Query 022384
Match_columns 298
No_of_seqs 276 out of 3140
Neff 10.4
Searched_HMMs 46136
Date Fri Mar 29 03:07:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022384hhsearch_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 1.1E-18 2.4E-23 167.2 18.9 183 7-290 194-379 (807)
2 TIGR02040 PpsR-CrtJ transcript 99.8 5.5E-19 1.2E-23 157.9 15.4 172 15-294 130-303 (442)
3 PRK09776 putative diguanylate 99.8 5.7E-18 1.2E-22 167.3 17.6 186 8-295 401-587 (1092)
4 TIGR02938 nifL_nitrog nitrogen 99.8 5.3E-18 1.1E-22 153.5 14.2 176 18-293 4-179 (494)
5 PF13426 PAS_9: PAS domain; PD 99.7 6.9E-17 1.5E-21 114.5 13.6 104 28-135 1-104 (104)
6 TIGR02040 PpsR-CrtJ transcript 99.7 1.1E-17 2.3E-22 149.6 9.2 181 24-293 2-183 (442)
7 PRK09776 putative diguanylate 99.7 5E-16 1.1E-20 153.6 17.5 125 15-143 280-405 (1092)
8 PF08448 PAS_4: PAS fold; Int 99.7 9.6E-16 2.1E-20 109.8 12.0 110 24-138 1-110 (110)
9 PRK13560 hypothetical protein; 99.7 1.3E-15 2.9E-20 146.0 16.5 176 17-293 66-253 (807)
10 PRK11359 cyclic-di-GMP phospho 99.7 1.8E-15 4E-20 145.0 14.8 170 18-293 12-185 (799)
11 PF00989 PAS: PAS fold; Inter 99.6 3.4E-15 7.4E-20 107.5 12.3 112 18-133 1-113 (113)
12 PRK11091 aerobic respiration c 99.5 1.3E-13 2.8E-18 131.8 14.6 125 15-143 152-276 (779)
13 PRK13559 hypothetical protein; 99.5 4.6E-13 9.9E-18 116.7 15.8 126 16-142 41-166 (361)
14 PRK10060 RNase II stability mo 99.5 6E-13 1.3E-17 124.5 16.0 137 16-157 109-253 (663)
15 PRK13557 histidine kinase; Pro 99.5 5.9E-13 1.3E-17 122.1 15.4 128 15-143 27-154 (540)
16 PRK13558 bacterio-opsin activa 99.4 5.6E-12 1.2E-16 118.6 15.9 125 19-144 149-273 (665)
17 TIGR00229 sensory_box PAS doma 99.3 7.3E-11 1.6E-15 83.4 13.0 120 18-142 3-123 (124)
18 PRK11359 cyclic-di-GMP phospho 99.2 2.2E-10 4.7E-15 110.2 13.3 123 16-142 134-257 (799)
19 PF08447 PAS_3: PAS fold; Int 99.2 1.5E-10 3.2E-15 79.9 9.0 86 43-130 1-91 (91)
20 cd00130 PAS PAS domain; PAS mo 99.0 1.6E-08 3.4E-13 68.0 13.4 103 27-133 1-103 (103)
21 PRK11360 sensory histidine kin 99.0 1.4E-08 3E-13 94.3 14.0 121 16-143 260-381 (607)
22 TIGR02966 phoR_proteo phosphat 98.9 9.5E-09 2.1E-13 88.2 11.3 112 15-143 3-114 (333)
23 PF12860 PAS_7: PAS fold 98.9 5.4E-09 1.2E-13 75.5 8.3 105 24-141 1-115 (115)
24 PF13596 PAS_10: PAS domain; P 98.9 1.4E-08 3E-13 72.2 9.5 106 20-134 1-106 (106)
25 PRK11073 glnL nitrogen regulat 98.9 1.5E-08 3.2E-13 87.9 10.7 114 19-143 8-121 (348)
26 PF14598 PAS_11: PAS domain; P 98.8 2E-07 4.4E-12 66.5 12.4 101 32-135 6-108 (111)
27 COG3829 RocR Transcriptional r 98.7 9.3E-08 2E-12 84.0 10.4 163 21-293 4-166 (560)
28 COG5002 VicK Signal transducti 98.7 3.6E-07 7.7E-12 75.7 11.1 118 15-143 108-225 (459)
29 KOG0501 K+-channel KCNQ [Inorg 98.6 1.5E-07 3.2E-12 82.6 9.1 121 18-139 14-139 (971)
30 PF00989 PAS: PAS fold; Inter 98.6 1.9E-08 4.2E-13 71.9 1.8 49 243-294 3-51 (113)
31 PRK11006 phoR phosphate regulo 98.5 4.7E-07 1E-11 80.9 9.2 110 15-143 95-204 (430)
32 TIGR02938 nifL_nitrog nitrogen 98.5 1.2E-07 2.5E-12 86.0 5.3 127 8-143 121-258 (494)
33 PF13426 PAS_9: PAS domain; PD 98.5 5E-08 1.1E-12 68.5 1.6 41 251-294 1-41 (104)
34 PRK10820 DNA-binding transcrip 98.4 1.8E-06 4E-11 78.5 10.2 110 15-138 77-190 (520)
35 COG2202 AtoS FOG: PAS/PAC doma 98.3 4.1E-05 9E-10 59.1 14.3 119 16-139 110-231 (232)
36 PF13188 PAS_8: PAS domain; PD 98.3 1.6E-06 3.4E-11 55.3 4.9 42 18-66 1-42 (64)
37 PRK11086 sensory histidine kin 98.3 8.6E-06 1.9E-10 74.9 11.4 112 16-143 219-333 (542)
38 PRK10060 RNase II stability mo 98.2 1.2E-06 2.5E-11 82.5 3.6 46 245-293 115-160 (663)
39 COG3829 RocR Transcriptional r 98.2 9.6E-06 2.1E-10 71.7 8.4 116 15-143 114-229 (560)
40 KOG1229 3'5'-cyclic nucleotide 98.1 1.5E-06 3.2E-11 74.0 3.2 105 20-128 159-264 (775)
41 PRK11388 DNA-binding transcrip 98.1 4.4E-05 9.6E-10 71.7 12.8 46 246-294 208-253 (638)
42 PF13188 PAS_8: PAS domain; PD 97.8 9.5E-06 2.1E-10 51.6 2.0 41 243-290 3-43 (64)
43 COG3290 CitA Signal transducti 97.8 9.6E-05 2.1E-09 65.4 8.4 113 16-143 213-327 (537)
44 PF08448 PAS_4: PAS fold; Int 97.8 1.1E-05 2.3E-10 57.1 2.2 44 247-293 1-44 (110)
45 PRK13557 histidine kinase; Pro 97.8 1.4E-05 3E-10 73.4 3.3 51 243-293 32-82 (540)
46 KOG3558 Hypoxia-inducible fact 97.8 0.00023 5E-09 64.3 10.5 58 23-83 124-181 (768)
47 PRK15053 dpiB sensor histidine 97.8 0.00015 3.4E-09 66.8 10.0 110 17-143 221-332 (545)
48 PRK11388 DNA-binding transcrip 97.8 0.00032 6.9E-09 66.0 12.1 109 18-138 203-311 (638)
49 COG5000 NtrY Signal transducti 97.8 0.00033 7.2E-09 62.8 11.1 115 16-142 368-483 (712)
50 PRK09959 hybrid sensory histid 97.7 0.00074 1.6E-08 68.3 13.7 43 15-60 573-615 (1197)
51 TIGR02966 phoR_proteo phosphat 97.7 3.2E-05 6.9E-10 66.2 3.4 48 243-293 8-55 (333)
52 PRK13559 hypothetical protein; 97.5 6.2E-05 1.3E-09 65.6 3.1 51 243-293 45-95 (361)
53 PF08670 MEKHLA: MEKHLA domain 97.5 0.0045 9.7E-08 46.1 11.7 112 18-132 32-144 (148)
54 KOG3558 Hypoxia-inducible fact 97.5 0.00015 3.3E-09 65.4 4.7 77 41-117 284-360 (768)
55 PRK11073 glnL nitrogen regulat 97.4 8.6E-05 1.9E-09 64.3 2.9 48 243-293 9-56 (348)
56 KOG1229 3'5'-cyclic nucleotide 97.4 2.9E-05 6.3E-10 66.3 -0.5 47 243-292 159-205 (775)
57 PRK11006 phoR phosphate regulo 97.3 0.00012 2.6E-09 65.5 2.5 49 243-294 100-148 (430)
58 PF12860 PAS_7: PAS fold 97.3 0.00019 4.1E-09 51.5 3.1 46 247-295 1-47 (115)
59 smart00091 PAS PAS domain. PAS 97.3 0.00074 1.6E-08 40.6 5.5 54 20-76 3-56 (67)
60 TIGR00229 sensory_box PAS doma 97.2 0.00031 6.8E-09 48.6 2.9 47 244-293 6-52 (124)
61 PRK10820 DNA-binding transcrip 97.2 0.0002 4.3E-09 65.4 2.2 49 243-294 82-130 (520)
62 TIGR02373 photo_yellow photoac 97.1 0.0067 1.5E-07 43.2 9.0 67 21-90 19-86 (124)
63 PRK11091 aerobic respiration c 97.1 0.00029 6.3E-09 68.0 2.9 48 243-293 157-204 (779)
64 COG3852 NtrB Signal transducti 97.1 0.0036 7.9E-08 51.7 8.6 108 21-138 10-118 (363)
65 COG2461 Uncharacterized conser 96.9 0.0035 7.5E-08 53.3 7.2 114 17-140 289-402 (409)
66 cd00130 PAS PAS domain; PAS mo 96.9 0.00081 1.7E-08 44.2 2.8 39 252-293 3-41 (103)
67 COG2202 AtoS FOG: PAS/PAC doma 96.7 0.026 5.6E-07 43.1 10.6 45 246-293 117-161 (232)
68 PRK11360 sensory histidine kin 96.3 0.0034 7.4E-08 58.4 3.2 47 244-293 265-311 (607)
69 KOG3559 Transcriptional regula 96.2 0.032 6.9E-07 47.6 8.4 55 21-78 82-136 (598)
70 smart00091 PAS PAS domain. PAS 96.2 0.0048 1E-07 36.8 2.8 45 246-293 6-50 (67)
71 smart00086 PAC Motif C-termina 96.2 0.054 1.2E-06 28.5 7.0 41 95-136 3-43 (43)
72 PRK13558 bacterio-opsin activa 96.1 0.0044 9.6E-08 58.7 3.1 49 245-293 152-200 (665)
73 COG3283 TyrR Transcriptional r 96.0 0.022 4.8E-07 48.4 6.4 58 16-76 78-135 (511)
74 PF07310 PAS_5: PAS domain; I 95.5 0.36 7.8E-06 35.7 10.6 87 40-130 50-136 (137)
75 PRK15053 dpiB sensor histidine 95.3 0.015 3.3E-07 53.7 3.3 48 243-293 224-273 (545)
76 KOG3560 Aryl-hydrocarbon recep 95.3 0.079 1.7E-06 47.1 7.3 93 41-135 293-385 (712)
77 PF08447 PAS_3: PAS fold; Int 95.1 0.0078 1.7E-07 40.8 0.6 22 266-288 1-22 (91)
78 TIGR02373 photo_yellow photoac 95.0 0.022 4.8E-07 40.6 2.6 42 246-290 21-62 (124)
79 KOG0501 K+-channel KCNQ [Inorg 94.8 0.0085 1.8E-07 53.6 0.3 38 253-290 29-66 (971)
80 COG5002 VicK Signal transducti 94.7 0.025 5.4E-07 47.8 2.7 46 249-297 119-164 (459)
81 PF14598 PAS_11: PAS domain; P 94.2 0.021 4.6E-07 40.6 1.1 31 263-293 11-42 (111)
