
45 PRK11388 DNA-binding transcrip 97.9 0.00017 3.7E-09 66.4 11.4 108 19-138 204-311 (638)
46 PRK15053 dpiB sensor histidine 97.8 0.00012 2.6E-09 66.2 9.7 110 17-143 221-332 (545)
47 COG3290 CitA Signal transducti 97.8 0.00012 2.7E-09 63.5 8.4 112 17-143 214-327 (537)
48 PRK13559 hypothetical protein; 97.8 4.3E-05 9.3E-10 65.3 5.3 46 243-288 45-90 (361)
49 COG5000 NtrY Signal transducti 97.7 0.00035 7.7E-09 61.4 10.3 115 15-141 367-482 (712)
50 PF08670 MEKHLA: MEKHLA domain 97.7 0.0016 3.5E-08 47.3 12.0 112 18-132 32-144 (148)
51 PRK09959 hybrid sensory histid 97.7 0.00065 1.4E-08 67.4 12.8 44 15-61 573-616 (1197)
52 KOG3558 Hypoxia-inducible fact 97.6 0.00078 1.7E-08 59.8 10.5 59 22-83 123-181 (768)
53 KOG3558 Hypoxia-inducible fact 97.5 0.00016 3.5E-09 63.9 5.6 89 41-129 284-372 (768)
54 smart00091 PAS PAS domain. PAS 97.5 0.00038 8.2E-09 41.3 5.5 54 19-75 2-55 (67)
55 COG3852 NtrB Signal transducti 97.4 0.0014 3.1E-08 52.9 8.9 96 21-123 10-106 (363)
56 PRK11006 phoR phosphate regulo 97.4 0.00014 3E-09 63.8 3.4 42 243-287 100-141 (430)
57 PRK11091 aerobic respiration c 97.3 0.00028 6.1E-09 66.7 4.9 43 243-288 157-199 (779)
58 TIGR00229 sensory_box PAS doma 97.3 0.00045 9.8E-09 46.9 4.8 42 243-287 5-46 (124)
59 TIGR02373 photo_yellow photoac 97.2 0.006 1.3E-07 42.6 8.9 67 21-90 19-86 (124)
60 COG2461 Uncharacterized conser 97.1 0.0018 4E-08 53.8 7.2 114 17-140 289-402 (409)
61 PRK10820 DNA-binding transcrip 97.1 0.00055 1.2E-08 61.3 3.7 43 243-288 82-124 (520)
62 KOG1229 3'5'-cyclic nucleotide 97.0 0.00019 4.2E-09 60.2 0.3 42 243-287 159-200 (775)
63 cd00130 PAS PAS domain; PAS mo 97.0 0.0012 2.7E-08 42.5 4.2 34 251-287 2-35 (103)
64 COG2202 AtoS FOG: PAS/PAC doma 97.0 0.019 4.2E-07 43.1 11.5 42 243-287 114-155 (232)
65 PF12860 PAS_7: PAS fold 96.9 0.0013 2.8E-08 46.2 3.8 37 247-286 1-38 (115)
66 COG3283 TyrR Transcriptional r 96.6 0.0057 1.2E-07 50.8 6.0 56 16-74 78-133 (511)
67 smart00091 PAS PAS domain. PAS 96.6 0.0059 1.3E-07 35.7 4.7 41 244-287 4-44 (67)
68 PRK13558 bacterio-opsin activa 96.6 0.0036 7.8E-08 58.2 5.2 45 244-288 151-195 (665)
69 PRK11360 sensory histidine kin 96.3 0.0056 1.2E-07 55.9 4.9 43 243-288 264-306 (607)
70 smart00086 PAC Motif C-termina 96.3 0.049 1.1E-06 28.1 7.1 41 95-136 3-43 (43)
71 PF07310 PAS_5: PAS domain; I 95.9 0.2 4.2E-06 36.4 10.5 86 41-130 51-136 (137)
72 KOG3560 Aryl-hydrocarbon recep 95.4 0.071 1.5E-06 46.5 7.3 93 41-135 293-385 (712)
73 PRK15053 dpiB sensor histidine 95.1 0.025 5.4E-07 51.3 4.0 42 243-287 224-267 (545)
74 KOG3559 Transcriptional regula 95.0 0.26 5.7E-06 41.5 9.2 55 21-78 82-136 (598)
75 KOG0501 K+-channel KCNQ [Inorg 94.9 0.016 3.5E-07 50.9 2.0 35 253-287 29-63 (971)
76 PRK11086 sensory histidine kin 94.0 0.057 1.2E-06 48.8 3.8 42 243-287 223-267 (542)
77 TIGR02373 photo_yellow photoac 93.8 0.081 1.8E-06 37.0 3.3 40 246-288 21-60 (124)
78 PF08670 MEKHLA: MEKHLA domain 93.2 0.19 4.1E-06 36.8 4.5 43 243-286 33-75 (148)
79 PF13596 PAS_10: PAS domain; P 93.1 0.074 1.6E-06 36.5 2.2 40 244-287 2-41 (106)
80 KOG3561 Aryl-hydrocarbon recep 93.0 0.078 1.7E-06 49.2 2.8 53 22-77 99-151 (803)
81 COG5002 VicK Signal transducti 92.7 0.19 4E-06 41.9 4.2 43 243-288 113-155 (459)
82 PRK10841 hybrid sensory kinase 92.3 3 6.5E-05 40.7 12.6 102 15-143 331-433 (924)
83 COG3290 CitA Signal transducti 91.5 0.22 4.8E-06 43.9 3.6 42 243-287 217-260 (537)
84 KOG3559 Transcriptional regula 91.3 0.46 9.9E-06 40.1 5.0 84 30-116 227-310 (598)
85 PF14598 PAS_11: PAS domain; P 91.1 0.25 5.5E-06 34.3 3.1 26 263-288 11-37 (111)
86 COG3283 TyrR Transcriptional r 91.0 0.33 7.1E-06 40.8 3.9 44 242-288 81-124 (511)
87 PF08446 PAS_2: PAS fold; Int 87.0 0.67 1.4E-05 32.1 2.7 42 30-73 17-61 (110)
88 PRK09959 hybrid sensory histid 85.8 0.98 2.1E-05 45.3 4.3 36 243-281 578-613 (1197)
89 PRK10618 phosphotransfer inter 84.2 2.6 5.6E-05 40.8 6.0 39 15-56 340-379 (894)
90 KOG3561 Aryl-hydrocarbon recep 83.0 1.3 2.8E-05 41.6 3.3 38 247-287 101-138 (803)
91 COG5388 Uncharacterized protei 82.3 11 0.00024 28.7 7.4 107 22-133 52-159 (209)
92 KOG3753 Circadian clock protei 81.2 4.1 8.9E-05 38.3 5.7 82 31-113 332-416 (1114)
93 COG5000 NtrY Signal transducti 80.9 2.5 5.3E-05 38.3 4.2 42 243-287 372-413 (712)
94 KOG3560 Aryl-hydrocarbon recep 79.6 2.4 5.3E-05 37.5 3.6 58 23-83 116-173 (712)
95 PRK13719 conjugal transfer tra 78.7 5 0.00011 31.4 4.8 39 17-58 18-56 (217)
96 COG3887 Predicted signaling pr 74.0 7.5 0.00016 35.2 5.2 40 14-56 71-110 (655)
97 PRK14538 putative bifunctional 73.2 7 0.00015 37.5 5.2 48 16-69 100-148 (838)
98 COG3284 AcoR Transcriptional a 70.6 89 0.0019 28.8 11.2 30 249-281 230-259 (606)
99 PF08446 PAS_2: PAS fold; Int 65.6 10 0.00023 26.1 3.6 33 254-288 18-53 (110)
100 PF06785 UPF0242: Uncharacteri 65.4 13 0.00028 31.0 4.4 88 20-115 285-378 (401)
101 PF08348 PAS_6: YheO-like PAS 60.7 45 0.00097 23.4 6.0 48 91-141 67-114 (118)
102 KOG3753 Circadian clock protei 59.4 8.7 0.00019 36.3 2.8 44 31-77 195-238 (1114)
103 PRK10618 phosphotransfer inter 55.1 15 0.00032 35.8 3.8 36 243-280 345-380 (894)
104 PRK14538 putative bifunctional 44.2 28 0.00061 33.6 3.7 33 243-278 104-137 (838)
105 PF08587 UBA_2: Ubiquitin asso 39.5 18 0.00038 20.5 1.0 17 271-287 7-23 (46)
106 PF09308 LuxQ-periplasm: LuxQ, 36.0 2.3E+02 0.005 22.8 10.0 93 16-133 56-152 (238)
107 PF06785 UPF0242: Uncharacteri 29.9 22 0.00048 29.6 0.6 25 262-286 306-330 (401)
108 PF15660 Imm49: Immunity prote 24.9 45 0.00098 20.2 1.1 24 251-274 31-54 (84)
109 PRK13719 conjugal transfer tra 24.3 1.2E+02 0.0027 23.9 3.7 33 243-278 21-53 (217)
110 PF11479 Suppressor_P21: RNA s 22.2 55 0.0012 22.9 1.3 15 271-285 111-125 (177)
No 1
>PRK13560 hypothetical protein; Provisional
Probab=99.83 E-value=3.4e-19 Score=167.20 Aligned_cols=181 Identities=14% Similarity=0.123 Sum_probs=144.8
Q ss_pred chHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHH
Q 022961 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREA 85 (289)
Q Consensus 6 ~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~ 85 (289)
++.++.+. +++++++.+++++|+++++.|.+ |+++++|+++++++||++++++|+++..+.++.............
T Consensus 193 k~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~ 268 (807)
T PRK13560 193 KRAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAK 268 (807)
T ss_pred HHHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHH
Confidence 44455565 67789999999999999999999 999999999999999999999999988877654433333334445
Q ss_pred HHhCCCeEEEEEEEecCCCEEEEEEEE--EEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhc
Q 022961 86 IREERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSC 163 (289)
Q Consensus 86 ~~~~~~~~~e~~~~~~~g~~~~~~~~~--~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~ 163 (289)
+..+.....+..+.+++|..+|+.+.. .|+.+ ..|.+.+++++++|||++|++|+++...
T Consensus 269 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e~~L~~s----------------- 330 (807)
T PRK13560 269 FDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAERELLEK----------------- 330 (807)
T ss_pred hccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHHHHHHHH-----------------
Confidence 555666677888899999999776655 45567 7889999999999999999996654211
Q ss_pred ccccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhH
Q 022961 164 RREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSL 243 (289)
Q Consensus 164 ~~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 243 (289)
.. .+
T Consensus 331 ------------------------------------e~----------------------------------------~l 334 (807)
T PRK13560 331 ------------------------------------ED----------------------------------------ML 334 (807)
T ss_pred ------------------------------------HH----------------------------------------HH
Confidence 00 04
Q ss_pred HHHhhcccccEEEeCCCCCCCCEEEe-cHHHHHhhCCChHhHhhc
Q 022961 244 YISLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 244 ~~~~e~~~~~i~i~d~~~~~~~i~~v-N~~f~~~tGys~~E~~G~ 287 (289)
...++.++.++++.|. +++|+++ |+++++++||+.+|++|+
T Consensus 335 ~~l~~~~~~~i~~~d~---~g~i~~~nn~~~~~~~G~~~~e~~g~ 376 (807)
T PRK13560 335 RAIIEAAPIAAIGLDA---DGNICFVNNNAAERMLGWSAAEVMGK 376 (807)
T ss_pred HHHHHhCcccEEEEcC---CCCEEEecCHHHHHHhCCCHHHHcCC
Confidence 5578888999999999 9999998 578888999999999996
No 2
>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=99.83 E-value=1.9e-19 Score=157.45 Aligned_cols=166 Identities=18% Similarity=0.179 Sum_probs=126.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEeC-CCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (289)
..+++++.++++++++++++|. + |+++++|+++++++||++++++|+++..++++.+.......+......+....
T Consensus 130 ~~e~r~~~l~e~~~~~i~~~d~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~ 206 (442)
T TIGR02040 130 EMETRYRVVLEVSSDAVLLVDMST---GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAAP 206 (442)
T ss_pred HHHHHHHHHHhhCCceEEEEECCC---CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCcc
Confidence 4567899999999999999997 7 99999999999999999999999998777776665555566666665555544
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccce
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~ 173 (289)
.++. .++|...| .+.+.++.. .+. ..+++..+|||++++.|+++
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~e~~~------------------------------ 250 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPVGDEL------------------------------ 250 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhhhHHH------------------------------
Confidence 4443 34444444 345566654 333 35677889999988763321
Q ss_pred eccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhccccc
Q 022961 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (289)
Q Consensus 174 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 253 (289)
.. .+...++.++++
T Consensus 251 --------------------------~~----------------------------------------~~~~l~e~~~d~ 264 (442)
T TIGR02040 251 --------------------------SE----------------------------------------NLARLYHEAPDA 264 (442)
T ss_pred --------------------------HH----------------------------------------HHHHHHHhCCce
Confidence 00 156678999999
Q ss_pred EEEeCCCCCCCCEEEecHHHHHhhCCC-hHhHhhcc
Q 022961 254 FVLIDPHLPDMPMVYASDAFLKLTGAQ-IFTKITRI 288 (289)
Q Consensus 254 i~i~d~~~~~~~i~~vN~~f~~~tGys-~~E~~G~~ 288 (289)
|+++|. +|+|+++|++|++++||+ .++++|+-
T Consensus 265 I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~ 297 (442)
T TIGR02040 265 IVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRT 297 (442)
T ss_pred EEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCC
Confidence 999999 999999999999999997 67899973
No 3
>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=99.79 E-value=2.3e-18 Score=152.74 Aligned_cols=170 Identities=22% Similarity=0.384 Sum_probs=142.9
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 022961 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (289)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (289)
+.++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.++.........+...+..+..+..+..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80 (494)
T ss_pred HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence 46889999999999999999 999999999999999999999999876666665566666666777777777777777
Q ss_pred EEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccc
Q 022961 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (289)
Q Consensus 98 ~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~ 177 (289)
..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++++++...