82 PF13596 PAS_10: PAS domain; P 94.2 0.013 2.9E-07 41.1 0.1 44 245-292 3-46 (106)
83 PRK11086 sensory histidine kin 94.2 0.046 9.9E-07 50.4 3.5 48 243-293 223-273 (542)
84 KOG3561 Aryl-hydrocarbon recep 92.9 0.11 2.4E-06 49.2 3.8 56 19-77 96-151 (803)
85 COG3852 NtrB Signal transducti 92.9 0.065 1.4E-06 44.6 2.0 47 245-294 11-57 (363)
86 PRK10841 hybrid sensory kinase 92.7 3 6.5E-05 41.4 13.5 103 15-143 331-433 (924)
87 KOG3561 Aryl-hydrocarbon recep 89.9 0.19 4.1E-06 47.7 2.0 46 247-295 101-146 (803)
88 COG3283 TyrR Transcriptional r 89.3 0.35 7.5E-06 41.5 2.9 48 243-293 82-129 (511)
89 KOG3559 Transcriptional regula 88.9 0.93 2E-05 39.1 5.2 84 30-116 227-310 (598)
90 COG3290 CitA Signal transducti 88.0 0.28 6E-06 44.2 1.6 49 243-294 217-267 (537)
91 KOG3560 Aryl-hydrocarbon recep 87.1 0.8 1.7E-05 41.1 3.8 59 22-83 115-173 (712)
92 COG3284 AcoR Transcriptional a 86.6 7.6 0.00017 36.0 9.8 42 249-293 230-272 (606)
93 PF08446 PAS_2: PAS fold; Int 85.2 0.85 1.8E-05 32.3 2.6 43 30-74 17-62 (110)
94 PF08446 PAS_2: PAS fold; Int 84.2 0.69 1.5E-05 32.7 1.8 39 254-294 18-59 (110)
95 PRK10618 phosphotransfer inter 79.9 4.7 0.0001 39.8 6.3 40 15-56 340-379 (894)
96 PF08670 MEKHLA: MEKHLA domain 79.0 1.6 3.6E-05 32.6 2.2 44 244-288 34-77 (148)
97 KOG3753 Circadian clock protei 78.0 8.5 0.00018 37.0 6.8 78 31-109 332-412 (1114)
98 KOG3753 Circadian clock protei 77.9 1.7 3.8E-05 41.4 2.5 41 254-297 195-235 (1114)
99 COG5000 NtrY Signal transducti 76.8 2.2 4.8E-05 39.3 2.8 44 246-292 375-418 (712)
100 PRK09959 hybrid sensory histid 76.6 2.3 5E-05 43.5 3.2 36 244-282 579-614 (1197)
101 COG3887 Predicted signaling pr 67.1 14 0.0003 34.2 5.4 39 15-56 72-110 (655)
102 PRK14538 putative bifunctional 65.8 13 0.00028 36.4 5.4 45 18-68 102-147 (838)
103 PF08348 PAS_6: YheO-like PAS 65.2 29 0.00063 24.9 5.9 47 92-141 68-114 (118)
104 PRK13719 conjugal transfer tra 63.3 16 0.00035 29.2 4.6 38 18-58 19-56 (217)
105 PF06785 UPF0242: Uncharacteri 57.5 19 0.0004 30.6 4.2 90 20-115 285-378 (401)
106 COG5388 Uncharacterized protei 57.3 89 0.0019 24.5 7.4 105 23-133 53-159 (209)
107 PF09884 DUF2111: Uncharacteri 41.6 1E+02 0.0022 20.4 6.2 47 82-134 37-83 (84)
108 PRK14538 putative bifunctional 35.7 37 0.00081 33.4 3.2 43 244-292 105-148 (838)
109 PRK10618 phosphotransfer inter 32.8 37 0.0008 33.8 2.7 36 243-280 345-380 (894)
110 PF06785 UPF0242: Uncharacteri 32.3 14 0.00031 31.3 -0.1 25 262-286 306-330 (401)
111 COG4004 Uncharacterized protei 26.8 23 0.00049 23.8 0.1 17 268-284 73-89 (96)
112 PF15660 Imm49: Immunity prote 21.1 59 0.0013 20.1 1.2 23 252-274 32-54 (84)
No 1
>PRK13560 hypothetical protein; Provisional
Probab=99.81 E-value=1.1e-18 Score=167.18 Aligned_cols=183 Identities=13% Similarity=0.091 Sum_probs=143.6
Q ss_pred hHHHhhhhHHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHH
Q 022384 7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI 86 (298)
Q Consensus 7 ~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~ 86 (298)
..++.+. +..++++.+++++|++++++|.+ |+++++|+++++++||++++++|+++..+.++.............+
T Consensus 194 ~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~ 269 (807)
T PRK13560 194 RAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKF 269 (807)
T ss_pred HHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHh
Confidence 3444554 56778999999999999999999 9999999999999999999999999888876655444434444555
Q ss_pred HhCCCEEEEEEEEccCCCEEEEEEEE--EEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhh
Q 022384 87 REERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCR 164 (298)
Q Consensus 87 ~~~~~~~~e~~~~~~dg~~~~~~~~~--~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~ 164 (298)
..+.....+..+.+++|..+|+.+.. .|+.+ .+|.+.+++++++|||++|++|+++... .
T Consensus 270 ~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e~~L~~s-----------------e 331 (807)
T PRK13560 270 DADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAERELLEK-----------------E 331 (807)
T ss_pred ccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHHHHHHHH-----------------H
Confidence 56666777888899999999765554 55667 7888999999999999999995554111 1
Q ss_pred hhccccchhhcccceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhh
Q 022384 165 REVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLY 244 (298)
Q Consensus 165 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 244 (298)
. + +.
T Consensus 332 ~-----------------------------------~-----------------------------------------l~ 335 (807)
T PRK13560 332 D-----------------------------------M-----------------------------------------LR 335 (807)
T ss_pred H-----------------------------------H-----------------------------------------HH
Confidence 0 0 22
Q ss_pred hhhcccccceEeeCCCCCCCceeee-hhhhhhhccccceeccchhhH
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTDKGKHSNRASMHS 290 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~-N~af~~itGys~eE~~G~~~~ 290 (298)
..++.+..+++++|. ++.|+++ |+++++++||+.+|++|++..
T Consensus 336 ~l~~~~~~~i~~~d~---~g~i~~~nn~~~~~~~G~~~~e~~g~~~~ 379 (807)
T PRK13560 336 AIIEAAPIAAIGLDA---DGNICFVNNNAAERMLGWSAAEVMGKPLP 379 (807)
T ss_pred HHHHhCcccEEEEcC---CCCEEEecCHHHHHHhCCCHHHHcCCCcc
Confidence 345667788899999 9999987 678889999999999998754
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=99.81 E-value=5.5e-19 Score=157.89 Aligned_cols=172 Identities=19% Similarity=0.201 Sum_probs=130.3
Q ss_pred HHHHHHHHHHhhCCCEEEEEeC-CCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEE
Q 022384 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~-~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (298)
..+++++.+++.++++++++|. + |+++++|+++++++||+.++++|+++..++++.+.......+......+....
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 3467899999999999999997 7 99999999999999999999999987777777666656666666666665544
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhhccccchh
Q 022384 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (298)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~~~~~~l~ 173 (298)
.++. .++|...| .+.+.++.. .|. ..+++..+|||+++++|+++ .
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~e~~~-----------------~------------ 251 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPVGDEL-----------------S------------ 251 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhhhHHH-----------------H------------
Confidence 4443 33444444 345566654 343 35677889999998873321 0
Q ss_pred hcccceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhhhcccccc
Q 022384 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (298)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (298)
. .+...++.+.++
T Consensus 252 --------------------------~-----------------------------------------~~~~l~e~~~d~ 264 (442)
T TIGR02040 252 --------------------------E-----------------------------------------NLARLYHEAPDA 264 (442)
T ss_pred --------------------------H-----------------------------------------HHHHHHHhCCce
Confidence 0 033466778899
Q ss_pred eEeeCCCCCCCceeeehhhhhhhcccc-ceeccchhhHHHHh
Q 022384 254 FVLIDPHLPDMPMVYASDAFLKLTDKG-KHSNRASMHSTYLK 294 (298)
Q Consensus 254 i~i~d~~~~~~~i~~~N~af~~itGys-~eE~~G~~~~~~~~ 294 (298)
|+++|. +|.|+++|++|++++||+ .++++|+++.+++.