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~l~~~------------------------------- 128 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQVVANQ------------------------------- 128 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHHHHHH-------------------------------
Confidence 78899999999999999998 8999999999999999999985543110
Q ss_pred hhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEe
Q 022961 178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI 257 (289)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~ 257 (289)
.. .+...++.++.++++.
T Consensus 129 ----------------------~~----------------------------------------~~~~~~~~~~~~i~~~ 146 (494)
T TIGR02938 129 ----------------------KL----------------------------------------LIESVVDAAPVAFVLL 146 (494)
T ss_pred ----------------------HH----------------------------------------HHHHHHhcccceEEEE
Confidence 00 0455778889999999
Q ss_pred CCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 258 DPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 258 d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
|. +++|+++|++|++++||...+..+.
T Consensus 147 d~---~~~i~~~N~~~~~~~g~~~~~~~~~ 173 (494)
T TIGR02938 147 DP---TGRVILDNQEYKKLATDLRVKEPAH 173 (494)
T ss_pred cC---CCCEEEechhHHHhhchhhhhHHHH
Confidence 99 9999999999999999998876653
No 4
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.78 E-value=5.4e-18 Score=163.97 Aligned_cols=180 Identities=16% Similarity=0.145 Sum_probs=147.7
Q ss_pred chHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC-CCCccCCCCCHHHHHHHHH
Q 022961 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIRE 84 (289)
Q Consensus 6 ~~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~ 84 (289)
++.++.+. +.+++++.+++..+++++.+|.+ +.++++|+++++++||++++..+.. +....+|++.......+..
T Consensus 399 k~~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~ 474 (1092)
T PRK09776 399 KRTEQVNE-RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRD 474 (1092)
T ss_pred HHHHHHHH-HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHH
Confidence 34455554 66778899999999999999999 9999999999999999988844322 2334456655556666677
Q ss_pred HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcc
Q 022961 85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCR 164 (289)
Q Consensus 85 ~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~ 164 (289)
....+..+..+++..+++| ..|+.....|+.+ .+|.+.+++++.+|||++|++|+++...
T Consensus 475 ~~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e~~L~~~------------------ 534 (1092)
T PRK09776 475 ALQGRSPFKLEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLNEALFQE------------------ 534 (1092)
T ss_pred HHhcCCCeeEEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHHHHHHHH------------------
Confidence 7777888889999999999 9999999999998 8999999999999999999996554110
Q ss_pred cccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHH
Q 022961 165 REVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLY 244 (289)
Q Consensus 165 ~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 244 (289)
.. .+.
T Consensus 535 -----------------------------------~~----------------------------------------~l~ 539 (1092)
T PRK09776 535 -----------------------------------KE----------------------------------------RLH 539 (1092)
T ss_pred -----------------------------------HH----------------------------------------HHH
Confidence 00 045
Q ss_pred HHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 245 ~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
..++.++++++++|. +++|+++|+++++++||+.+|++|+
T Consensus 540 ~~l~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~e~iG~ 579 (1092)
T PRK09776 540 ITLDSIGEAVVCTDM---AMKVTFMNPVAEKMTGWTQEEALGV 579 (1092)
T ss_pred HHHhccccEEEEECC---CCeEEEEcHHHHHHhCCCHHHHcCC
Confidence 567888999999999 9999999999999999999999997
No 5
>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=99.77 E-value=2.1e-17 Score=114.87 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=95.1
Q ss_pred CCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEE
Q 022961 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (289)
Q Consensus 28 ~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 107 (289)
|++++++|.+ |+|+++|+++++++||++++++|+++..++++.........+.+.+..+..+..+..+.+++|..+|
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 7899999999 9999999999999999999999999988888777788888899999888889999999999999999
Q ss_pred EEEEEEEeecCCCCcEEEEEEEEecccc
Q 022961 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (289)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe 135 (289)
+.+++.|+.+ ++|.+.+++++++|||+
T Consensus 78 ~~~~~~~i~~-~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 78 VEVSASPIRD-EDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEE-TTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEC-CCCCEEEEEEEEEECCC
Confidence 9999999999 89999999999999996
No 6
>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=99.73 E-value=1.1e-17 Score=146.44 Aligned_cols=175 Identities=14% Similarity=0.095 Sum_probs=124.1
Q ss_pred HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC-CeEEEEEEEecC
Q 022961 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD 102 (289)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~~ 102 (289)
+++++++++++|.+ |+++++|+.++.++||+.++++|+++..+++|++.+.....+......+. .+..+.....++
T Consensus 2 ~~~~~d~~~~~d~~---g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 78 (442)
T TIGR02040 2 LATAADVTLLLDAE---GVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPS 78 (442)
T ss_pred CcccCcEEEEECCC---CcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCC
Confidence 57889999999999 99999999999999999999999999888887665555444545554443 355555555666
Q ss_pred CCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccchhccc
Q 022961 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD 182 (289)
Q Consensus 103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~~~~~~ 182 (289)
|..+|+.++..++.+ + .+++++.+|||++++.++++... ..++.
T Consensus 79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~~----------~~~~e--------------------- 122 (442)
T TIGR02040 79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVAA----------QQAME--------------------- 122 (442)
T ss_pred CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHHH----------HHHHH---------------------
Confidence 767777777666643 2 25678899999988875443110 00000
Q ss_pred CCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEeCCCCC
Q 022961 183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLP 262 (289)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~d~~~~ 262 (289)
.....+...+ ..+...++.+++++++.|. .
T Consensus 123 -----------------~~~~~l~~~e-------------------------------~r~~~l~e~~~~~i~~~d~--~ 152 (442)
T TIGR02040 123 -----------------RDYWTLREME-------------------------------TRYRVVLEVSSDAVLLVDM--S 152 (442)
T ss_pred -----------------HHHHHHHHHH-------------------------------HHHHHHHhhCCceEEEEEC--C
Confidence 0000000000 0156678899999999995 2
Q ss_pred CCCEEEecHHHHHhhCCChHhHhhc
Q 022961 263 DMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 263 ~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+|+|+++|++|++++||+.+|++|+
T Consensus 153 ~g~i~~~N~a~~~l~G~~~~el~g~ 177 (442)
T TIGR02040 153 TGRIVEANSAAAALLGGVGQSLVGR 177 (442)
T ss_pred CCEEEEEcHHHHHHhCcCHHHHcCC
Confidence 5899999999999999999999997
No 7
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.73 E-value=7.5e-17 Score=156.09 Aligned_cols=170 Identities=14% Similarity=0.190 Sum_probs=140.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (289)
+++++++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.+|++.......+....... ..+.
T Consensus 280 ~~e~r~~~l~e~~~~~i~~~d~d---G~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~ 356 (1092)
T PRK09776 280 ESETRFRNAMEYSAIGMALVGTE---GQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYS 356 (1092)
T ss_pred HHHHHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCcccee
Confidence 57788999999999999999999 9999999999999999999999999888877776555544444444332 3466
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccce
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~ 173 (289)
.+.+..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+++...
T Consensus 357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l~~~--------------------------- 408 (1092)
T PRK09776 357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVNERL--------------------------- 408 (1092)
T ss_pred eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHHHHH---------------------------
Confidence 788889999999999999999998 7899999999999999999996654111
Q ss_pred eccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhccccc
Q 022961 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (289)
Q Consensus 174 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 253 (289)
.. .+...++..+.+
T Consensus 409 --------------------------~~----------------------------------------~~~~~~~~~~~~ 422 (1092)
T PRK09776 409 --------------------------ME----------------------------------------RITLANEAGGIG 422 (1092)
T ss_pred --------------------------HH----------------------------------------HHHHHHHhcCce
Confidence 00 033456667789
Q ss_pred EEEeCCCCCCCCEEEecHHHHHhhCCChHhH
Q 022961 254 FVLIDPHLPDMPMVYASDAFLKLTGAQIFTK 284 (289)
Q Consensus 254 i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~ 284 (289)
++..|. +++++++|+++++++||+.+|.
T Consensus 423 i~~~d~---~~~~~~~n~~~~~l~G~~~~~~ 450 (1092)
T PRK09776 423 IWEWDL---KPNIISWDKRMFELYEIPPHIK 450 (1092)
T ss_pred EEEEec---CCCeEeeCHHHHHHhCCCcccC
Confidence 999999 9999999999999999998874
No 8
>PRK13560 hypothetical protein; Provisional
Probab=99.70 E-value=6.9e-16 Score=144.97 Aligned_cols=177 Identities=11% Similarity=0.006 Sum_probs=126.9
Q ss_pred HhhchHHHHHH-HHHHhhCCCEEEEEeCCCCCcc--EEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHH----
Q 022961 10 QSFNNRYTLWV-HEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM---- 80 (289)
Q Consensus 10 ~~l~~~~~~~l-~~~~~~~~~~i~~~d~~~~~g~--i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~---- 80 (289)
..+. ..++++ +.+++++|.+++.++.+ ++|. +.+++++...++||.+.++++.. +..+.+|++......
T Consensus 60 ~~l~-~~~e~~~r~l~~~~p~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~ 137 (807)
T PRK13560 60 AEAQ-DCREQCERNLKANIPGGMFLFALD-GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFR 137 (807)
T ss_pred HHHH-HHHHHHHHHHHhcCCceEEEEEEc-CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhh
Confidence 4444 334445 99999999999998876 1133 33477777888888887766543 344566666554332
Q ss_pred ---HHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhh
Q 022961 81 ---EIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLRE 157 (289)
Q Consensus 81 ---~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~ 157 (289)
.+..++..+.....++++++++|. |+.....|..+ .+|.. .+.+++.|||++|++|+++...
T Consensus 138 ~~~~~~~~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae~~l~~~----------- 202 (807)
T PRK13560 138 SAETIAMALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAEERIDEA----------- 202 (807)
T ss_pred HHHHHHHHhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHHHHHHHH-----------
Confidence 222233334455678888999996 55566777777 56764 6899999999999996654111
Q ss_pred hHHhhcccccccccceeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCC
Q 022961 158 IVFGSCRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMG 237 (289)
Q Consensus 158 ~~~~~~~~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~ 237 (289)
..
T Consensus 203 ------------------------------------------~~------------------------------------ 204 (807)
T PRK13560 203 ------------------------------------------LH------------------------------------ 204 (807)
T ss_pred ------------------------------------------HH------------------------------------
Confidence 00
Q ss_pred CcchhHHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 238 FISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 238 ~~~~~~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
.+...++++++++++.|. +|+|+++|++|++++||+.+|++|+.
T Consensus 205 ----~l~~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~ 248 (807)
T PRK13560 205 ----FLQQLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMS 248 (807)
T ss_pred ----HHHHHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCc
Confidence 056678999999999999 99999999999999999999999973
No 9
>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=99.68 E-value=7.4e-16 Score=108.23 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=96.8
Q ss_pred HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCC
Q 022961 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (289)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g 103 (289)
++++|++++++|.+ |+++++|+++.+++|++.++++|+++..++++...+.....+.+++..+.....+..... +|
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 76 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG 76 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence 68899999999999 999999999999999999999999988888777777777788888888777666555444 89
Q ss_pred CEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (289)
Q Consensus 104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~ 138 (289)
...|+.+++.|+.+ .+|.+.+++++.+|||++|+
T Consensus 77 ~~~~~~~~~~Pi~~-~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 77 EERWFEVSISPIFD-EDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp CEEEEEEEEEEEEC-TTTCEEEEEEEEEEECCHHH
T ss_pred CcEEEEEEEEEeEc-CCCCEEEEEEEEEECchhhC
Confidence 99999999999998 89999999999999999985
No 10
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.68 E-value=1.3e-15 Score=142.96 Aligned_cols=166 Identities=20% Similarity=0.288 Sum_probs=130.3
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCC----Ce
Q 022961 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PI 92 (289)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~ 92 (289)
+..+..+++.++++++++|.+ |+++++|+++++++||++++++|++...+.++.........+......+. .+
T Consensus 11 ~~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (799)
T PRK11359 11 DGIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGM 87 (799)
T ss_pred hhhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCcccccc
Confidence 345667899999999999999 99999999999999999999999998877776654444444444333322 23
Q ss_pred EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccc
Q 022961 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSL 172 (289)
Q Consensus 93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l 172 (289)
..+.+..+++|..+|+.....|+.. .|. ..++++.+|||++++.+++.