T Consensus 265 I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~ 303 (442)
T TIGR02040 265 IVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRTLDRWLG 303 (442)
T ss_pred EEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCCHHHHhC
Confidence 999999 999999999999999997 57899999988764
No 3
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.78 E-value=5.7e-18 Score=167.29 Aligned_cols=186 Identities=17% Similarity=0.147 Sum_probs=151.0
Q ss_pred HHHhhhhHHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCC-CCCCcCCCCCHHHHHHHHHHH
Q 022384 8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAI 86 (298)
Q Consensus 8 ~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~-~~~l~~~~~~~~~~~~~~~~~ 86 (298)
.++.+. +..++++.+++..+.+++.+|.+ +.++++|+++++++||+.++..+.. +....+|++.......+...+
T Consensus 401 ~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~ 476 (1092)
T PRK09776 401 TEQVNE-RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDAL 476 (1092)
T ss_pred HHHHHH-HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHH
Confidence 344444 55678888999999999999999 9999999999999999998844322 333455666666666677778
Q ss_pred HhCCCEEEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhh
Q 022384 87 REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRRE 166 (298)
Q Consensus 87 ~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~ 166 (298)
..+..+..+++..+++| ..|+.....|+.+ .+|.+.+++++.+|||++|++|+++ ....
T Consensus 477 ~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e~~L-----------------~~~~-- 535 (1092)
T PRK09776 477 QGRSPFKLEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLNEAL-----------------FQEK-- 535 (1092)
T ss_pred hcCCCeeEEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHHHHH-----------------HHHH--
Confidence 88888999999999999 9999999999998 8999999999999999999995543 1111
Q ss_pred ccccchhhcccceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhh
Q 022384 167 VCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYIS 246 (298)
Q Consensus 167 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 246 (298)
++ +...
T Consensus 536 ---------------------------------~~-----------------------------------------l~~~ 541 (1092)
T PRK09776 536 ---------------------------------ER-----------------------------------------LHIT 541 (1092)
T ss_pred ---------------------------------HH-----------------------------------------HHHH
Confidence 00 2335
Q ss_pred hcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHhh
Q 022384 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLKL 295 (298)
Q Consensus 247 ~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~~ 295 (298)
++.+.++++++|. ++.|+++|++|++++||+.+|++|+++.+++.+
T Consensus 542 l~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~ 587 (1092)
T PRK09776 542 LDSIGEAVVCTDM---AMKVTFMNPVAEKMTGWTQEEALGVPLLTVLHI 587 (1092)
T ss_pred HhccccEEEEECC---CCeEEEEcHHHHHHhCCCHHHHcCCCHHHHccc
Confidence 5677888999999 999999999999999999999999998887654
No 4
>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=99.77 E-value=5.3e-18 Score=153.47 Aligned_cols=176 Identities=22% Similarity=0.380 Sum_probs=144.2
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (298)
++++.+++.+|.+++++|.+ |+++++|+++++++||++++++|+....+.++.........+...+..+.++..++.
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 46888999999999999999 999999999999999999999998866666655556566666677777777877887
Q ss_pred EEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhhccccchhhccc
Q 022384 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (298)
Q Consensus 98 ~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~~~~~~l~~~~~ 177 (298)
..+++|..+|+.....|+.+ .+|.+.+++++.+|||++|++++++... .
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~l~~~-----------------~------------- 129 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQVVANQ-----------------K------------- 129 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHHHHHH-----------------H-------------
Confidence 88899999999999999998 8899999999999999999995543111 0
Q ss_pred ceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhhhcccccceEee
Q 022384 178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI 257 (298)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~ 257 (298)
.+ +...++.+..++++.
T Consensus 130 ----------------------~~-----------------------------------------~~~~~~~~~~~i~~~ 146 (494)
T TIGR02938 130 ----------------------LL-----------------------------------------IESVVDAAPVAFVLL 146 (494)
T ss_pred ----------------------HH-----------------------------------------HHHHHhcccceEEEE
Confidence 00 223456677888999
Q ss_pred CCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 258 DPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 258 d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
|. ++.|+++|++|++++||...+..+....+++
T Consensus 147 d~---~~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~ 179 (494)
T TIGR02938 147 DP---TGRVILDNQEYKKLATDLRVKEPAHTVLDLL 179 (494)
T ss_pred cC---CCCEEEechhHHHhhchhhhhHHHHHHHHHh
Confidence 99 9999999999999999999988887655443
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=99.74 E-value=6.9e-17 Score=114.55 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=95.4
Q ss_pred CCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEEE
Q 022384 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (298)
Q Consensus 28 ~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (298)
|++++++|.+ |+++++|+++++++||++++++|+++..++++.........+.+.+..+..+..++.+.+++|..+|
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 9999999999999999999999999988888887888888899999988889999999999999999
Q ss_pred EEEEEEEeecCCCCcEEEEEEEEecCch
Q 022384 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (298)
Q Consensus 108 ~~~~~~p~~~~~~g~~~~~~~~~~DITe 135 (298)
+.+++.|+.+ .+|.+.+++++++|||+
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=149.62 Aligned_cols=181 Identities=13% Similarity=0.070 Sum_probs=127.5
Q ss_pred HhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCC-CEEEEEEEEccC
Q 022384 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD 102 (298)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~d 102 (298)
+++++++++++|.+ |+++++|+.++.++||+.++++|+++..++++++.......+......+. .+..+.....++
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 56789999999999 99999999999999999999999999888887765555555555555543 344555555566
Q ss_pred CCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhhccccchhhcccceeec
Q 022384 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD 182 (298)
Q Consensus 103 g~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 182 (298)
|..+|+.++..++.+ + .+++++.+|||++++.+.++... ...+.. .
T Consensus 79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~~----------~~~~e~---~---------------- 124 (442)
T TIGR02040 79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVAA----------QQAMER---D---------------- 124 (442)
T ss_pred CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHHH----------HHHHHH---H----------------
Confidence 667777777666643 2 25678899999988874443111 000000 0
Q ss_pred CCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhhhcccccceEeeCCCCC
Q 022384 183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLP 262 (298)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~~~ 262 (298)
...+..... .+...++.+.+++++.|. .
T Consensus 125 -------------------~~~l~~~e~-------------------------------r~~~l~e~~~~~i~~~d~--~ 152 (442)
T TIGR02040 125 -------------------YWTLREMET-------------------------------RYRVVLEVSSDAVLLVDM--S 152 (442)
T ss_pred -------------------HHHHHHHHH-------------------------------HHHHHHhhCCceEEEEEC--C
Confidence 000000000 034466777888999986 2
Q ss_pred CCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 263 DMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 263 ~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
++.|+++|++|++++||+.+|++|+++.+++
T Consensus 153 ~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~ 183 (442)
T TIGR02040 153 TGRIVEANSAAAALLGGVGQSLVGRAFPQEF 183 (442)
T ss_pred CCEEEEEcHHHHHHhCcCHHHHcCCCHHHhC
Confidence 5899999999999999999999999887765
No 7
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.70 E-value=5e-16 Score=153.60 Aligned_cols=125 Identities=17% Similarity=0.286 Sum_probs=107.2
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhC-CCEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (298)
+.+++++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.+|++.......+.....+. ..+.
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 56678999999999999999999 9999999999999999999999999888887776665555555544433 3467
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
.+.+..+++|+.+|+.....|+.+ .+|.+.+++++.+|||++|++|+++
T Consensus 357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l 405 (1092)
T PRK09776 357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVN 405 (1092)
T ss_pred eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHH
Confidence 788889999999999999999998 8899999999999999999996654
No 8
>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=9.6e-16 Score=109.83 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=98.1
Q ss_pred HhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCC
Q 022384 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (298)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg 103 (298)
|+++|++++++|.+ |+++++|+++.+++|++.++++|+++..++++.....+...+.+++.++.....+..... +|
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 999999999999999999999999988888877777788888888888887766655555 89
Q ss_pred CEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhh
Q 022384 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (298)
Q Consensus 104 ~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~ 138 (298)
...|+.+...|+.+ .+|.+.+++++++|||++|+
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 89999999999999999986
No 9
>PRK13560 hypothetical protein; Provisional
Probab=99.67 E-value=1.3e-15 Score=145.99 Aligned_cols=176 Identities=10% Similarity=0.003 Sum_probs=126.1
Q ss_pred HHHH-HHHHhhCCCEEEEEeCCCCCCc--EEEcchHHHHHhCCCccccCCCC--CCCCcCCCCCHHHHH-------HHHH
Q 022384 17 TLWV-HEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM-------EIRE 84 (298)
Q Consensus 17 ~~~l-~~~~~~~~~~i~~~d~~~~~g~--i~~~N~~~~~~~g~~~~e~ig~~--~~~l~~~~~~~~~~~-------~~~~ 84 (298)
.+++ +.+++++|.+++.++.+ ++|. +.+++++...++|+...++++.. +..+.+|++...... .+..
T Consensus 66 ~e~~~r~l~~~~p~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~ 144 (807)
T PRK13560 66 REQCERNLKANIPGGMFLFALD-GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAETIAM 144 (807)
T ss_pred HHHHHHHHHhcCCceEEEEEEc-CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHHHHHH
Confidence 3444 99999999999998877 1233 33477778888888887776543 344566666554332 2222
Q ss_pred HHHhCCCEEEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhh
Q 022384 85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCR 164 (298)
Q Consensus 85 ~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~ 164 (298)
.+..+.....+++++++||+ |+.....|..+ .+|.. .+.|+..|||++|++|+++... .
T Consensus 145 ~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae~~l~~~-----------------~ 203 (807)
T PRK13560 145 ALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAEERIDEA-----------------L 203 (807)
T ss_pred HhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHHHHHHHH-----------------H
Confidence 33334455677888899996 55567778877 66765 6899999999999996554111 0
Q ss_pred hhccccchhhcccceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhh
Q 022384 165 REVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLY 244 (298)
Q Consensus 165 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 244 (298)
+. +.
T Consensus 204 ~~----------------------------------------------------------------------------l~ 207 (807)
T PRK13560 204 HF----------------------------------------------------------------------------LQ 207 (807)
T ss_pred HH----------------------------------------------------------------------------HH
Confidence 00 33
Q ss_pred hhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
..++++..+++++|. +++|+++|++|++++||+.+|++|++..++.
T Consensus 208 ~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~ 253 (807)
T PRK13560 208 QLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMSIHDFA 253 (807)
T ss_pred HHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCcchhcC
Confidence 456778888999999 9999999999999999999999999876653
No 10
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.65 E-value=1.8e-15 Score=145.00 Aligned_cols=170 Identities=19% Similarity=0.268 Sum_probs=132.2
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCC----CEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIE 93 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~ 93 (298)
..+..+++..+.+++++|.+ |.++++|+++++++||++++++|+++..+.++.........+......+. .+.
T Consensus 12 ~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMS 88 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccc
Confidence 34567889999999999999 99999999999999999999999998877776655443333443333332 244
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhhccccchh
Q 022384 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (298)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~~~~~~l~ 173 (298)
.+++..+++|..+|+.....|+.. .|. .+++++.+|||++++.+++. ..
T Consensus 89 ~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~~~--------------~~-------------- 137 (799)
T PRK11359 89 RELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKEQT--------------RQ-------------- 137 (799)
T ss_pred eeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHHHH--------------HH--------------
Confidence 577888999999999998888853 555 45788899999988773321 00
Q ss_pred hcccceeecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhhhcccccc
Q 022384 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (298)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (298)
+...++....+
T Consensus 138 ---------------------------------------------------------------------~~~~~~~~~~~ 148 (799)
T PRK11359 138 ---------------------------------------------------------------------LIIAVDHLDRP 148 (799)
T ss_pred ---------------------------------------------------------------------HHHHHhcCCCc
Confidence 11234556778
Q ss_pred eEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 254 FVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 254 i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
++++|. ++.|+++|++|++++||+.+|++|++...++
T Consensus 149 i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~ 185 (799)
T PRK11359 149 VIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQPDTLL 185 (799)
T ss_pred EEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCChHHhc
Confidence 889999 9999999999999999999999999887765
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=99.65 E-value=3.4e-15 Score=107.49 Aligned_cols=112 Identities=23% Similarity=0.366 Sum_probs=94.0
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEE-EEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL 96 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~ 96 (298)
++++.+++++|++++++|.+ |+|+++|+++++++||+.++++|++...++++.+.......+...+..+.... ...
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 99999999999999999999999998888877655556677777777766543 344
Q ss_pred EEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecC
Q 022384 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (298)
Q Consensus 97 ~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DI 133 (298)
....++|..+|+.+...|+.+ .+|.+.+++++++||
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=99.53 E-value=1.3e-13 Score=131.82 Aligned_cols=125 Identities=14% Similarity=0.186 Sum_probs=109.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
+..++++.+++++|++++++|.+ |+++++|+++++++||+.++++|+++..++++.............+..+..+..
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 35567889999999999999999 999999999999999999999999987777765555555555666777778888
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
+.....++|...|+.+...|+.+ .+|...+++++.+|||++|++|+++
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 7899999999999999999998765
No 13
>PRK13559 hypothetical protein; Provisional
Probab=99.52 E-value=4.6e-13 Score=116.71 Aligned_cols=126 Identities=37% Similarity=0.666 Sum_probs=107.1
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (298)
....++.+++.++++++++|.+..+|.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..+
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 45678889999999999999742237899999999999999999999999777766666666666677777777788888
Q ss_pred EEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhh
Q 022384 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (298)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~ 142 (298)
....+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++|++
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 789988999999999999987554
No 14
>PRK10060 RNase II stability modulator; Provisional
Probab=99.50 E-value=6e-13 Score=124.48 Aligned_cols=137 Identities=14% Similarity=0.211 Sum_probs=108.7
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCc-CCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
...+++.+++.++++|+++|.+ |+++++|+++++++||+.++++|+++..++ ++.+.......+...+..+..+..
T Consensus 109 ~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (663)
T PRK10060 109 GLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV 185 (663)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence 3457788999999999999999 999999999999999999999999865544 444444455566677778888999
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCc-EEEEEEEEecCchhhhhhhhc--cccccc--C--Ccchhhh
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGR-ATHFVAVQVPIVSRKHMRNSG--MSYSED--G--GGSRLRE 157 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~-~~~~~~~~~DITe~k~~ee~l--~~~~~~--~--nr~~~~~ 157 (298)
+.+..+++|..+|+.....+. + ..|. ...++++.+|||++|++++++ ++.+|. | ||..|.+
T Consensus 186 e~~~~~~~G~~~~~~~~~~~~-~-~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~ 253 (663)
T PRK10060 186 ERWIKTRKGQRLFLFRNKFVH-S-GSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQE 253 (663)
T ss_pred EEEEEeCCCCEEEEEeeeEEE-c-CCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHH
Confidence 999999999988876554443 3 3444 356788899999999999988 455666 4 9998883
No 15
>PRK13557 histidine kinase; Provisional
Probab=99.50 E-value=5.9e-13 Score=122.07 Aligned_cols=128 Identities=37% Similarity=0.672 Sum_probs=111.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
....+|+.+++.++.+++++|.+..+|+++|+|+++++++||+.++++|+++..+.++.........++..+..+..+..
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 44678999999999999999963233999999999999999999999999988887777777777777788887877888
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
+....+++|..+|+.+...|+.+ .+|.+.+++++.+|||+++++|+++
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 7899999999999999999987765
No 16
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.42 E-value=5.6e-12 Score=118.55 Aligned_cols=125 Identities=38% Similarity=0.695 Sum_probs=107.9
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEE
Q 022384 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (298)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (298)
+++.+++.++.++++.+...++|.++++|+++++++||++++++|+++..+.++.........+...+..+..+..+++.
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 45678999999999998532338999999999999999999999998877777666666666667777778888889999
Q ss_pred EccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcc
Q 022384 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM 144 (298)
Q Consensus 99 ~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~ 144 (298)
.+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++|+++.
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 79999999999999999999988774
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=99.31 E-value=7.3e-11 Score=83.45 Aligned_cols=120 Identities=21% Similarity=0.347 Sum_probs=93.3
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhC-CCEEEEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (298)
+.++.+++.++.+++++|.+ +.++++|+++.+++|++..+++|.....+.++.........+......+ .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 35677899999999999999 9999999999999999999999988766666555554444455555433 2233444
Q ss_pred EEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhh
Q 022384 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (298)
Q Consensus 97 ~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~ 142 (298)
.....+|...|+.....|+.. +|...+++++..|||++++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHHhc
Confidence 555788999999888888863 67778899999999999998654
No 18
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.20 E-value=2.2e-10 Score=110.20 Aligned_cols=123 Identities=19% Similarity=0.291 Sum_probs=102.1
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcC-CCCCHHHHHHHHHHHHhCCCEEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
..+++..+++.++.+++++|.+ |+++++|+++++++||+.++++|++...+.+ +.........+...+..+..+..
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 3455667899999999999999 9999999999999999999999998655543 44444455555666666667777
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhh
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~ 142 (298)
+.+..+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++++.
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 788899999999999999988653
No 19
>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=99.20 E-value=1.5e-10 Score=79.86 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=71.9
Q ss_pred EEEcchHHHHHhCCCccccCCCC----CCCCcCCCCCHHHHHHHHH-HHHhCCCEEEEEEEEccCCCEEEEEEEEEEeec
Q 022384 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (298)
Q Consensus 43 i~~~N~~~~~~~g~~~~e~ig~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~ 117 (298)
++++|+.+++++||+++++ +.. +..+++|++...+...+.. ....+..+..++++++++|+..|+...+.++.+
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 6667889999999888888 677778899999999999999999999999998
Q ss_pred CCCCcEEEEEEEE
Q 022384 118 KEDGRATHFVAVQ 130 (298)
Q Consensus 118 ~~~g~~~~~~~~~ 130 (298)
.+|.+..++|+.
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999988874
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=99.03 E-value=1.6e-08 Score=68.00 Aligned_cols=103 Identities=21% Similarity=0.404 Sum_probs=83.4
Q ss_pred CCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEE
Q 022384 27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF 106 (298)
Q Consensus 27 ~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~ 106 (298)
++.++++++.+ +.++++|+.+.+++|++..+++|.....+.++.........+......+.....+......+|...
T Consensus 1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (103)
T cd00130 1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77 (103)
T ss_pred CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence 36789999999 999999999999999999999998876677666665555555555555556667777778889999
Q ss_pred EEEEEEEEeecCCCCcEEEEEEEEecC
Q 022384 107 WMLFKMSLVFGKEDGRATHFVAVQVPI 133 (298)
Q Consensus 107 ~~~~~~~p~~~~~~g~~~~~~~~~~DI 133 (298)
|+.+...|+.+ ..|...+++++..||
T Consensus 78 ~~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 78 WVLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEec-CCCCEEEEEEEEecC
Confidence 99999999987 677888888888875
No 21
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.95 E-value=1.4e-08 Score=94.33 Aligned_cols=121 Identities=14% Similarity=0.181 Sum_probs=96.9
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCC-EEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV 94 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~ 94 (298)
....++.++++++++++++|.+ |.++++|+++++++|+++++++|+++..++++.. .....+...+..+.. ...
T Consensus 260 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 334 (607)
T PRK11360 260 TRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVDL 334 (607)
T ss_pred HHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccce
Confidence 4456788999999999999999 9999999999999999999999998777766432 223344445554443 334
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
+.....++|... +.+...|+.+ .+|.+.+++++++|||+++++|+++
T Consensus 335 ~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l 381 (607)
T PRK11360 335 EISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRV 381 (607)
T ss_pred EEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHH
Confidence 566677777766 7889999998 8999999999999999999998776
No 22
>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=98.94 E-value=9.5e-09 Score=88.17 Aligned_cols=112 Identities=11% Similarity=0.063 Sum_probs=84.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
+..++++.++++++++++++|.+ |.++++|+++++++|+++++.+|+++..+..+ +. +...+..+.. ..
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 99999999999999999999999886665443 22 2233333222 22
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
......++|...|+.+...|+.+ +. ++++.+|||++++.++..
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~---~~---~~~~~~dit~~~~~~~~~ 114 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE---EQ---KLLVARDVTRLRRLEQMR 114 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC---Cc---eEEEEeCchHHHHHHHHH
Confidence 24445578888899999999865 22 667889999999886543
No 23
>PF12860 PAS_7: PAS fold
Probab=98.94 E-value=5.4e-09 Score=75.46 Aligned_cols=105 Identities=21% Similarity=0.351 Sum_probs=71.6
Q ss_pred HhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCcccc-CCCCCCCCc---------CCCCCHHHHHHHHHHHHhCCCEE
Q 022384 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (298)
Q Consensus 24 ~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~-ig~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (298)
+++++.||+++|.+ ++++++|+++.++++++.+.+ .|.+...+. ++.....................