T Consensus 88 ~~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~~~----------------------------- 135 (799)
T PRK11359 88 SRELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKEQT----------------------------- 135 (799)
T ss_pred ceeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHHHH-----------------------------
Confidence 4577888999999999999888753 555 45788899999987763321
Q ss_pred eeccchhcccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccc
Q 022961 173 LDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQ 252 (289)
Q Consensus 173 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 252 (289)
+. +...++..++
T Consensus 136 ----------------------------~~----------------------------------------~~~~~~~~~~ 147 (799)
T PRK11359 136 ----------------------------RQ----------------------------------------LIIAVDHLDR 147 (799)
T ss_pred ----------------------------HH----------------------------------------HHHHHhcCCC
Confidence 00 2335677889
Q ss_pred cEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 253 SFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 253 ~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+++++|. +++|+++|++|++++||+.+|++|+.
T Consensus 148 ~i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~ 180 (799)
T PRK11359 148 PVIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQ 180 (799)
T ss_pred cEEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCC
Confidence 9999999 99999999999999999999999973
No 11
>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=99.68 E-value=1.3e-15 Score=107.46 Aligned_cols=112 Identities=23% Similarity=0.366 Sum_probs=93.9
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE-EEE
Q 022961 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL 96 (289)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~ 96 (289)
++++.++++++++++++|.+ |+|+++|+++++++||++++++|+++..++++.+.......+...+..+.... ...
T Consensus 1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV 77 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence 46889999999999999999 99999999999999999999999998888877655556667777777666543 344
Q ss_pred EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (289)
Q Consensus 97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (289)
....++|+.+|+.+...|+.+ .+|.+.+++++++||
T Consensus 78 ~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 78 RFRLRDGRPRWVEVRASPVRD-EDGQIIGILVIFRDI 113 (113)
T ss_dssp EEEETTSCEEEEEEEEEEEEE-TTEEEEEEEEEEEE-
T ss_pred EEEecCCcEEEEEEEEEEEEe-CCCCEEEEEEEEEeC
Confidence 444469999999999999999 788888999999997
No 12
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.56 E-value=5e-14 Score=131.81 Aligned_cols=125 Identities=14% Similarity=0.186 Sum_probs=108.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
+.+++++.+++++|++++++|.+ |+++++|+++++++||+.++++|+++..++++.............+..+..+..
T Consensus 152 ~~~~~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (779)
T PRK11091 152 QQSSLLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTY 228 (779)
T ss_pred HHHHHHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEE
Confidence 45678899999999999999999 999999999999999999999999988777665444455555566667777888
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|++|+++
T Consensus 229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~l 276 (779)
T PRK11091 229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQDAL 276 (779)
T ss_pred EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHHHHH
Confidence 88888999999999999999998 7899999999999999999997765
No 13
>PRK13559 hypothetical protein; Provisional
Probab=99.55 E-value=2.2e-13 Score=116.29 Aligned_cols=126 Identities=37% Similarity=0.666 Sum_probs=107.0
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEE
Q 022961 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (289)
..+.++.++++++++++++|.+..+|.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..+
T Consensus 41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 120 (361)
T PRK13559 41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVE 120 (361)
T ss_pred hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEE
Confidence 45678889999999999999742237899999999999999999999999877766666666666677777777778788
Q ss_pred EEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (289)
Q Consensus 96 ~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~ 142 (289)
....+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+.
T Consensus 121 ~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e~~ 166 (361)
T PRK13559 121 LLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVRAL 166 (361)
T ss_pred EEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhHHH
Confidence 8888999999999999999998 789999999999999999987543
No 14
>PRK13557 histidine kinase; Provisional
Probab=99.53 E-value=2.1e-13 Score=122.57 Aligned_cols=128 Identities=37% Similarity=0.672 Sum_probs=112.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
.....|+.+++.++++++++|.+..+|+|+|+|++|++++||+.++++|+++..+.++.........++..+..+..+..
T Consensus 27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (540)
T PRK13557 27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIAT 106 (540)
T ss_pred hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceE
Confidence 45678999999999999999963233899999999999999999999999988888777777777777888877777777
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
+.+..+++|..+|+.....|+.+ .+|.+.+++++.+|||+++++|+++
T Consensus 107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~l 154 (540)
T PRK13557 107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDAL 154 (540)
T ss_pred EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHHH
Confidence 88888999999999999999998 7899999999999999999887655
No 15
>PRK10060 RNase II stability modulator; Provisional
Probab=99.52 E-value=3.7e-13 Score=123.24 Aligned_cols=137 Identities=13% Similarity=0.208 Sum_probs=108.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCcc-CCCCCHHHHHHHHHHHHhCCCeE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~ 93 (289)
....+++.+++.++++++++|.+ |+|+++|+++++++||+.++++|+++..++ ++.+.......+...+..+..+.
T Consensus 108 ~~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (663)
T PRK10060 108 HGLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYE 184 (663)
T ss_pred HHHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceE
Confidence 34457788999999999999999 999999999999999999999999965544 44444445556667777888888
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCc-EEEEEEEEecccccHHHHhcc--cccccC--C--Ccchhh
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGR-ATHFVAVQVPIVSRKHMRNSG--MSYSED--G--GGSRLR 156 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~-~~~~~~~~~DITe~k~~e~~l--~~~~~~--~--n~~~~~ 156 (289)
.+.+..+++|..+|+.....+ .+ ..|. ...++++.+|||++|++++++ ++.+|. | ||..|.
T Consensus 185 ~e~~~~~~~G~~~~~~~~~~~-~~-~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~ 252 (663)
T PRK10060 185 VERWIKTRKGQRLFLFRNKFV-HS-GSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQ 252 (663)
T ss_pred EEEEEEeCCCCEEEEEeeeEE-Ec-CCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHH
Confidence 999999999998887655444 33 3443 456788999999999999888 455555 4 998888
No 16
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.44 E-value=3.4e-12 Score=117.50 Aligned_cols=125 Identities=38% Similarity=0.695 Sum_probs=107.6
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (289)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (289)
.++.+++.++.++++.|...++|.++++|+++++++||++++++|+++..+.++.........+...+..+..+..+++.
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 228 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRN 228 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEE
Confidence 45678999999999998532338999999999999999999999999877777666666666667777777788889999
Q ss_pred EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhccc
Q 022961 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM 144 (289)
Q Consensus 99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~ 144 (289)
++++|..+|+.....|+.+ .+|.+.+++++.+|||++|++|+++.
T Consensus 229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L~ 273 (665)
T PRK13558 229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELALQ 273 (665)
T ss_pred ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHHH
Confidence 9999999999999999998 79999999999999999999988773
No 17
>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=99.35 E-value=3.2e-11 Score=83.84 Aligned_cols=120 Identities=21% Similarity=0.347 Sum_probs=93.4
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeEEEE
Q 022961 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (289)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (289)
+.++.+++.++.+++++|.+ +.++++|+++.+++|++..+++|.+...+.++.........+....... .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 45778999999999999999 9999999999999999999999988776666555444444444544422 2233444
Q ss_pred EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (289)
Q Consensus 97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~ 142 (289)
.+...+|...|+.....|+.. +|...+++++..|||++++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHHhc
Confidence 555788999999988888863 67778889999999999998664
No 18
>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=99.28 E-value=3.4e-11 Score=81.38 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=71.7
Q ss_pred EEEccHHHHHHhCCCccccCCCC----CCCccCCCCCHHHHHHHHH-HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeec
Q 022961 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (289)
Q Consensus 43 i~~~N~~~~~~~G~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~ 117 (289)
++++|+.+++++||+++++ +.+ +..+++|++.......+.. ....+..+..++++++++|...|+...+.++.+
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d 79 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFD 79 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEET
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEEC
Confidence 5899999999999999999 665 6667889998888888888 677777899999999999999999999999998
Q ss_pred CCCCcEEEEEEEE
Q 022961 118 KEDGRATHFVAVQ 130 (289)
Q Consensus 118 ~~~g~~~~~~~~~ 130 (289)
.+|.+..++|++
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999998874
No 19
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.23 E-value=1.3e-10 Score=109.40 Aligned_cols=123 Identities=19% Similarity=0.291 Sum_probs=102.0
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccC-CCCCHHHHHHHHHHHHhCCCeEE
Q 022961 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
.++.+..+++.++++++++|.+ |+++++|+++++++||+.++++|++...+.+ +.........+...+..+..+..
T Consensus 134 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (799)
T PRK11359 134 QTRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQD 210 (799)
T ss_pred HHHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcc
Confidence 4456667899999999999999 9999999999999999999999998665543 44444455555666666666777
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~ 142 (289)
+.+..+++|..+|+.....|+.+ ..|.+.+++++.+|||++|++++.
T Consensus 211 e~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 211 EFLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred eeEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHHHH
Confidence 88888999999999999999998 789999999999999999987543
No 20
>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=99.08 E-value=9e-09 Score=68.05 Aligned_cols=103 Identities=21% Similarity=0.404 Sum_probs=82.9
Q ss_pred CCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 022961 27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF 106 (289)
Q Consensus 27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~ 106 (289)
++++++++|.+ +.++++|+.++.++|++..+++|.+...+.++.........+......+..+..+......+|...
T Consensus 1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (103)
T cd00130 1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77 (103)
T ss_pred CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence 36789999999 999999999999999999999998877677666655555555555555555667777778889999
Q ss_pred EEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961 107 WMLFKMSLVFGKEDGRATHFVAVQVPI 133 (289)
Q Consensus 107 ~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (289)
|+.....++.+ ..|...+++++..||
T Consensus 78 ~~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 78 WVLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEec-CCCCEEEEEEEEecC
Confidence 99999999887 677888888888875
No 21
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.01 E-value=6.7e-09 Score=94.55 Aligned_cols=122 Identities=14% Similarity=0.181 Sum_probs=97.7
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC-eE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~ 93 (289)
..+..++.++++++++++++|.+ |.++++|+++++++||++++++|++...++++.. .....+.+.+..+.. ..
T Consensus 259 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 333 (607)
T PRK11360 259 ETRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVD 333 (607)
T ss_pred HHHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccc
Confidence 44567788999999999999999 9999999999999999999999999777765432 233344455554443 33
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
.+.....++|... +.++..|+.+ .+|.+.+++++.+|||+++++|+++
T Consensus 334 ~~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l 381 (607)
T PRK11360 334 LEISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRV 381 (607)
T ss_pred eEEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHH
Confidence 4566667777766 8899999998 7999999999999999999998776
No 22
>PF12860 PAS_7: PAS fold
Probab=98.99 E-value=3.1e-09 Score=75.16 Aligned_cols=105 Identities=21% Similarity=0.356 Sum_probs=71.8
Q ss_pred HhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcccc-CCCCCCCcc---------CCCCCHHHHHHHHHHHHhCCCeE
Q 022961 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (289)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (289)
+++++.|+++.|.+ ++++++|+.|.+++|++.+.+ .|.++..+. .+.....................
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRRRQPRS 77 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhcCCCce
Confidence 47899999999999 999999999999999999887 677755442 11222222222222233333333
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~ 141 (289)
.+ ....+|. |+.+...|.. +| +++.+..|||+++++|+
T Consensus 78 ~~--~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 78 FE--LRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred eE--EECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhcC
Confidence 33 3456775 5677788885 34 46788999999999864
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=98.98 E-value=5.1e-09 Score=88.07 Aligned_cols=111 Identities=12% Similarity=0.073 Sum_probs=84.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
+..+.++.++++++++++++|.+ |+++++|+++++++||++++.+|+++..+..+ +. +...+..+.. ..
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~---~~----~~~~l~~~~~-~~ 71 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRH---PE----FVEYLAAGRF-SE 71 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccC---HH----HHHHHHhccc-CC
Confidence 45567899999999999999999 99999999999999999999999987666543 22 2333333222 22
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~ 142 (289)
......++|...|+.+...|+.+ . + ++++.+|||++++.++.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~~~~ 113 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRLEQM 113 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHHHHH
Confidence 34445578888899999999875 2 2 67888999999887654
No 24
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.94 E-value=7.5e-09 Score=87.94 Aligned_cols=114 Identities=13% Similarity=0.138 Sum_probs=85.9
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (289)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (289)
.+..++++++++++++|.+ |+|+++|+++++++||+.++++|+++..+.++.. .....+...+..+..+......
T Consensus 8 ~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 82 (348)
T PRK11073 8 DAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEVT 82 (348)
T ss_pred hHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccceE
Confidence 5678999999999999999 9999999999999999999999999777765322 2223344555555444333334
Q ss_pred EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
...+|..+|+.++..|+.. .+++...+|+|++++.++++
T Consensus 83 ~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~~~~~ 121 (348)
T PRK11073 83 LVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRLSQEQ 121 (348)
T ss_pred EEECCceEEEEEEEEEccC------ceeEEEEechhHHHHHHHHH
Confidence 4579999999999998853 23567789999998875544
No 25
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.92 E-value=1.4e-08 Score=70.72 Aligned_cols=106 Identities=21% Similarity=0.259 Sum_probs=71.2
Q ss_pred HHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 022961 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (289)
Q Consensus 20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (289)
+..++++++.++.++|.+ +++.+.|+++.++++..+ ..+|++...+.++...+.... +.+.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~-~i~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKK-IIEQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHH-HHHHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHH-HHHHHHcCCCceEEEEe-
Confidence 467899999999999999 999999999999999775 457999887765432233333 33444555543333333
Q ss_pred ecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccc
Q 022961 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (289)
Q Consensus 100 ~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT 134 (289)
..+|. |+.+...|+.+ .+|...|++.+..|||
T Consensus 75 ~~~~~--~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGGR--WYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETTE--EEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCCE--EEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 24443 56789999998 7999999999999998
No 26
>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=98.89 E-value=8.6e-08 Score=66.93 Aligned_cols=100 Identities=16% Similarity=0.257 Sum_probs=82.0
Q ss_pred EEeCCCCCccEEEccHH-HHHHhCCCccccCCCCCCCccCCCCCHH-HHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEE
Q 022961 33 ITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWMLF 110 (289)
Q Consensus 33 ~~d~~~~~g~i~~~N~~-~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~ 110 (289)
-.+.+ |+|+++.+. ...++||.+++++|+++..+++|++... ........+..|.....-+++..++|...|+..