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 46889999999999 999999999999999999887 677644332 11222222222222233333332
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhh
Q 022384 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (298)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee 141 (298)
......+|. |+.+...|.. +| +++.+..|||+++++|+
T Consensus 78 --~~~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 78 --FELRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred --eEEECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhcC
Confidence 334556776 6677888884 44 46788999999999864
No 24
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.91 E-value=1.4e-08 Score=72.20 Aligned_cols=106 Identities=21% Similarity=0.249 Sum_probs=71.3
Q ss_pred HHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEE
Q 022384 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (298)
Q Consensus 20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (298)
+..++++++.+++++|.+ +++.++|+++.++++... ..+|++...+.++...+.....+ +.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i-~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKII-EQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHH-HHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHH-HHHHcCCCceEEEEe-
Confidence 457899999999999999 999999999999999765 45799988877653333333333 344455543333332
Q ss_pred ccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCc
Q 022384 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (298)
Q Consensus 100 ~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DIT 134 (298)
..+| .|+.+...|+.+ .+|...|++.++.|||
T Consensus 75 ~~~~--~~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGG--RWYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETT--EEEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCC--EEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 2344 366789999999 8999999999999998
No 25
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.88 E-value=1.5e-08 Score=87.85 Aligned_cols=114 Identities=13% Similarity=0.138 Sum_probs=85.8
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEE
Q 022384 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (298)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (298)
.+..+++++++|++++|.+ |+++++|+++++++||+.++++|+++..+.++.. .....+...+..+..+......
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 9999999999999999999999998776665332 1223344555555544433334
Q ss_pred EccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 99 ~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
...+|..+|+.++..|+.. .+++..++|+|++++.++++
T Consensus 83 ~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~~~~~ 121 (348)
T PRK11073 83 LVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRLSQEQ 121 (348)
T ss_pred EEECCceEEEEEEEEEccC------ceeEEEEechhHHHHHHHHH
Confidence 4569999999999998842 24566789999998875543
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=98.80 E-value=2e-07 Score=66.50 Aligned_cols=101 Identities=17% Similarity=0.262 Sum_probs=82.8
Q ss_pred EEEeCCCCCCcEEEcchH-HHHHhCCCccccCCCCCCCCcCCCCCHH-HHHHHHHHHHhCCCEEEEEEEEccCCCEEEEE
Q 022384 32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (298)
Q Consensus 32 ~~~d~~~~~g~i~~~N~~-~~~~~g~~~~e~ig~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (298)
...+.+ |+|+++.+. ...++||.+++++|+++..+++|++... ........+..|.....-++++.++|..+|+.
T Consensus 6 trhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq 82 (111)
T PF14598_consen 6 TRHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ 82 (111)
T ss_dssp EEEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred EEECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence 345677 999999999 6999999999999999999999999886 77788888888888777899999999999999
Q ss_pred EEEEEeecCCCCcEEEEEEEEecCch
Q 022384 110 FKMSLVFGKEDGRATHFVAVQVPIVS 135 (298)
Q Consensus 110 ~~~~p~~~~~~g~~~~~~~~~~DITe 135 (298)
....+..+|..+.+..++++-.=|++
T Consensus 83 t~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 83 TKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEEECCCCCCccEEEEEEEEecc
Confidence 99998886445677777776554444
No 27
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.73 E-value=9.3e-08 Score=84.02 Aligned_cols=163 Identities=18% Similarity=0.113 Sum_probs=116.9
Q ss_pred HHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEc
Q 022384 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (298)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (298)
..+++..++++++++.. ..+..+|..+..+.+-....++|++...+.++...+... .+..+........
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 34789999999999998 999999999999999999999999877776654433221 2222222233333
Q ss_pred cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhcccccccCCcchhhhHHHHhhhhhccccchhhccccee
Q 022384 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180 (298)
Q Consensus 101 ~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l~~~~~~~nr~~~~~~~~~~~~~~~~~~~l~~~~~~~~ 180 (298)
+ + ...+.+...|+. +.+.+.+++++..|+++....-+ ......+
T Consensus 73 ~-~-~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~~~-----------------~~l~~~~--------------- 116 (560)
T COG3829 73 K-V-KRIVVVGKTPVD--EQGRVVGVLEVFLDISEALELIE-----------------ENLRQLR--------------- 116 (560)
T ss_pred c-c-eeEEEcCCceee--cCCceeeeehhhhhhHHHHHHHH-----------------HHHHHHH---------------
Confidence 3 2 333334445554 47899999999999998555411 1100000
Q ss_pred ecCCCCCcccccCccccHHHHHHHHhhhhhhhHhhhhcccccceeeeccccCCCCCCccchhhhhhhcccccceEeeCCC
Q 022384 181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH 260 (298)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~ 260 (298)
..+...++.+.++++++|.
T Consensus 117 ------------------------------------------------------------~~l~~il~~~~~~l~vvD~- 135 (560)
T COG3829 117 ------------------------------------------------------------QRLEAILDSIDDGLLVVDE- 135 (560)
T ss_pred ------------------------------------------------------------HHHHHHHhhccCceEEEcC-
Confidence 0034466778899999999
Q ss_pred CCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 261 LPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 261 ~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+|.+++.|++..+++|++.++++|++..++.
T Consensus 136 --~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~ 166 (560)
T COG3829 136 --DGIIIYYNKAYAKLLGLSPEEVLGKHLLDVV 166 (560)
T ss_pred --CCcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence 9999999999999999999999999988885
No 28
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.66 E-value=3.6e-07 Score=75.74 Aligned_cols=118 Identities=14% Similarity=0.224 Sum_probs=90.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
...+++.+++..+.+|++..|+. |+++.+|..+.+++|.+.++++|++...+..-.+.-.+ .+.+........
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---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTF----EDLVEKNDSLLL 180 (459)
T ss_pred HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeH----HHHHhcCCcEEE
Confidence 44578999999999999999999 99999999999999999999999986555543332222 222333333322
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
+. ...++.+.+++..+.+.. +.|-+.|++++..|+||+.+.|.+.
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 22 226777778888888888 8999999999999999999886664
No 29
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.65 E-value=1.5e-07 Score=82.61 Aligned_cols=121 Identities=25% Similarity=0.502 Sum_probs=96.2
Q ss_pred HHHHHHHhhCC--CEE-EEEeCCCCCCcEEEcchHHHHHhCCCccccCCCC--CCCCcCCCCCHHHHHHHHHHHHhCCCE
Q 022384 18 LWVHEALDELP--DSF-TITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI 92 (298)
Q Consensus 18 ~~l~~~~~~~~--~~i-~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (298)
.+++.++..+. +.- ++.+.+.-|..|+|+|+.||++.||.+.|++.++ +..++.........+.+.+.+.+.+.-
T Consensus 14 TFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~ 93 (971)
T KOG0501|consen 14 TFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETN 93 (971)
T ss_pred hHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhc
Confidence 34555555444 433 3334433347899999999999999999999887 455566666666777888888887878
Q ss_pred EEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhh
Q 022384 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (298)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ 139 (298)
++|+.++.++..+.|+.+.+.|++. +...++.+++.+.|||..|+-
T Consensus 94 qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 94 QFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred ceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence 8899999999999999999999998 888899999999999998875
No 30
>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=98.59 E-value=1.9e-08 Score=71.91 Aligned_cols=49 Identities=14% Similarity=0.130 Sum_probs=43.5
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
+...++++.++++++|. +++|+++|++|++++||+++|++|+++.+++-
T Consensus 3 ~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~ 51 (113)
T PF00989_consen 3 YRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKSLFDLIH 51 (113)
T ss_dssp HHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSBGGGGCS
T ss_pred HHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCcHHHhcC
Confidence 34567889999999999 99999999999999999999999999988764
No 31
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.52 E-value=4.7e-07 Score=80.89 Aligned_cols=110 Identities=13% Similarity=0.145 Sum_probs=75.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
+..++++.+++++|++++++|.+ |+++++|+++++++||+.++.+|++...+..+. ..... +... ....
T Consensus 95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~~~----~~~~-~~~~ 163 (430)
T PRK11006 95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFTQY----LKTR-DFSR 163 (430)
T ss_pred HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHHHH----HHhc-ccCC
Confidence 45678999999999999999999 999999999999999999999999865554322 12111 1111 1111
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
.......+|. ++.+...|..+ + .++.+.+|||+++++|+..
T Consensus 164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e~~~ 204 (430)
T PRK11006 164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLEGAR 204 (430)
T ss_pred CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHHHHH
Confidence 2233344554 44555666643 3 2566789999999987654
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=98.52 E-value=1.2e-07 Score=85.97 Aligned_cols=127 Identities=13% Similarity=0.168 Sum_probs=81.3
Q ss_pred HHHhhhhHHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHH
Q 022384 8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87 (298)
Q Consensus 8 ~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~ 87 (298)
.++.+. +...+++.++++++.+++++|.+ |.++++|+++++++|+...+..+..+....++.... .+.....
T Consensus 121 ~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~~ 192 (494)
T TIGR02938 121 LEQVVA-NQKLLIESVVDAAPVAFVLLDPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWRE----ALAENWP 192 (494)
T ss_pred HHHHHH-HHHHHHHHHHhcccceEEEEcCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhh----hhhhcch
Confidence 334444 45678899999999999999999 999999999999999887766554432222222111 1111111
Q ss_pred hCCCEE-EEEEEEccCCC-EEEEEEEEEEeecCCCCcE---------EEEEEEEecCchhhhhhhhc
Q 022384 88 EERPIE-VNLLNYKKDGT-PFWMLFKMSLVFGKEDGRA---------THFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 88 ~~~~~~-~e~~~~~~dg~-~~~~~~~~~p~~~~~~g~~---------~~~~~~~~DITe~k~~ee~l 143 (298)
.+..+. .+......+|. .+|+.....|+.. ..|.. .+++++++|||++|++|+++
T Consensus 193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l 258 (494)
T TIGR02938 193 QQLAFSNREARFDRGGGRPARWLSCTGSVIGM-ESDCADSFFCAAEQPYLLLTIADISNLREEQERA 258 (494)
T ss_pred hhhccccceeeeccCCCceeeEEEecCceEEe-ecchhhheeccCCCchheehHHHHHHHHHHHHHH
Confidence 111222 23333444444 6888888777765 44433 34566789999999998765
No 33
>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=98.49 E-value=5e-08 Score=68.52 Aligned_cols=41 Identities=20% Similarity=0.371 Sum_probs=35.4
Q ss_pred ccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 251 KQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 251 ~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
+++++++|+ ++.|+++|++|++++||+++|++|+++.+++.
T Consensus 1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~ 41 (104)
T PF13426_consen 1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGKSISDFFP 41 (104)
T ss_dssp -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCS
T ss_pred CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCCCcccccC
Confidence 367899999 99999999999999999999999999988765
No 34
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.41 E-value=1.8e-06 Score=78.54 Aligned_cols=110 Identities=14% Similarity=0.138 Sum_probs=78.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
+....+..+++++++||+++|.+ |+|+++|+++++++|++.++++|++...+++... +.+.+..+.....
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 34567889999999999999999 9999999999999999999999999777765432 2233344433111
Q ss_pred EEEEEccCCCEEEEEEEEEEee--cCCCCc--EEEEEEEEecCchhhh
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRKH 138 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~--~~~~g~--~~~~~~~~~DITe~k~ 138 (298)
. .....+|..++ +...|+. + ++|. ..|.+.+++|+++..+
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 11233566554 5567776 4 4454 3788999999987643
No 35
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.29 E-value=4.1e-05 Score=59.13 Aligned_cols=119 Identities=24% Similarity=0.359 Sum_probs=85.5
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHH-HHHHHHHH-HHhCCCEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREA-IREERPIE 93 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~-~~~~~~~~-~~~~~~~~ 93 (298)
...++..+++..+.+++..|.+ +.+.++|+++.+++|++..+..+.....+........ ........ ........
T Consensus 110 ~~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (232)
T COG2202 110 SEERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLE 186 (232)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcc
Confidence 3445888999999999999999 9999999999999999988777766544433222221 11111222 22233466
Q ss_pred EEEEEEccCCCE-EEEEEEEEEeecCCCCcEEEEEEEEecCchhhhh
Q 022384 94 VNLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (298)
Q Consensus 94 ~e~~~~~~dg~~-~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ 139 (298)
.+.....++|.. .+......+... .|.+..+.....|+++++++
T Consensus 187 ~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 187 IEYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred eEEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence 777888899986 777777777653 68888888999999998875
No 36
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.29 E-value=1.6e-06 Score=55.31 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.3
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCC
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~ 66 (298)
++++.+++++|.+|+++| + ++++++|+++++++||+ ..|...
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 368899999999999999 9 99999999999999998 455543
No 37
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.27 E-value=8.6e-06 Score=74.93 Aligned_cols=112 Identities=10% Similarity=0.124 Sum_probs=78.0
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCc---cccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~---~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (298)
..+.++.+++++++|++++|.+ |+++++|+++++++|++. .+.+|.....+.++ ..+...+..+.+.
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 34555554333321 1233444444443
Q ss_pred EEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
.... ...+|. ++.+...|+.+ +|.+.+++.+++|+|+.+++++++
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 112444 34466788886 788899999999999999887665
No 38
>PRK10060 RNase II stability modulator; Provisional
Probab=98.18 E-value=1.2e-06 Score=82.55 Aligned_cols=46 Identities=9% Similarity=0.019 Sum_probs=41.0
Q ss_pred hhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
..++...++|+++|. +|+|+++|++|+++|||+.+|++|++..+++
T Consensus 115 ~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~ 160 (663)
T PRK10060 115 QVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQSVFKLF 160 (663)
T ss_pred HHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCCHHHHh
Confidence 356677889999999 9999999999999999999999999876654
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.15 E-value=9.6e-06 Score=71.66 Aligned_cols=116 Identities=16% Similarity=0.342 Sum_probs=87.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
+..+.|+.+++.+.++++++|.+ |.++++|.++..++|++.++++|++..++...... ....+++..+.+...
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 45678999999999999999999 99999999999999999999999986655411111 123455667776555
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
.......+.. .....|+.. +|.+.+.+++..|+++.+.+..++
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 4443333322 356677764 789999999999999988886665
No 40
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=98.15 E-value=1.5e-06 Score=74.04 Aligned_cols=105 Identities=23% Similarity=0.386 Sum_probs=86.6
Q ss_pred HHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCC-CCCHHHHHHHHHHHHhCCCEEEEEEE
Q 022384 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGP-RTNRRTIMEIREAIREERPIEVNLLN 98 (298)
Q Consensus 20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (298)
+...++....+|-+.|.+ ..+.|+|++|++|+||...|++|++..++.-. .........+..+++.|..|+++...
T Consensus 159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~a 235 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA 235 (775)
T ss_pred HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence 445678888899999998 99999999999999999999999997776432 23445677788899999999999888
Q ss_pred EccCCCEEEEEEEEEEeecCCCCcEEEEEE
Q 022384 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128 (298)
Q Consensus 99 ~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~ 128 (298)
+++.|...-..+...|+.. ..|.+..++.
T Consensus 236 RRksgdS~dqh~~itP~~g-qggkirhfvs 264 (775)
T KOG1229|consen 236 RRKSGDSCDQHFIITPFAG-QGGKIRHFVS 264 (775)
T ss_pred hhccCCcccceEEEeeecC-CCCceeeehh
Confidence 8999988877888899987 6777776654
No 41
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.12 E-value=4.4e-05 Score=71.67 Aligned_cols=46 Identities=9% Similarity=0.125 Sum_probs=41.6
Q ss_pred hhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 246 ~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
.++.+.++|+++|. +|+|+++|+++++++|++.++++|++..+++.
T Consensus 208 il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~ 253 (638)
T PRK11388 208 LLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRAITELLT 253 (638)
T ss_pred HHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence 55667889999999 99999999999999999999999999888764
No 42
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.84 E-value=9.5e-06 Score=51.63 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=31.6
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHS 290 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~ 290 (298)
+...+++++.+|++.| +++|+++|++|++++||+ +.|+...
T Consensus 3 ~~~l~~~~~~~i~i~d----~~~i~~~N~~~~~l~g~~---~~~~~~~ 43 (64)
T PF13188_consen 3 YRSLFDNSPDGILIID----GGRIIYVNPAFEELFGYS---LEGEDIG 43 (64)
T ss_dssp HHHHHCCSSSEEEEEE----TSBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred HHHHHHcCccceEEEE----CCChHHhhHHHHHHhCCC---CCCCCHH
Confidence 3457888999999999 348999999999999999 5565544
No 43
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.82 E-value=9.6e-05 Score=65.43 Aligned_cols=113 Identities=12% Similarity=0.155 Sum_probs=85.2
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCcc--ccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~--e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (298)
..+...+++++...|++.+|.. |.+..+|.++++|+|+... +.+|++...+.+|+.. +...++.+.+..
T Consensus 213 l~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~ 283 (537)
T COG3290 213 LLEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQH 283 (537)
T ss_pred HHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCccc
Confidence 3445567899999999999999 9999999999999999776 6889887777776322 122344454433
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
.+. .+-+|. ++.....|+.. .|++.|++.+++|-|+-++.-+++
T Consensus 284 ~~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L~eqL 327 (537)
T COG3290 284 DEE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKLTEQL 327 (537)
T ss_pred chh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHHHHHH
Confidence 322 122444 55678889986 889999999999999999987777
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=97.81 E-value=1.1e-05 Score=57.10 Aligned_cols=44 Identities=25% Similarity=0.257 Sum_probs=39.4
Q ss_pred hcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 247 ~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
++++..++++.|. +++|+++|+++.+++|++.++++|++..+++
T Consensus 1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~ 44 (110)
T PF08448_consen 1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRSLFDLL 44 (110)
T ss_dssp HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSBHHHHS
T ss_pred CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhccchhcc
Confidence 4677889999999 9999999999999999999999999988764
No 45
>PRK13557 histidine kinase; Provisional
Probab=97.80 E-value=1.4e-05 Score=73.41 Aligned_cols=51 Identities=22% Similarity=0.436 Sum_probs=44.3
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++.+..+++++|+..++++|+|+|++|++++||+.+|++|+++..+.
T Consensus 32 ~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~ 82 (540)
T PRK13557 32 FFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQ 82 (540)
T ss_pred HHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhc
Confidence 556778888999999975568899999999999999999999999887654
No 46
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.80 E-value=0.00023 Score=64.28 Aligned_cols=58 Identities=16% Similarity=0.174 Sum_probs=49.7
Q ss_pred HHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHH
Q 022384 23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (298)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~ 83 (298)
+++.+..-|++++.+ |.++|+++.....+|++.-|+.|....++++|.+..++.+.+.
T Consensus 124 iLqsLDGFVm~l~~d---G~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~ 181 (768)
T KOG3558|consen 124 ILQSLDGFVMALTQD---GDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLG 181 (768)
T ss_pred HHhhccceEEEEccC---CCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhc
Confidence 556666667888888 9999999999999999999999999999999988877665543
No 47
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.79 E-value=0.00015 Score=66.83 Aligned_cols=110 Identities=14% Similarity=0.069 Sum_probs=75.3
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCc--cccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~--~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
.+.++.+++++++|++++|.+ |+++++|+++++++|++. ++++|++...+.++.... ..... ......
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~~------~~~~~-~~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADFF------TEQID-EKRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchhh------hhhcC-Ccccce
Confidence 456678999999999999999 999999999999999975 468898866555432111 01111 111111
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
. ...+|. .+.....|+.. .|.+.+.+.+++|+|+.++.++++
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 112342 34466778875 667789999999999998876665
No 48
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.79 E-value=0.00032 Score=65.99 Aligned_cols=109 Identities=12% Similarity=0.217 Sum_probs=76.0
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (298)
..+..+++..+++++++|.+ |+|+++|+++++++|++.++++|++...+++.. . .+..++..+..+.....
T Consensus 203 ~~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~--~----~l~~vl~~~~~~~~~~~ 273 (638)
T PRK11388 203 NQLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP--A----VLQQAIKQAHPLKHVEV 273 (638)
T ss_pred HHHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc--h----HHHHHHhcCCceeeEEE
Confidence 34456889999999999999 999999999999999999999999866665321 1 22344555554433222
Q ss_pred EEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhh
Q 022384 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (298)
Q Consensus 98 ~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~ 138 (298)
....+|..+++.+...|+.+ ..|. +++.+..|++..++
T Consensus 274 ~l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 274 TFESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EEecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 23345676778888899865 3443 35555678877554
No 49
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.77 E-value=0.00033 Score=62.79 Aligned_cols=115 Identities=13% Similarity=0.057 Sum_probs=77.0
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCC-CEEE
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEV 94 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~ 94 (298)
..+.++.+++..+.|++..|.+ |.+..+|+++++|+|.+-++++|.+...+.| .+.+.+...-..+. ....