T Consensus 7 rhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt 83 (111)
T PF14598_consen 7 RHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT 83 (111)
T ss_dssp EEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred EECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence 45677 999999999 6999999999999999999999998886 667778888888877777999999999999999
Q ss_pred EEEEeecCCCCcEEEEEEEEecccc
Q 022961 111 KMSLVFGKEDGRATHFVAVQVPIVS 135 (289)
Q Consensus 111 ~~~~~~~~~~g~~~~~~~~~~DITe 135 (289)
...++.+|..+.+..++++-+=|++
T Consensus 84 ~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 84 KATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEECCCCCCccEEEEEEEEecc
Confidence 9999886456677777776655554
No 27
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.76 E-value=4.6e-08 Score=83.92 Aligned_cols=122 Identities=25% Similarity=0.526 Sum_probs=99.1
Q ss_pred HHHHHHHHhhCC--CE-EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCC--CCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961 17 TLWVHEALDELP--DS-FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERP 91 (289)
Q Consensus 17 ~~~l~~~~~~~~--~~-i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~ 91 (289)
+-+++.++..+. +. ++..+.+..|..|+|+|+.||++.||.+.|++.++ +.+++....+....+.+.+.+.+.+.
T Consensus 13 NTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~ 92 (971)
T KOG0501|consen 13 NTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYET 92 (971)
T ss_pred hhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhh
Confidence 345666666555 43 33344444457899999999999999999999987 45566666667777888888888888
Q ss_pred eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (289)
Q Consensus 92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (289)
-++|+.++.++..+.|+.+.+.|+++ +...++.+++...|||..|+-
T Consensus 93 ~qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 93 NQFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred cceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence 88999999999999999999999998 888899999999999988864
No 28
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.74 E-value=1.3e-07 Score=76.58 Aligned_cols=118 Identities=14% Similarity=0.233 Sum_probs=92.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
...+++.+++.++.||++.+|.. |+|+.+|..+.+++|.+.++++|++...+..-.+.-. +.+.+....+...
T Consensus 108 ~Er~kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~----~~dL~e~~~s~ll 180 (459)
T COG5002 108 QERRKLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYT----FEDLVEKNDSLLL 180 (459)
T ss_pred HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee----HHHHHhcCCcEEE
Confidence 45678999999999999999999 9999999999999999999999999766654433222 2333333333333
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
+. +..++.+.+++..+.+.. +.|-+.|++++..|+|++.+.|++.
T Consensus 181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~e~Er 225 (459)
T COG5002 181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKVERER 225 (459)
T ss_pred ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHHHHHH
Confidence 32 226777778888899988 8999999999999999999887765
No 29
>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=98.64 E-value=4.1e-08 Score=68.79 Aligned_cols=43 Identities=21% Similarity=0.192 Sum_probs=39.6
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...+++++++++++|. +|+|+++|++|++++||+.+|++|+.
T Consensus 3 ~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~ 45 (113)
T PF00989_consen 3 YRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKS 45 (113)
T ss_dssp HHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSB
T ss_pred HHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCc
Confidence 56789999999999999 99999999999999999999999974
No 30
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.61 E-value=4.6e-07 Score=78.08 Aligned_cols=157 Identities=19% Similarity=0.175 Sum_probs=112.3
Q ss_pred HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEe
Q 022961 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (289)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (289)
..+++.+++++++++.. ..+..+|..+..+++-....++|++...+.++...+... .+..+........
T Consensus 4 ~~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~ 72 (560)
T COG3829 4 EGILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKL 72 (560)
T ss_pred hhhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeec
Confidence 34899999999999998 999999999999999999999999877776554332221 2222222223333
Q ss_pred cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcccccccCCCcchhhhhHHhhcccccccccceeccchhc
Q 022961 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180 (289)
Q Consensus 101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l~~~~~~~n~~~~~~~~~~~~~~~~~~~~l~e~~~~~~ 180 (289)
+ + ...+.....|+. +.+++.+++.+..|+++....-++.+
T Consensus 73 ~-~-~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~~~~~l------------------------------------ 112 (560)
T COG3829 73 K-V-KRIVVVGKTPVD--EQGRVVGVLEVFLDISEALELIEENL------------------------------------ 112 (560)
T ss_pred c-c-eeEEEcCCceee--cCCceeeeehhhhhhHHHHHHHHHHH------------------------------------
Confidence 3 2 223333344444 58899999999999998555411100
Q ss_pred ccCCCCCCccccCccccHHHHHHHHHHhhHHHHhhhcccccccceecccccCCCCCCCcchhHHHHhhcccccEEEeCCC
Q 022961 181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH 260 (289)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~i~i~d~~ 260 (289)
+ .....+...++.+.++++++|.
T Consensus 113 --------------------~------------------------------------~~~~~l~~il~~~~~~l~vvD~- 135 (560)
T COG3829 113 --------------------R------------------------------------QLRQRLEAILDSIDDGLLVVDE- 135 (560)
T ss_pred --------------------H------------------------------------HHHHHHHHHHhhccCceEEEcC-
Confidence 0 0000156678889999999999
Q ss_pred CCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 261 LPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 261 ~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+|++++.|++..+++|++.++++|+
T Consensus 136 --~G~~i~~N~~~~~~~gl~~e~~~gk 160 (560)
T COG3829 136 --DGIIIYYNKAYAKLLGLSPEEVLGK 160 (560)
T ss_pred --CCcEEEEcHHHHHHhCCCHHHHcCC
Confidence 9999999999999999999999997
No 31
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.61 E-value=1.2e-07 Score=82.99 Aligned_cols=110 Identities=13% Similarity=0.147 Sum_probs=75.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
..+++++.+++++|++++++|.+ |+|+++|+++++++||+.++..|++...+..+. .... .+... ....
T Consensus 95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~~----~~~~~-~~~~ 163 (430)
T PRK11006 95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFTQ----YLKTR-DFSR 163 (430)
T ss_pred HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHHH----HHHhc-ccCC
Confidence 45678999999999999999999 999999999999999999999999866554322 2211 11111 1111
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
.......+|. ++.+...|..+ + .++.+.+|||++++.|+..
T Consensus 164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e~~~ 204 (430)
T PRK11006 164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLEGAR 204 (430)
T ss_pred CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHHHHH
Confidence 2223344554 44556666643 2 2467789999999886543
No 32
>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=98.57 E-value=4.2e-08 Score=87.16 Aligned_cols=128 Identities=13% Similarity=0.161 Sum_probs=82.4
Q ss_pred hHHHhhchHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHH
Q 022961 7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86 (289)
Q Consensus 7 ~~~~~l~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~ 86 (289)
+.++.+. +.+..++.++++++++++++|.+ |+++++|+++++++|+...+..+.......++.... .+....
T Consensus 120 ~~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~ 191 (494)
T TIGR02938 120 RLEQVVA-NQKLLIESVVDAAPVAFVLLDPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWRE----ALAENW 191 (494)
T ss_pred HHHHHHH-HHHHHHHHHHhcccceEEEEcCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhh----hhhhcc
Confidence 3344444 56678899999999999999999 999999999999999987766655433222222111 111111
Q ss_pred HhCCCeE-EEEEEEecCCC-EEEEEEEEEEeecCCCCcE---------EEEEEEEecccccHHHHhcc
Q 022961 87 REERPIE-VNLLNYKKDGT-PFWMLFKMSLVFGKEDGRA---------THFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 87 ~~~~~~~-~e~~~~~~~g~-~~~~~~~~~~~~~~~~g~~---------~~~~~~~~DITe~k~~e~~l 143 (289)
..+..+. .+......+|. .+|+.....|+.. ..|.. .+++++++|||++|++|+++
T Consensus 192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l 258 (494)
T TIGR02938 192 PQQLAFSNREARFDRGGGRPARWLSCTGSVIGM-ESDCADSFFCAAEQPYLLLTIADISNLREEQERA 258 (494)
T ss_pred hhhhccccceeeeccCCCceeeEEEecCceEEe-ecchhhheeccCCCchheehHHHHHHHHHHHHHH
Confidence 1111111 23334444544 6888888777765 44433 34566789999999987764
No 33
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.52 E-value=7.2e-07 Score=79.47 Aligned_cols=110 Identities=14% Similarity=0.139 Sum_probs=78.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
+....+..+++++++||+++|.+ |+|+++|+++++++|++.++++|+++..+++... +...+..+.....
T Consensus 77 ~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~ 146 (520)
T PRK10820 77 REHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccc
Confidence 44567899999999999999999 9999999999999999999999999887765422 2233444433111
Q ss_pred EEEEEecCCCEEEEEEEEEEee--cCCCCcE--EEEEEEEecccccHH
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGRA--THFVAVQVPIVSRKH 138 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~--~~~~g~~--~~~~~~~~DITe~k~ 138 (289)
. .....+|..++ +...|+. + +.|.. .|.+.+.+|+++..+
T Consensus 147 ~-~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 N-EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred e-EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHHH
Confidence 1 12234566555 5556765 5 45543 788999999987643
No 34
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=98.48 E-value=1.3e-07 Score=65.03 Aligned_cols=34 Identities=26% Similarity=0.444 Sum_probs=30.1
Q ss_pred cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
|+|+++.|+ +|+|+++|++|++++||+++|++|+
T Consensus 1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~ 34 (104)
T PF13426_consen 1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGK 34 (104)
T ss_dssp -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTS
T ss_pred CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCC
Confidence 579999999 9999999999999999999999997
No 35
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.41 E-value=5.9e-07 Score=56.11 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.5
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCC
Q 022961 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66 (289)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~ 66 (289)
++++.+++++|.+++++| + ++|+++|+++++++||+ ..|+..
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence 468899999999999999 9 99999999999999998 555554
No 36
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.32 E-value=2.6e-05 Score=59.25 Aligned_cols=119 Identities=24% Similarity=0.365 Sum_probs=85.4
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHH-HHHHHHHHH-HhCCCeE
Q 022961 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAI-REERPIE 93 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~-~~~~~~~ 93 (289)
...++..+++..+++++..|.+ +.+.++|+.+..++|++..+..+.....+........ ......... .......
T Consensus 110 ~~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (232)
T COG2202 110 SEERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLE 186 (232)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcc
Confidence 4445888999999999999999 9999999999999999987777776554443322221 111112222 2223456
Q ss_pred EEEEEEecCCCE-EEEEEEEEEeecCCCCcEEEEEEEEecccccHHH
Q 022961 94 VNLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (289)
Q Consensus 94 ~e~~~~~~~g~~-~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (289)
.+.....++|.. .+......+... .|.+..+.....|+++++..
T Consensus 187 ~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 187 IEYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred eEEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence 777788899986 777777776653 67888888999999988764
No 37
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.30 E-value=5.9e-06 Score=74.54 Aligned_cols=112 Identities=10% Similarity=0.124 Sum_probs=78.1
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCc---cccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCe
Q 022961 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (289)
..+.++.++++++++++++|.+ |+|+++|+++++++|++. .+.+|+....+.++ ..+...+..+...
T Consensus 219 l~~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~ 288 (542)
T PRK11086 219 LFEQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPV-------SRLKEVLRTGTPR 288 (542)
T ss_pred HHHHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCc-------hhHHHHHhcCCCc
Confidence 3456688999999999999999 999999999999998753 35556554443321 1233444444433
Q ss_pred EEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 93 ~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
.... ...+|. ++.+...|+.+ +|.+.+++.+.+|+|+.++.++++
T Consensus 289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~~l 333 (542)
T PRK11086 289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQRL 333 (542)
T ss_pred cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHHHH
Confidence 2211 122444 34566778886 788899999999999999886665
No 38
>PRK10060 RNase II stability modulator; Provisional
Probab=98.21 E-value=1.9e-06 Score=79.52 Aligned_cols=43 Identities=12% Similarity=0.055 Sum_probs=39.3
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+..+++.++++|+++|. +|+|+++|++|+++|||+.+|++|+-
T Consensus 113 ~~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~ 155 (663)
T PRK10060 113 AEQVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQS 155 (663)
T ss_pred HHHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCC
Confidence 44578888999999999 99999999999999999999999973
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.17 E-value=6.9e-06 Score=71.04 Aligned_cols=116 Identities=16% Similarity=0.342 Sum_probs=86.1
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
+..+.|..+++.+.++++++|.+ |.++++|.+...++|++.++++|++...+.....+ ....+++..+.+...
T Consensus 114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~~~ 186 (560)
T COG3829 114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCccee
Confidence 45578899999999999999999 99999999999999999999999986665411111 123456667776555
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
....+..+.. .....|+.. +|.+.+.+++..|+++.+....++
T Consensus 187 ~~~~~~~~~~----i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l~~~~ 229 (560)
T COG3829 187 VVQTYNGNKI----IVNVAPVYA--DGQLIGVVGISKDVSELERLTREL 229 (560)
T ss_pred eeeeecCCce----eEeeccEec--CCcEEEEEEeecchHHHHHHHHHH
Confidence 4433332222 355566764 779999999999999888775555
No 40
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.12 E-value=4e-05 Score=70.53 Aligned_cols=42 Identities=10% Similarity=0.071 Sum_probs=37.8
Q ss_pred HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
...++...++|++.|. +|+|+++|+++++++|++.++++|+.
T Consensus 206 ~~il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~ 247 (638)
T PRK11388 206 NALLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRA 247 (638)
T ss_pred HHHHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCc
Confidence 3456777899999999 99999999999999999999999974
No 41
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.10 E-value=4.7e-06 Score=51.96 Aligned_cols=34 Identities=21% Similarity=0.330 Sum_probs=29.0
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCC
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys 280 (289)
+...++++++||++.| +++|+++|++|++++||+
T Consensus 3 ~~~l~~~~~~~i~i~d----~~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 3 YRSLFDNSPDGILIID----GGRIIYVNPAFEELFGYS 36 (64)
T ss_dssp HHHHHCCSSSEEEEEE----TSBEEEE-HHHHHHHCS-
T ss_pred HHHHHHcCccceEEEE----CCChHHhhHHHHHHhCCC
Confidence 5678999999999999 348999999999999999
No 42
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=98.07 E-value=2.5e-06 Score=71.18 Aligned_cols=106 Identities=23% Similarity=0.362 Sum_probs=86.4
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCC-CCHHHHHHHHHHHHhCCCeEEEEE
Q 022961 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLL 97 (289)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~ 97 (289)
.+..+++....++-+.|.+ ..|.|+|++|+.|+||-..|++|++..++...+ ....+.+.+...++.|..|+++..
T Consensus 158 alFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~ 234 (775)
T KOG1229|consen 158 ALFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEE 234 (775)
T ss_pred HHHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHH
Confidence 3445788888999999998 999999999999999999999999988776433 234566777788888999999888
Q ss_pred EEecCCCEEEEEEEEEEeecCCCCcEEEEEE
Q 022961 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128 (289)
Q Consensus 98 ~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~ 128 (289)
.+++.|......+.+.|+.. ..|.+..++.
T Consensus 235 aRRksgdS~dqh~~itP~~g-qggkirhfvs 264 (775)
T KOG1229|consen 235 ARRKSGDSCDQHFIITPFAG-QGGKIRHFVS 264 (775)
T ss_pred HhhccCCcccceEEEeeecC-CCCceeeehh
Confidence 88888888777788899987 6777766653
No 43
>PRK13557 histidine kinase; Provisional
Probab=97.91 E-value=1.5e-05 Score=71.85 Aligned_cols=46 Identities=28% Similarity=0.557 Sum_probs=41.8
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...++.++++++++|+..++|+|+|+|++|++++||+.+|++|+.
T Consensus 32 ~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~ 77 (540)
T PRK13557 32 FFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNN 77 (540)
T ss_pred HHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCC
Confidence 6778999999999999755689999999999999999999999973
No 44
>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=97.89 E-value=1.5e-05 Score=55.28 Aligned_cols=39 Identities=33% Similarity=0.395 Sum_probs=35.4
Q ss_pred hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
++++++++++.|. +++|+++|+++.+++|++.++++|+-
T Consensus 1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~ 39 (110)
T PF08448_consen 1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRS 39 (110)
T ss_dssp HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSB
T ss_pred CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhcc
Confidence 4678999999999 99999999999999999999999973
No 45
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.86 E-value=0.00017 Score=66.41 Aligned_cols=108 Identities=12% Similarity=0.228 Sum_probs=75.7
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 022961 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (289)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (289)
.+..++++++++++++|.+ |+|+++|+++++++|++.++++|++...+++.. ..+..++..+..+......
T Consensus 204 ~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~~ 274 (638)
T PRK11388 204 QLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEVT 274 (638)
T ss_pred HHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEEE
Confidence 3455899999999999999 999999999999999999999999877665321 1233455555544332222
Q ss_pred EecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHH
Q 022961 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (289)
Q Consensus 99 ~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~ 138 (289)
...+|..+++.+...|+.+ ..|. +++.+..|++..++
T Consensus 275 l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 275 FESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 3345777788888899865 3443 24555678776544
No 46
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.83 E-value=0.00012 Score=66.19 Aligned_cols=110 Identities=14% Similarity=0.072 Sum_probs=75.1
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCc--cccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
...+..+++++++|++++|.+ |+|+++|+++++++|++. ++++|++...+.++... . ..... ......
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~--~----~~~~~-~~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF--F----TEQID-EKRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh--h----hhhcC-Ccccce
Confidence 345678999999999999999 999999999999999965 46889886666543211 1 11111 111111
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
. ...+|. .+.....|+.. .+.+.+.+...+|+|+.++.++++
T Consensus 291 ~---~~~~~~--~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l~~~l 332 (545)
T PRK15053 291 V---ANFNGL--SVIANREAIRS--GDDLLGAIISFRSKDEISTLNAQL 332 (545)
T ss_pred E---EEECCE--EEEEEeeeEEE--CCeEEEEEEEEEchHHHHHHHHHH
Confidence 1 122443 34466777775 667788999999999988776555
No 47
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.78 E-value=0.00012 Score=63.46 Aligned_cols=112 Identities=13% Similarity=0.156 Sum_probs=83.8
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcc--ccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEE
Q 022961 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (289)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (289)
-+.-..+++++..|++.+|.. |.+..+|.++++|+|+... +.+|++...+.+|+.. +...++.+++...
T Consensus 214 ~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~~ 284 (537)
T COG3290 214 LEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQHD 284 (537)
T ss_pred HHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCcccc
Confidence 344567899999999999999 9999999999999999765 6889988887776221 2233445544332
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
+. .+-+|. ++.+...|+.. .|++.+.+.+++|-|+-++.-++|
T Consensus 285 ~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L~eqL 327 (537)
T COG3290 285 EE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKLTEQL 327 (537)
T ss_pred hh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHHHHHH
Confidence 22 223454 45577788886 889999999999999998886666
No 48
>PRK13559 hypothetical protein; Provisional
Probab=97.75 E-value=4.3e-05 Score=65.31 Aligned_cols=46 Identities=33% Similarity=0.577 Sum_probs=40.7
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...++.++++++++|...++++|+++|++|++++||+.+|++|+.
T Consensus 45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~ 90 (361)
T PRK13559 45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRN 90 (361)
T ss_pred HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCC
Confidence 5667899999999999744567899999999999999999999974
No 49
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.73 E-value=0.00035 Score=61.35 Aligned_cols=115 Identities=11% Similarity=0.046 Sum_probs=78.7
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhC-CCeE
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (289)
+..+.++.+++..+.|++..|.+ |.+.-+|++.++|+|.+.++++|.+.+.+.+ .+...+...-..+ ....
T Consensus 367 ~rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap-----~~~~vf~~~~a~~~~~~~ 438 (712)
T COG5000 367 QRRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAP-----ELEEVFAEAGAAARTDKR 438 (712)
T ss_pred HHHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhh-----HHHHHHHHhhhhcCCCcc
Confidence 34567788999999999999999 9999999999999999999999998665532 1222222222221 2223
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~ 141 (289)
.+..+ ...|+...+.+..+.... ++| .+++.++-|||+...+|.
T Consensus 439 ~ev~~-~r~g~~rtl~Vq~t~~~~-d~~--~gyVvt~DDITdLV~AQR 482 (712)
T COG5000 439 VEVKL-AREGEERTLNVQATREPE-DNG--NGYVVTFDDITDLVIAQR 482 (712)
T ss_pred ceeec-ccCCCceeeeeeeeeccc-ccC--CceEEEecchHHHHHHHH
Confidence 34333 344555566666555544 322 468889999999988854
No 50
>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=97.72 E-value=0.0016 Score=47.34 Aligned_cols=112 Identities=11% Similarity=0.102 Sum_probs=77.3
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 022961 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (289)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (289)
..++.++. .|.+|+-.+.. ++-.++|.|.++.+|++++-+++.+.+.+.-..+.........+.++.+.|-.....-.
T Consensus 32 ~~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~Gi 109 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGI 109 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence 44555555 88888877654 44789999999999999999999999877655555555555666666666654333333
Q ss_pred EEecCCCEEEEEE-EEEEeecCCCCcEEEEEEEEec
Q 022961 98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVP 132 (289)
Q Consensus 98 ~~~~~g~~~~~~~-~~~~~~~~~~g~~~~~~~~~~D 132 (289)
-..+.|+.++++- ++-.+.| ++|...+.-.+..+
T Consensus 110 Riss~Grrf~ie~a~vW~l~D-~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 110 RISSTGRRFRIERATVWNLID-EDGNYCGQAAMFSN 144 (148)
T ss_pred EEcCCCCeEEEeceEEEEEEc-CCCCEEEEEEEEee
Confidence 4578898887763 4455666 68877766554443
No 51
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.67 E-value=0.00065 Score=67.38 Aligned_cols=44 Identities=9% Similarity=0.041 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCcccc
Q 022961 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI 61 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~ 61 (289)
....+++.+++++|++++++|.+ |+++++|+++++++|++....
T Consensus 573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~ 616 (1197)
T PRK09959 573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKN 616 (1197)
T ss_pred HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccc
Confidence 45567788999999999999999 999999999999999875433
No 52
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.59 E-value=0.00078 Score=59.77 Aligned_cols=59 Identities=15% Similarity=0.173 Sum_probs=50.2
Q ss_pred HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (289)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~ 83 (289)
.+++++..-+++++.+ |.++|+++.....+|++.-|+.|.++.+++||.+...+.+.+.
T Consensus 123 ~iLqsLDGFVm~l~~d---G~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~ 181 (768)
T KOG3558|consen 123 HILQSLDGFVMALTQD---GDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLG 181 (768)
T ss_pred hHHhhccceEEEEccC---CCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhc
Confidence 3566666667888999 9999999999999999999999999999999998877665543
No 53
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.53 E-value=0.00016 Score=63.89 Aligned_cols=89 Identities=11% Similarity=0.277 Sum_probs=75.6
Q ss_pred ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (289)
Q Consensus 41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~ 120 (289)
-+|.|+.+.+..++||.+++++|+++..++|+.+...+.....+.+..|.....-+++..++|...|+...++.+....+
T Consensus 284 mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn 363 (768)
T KOG3558|consen 284 MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKN 363 (768)
T ss_pred eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCC
Confidence 78999999999999999999999999999999888888888888888888888889999999999999999888865223
Q ss_pred CcEEEEEEE
Q 022961 121 GRATHFVAV 129 (289)
Q Consensus 121 g~~~~~~~~ 129 (289)
++-..++++
T Consensus 364 ~q~q~IicV 372 (768)
T KOG3558|consen 364 PQEQNIICV 372 (768)
T ss_pred CCcceEEEE
Confidence 333344443
No 54
>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=97.48 E-value=0.00038 Score=41.26 Aligned_cols=54 Identities=24% Similarity=0.417 Sum_probs=44.8
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCC
Q 022961 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN 75 (289)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~ 75 (289)
+++.+++.+++++++++.. +.+.++|+.+..++|++..++.+..+..+.++.+.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (67)
T smart00091 2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDR 55 (67)
T ss_pred hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccH
Confidence 3566888999999999998 99999999999999999988888776555555443
No 55
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=97.40 E-value=0.0014 Score=52.91 Aligned_cols=96 Identities=13% Similarity=0.124 Sum_probs=74.5
Q ss_pred HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE-EEEEEE
Q 022961 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY 99 (289)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~ 99 (289)
..++++.+..++++|.+ +.|.|+|++++.+||.+...+.+.+.+.+++.. ......+.+....+..+. .+..+
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l- 83 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTL- 83 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeee-
Confidence 46899999999999999 999999999999999999999999988877543 344555666666665543 23333
Q ss_pred ecCCCEEEEEEEEEEeecCCCCcE
Q 022961 100 KKDGTPFWMLFKMSLVFGKEDGRA 123 (289)
Q Consensus 100 ~~~g~~~~~~~~~~~~~~~~~g~~ 123 (289)
..+|....+...+.|+.. ..|.+
T Consensus 84 ~~~g~~~~v~~~v~~v~~-~~G~v 106 (363)
T COG3852 84 VILGRSHIVDLTVAPVPE-EPGSV 106 (363)
T ss_pred eecCccceEEEEEeeccC-CCCeE
Confidence 268888899999999986 56654
No 56
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.38 E-value=0.00014 Score=63.78 Aligned_cols=42 Identities=10% Similarity=0.090 Sum_probs=39.3
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+...++.+++++++.|. +|+|+++|+++++++||+.+|++|+
T Consensus 100 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~ 141 (430)
T PRK11006 100 FRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQ 141 (430)
T ss_pred HHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCC
Confidence 56678999999999999 9999999999999999999999886
No 57
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.32 E-value=0.00028 Score=66.73 Aligned_cols=43 Identities=19% Similarity=-0.011 Sum_probs=40.3
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...++.++++|++.|. +|+|+++|++|++++||+.+|++|+.