T Consensus 368 rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap-----~~~~vf~~~~a~~~~~~~~ 439 (712)
T COG5000 368 RRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAP-----ELEEVFAEAGAAARTDKRV 439 (712)
T ss_pred HHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhh-----HHHHHHHHhhhhcCCCccc
Confidence 4567788999999999999999 9999999999999999999999998654432 12222222211211 2233
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhh
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~ 142 (298)
+..+.+ .|+...+.+....... ++| .+++.++.|||....+|..
T Consensus 440 ev~~~r-~g~~rtl~Vq~t~~~~-d~~--~gyVvt~DDITdLV~AQRs 483 (712)
T COG5000 440 EVKLAR-EGEERTLNVQATREPE-DNG--NGYVVTFDDITDLVIAQRS 483 (712)
T ss_pred eeeccc-CCCceeeeeeeeeccc-ccC--CceEEEecchHHHHHHHHH
Confidence 344333 4455555555554433 222 3688899999999988543
No 50
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.69 E-value=0.00074 Score=68.33 Aligned_cols=43 Identities=9% Similarity=0.063 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccc
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e 60 (298)
....+++.+++++|.+++++|.+ |+++++|+++++++|++...
T Consensus 573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~ 615 (1197)
T PRK09959 573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYK 615 (1197)
T ss_pred HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCccccc
Confidence 44567788999999999999999 99999999999999987543
No 51
>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=97.68 E-value=3.2e-05 Score=66.25 Aligned_cols=48 Identities=8% Similarity=0.112 Sum_probs=43.8
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++.++.++++.|. ++.|+++|++|++++||+++|++|+++.+++
T Consensus 8 l~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~ 55 (333)
T TIGR02966 8 FRAAAQALPDAVVVLDE---EGQIEWCNPAAERLLGLRWPDDLGQRITNLI 55 (333)
T ss_pred HHHHHHhCcCcEEEECC---CCcEEEEcHHHHHHhCCChHHHcCCcHHHHc
Confidence 55678889999999999 9999999999999999999999999887664
No 52
>PRK13559 hypothetical protein; Provisional
Probab=97.53 E-value=6.2e-05 Score=65.63 Aligned_cols=51 Identities=25% Similarity=0.427 Sum_probs=42.7
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++.+..+++++|...++++|+++|++|++++||+.+|++|++...+.
T Consensus 45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~ 95 (361)
T PRK13559 45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQ 95 (361)
T ss_pred HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhc
Confidence 445678888999999974446789999999999999999999999876543
No 53
>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=97.47 E-value=0.0045 Score=46.07 Aligned_cols=112 Identities=11% Similarity=0.102 Sum_probs=76.1
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEE
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (298)
..++.+++ .|.+|+-.+.. +|-.++|.|.++.+|++++-+++.+.+.+.-..+.........+.++.+.|-.....-.
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 34555555 88888887765 44689999999999999999999999877666665566666667777766653222222
Q ss_pred EEccCCCEEEEEE-EEEEeecCCCCcEEEEEEEEec
Q 022384 98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVP 132 (298)
Q Consensus 98 ~~~~dg~~~~~~~-~~~p~~~~~~g~~~~~~~~~~D 132 (298)
...+.|+.++++- .+=.+.| ++|...|.-..+.+
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 3567888877643 2334456 67777665555443
No 54
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.47 E-value=0.00015 Score=65.37 Aligned_cols=77 Identities=12% Similarity=0.265 Sum_probs=71.5
Q ss_pred CcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEEEEEEEEEEeec
Q 022384 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (298)
Q Consensus 41 g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~ 117 (298)
-+|.||.+++..++||.+++++|++...++++.+...+.....+.+..|....+.+++..++|...|+...+..+..
T Consensus 284 mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~ 360 (768)
T KOG3558|consen 284 MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYN 360 (768)
T ss_pred eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEec
Confidence 89999999999999999999999999999999998888888888999999999999999999999999998888765
No 55
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=97.45 E-value=8.6e-05 Score=64.32 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=44.2
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++.+.+++++.|. ++.|+++|+++++++||+.++++|+++.+++
T Consensus 9 ~~~il~~~~~gi~~~d~---~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~ 56 (348)
T PRK11073 9 AGQILNSLINSILLLDD---DLAIHYANPAAQQLLAQSSRKLFGTPLPELL 56 (348)
T ss_pred HHHHHhcCcCeEEEECC---CCeEeeEcHHHHHHhCCCHHHHcCCCHHHHc
Confidence 55678899999999999 9999999999999999999999999988775
No 56
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=97.41 E-value=2.9e-05 Score=66.33 Aligned_cols=47 Identities=17% Similarity=0.241 Sum_probs=42.1
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTY 292 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~ 292 (298)
+-.+++...++|-|+|. +..|.||||||++|+||-+.|++||.-.++
T Consensus 159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGke~adl 205 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGKEEADL 205 (775)
T ss_pred HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCCchhhc
Confidence 55677888899999999 999999999999999999999999976654
No 57
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.34 E-value=0.00012 Score=65.54 Aligned_cols=49 Identities=8% Similarity=0.057 Sum_probs=43.7
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
+...++.+++++++.|. ++.|+++|+++++++||+.+|++|+++.+++.
T Consensus 100 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~ 148 (430)
T PRK11006 100 FRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQNILNLLR 148 (430)
T ss_pred HHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCCcHHHHhc
Confidence 44567888999999999 99999999999999999999999998877654
No 58
>PF12860 PAS_7: PAS fold
Probab=97.33 E-value=0.00019 Score=51.55 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=42.0
Q ss_pred hcccccceEeeCCCCCCCceeeehhhhhhhccccceec-cchhhHHHHhh
Q 022384 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSN-RASMHSTYLKL 295 (298)
Q Consensus 247 ~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~-~G~~~~~~~~~ 295 (298)
++++.+||++.|+ +++++++|++|.+++|++.+.+ .|.++.+++..
T Consensus 1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~ 47 (115)
T PF12860_consen 1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRR 47 (115)
T ss_pred CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHH
Confidence 4678899999999 9999999999999999999998 89999988764
No 59
>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=97.32 E-value=0.00074 Score=40.64 Aligned_cols=54 Identities=24% Similarity=0.429 Sum_probs=44.7
Q ss_pred HHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCH
Q 022384 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR 76 (298)
Q Consensus 20 l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~ 76 (298)
++.+++..+.++++++.. +.+.++|+.+..++|++..++.+..+..+.++.+..
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRE 56 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHH
Confidence 566788999999999999 999999999999999998888887665555554443
No 60
>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=97.19 E-value=0.00031 Score=48.58 Aligned_cols=47 Identities=11% Similarity=0.126 Sum_probs=40.5
Q ss_pred hhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
...++.+..+++++|. ++.|+++|++|++++||+.++++|+....++
T Consensus 6 ~~~~~~~~~~~~~~d~---~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~ 52 (124)
T TIGR00229 6 RAIFESSPDAIIVIDL---EGNILYVNPAFEEIFGYSAEELIGRNVLELI 52 (124)
T ss_pred HHHHhhCCceEEEEcC---CCcEEEEchHHHHHhCCChHHhcCcchhhhc
Confidence 3456777888999999 9999999999999999999999998776643
No 61
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.18 E-value=0.0002 Score=65.43 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=45.4
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
+...++.+.++|+++|. +|.|+++|+++++++|++.++++|+++.+++.
T Consensus 82 L~aIL~sm~eGVi~vD~---~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~ 130 (520)
T PRK10820 82 LSALLEALPEPVLSIDM---KGKVELANPASCQLFGQSEEKLRNHTAAQLIN 130 (520)
T ss_pred HHHHHHhCCCcEEEECC---CCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcC
Confidence 66788999999999999 99999999999999999999999999988753
No 62
>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=97.13 E-value=0.0067 Score=43.23 Aligned_cols=67 Identities=18% Similarity=0.106 Sum_probs=54.5
Q ss_pred HHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCC-CCCcCCCCCHHHHHHHHHHHHhCC
Q 022384 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG-RMFQGPRTNRRTIMEIREAIREER 90 (298)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~-~~l~~~~~~~~~~~~~~~~~~~~~ 90 (298)
..-++.+|-|++-+|.+ |.++..|.+-..+.|++++.++|++. .++-|....+.+...+.+....|.
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 99999999999999999999999984 445555566667777776555554
No 63
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.12 E-value=0.00029 Score=67.97 Aligned_cols=48 Identities=15% Similarity=-0.027 Sum_probs=43.4
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++.+.++++++|. +++|+++|++|++++||+.+|++|++..+++
T Consensus 157 l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~ 204 (779)
T PRK11091 157 LRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLTPKDVY 204 (779)
T ss_pred HHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCChHHhC
Confidence 45577889999999999 9999999999999999999999999877664
No 64
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=97.12 E-value=0.0036 Score=51.70 Aligned_cols=108 Identities=12% Similarity=0.112 Sum_probs=78.3
Q ss_pred HHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEE-EEEEEE
Q 022384 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY 99 (298)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~ 99 (298)
..++++++..++++|.+ +.|.|+|++++.++|.+...+.|.+.+.+++.. ......+.+....+.++. .++.+.