T Consensus 157 l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~ 199 (779)
T PRK11091 157 LRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLT 199 (779)
T ss_pred HHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCC
Confidence 66788999999999999 99999999999999999999999973
No 58
>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=97.30 E-value=0.00045 Score=46.92 Aligned_cols=42 Identities=19% Similarity=0.263 Sum_probs=38.2
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+...++.++.+++++|. +++|+++|++|++++||+.++++|+
T Consensus 5 ~~~~~~~~~~~~~~~d~---~~~i~~~n~~~~~~~g~~~~~~~~~ 46 (124)
T TIGR00229 5 YRAIFESSPDAIIVIDL---EGNILYVNPAFEEIFGYSAEELIGR 46 (124)
T ss_pred HHHHHhhCCceEEEEcC---CCcEEEEchHHHHHhCCChHHhcCc
Confidence 45678888999999999 9999999999999999999998875
No 59
>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=97.17 E-value=0.006 Score=42.55 Aligned_cols=67 Identities=18% Similarity=0.076 Sum_probs=52.9
Q ss_pred HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCC-CccCCCCCHHHHHHHHHHHHhCC
Q 022961 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREER 90 (289)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~ 90 (289)
..-++..|-|++-+|.+ |.|+..|.+-..+.|++++.++|+++. ++-+.-..+.+...+.+..+.+.
T Consensus 19 ~eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 19 DAQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred HhHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 34589999999999999 999999999999999999999999844 44443444556666666555554
No 60
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=97.14 E-value=0.0018 Score=53.82 Aligned_cols=114 Identities=16% Similarity=0.187 Sum_probs=86.6
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 022961 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (289)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (289)
.+.+..++.+.|.-+..+|.+ +.+.+.|+. .++|-.++. .+|++.. +.+|.........+.+.+++|..-..++
T Consensus 289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~-~chpPksv~iv~ki~~~fksG~kd~~ef 362 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQ-LCHPPKSVHIVEKILKDFKSGEKDFAEF 362 (409)
T ss_pred HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCccc-CCCCCchHHHHHHHHHHhhcCCcchHHH
Confidence 456888999999777788999 999999997 777877765 4688755 3455556666677777778877655565
Q ss_pred EEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHH
Q 022961 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (289)
Q Consensus 97 ~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e 140 (289)
.. ...+. .+.++..+++| +.|...|.+.+++|||..|+.+
T Consensus 363 w~-~~~~~--~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 363 WI-NMGDK--FIHIRYFAVKD-EEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred hc-cCCCc--eEEEEEEEEEc-CCCceeeeehhhhhhHHHHhcc
Confidence 52 22222 45688889999 8999999999999999998874
No 61
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.05 E-value=0.00055 Score=61.32 Aligned_cols=43 Identities=19% Similarity=0.067 Sum_probs=40.6
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...++.+++||+++|. +|+|+++|+++++++|++.++++|+.
T Consensus 82 L~aIL~sm~eGVi~vD~---~G~I~~iN~aA~~Llg~~~eel~Gk~ 124 (520)
T PRK10820 82 LSALLEALPEPVLSIDM---KGKVELANPASCQLFGQSEEKLRNHT 124 (520)
T ss_pred HHHHHHhCCCcEEEECC---CCeeeHhHHHHHHHHCcCHHHHCCCc
Confidence 77889999999999999 99999999999999999999999973
No 62
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.99 E-value=0.00019 Score=60.24 Aligned_cols=42 Identities=21% Similarity=0.363 Sum_probs=38.7
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+-.+++...++|-|+|. +..|.||||||++|+||-+.|+|||
T Consensus 159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGk 200 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGK 200 (775)
T ss_pred HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCC
Confidence 55677888899999999 8899999999999999999999997
No 63
>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=96.98 E-value=0.0012 Score=42.48 Aligned_cols=34 Identities=24% Similarity=0.285 Sum_probs=31.2
Q ss_pred cccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 251 ~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+.++++.|. ++.++++|+++++++||+.++++|+
T Consensus 2 ~~~i~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~ 35 (103)
T cd00130 2 PDGVIVLDL---DGRILYANPAAEQLLGYSPEELIGK 35 (103)
T ss_pred CceEEEECC---CCcEEEECHHHHHHhCCCHHHHcCc
Confidence 467889999 9999999999999999999999886
No 64
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.98 E-value=0.019 Score=43.05 Aligned_cols=42 Identities=24% Similarity=0.238 Sum_probs=36.2
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+...++..++++++.|. ++.++++|+++++++||+..+.+++
T Consensus 114 ~~~~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~ 155 (232)
T COG2202 114 LRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGR 155 (232)
T ss_pred HHHHHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCC
Confidence 34567777899999999 9999999999999999998877654
No 65
>PF12860 PAS_7: PAS fold
Probab=96.89 E-value=0.0013 Score=46.19 Aligned_cols=37 Identities=22% Similarity=0.241 Sum_probs=33.5
Q ss_pred hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhH-hh
Q 022961 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTK-IT 286 (289)
Q Consensus 247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~-~G 286 (289)
++++++||++-|+ +++++++|++|.+++|++.+.+ .|
T Consensus 1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G 38 (115)
T PF12860_consen 1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPG 38 (115)
T ss_pred CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCC
Confidence 3678899999999 9999999999999999999887 45
No 66
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.62 E-value=0.0057 Score=50.80 Aligned_cols=56 Identities=14% Similarity=0.158 Sum_probs=49.3
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCC
Q 022961 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~ 74 (289)
..-.+..+++++|++++.+|.. |.+..+|++++.++|.+++.+.|.+...++...+
T Consensus 78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n 133 (511)
T COG3283 78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN 133 (511)
T ss_pred HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence 3446788999999999999999 9999999999999999999999999777765443
No 67
>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=96.57 E-value=0.0059 Score=35.73 Aligned_cols=41 Identities=22% Similarity=0.229 Sum_probs=36.0
Q ss_pred HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
...++..+.+++++|. ++.++++|+.+.+++||+..++.|+
T Consensus 4 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (67)
T smart00091 4 RAILESLPDGIFVLDL---DGRILYANPAAEELLGYSPEELIGK 44 (67)
T ss_pred HHHHhhCCceEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCC
Confidence 4456778889999998 9999999999999999999888875
No 68
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.55 E-value=0.0036 Score=58.19 Aligned_cols=45 Identities=29% Similarity=0.445 Sum_probs=39.4
Q ss_pred HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
...++..+.++++.|...++++|+++|++|++++||+.+|++|+.
T Consensus 151 ~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~ 195 (665)
T PRK13558 151 ERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRN 195 (665)
T ss_pred HHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCC
Confidence 456788899999998655689999999999999999999999973
No 69
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.32 E-value=0.0056 Score=55.89 Aligned_cols=43 Identities=19% Similarity=0.128 Sum_probs=38.8
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
+...++.++++++++|. +++|+++|+++++++||+.++++|+.
T Consensus 264 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~ 306 (607)
T PRK11360 264 NELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKP 306 (607)
T ss_pred HHHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCc
Confidence 44567889999999999 99999999999999999999999873
No 70
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=96.28 E-value=0.049 Score=28.11 Aligned_cols=41 Identities=29% Similarity=0.448 Sum_probs=33.2
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEeccccc
Q 022961 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (289)
Q Consensus 95 e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~ 136 (289)
++.....+|..+|+.....++.+ ..+.+.+++++..|||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence 34556778888899888888887 678888899999999863
No 71
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=95.94 E-value=0.2 Score=36.37 Aligned_cols=86 Identities=13% Similarity=0.147 Sum_probs=69.1
Q ss_pred ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (289)
Q Consensus 41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~ 120 (289)
-++..+=..+++++|++ +-|+++..++.+.........+..++....+..........+|....++....|+.+ +.
T Consensus 51 ~r~RLaGt~i~~~~G~d---~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~ 126 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGRD---LTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG 126 (137)
T ss_pred eEEEEecHHHHHHhCCC---CCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence 45667889999999984 568988888777776667777777777777777777777888988888999999998 77
Q ss_pred CcEEEEEEEE
Q 022961 121 GRATHFVAVQ 130 (289)
Q Consensus 121 g~~~~~~~~~ 130 (289)
|.+..++|..
T Consensus 127 ~~v~rilG~~ 136 (137)
T PF07310_consen 127 GTVDRILGAL 136 (137)
T ss_pred CCccEEEEec
Confidence 8888888764
No 72
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=95.43 E-value=0.071 Score=46.50 Aligned_cols=93 Identities=14% Similarity=0.170 Sum_probs=73.1
Q ss_pred ccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 022961 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (289)
Q Consensus 41 g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~ 120 (289)
+..+.+......++||...|+.|++...+++.++..-....-.+.+++|.+--..++..+++|++.|+..+...+. .+
T Consensus 293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly--kn 370 (712)
T KOG3560|consen 293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY--KN 370 (712)
T ss_pred cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee--ec
Confidence 5666677778899999999999988777777666554555566778888887788889999999999987766665 48
Q ss_pred CcEEEEEEEEecccc
Q 022961 121 GRATHFVAVQVPIVS 135 (289)
Q Consensus 121 g~~~~~~~~~~DITe 135 (289)
|+...++...+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 888877777766665
No 73
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=95.08 E-value=0.025 Score=51.25 Aligned_cols=42 Identities=10% Similarity=0.103 Sum_probs=36.9
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh--HhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI--FTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~--~E~~G~ 287 (289)
+...++...+|+++.|. +|+|+++|+++++++|+.. ++++|+
T Consensus 224 ~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~~~~~~~~~~g~ 267 (545)
T PRK15053 224 QEALFSSVYEGLIAVDP---HGYITAINRNARKMLGLSSPGRQWLGK 267 (545)
T ss_pred HHHHHHHhCceEEEECC---CCeEEeecHHHHHHhCCCCcchhhcCC
Confidence 45578888999999999 9999999999999999975 468886
No 74
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=95.00 E-value=0.26 Score=41.51 Aligned_cols=55 Identities=18% Similarity=0.264 Sum_probs=46.1
Q ss_pred HHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHH
Q 022961 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78 (289)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~ 78 (289)
..+++.+..-+++++++ |.|.|+++.+.--+|++.-|+.|....+.+++.+....
T Consensus 82 shlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~dem 136 (598)
T KOG3559|consen 82 SHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEM 136 (598)
T ss_pred HhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHHH
Confidence 34566666678889999 99999999999999999999999998888888776544
No 75
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=94.85 E-value=0.016 Score=50.91 Aligned_cols=35 Identities=34% Similarity=0.657 Sum_probs=28.8
Q ss_pred cEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 253 SFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 253 ~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
++++..+..-|.+|+|.|++||+++||.+.|+..|
T Consensus 29 sFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQK 63 (971)
T KOG0501|consen 29 SFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQK 63 (971)
T ss_pred ceeeccceeeccceEEecCcchhccCccHHHHhcc
Confidence 34555555558899999999999999999999876
No 76
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=94.03 E-value=0.057 Score=48.81 Aligned_cols=42 Identities=14% Similarity=0.092 Sum_probs=35.2
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh---HhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI---FTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~---~E~~G~ 287 (289)
....++.+++||+++|. +|+|+++|+++++++||.. .+.+|+
T Consensus 223 ~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~ 267 (542)
T PRK11086 223 RQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGT 267 (542)
T ss_pred HHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCC
Confidence 45678899999999999 9999999999999998763 345543
No 77
>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=93.84 E-value=0.081 Score=37.04 Aligned_cols=40 Identities=15% Similarity=0.071 Sum_probs=36.5
Q ss_pred HhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 246 ~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
.++..+-|++-.|. +|.|+.-|.+=.+++|++++.++||.
T Consensus 21 elD~lpFGvI~lD~---~G~V~~YN~aE~~~sg~~p~~vlGr~ 60 (124)
T TIGR02373 21 QFDALPFGAIQLDG---SGVILRYNAAEGRITGRDPERVIGRN 60 (124)
T ss_pred HhhcCCcceEEECC---CCEEEEEecchhhhcCCChhhhhchh
Confidence 36677889999999 99999999999999999999999983
No 78
>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=93.21 E-value=0.19 Score=36.75 Aligned_cols=43 Identities=19% Similarity=0.091 Sum_probs=36.4
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhh
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKIT 286 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G 286 (289)
....+-+.+.+|+..+. .+|=..+|+|.+.++|++|+.+|++|
T Consensus 33 ~~~~L~~ap~ailsh~~-~~dP~f~yaN~aaL~l~e~~w~el~~ 75 (148)
T PF08670_consen 33 LAKALWHAPFAILSHGT-KADPIFIYANQAALDLFETTWDELVG 75 (148)
T ss_pred HHHHHHcCCCEEEEcCC-CCCCEEEehhHHHHHHhcCCHHHHhc
Confidence 55666668899988886 55667999999999999999999987
No 79
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=93.07 E-value=0.074 Score=36.50 Aligned_cols=40 Identities=18% Similarity=0.263 Sum_probs=29.9
Q ss_pred HHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 244 ~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
...++..+.++++.|. +++|.++|++..++++.+. ..+||
T Consensus 2 ~~il~s~~~~i~~vD~---~~~I~~~n~~a~~~f~~~~-~~iGr 41 (106)
T PF13596_consen 2 NNILDSMPIGIIFVDR---NLRIRYFNPAAARLFNLSP-SDIGR 41 (106)
T ss_dssp HHHHHHSSSEEEEEET---TSBEEEE-SCGC-SS---G-GGTTS
T ss_pred hHHHhcCCCCEEEEcC---CCeEEEeChhHhhhcCCCh-HHCCC
Confidence 4567888999999999 9999999999999999765 44676
No 80
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=92.98 E-value=0.078 Score=49.22 Aligned_cols=53 Identities=17% Similarity=0.300 Sum_probs=45.1
Q ss_pred HHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHH
Q 022961 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR 77 (289)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~ 77 (289)
.+++++..-++++.-+ |+|+||++....++||..++++|+++..+.+|.+...
T Consensus 99 LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~ 151 (803)
T KOG3561|consen 99 LILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDK 151 (803)
T ss_pred HHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCc
Confidence 4567776677888999 9999999999999999999999999888887766443
No 81
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=92.66 E-value=0.19 Score=41.89 Aligned_cols=43 Identities=16% Similarity=0.186 Sum_probs=39.3
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
|..++.-..+|++-||. .|+|+.+|..++++.|-+.++++|+.
T Consensus 113 L~SvlayMtDGViATdR---rG~iI~iN~~A~k~L~~~~E~~~~~~ 155 (459)
T COG5002 113 LDSVLAYMTDGVIATDR---RGKIILINKPALKMLGVSKEDALGRS 155 (459)
T ss_pred HHHHHHHHcCceEeecC---CCcEEEeccHHHHHhCcCHHHHhccc
Confidence 66677778899999999 99999999999999999999999974
No 82
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=92.34 E-value=3 Score=40.68 Aligned_cols=102 Identities=10% Similarity=0.044 Sum_probs=61.3
Q ss_pred HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeE
Q 022961 15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (289)
..+++++.+++.+|.++++++ .+ |.++++|+.+..++|+...+. . ..+......... .
T Consensus 331 e~e~~~r~iv~~~p~gi~i~~~~~---g~~~~~N~~a~~~~~l~~~~~-------------~----~~~~~~~~~~~~-~ 389 (924)
T PRK10841 331 EHEQFNRKIVASAPVGICILRTSD---GTNILSNELAHNYLNMLTHED-------------R----QRLTQIICGQQV-N 389 (924)
T ss_pred HHHHHHHHHHHhCCccEEEEEcCC---CcEEEehHHHHHHhccCChhH-------------H----HHHHHHHhcccc-c
Confidence 566788999999999999997 45 999999999999887643211 0 111111111111 1
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHhcc
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~~l 143 (289)
. ......++.... +...+... .+. ...+++..|||+++++|+++
T Consensus 390 ~-~~~~~~~~~~~~--i~~~~~~~--~~~-~~~i~~~~Dit~r~~~e~~L 433 (924)
T PRK10841 390 F-VDVLTSNNTNLQ--ISFVHSRY--RNE-NVAICVLVDVSARVKMEESL 433 (924)
T ss_pred e-eeEEcCCCcEEE--EEEEeeee--cCc-eEEEEEEEEhhHHHHHHHHH
Confidence 1 112234444433 33333332 222 34578889999999987766
No 83
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=91.48 E-value=0.22 Score=43.94 Aligned_cols=42 Identities=24% Similarity=0.212 Sum_probs=36.3
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChH--hHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIF--TKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~--E~~G~ 287 (289)
....++.+.+||+..|. .|.|..+|.++++|.|+... +.+|+
T Consensus 217 r~A~l~si~EGviAvd~---~G~It~~N~~A~~ll~~~~~~~~~ig~ 260 (537)
T COG3290 217 RQAMLQSIKEGVIAVDK---KGVITLINQAAQKLLGLRQPSGDPIGR 260 (537)
T ss_pred HHHHHHHhhceEEEECC---CCeEeehhHHHHHHhcccCcCcccccc
Confidence 34567888999999999 99999999999999999876 46664
No 84
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=91.28 E-value=0.46 Score=40.13 Aligned_cols=84 Identities=8% Similarity=0.050 Sum_probs=56.9
Q ss_pred EEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 022961 30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (289)
Q Consensus 30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~ 109 (289)
-++....+ -.+++.......++||.+.++++++.-.+++..+.......-...+..|....--+++..+.|.+.|+.
T Consensus 227 FmfraslD---lkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvq 303 (598)
T KOG3559|consen 227 FMFRASLD---LKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQ 303 (598)
T ss_pred EEEEeecc---eEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEE
Confidence 34555667 889999999999999999999999866666555443333332333444443333456777888888887
Q ss_pred EEEEEee
Q 022961 110 FKMSLVF 116 (289)
Q Consensus 110 ~~~~~~~ 116 (289)
-....+.
T Consensus 304 syat~vH 310 (598)
T KOG3559|consen 304 SYATFVH 310 (598)
T ss_pred EeeEEEe
Confidence 6655554
No 85
>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=91.14 E-value=0.25 Score=34.32 Aligned_cols=26 Identities=19% Similarity=0.146 Sum_probs=23.4
Q ss_pred CCCEEEecHH-HHHhhCCChHhHhhcc
Q 022961 263 DMPMVYASDA-FLKLTGAQIFTKITRI 288 (289)
Q Consensus 263 ~~~i~~vN~~-f~~~tGys~~E~~G~~ 288 (289)
||+|+++-+. ...++||..+|++|+.
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s 37 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRS 37 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSB
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCc
Confidence 9999999999 6999999999999985
No 86
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=90.96 E-value=0.33 Score=40.82 Aligned_cols=44 Identities=16% Similarity=0.050 Sum_probs=40.7
Q ss_pred hHHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhcc
Q 022961 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITRI 288 (289)
Q Consensus 242 ~~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~~ 288 (289)
.+...++..++.+.-.|. .|.|..+|||++..+|-+.+++.|+-
T Consensus 81 ~L~aLL~al~~pVlsvd~---kg~v~~aNpAa~~l~~~~~~~~~g~~ 124 (511)
T COG3283 81 ALSALLEALPEPVLSVDM---KGKVDMANPAACQLFGRKEDRLRGHT 124 (511)
T ss_pred HHHHHHHhCCCceEEecc---cCceeecCHHHHHHhCCChhhhcCcc
Confidence 377889999999999999 99999999999999999999999864
No 87
>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=86.96 E-value=0.67 Score=32.14 Aligned_cols=42 Identities=26% Similarity=0.394 Sum_probs=33.9
Q ss_pred EEEEEeCCCCCccEEEccHHHHHHhCCC---ccccCCCCCCCccCCC
Q 022961 30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPR 73 (289)
Q Consensus 30 ~i~~~d~~~~~g~i~~~N~~~~~~~G~~---~~e~~g~~~~~l~~~~ 73 (289)
.++++|.+ +++|+.++..+..++|.+ .++++|++...++.+.
T Consensus 17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~ 61 (110)
T PF08446_consen 17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAE 61 (110)
T ss_dssp EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCC
T ss_pred EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHH
Confidence 45566653 389999999999999999 9999999988887654
No 88
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=85.84 E-value=0.98 Score=45.33 Aligned_cols=36 Identities=8% Similarity=-0.006 Sum_probs=32.0
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCCh
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI 281 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~ 281 (289)
....++.++.+|++.|. +|+|+++|++|++++|+..
T Consensus 578 ~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~ 613 (1197)
T PRK09959 578 RKALSDSLPNPTYVVNW---QGNVISHNSAFEHYFTADY 613 (1197)
T ss_pred HHHHHhhCCCcEEEEcC---CCcEEEehHHHHHHhCccc
Confidence 34567889999999999 9999999999999999874
No 89
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=84.20 E-value=2.6 Score=40.85 Aligned_cols=39 Identities=15% Similarity=0.118 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCC
Q 022961 15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGF 56 (289)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~ 56 (289)
..+...+.+++++|+|++++| .+ |+++++|+++.+++|+
T Consensus 340 ~~~~l~~~Ii~~lp~Gilv~D~~~---~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 340 ILRALNEEIVSNLPLGLLVYDFES---NRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHhCCceEEEEECCC---CeEEEEhHHHHHHhCc
Confidence 566788899999999999999 45 8999999999999975
No 90
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=83.01 E-value=1.3 Score=41.58 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=30.9
Q ss_pred hhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 247 ~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+|.....+++..- +|+|+||.+.-+.++||..+|++|+
T Consensus 101 LeAlDGF~fvV~c---dG~IvyVSeSVT~~L~y~QsDL~~q 138 (803)
T KOG3561|consen 101 LEALDGFLFVVNC---DGRIVYVSESVTSVLGYLQSDLMGQ 138 (803)
T ss_pred HHHhcCeEEEEec---CceEEEEecchHHhhCcCHHHHhcc
Confidence 4545444555566 7999999999999999999999996
No 91
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.31 E-value=11 Score=28.71 Aligned_cols=107 Identities=17% Similarity=0.220 Sum_probs=72.1
Q ss_pred HHHhhCCCEEEEEeCC-CCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCCeEEEEEEEe
Q 022961 22 EALDELPDSFTITDPS-ISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (289)
Q Consensus 22 ~~~~~~~~~i~~~d~~-~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (289)
.+-...++.++ +..+ ..+-.+..+-...|.+||- |+-|.++..+..+.+.......+..+.....+.-.......
T Consensus 52 ~l~slL~d~Fi-L~~~~~G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s 127 (209)
T COG5388 52 KLKSLLPDVFI-LERDGRGKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRS 127 (209)
T ss_pred HHHhhcCceEE-EeccCCCCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhh
Confidence 34556666544 4433 1112345577778888884 67788888787777666666666666666666666666667
Q ss_pred cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (289)
Q Consensus 101 ~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (289)
..|...-+++-..|+.. ..|+...++|...-+
T Consensus 128 ~~G~sl~fEmLl~PL~~-~~g~~~R~LGais~~ 159 (209)
T COG5388 128 HGGRSLGFEMLLAPLQG-ASGETDRFLGAISPI 159 (209)
T ss_pred ccCcccceeeeeecccC-CCCCccchhhhcccc
Confidence 77888888999999988 788767777766544
No 92
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=81.16 E-value=4.1 Score=38.30 Aligned_cols=82 Identities=10% Similarity=0.124 Sum_probs=59.4
Q ss_pred EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC--e-EEEEEEEecCCCEEE
Q 022961 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP--I-EVNLLNYKKDGTPFW 107 (289)
Q Consensus 31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~--~-~~e~~~~~~~g~~~~ 107 (289)
+|.+... +++.+..|..++..++||-+.++||+++-.++++.+.....+....+++.+.. + ...+++...+|....
T Consensus 332 iFtT~HT-ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ 410 (1114)
T KOG3753|consen 332 IFTTTHT-PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVR 410 (1114)
T ss_pred eeEeccC-CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEE
Confidence 4444332 34788899999999999999999999988888888877766666666665532 2 235778888998776
Q ss_pred EEEEEE
Q 022961 108 MLFKMS 113 (289)
Q Consensus 108 ~~~~~~ 113 (289)
+.....
T Consensus 411 ldTeWS 416 (1114)
T KOG3753|consen 411 LDTEWS 416 (1114)
T ss_pred Eechhh
Confidence 554433
No 93
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=80.90 E-value=2.5 Score=38.28 Aligned_cols=42 Identities=10% Similarity=0.052 Sum_probs=37.8
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCChHhHhhc
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQIFTKITR 287 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~~E~~G~ 287 (289)
+..+++...-|++..|. +|+|.-+||+.++|+|-+.++++|+
T Consensus 372 ~E~VLsgvtaGVi~~d~---~g~i~t~N~~ae~~l~~~~~~~~G~ 413 (712)
T COG5000 372 LEAVLSGLTAGVIGFDN---RGCITTVNPSAEQILGKPFDQLLGQ 413 (712)
T ss_pred HHHHHhcCceeEEEEcC---CCeeEeecchHHHHhcCChhHhhcc
Confidence 44567778899999999 9999999999999999999999995
No 94
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=79.59 E-value=2.4 Score=37.46 Aligned_cols=58 Identities=12% Similarity=0.165 Sum_probs=49.3
Q ss_pred HHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHH
Q 022961 23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (289)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~ 83 (289)
+++++..-++++..+ |.|.|++......+|+...+++-++..++++.++.+.+...+.
T Consensus 116 lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLh 173 (712)
T KOG3560|consen 116 LLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLH 173 (712)
T ss_pred HHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHh
Confidence 566777778888999 9999999999999999999999999888998887777655443
No 95
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=78.66 E-value=5 Score=31.43 Aligned_cols=39 Identities=18% Similarity=0.065 Sum_probs=34.3
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCCCc
Q 022961 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (289)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~ 58 (289)
.+.+..+++..|.++++-+.+ |.+++.|.+|.+.+.-+-
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhcC
Confidence 456778999999999999999 999999999999987543
No 96
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=74.00 E-value=7.5 Score=35.15 Aligned_cols=40 Identities=13% Similarity=0.107 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHhhCCCEEEEEeCCCCCccEEEccHHHHHHhCC
Q 022961 14 NRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (289)
Q Consensus 14 ~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~ 56 (289)
.+.+..+..++.++|.|+++.+.+ +.+.|+||-...+|+-
T Consensus 71 ~~~~~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~~ 110 (655)
T COG3887 71 YQAEKSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcCh
Confidence 356677888999999999999988 9999999998888763
No 97
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=73.24 E-value=7 Score=37.49 Aligned_cols=48 Identities=19% Similarity=0.101 Sum_probs=38.5
Q ss_pred HHHHHHHHHhhCCCEEEEEe-CCCCCccEEEccHHHHHHhCCCccccCCCCCCCc
Q 022961 16 YTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF 69 (289)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l 69 (289)
..+.-..++..+|.|++++| .+ |.|.|.|+.|..++| .+ ++|++...+
T Consensus 100 ~~~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 100 VSQIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HhHHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 34455678999999999999 68 999999999999987 23 788886653
No 98
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=70.58 E-value=89 Score=28.84 Aligned_cols=30 Identities=17% Similarity=0.134 Sum_probs=25.5
Q ss_pred cccccEEEeCCCCCCCCEEEecHHHHHhhCCCh
Q 022961 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQI 281 (289)
Q Consensus 249 ~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys~ 281 (289)
..+++.++.|. +++|+..|++...+.+-+.
T Consensus 230 ~~~~~~lavd~---~grvl~at~aA~~~La~~~ 259 (606)
T COG3284 230 SQSEALLAVDQ---DGRVLGATRAARQLLALTD 259 (606)
T ss_pred cccceeeeecC---cchhhhccHHHHHhhccch
Confidence 34577888899 9999999999999998873
No 99
>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=65.59 E-value=10 Score=26.15 Aligned_cols=33 Identities=27% Similarity=0.397 Sum_probs=26.1
Q ss_pred EEEeCCCCCCCCEEEecHHHHHhhCCC---hHhHhhcc
Q 022961 254 FVLIDPHLPDMPMVYASDAFLKLTGAQ---IFTKITRI 288 (289)
Q Consensus 254 i~i~d~~~~~~~i~~vN~~f~~~tGys---~~E~~G~~ 288 (289)
++..|. ++++|+++......++|.+ .++++|+-
T Consensus 18 LLa~d~--~~~~I~~~S~N~~~~lg~~~~~~~~llG~~ 53 (110)
T PF08446_consen 18 LLALDP--DDLRIVQASENIAELLGIPPELPEELLGRP 53 (110)
T ss_dssp EEEEET--TTTBEEEEETTHHHHHSS----HHHHTTCB
T ss_pred EEEEEC--CCCEEEEEcCCHHHHhCCccccchhhcccC
Confidence 344444 2689999999999999999 99999973
No 100
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=65.37 E-value=13 Score=30.97 Aligned_cols=88 Identities=14% Similarity=0.303 Sum_probs=53.8
Q ss_pred HHHHHhhCC----CEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHH--hCCCeE
Q 022961 20 VHEALDELP----DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR--EERPIE 93 (289)
Q Consensus 20 l~~~~~~~~----~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~ 93 (289)
+++++|+.. .++++..+. +.+.+|+|..|..++||+.+..+......+.. ....+...+. ......
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV~e------Gl~qW~~dL~~~s~~E~~ 356 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIVQE------GLAQWETDLQLLSRQERS 356 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHHHh------hHHHHHHHHHhhhhhhhh
Confidence 455666544 345555543 37899999999999999999887543222221 1112222221 223345
Q ss_pred EEEEEEecCCCEEEEEEEEEEe
Q 022961 94 VNLLNYKKDGTPFWMLFKMSLV 115 (289)
Q Consensus 94 ~e~~~~~~~g~~~~~~~~~~~~ 115 (289)
+.+.+.+++|...++......+
T Consensus 357 grlviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 357 GRLVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred ceEEEEecCCCceeeEEEEeec
Confidence 6777888999887776665555
No 101
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=60.68 E-value=45 Score=23.44 Aligned_cols=48 Identities=17% Similarity=0.222 Sum_probs=37.0
Q ss_pred CeEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecccccHHHHh
Q 022961 91 PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (289)
Q Consensus 91 ~~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~e~ 141 (289)
.+...+....++|+. +..+...+++ ++|.+.+++++=.|+|....+.+
T Consensus 67 ~~~~nY~~~~~~Gk~--lrSsT~~Ird-~~g~~iG~LCIN~D~s~~~~~~~ 114 (118)
T PF08348_consen 67 DYIINYKTKTKDGKI--LRSSTFFIRD-ENGKLIGALCINFDISALEQAQN 114 (118)
T ss_pred CccccccccCCCCCE--EEEEEEEEEC-CCCCEEEEEEEEeccHHHHHHHH
Confidence 344556667788865 4567778888 89999999999999998887743
No 102
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=59.39 E-value=8.7 Score=36.31 Aligned_cols=44 Identities=14% Similarity=0.099 Sum_probs=36.5
Q ss_pred EEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHH
Q 022961 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR 77 (289)
Q Consensus 31 i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~ 77 (289)
+++.+.+ |+++|+.+.+..++||.++-+.+.++.+++++.+...
T Consensus 195 ~~vS~~d---G~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~v 238 (1114)
T KOG3753|consen 195 VAVSFLD---GRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGV 238 (1114)
T ss_pred EEEeccC---CcEEEeechhhhhccCchhhhccchhhhhcchhhhhh
Confidence 4445567 9999999999999999999999999888887765443
No 103
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=55.12 E-value=15 Score=35.83 Aligned_cols=36 Identities=8% Similarity=-0.064 Sum_probs=31.1
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhCCC
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGAQ 280 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tGys 280 (289)
...++++++.|+++.|. .+++|+.+|+++.+++|+.
T Consensus 345 ~~~Ii~~lp~Gilv~D~--~~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 345 NEEIVSNLPLGLLVYDF--ESNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHhCCceEEEEEC--CCCeEEEEhHHHHHHhCcc
Confidence 46678999999999994 1678999999999999975
No 104
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=44.22 E-value=28 Score=33.59 Aligned_cols=33 Identities=15% Similarity=0.048 Sum_probs=28.8
Q ss_pred HHHHhhcccccEEEeC-CCCCCCCEEEecHHHHHhhC
Q 022961 243 LYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTG 278 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d-~~~~~~~i~~vN~~f~~~tG 278 (289)
...++.+.|-++++.| . ++.|+++|+.|.+++|
T Consensus 104 ~~~~l~~~p~gi~~~~~~---~~~i~W~N~~~~~~~~ 137 (838)
T PRK14538 104 GEEVLNELPIGIVLIDIS---SKEIQWLNPYANFILK 137 (838)
T ss_pred HHHHHHhCCceEEEEeCC---CCEEEEECHHHHHHhC
Confidence 4557788899999999 7 7899999999999987
No 105
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=39.46 E-value=18 Score=20.54 Aligned_cols=17 Identities=12% Similarity=-0.068 Sum_probs=10.0
Q ss_pred HHHHHhhCCChHhHhhc
Q 022961 271 DAFLKLTGAQIFTKITR 287 (289)
Q Consensus 271 ~~f~~~tGys~~E~~G~ 287 (289)
.+..+-+||.++|++.-
T Consensus 7 ~~Ls~tMGY~kdeI~ea 23 (46)
T PF08587_consen 7 SKLSKTMGYDKDEIYEA 23 (46)
T ss_dssp HHHHCTT---HHHHHHH
T ss_pred HHHHHHhCCCHHHHHHH
Confidence 35667789999998753
No 106
>PF09308 LuxQ-periplasm: LuxQ, periplasmic; InterPro: IPR015387 This entry represents the periplasmic sensor domain of the prokaryotic protein LuxQ, that assumes a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds []. ; GO: 0004673 protein histidine kinase activity, 0016791 phosphatase activity; PDB: 2HJ9_C 2HJE_A 1ZHH_B 3C30_A 3C38_A.
Probab=36.00 E-value=2.3e+02 Score=22.78 Aligned_cols=93 Identities=11% Similarity=0.139 Sum_probs=52.3
Q ss_pred HHHHHHHHHh----hCCCEEEEEeCCCCCccEEEccHHHHHHhCCCccccCCCCCCCccCCCCCHHHHHHHHHHHHhCCC
Q 022961 16 YTLWVHEALD----ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP 91 (289)
Q Consensus 16 ~~~~l~~~~~----~~~~~i~~~d~~~~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 91 (289)
.+..|..+-+ ++||--++.+.+ | ++|.++-..++|.+... ...+......+..
T Consensus 56 l~~ff~~idq~~p~~~pDfRFi~~~~---~--~~WdDgN~~FYGi~~~~------------------L~~ls~~~~~~~~ 112 (238)
T PF09308_consen 56 LDQFFSSIDQSDPSNAPDFRFISSHD---G--VIWDDGNAPFYGISESS------------------LQHLSQKVAFSNN 112 (238)
T ss_dssp HHHHHHHHHHCCCCCS-SEEEEEETT---C--EEEE-SHHHHCT--HHH------------------HHHHHHHT-STTS
T ss_pred HHHHHhhccccCccCCCCEEEEEeCC---C--cEEeCCCCcccCcCHHH------------------HHHHhhcccccCc
Confidence 3444554433 466777777776 5 44666667777765432 2333444445556
Q ss_pred eEEEEEEEecCCCEEEEEEEEEEeecCCCCcEEEEEEEEecc
Q 022961 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (289)
Q Consensus 92 ~~~e~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (289)
|...- .......+++.++-.|+.++.+|++.|++-++.-+
T Consensus 113 W~~i~--~~s~~g~~~lLvRR~pIi~~~tGEVlG~Ly~gvVL 152 (238)
T PF09308_consen 113 WHYIQ--TPSSMGNRYLLVRRTPIIDPKTGEVLGYLYIGVVL 152 (238)
T ss_dssp -EEEE--EEETTCEEEEEEEEEEEE-TTTSBEEEEEEEEEE-
T ss_pred eeEEE--ecCCCCceEEEEeecceeeCCCCeEEEEEEEEEEE
Confidence 65432 23456677788999999876789999976554433
No 107
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=29.91 E-value=22 Score=29.64 Aligned_cols=25 Identities=16% Similarity=0.223 Sum_probs=21.7
Q ss_pred CCCCEEEecHHHHHhhCCChHhHhh
Q 022961 262 PDMPMVYASDAFLKLTGAQIFTKIT 286 (289)
Q Consensus 262 ~~~~i~~vN~~f~~~tGys~~E~~G 286 (289)
.+.+.+++|.-|...|||+.|..+-
T Consensus 306 k~qRllFAN~~fk~wtGy~~edFl~ 330 (401)
T PF06785_consen 306 KSQRLLFANSQFKTWTGYSSEDFLK 330 (401)
T ss_pred hhhHHHHhHHHHHHHhccCHHHHHh
Confidence 4678999999999999999987653
No 108
>PF15660 Imm49: Immunity protein 49
Probab=24.90 E-value=45 Score=20.18 Aligned_cols=24 Identities=13% Similarity=0.239 Sum_probs=17.8
Q ss_pred cccEEEeCCCCCCCCEEEecHHHH
Q 022961 251 KQSFVLIDPHLPDMPMVYASDAFL 274 (289)
Q Consensus 251 ~~~i~i~d~~~~~~~i~~vN~~f~ 274 (289)
.+-+++|...-.+.+.+|.||-|.
T Consensus 31 adrlmvttsvgeearlvyfnpdfa 54 (84)
T PF15660_consen 31 ADRLMVTTSVGEEARLVYFNPDFA 54 (84)
T ss_pred cceEEEEeccCceeEEEEeCCCcC
Confidence 455677776556778999999874
No 109
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=24.33 E-value=1.2e+02 Score=23.89 Aligned_cols=33 Identities=12% Similarity=0.078 Sum_probs=26.9
Q ss_pred HHHHhhcccccEEEeCCCCCCCCEEEecHHHHHhhC
Q 022961 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (289)
Q Consensus 243 ~~~~~e~~~~~i~i~d~~~~~~~i~~vN~~f~~~tG 278 (289)
+...+...+.=+.|-+. +|.+++.|.+|.+.++
T Consensus 21 ~~~~i~~~~~P~CiR~~---~g~fi~~N~~F~~~f~ 53 (217)
T PRK13719 21 LTAFIDDYSYPACIRNE---SGKFIFYNTLFLKEFL 53 (217)
T ss_pred HHHHHHcCCCCeEEECC---CCCeeecchHHHHHHH
Confidence 44566667777788888 9999999999998775
No 110
>PF11479 Suppressor_P21: RNA silencing suppressor P21; InterPro: IPR021575 P21 is produced by Beet yellows virus to suppress the antiviral silencing response mounted by the host. P21 acts by binding directly to siRNA which is a mediator in the process. P21 has an octameric ring structure with a large central cavity []. ; PDB: 2CWO_B.
Probab=22.15 E-value=55 Score=22.87 Aligned_cols=15 Identities=13% Similarity=0.352 Sum_probs=9.9
Q ss_pred HHHHHhhCCChHhHh
Q 022961 271 DAFLKLTGAQIFTKI 285 (289)
Q Consensus 271 ~~f~~~tGys~~E~~ 285 (289)
..+|+|||.++++.+
T Consensus 111 eeycritgl~redal 125 (177)
T PF11479_consen 111 EEYCRITGLTREDAL 125 (177)
T ss_dssp HHHHHHH---HHHHC
T ss_pred HHHHHHhccchHHHH
Confidence 568999999998865
Done!