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~ 84 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV 84 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee
Confidence 35899999999999999 999999999999999999999998877776533 334455566666655543 233333
Q ss_pred ccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhh
Q 022384 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (298)
Q Consensus 100 ~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~ 138 (298)
.+|....+...+.|+.. ..|.+ +..+.-+....+
T Consensus 85 -~~g~~~~v~~~v~~v~~-~~G~v---lle~~~~~~~~r 118 (363)
T COG3852 85 -ILGRSHIVDLTVAPVPE-EPGSV---LLEFHPRDMQRR 118 (363)
T ss_pred -ecCccceEEEEEeeccC-CCCeE---EEEechhHHHhH
Confidence 68888889999999976 56643 334444444433
No 65
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.94 E-value=0.0035 Score=53.33 Aligned_cols=114 Identities=16% Similarity=0.183 Sum_probs=85.7
Q ss_pred HHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEE
Q 022384 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (298)
Q Consensus 17 ~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (298)
.+.+.+++.+.|.-+-.+|.+ +.+.+.|+. .++|..++. ++|++.....|| ........+...++.|..-..++
T Consensus 289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~~chpP-ksv~iv~ki~~~fksG~kd~~ef 362 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQLCHPP-KSVHIVEKILKDFKSGEKDFAEF 362 (409)
T ss_pred HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCcccCCCCC-chHHHHHHHHHHhhcCCcchHHH
Confidence 456888999999777778888 999999998 888877664 578887655544 44455666777777777655665
Q ss_pred EEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhh
Q 022384 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (298)
Q Consensus 97 ~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~e 140 (298)
+.. ..+ ..+.++..++.| ++|...|.+-+.+|||.-++.+
T Consensus 363 w~~-~~~--~~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 363 WIN-MGD--KFIHIRYFAVKD-EEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred hcc-CCC--ceEEEEEEEEEc-CCCceeeeehhhhhhHHHHhcc
Confidence 522 222 245678889999 8899999999999999988873
No 66
>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=96.91 E-value=0.00081 Score=44.16 Aligned_cols=39 Identities=15% Similarity=0.164 Sum_probs=34.4
Q ss_pred cceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 252 QSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 252 ~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
.+++++|. ++.++++|++|++++||+.++++|+....++
T Consensus 3 ~~i~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~ 41 (103)
T cd00130 3 DGVIVLDL---DGRILYANPAAEQLLGYSPEELIGKSLLDLI 41 (103)
T ss_pred ceEEEECC---CCcEEEECHHHHHHhCCCHHHHcCccHHHhc
Confidence 56788888 9999999999999999999999998776554
No 67
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.73 E-value=0.026 Score=43.07 Aligned_cols=45 Identities=18% Similarity=0.149 Sum_probs=36.6
Q ss_pred hhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 246 ~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
.++...+++++.|. ++.++++|+++++++||+..+..++....+.
T Consensus 117 ~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~ 161 (232)
T COG2202 117 LLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGRGLSDLI 161 (232)
T ss_pred HHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCCChhheE
Confidence 44556677888998 9999999999999999998888777655543
No 68
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.25 E-value=0.0034 Score=58.36 Aligned_cols=47 Identities=17% Similarity=0.107 Sum_probs=42.1
Q ss_pred hhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
...++.+.++++++|. ++.|+++|+++++++||+.++++|++..+++
T Consensus 265 ~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~ 311 (607)
T PRK11360 265 ELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKPYSELF 311 (607)
T ss_pred HHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCcHHHHc
Confidence 3456778899999999 9999999999999999999999999887765
No 69
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=96.23 E-value=0.032 Score=47.65 Aligned_cols=55 Identities=18% Similarity=0.264 Sum_probs=46.1
Q ss_pred HHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHH
Q 022384 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78 (298)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~ 78 (298)
..+++.+..-+++++++ |.|.|+++.+.-.+|++.-|+.|....+.+++.+...+
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 34566666778999999 99999999999999999999999988777777766554
No 70
>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=96.22 E-value=0.0048 Score=36.82 Aligned_cols=45 Identities=16% Similarity=0.149 Sum_probs=37.8
Q ss_pred hhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 246 ~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
.++....+++++|. ++.++++|+.+.+++||+.+++.|+.+..++
T Consensus 6 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (67)
T smart00091 6 ILESLPDGIFVLDL---DGRILYANPAAEELLGYSPEELIGKSLLELI 50 (67)
T ss_pred HHhhCCceEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCCcHHHhc
Confidence 45566778888998 8999999999999999999999998666553
No 71
>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=96.18 E-value=0.054 Score=28.50 Aligned_cols=41 Identities=29% Similarity=0.448 Sum_probs=32.9
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchh
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~ 136 (298)
++.....+|...|+.....++.+ ..+.+.+++++..|||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence 34556778888898888888887 678888899999999863
No 72
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.08 E-value=0.0044 Score=58.73 Aligned_cols=49 Identities=22% Similarity=0.343 Sum_probs=40.3
Q ss_pred hhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
..++....++++.|...+++.|+|+|++|++++||+.+|++|++...+.
T Consensus 152 ~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~ 200 (665)
T PRK13558 152 RALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQ 200 (665)
T ss_pred HHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhc
Confidence 3456677888888864468899999999999999999999999776543
No 73
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.00 E-value=0.022 Score=48.41 Aligned_cols=58 Identities=14% Similarity=0.122 Sum_probs=50.1
Q ss_pred HHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCH
Q 022384 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR 76 (298)
Q Consensus 16 ~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~ 76 (298)
..-.+.++++++|+.++.+|-. |.+..+|++++.++|.+.+++.|.+...+++..+..
T Consensus 78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~ 135 (511)
T COG3283 78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL 135 (511)
T ss_pred HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHH
Confidence 3446788999999999999999 999999999999999999999999877776655433
No 74
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=95.46 E-value=0.36 Score=35.71 Aligned_cols=87 Identities=13% Similarity=0.155 Sum_probs=70.1
Q ss_pred CCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEEEEEEEEEEeecCC
Q 022384 40 GHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKE 119 (298)
Q Consensus 40 ~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~~~ 119 (298)
+.++..+=...++++|+ ++.|++...++.+.........+..++..+.+..........+|....++....|+.+ .
T Consensus 50 ~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~ 125 (137)
T PF07310_consen 50 DFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-D 125 (137)
T ss_pred ceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-C
Confidence 35667788899999998 4668888888777777777777788888888877777777888888888889999998 6
Q ss_pred CCcEEEEEEEE
Q 022384 120 DGRATHFVAVQ 130 (298)
Q Consensus 120 ~g~~~~~~~~~ 130 (298)
.|.+..++|..
T Consensus 126 ~~~v~rilG~~ 136 (137)
T PF07310_consen 126 GGTVDRILGAL 136 (137)
T ss_pred CCCccEEEEec
Confidence 78888888764
No 75
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=95.29 E-value=0.015 Score=53.68 Aligned_cols=48 Identities=6% Similarity=0.019 Sum_probs=41.2
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccc--eeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGK--HSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~--eE~~G~~~~~~~ 293 (298)
+...++.+.+|++++|. +|+|+++|+++++++|+.. ++++|++..+++
T Consensus 224 ~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~ 273 (545)
T PRK15053 224 QEALFSSVYEGLIAVDP---HGYITAINRNARKMLGLSSPGRQWLGKPIAEVV 273 (545)
T ss_pred HHHHHHHhCceEEEECC---CCeEEeecHHHHHHhCCCCcchhhcCCcHHHhC
Confidence 34467788999999999 9999999999999999976 579999887764
No 76
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=95.26 E-value=0.079 Score=47.13 Aligned_cols=93 Identities=14% Similarity=0.162 Sum_probs=74.9
Q ss_pred CcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEEEEEEEEEEeecCCC
Q 022384 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (298)
Q Consensus 41 g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~~~~ 120 (298)
+..+.+......++||...|+.|.+...+++.++..-......+.+++|+..-.-++...++|++.|+..+...+.- +
T Consensus 293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarllyk--n 370 (712)
T KOG3560|consen 293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLYK--N 370 (712)
T ss_pred cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeeee--c
Confidence 67777888889999999999999887788887776656666678888888877788899999999999887776664 7
Q ss_pred CcEEEEEEEEecCch
Q 022384 121 GRATHFVAVQVPIVS 135 (298)
Q Consensus 121 g~~~~~~~~~~DITe 135 (298)
|.+..++..-+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 888777776665554
No 77
>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=95.10 E-value=0.0078 Score=40.77 Aligned_cols=22 Identities=18% Similarity=0.289 Sum_probs=17.0
Q ss_pred eeeehhhhhhhccccceeccchh
Q 022384 266 MVYASDAFLKLTDKGKHSNRASM 288 (298)
Q Consensus 266 i~~~N~af~~itGys~eE~~G~~ 288 (298)
|+|+|+.|++|+||+++++ |..
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~ 22 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKP 22 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCB
T ss_pred CEEEeHHHHHHhCCCHHHh-ccC
Confidence 7899999999999999999 543
No 78
>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=94.97 E-value=0.022 Score=40.64 Aligned_cols=42 Identities=7% Similarity=-0.013 Sum_probs=37.1
Q ss_pred hhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhH
Q 022384 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHS 290 (298)
Q Consensus 246 ~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~ 290 (298)
.++..+=|++-.|. +|.|+..|.+=.+++|++++.++||++=
T Consensus 21 elD~lpFGvI~lD~---~G~V~~YN~aE~~~sg~~p~~vlGr~FF 62 (124)
T TIGR02373 21 QFDALPFGAIQLDG---SGVILRYNAAEGRITGRDPERVIGRNFF 62 (124)
T ss_pred HhhcCCcceEEECC---CCEEEEEecchhhhcCCChhhhhchhhh
Confidence 35556678889999 9999999999999999999999999863
No 79
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=94.84 E-value=0.0085 Score=53.61 Aligned_cols=38 Identities=29% Similarity=0.511 Sum_probs=31.3
Q ss_pred ceEeeCCCCCCCceeeehhhhhhhccccceeccchhhH
Q 022384 253 SFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHS 290 (298)
Q Consensus 253 ~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~ 290 (298)
++++.++..-|.+|+|.|+.||++.||.+.|+.-|++.
T Consensus 29 sFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~t 66 (971)
T KOG0501|consen 29 SFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCT 66 (971)
T ss_pred ceeeccceeeccceEEecCcchhccCccHHHHhcccce
Confidence 34455555558899999999999999999999998763
No 80
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=94.74 E-value=0.025 Score=47.80 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=42.6
Q ss_pred ccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHhhhc
Q 022384 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLKLQE 297 (298)
Q Consensus 249 ~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~~~~ 297 (298)
-.-+||+-||. .|+|+-+|..+.++.|-+.|+++|++..++|+++|
T Consensus 119 yMtDGViATdR---rG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d 164 (459)
T COG5002 119 YMTDGVIATDR---RGKIILINKPALKMLGVSKEDALGRSILELLKIED 164 (459)
T ss_pred HHcCceEeecC---CCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcc
Confidence 34578899999 99999999999999999999999999999999976
No 81
>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=94.21 E-value=0.021 Score=40.58 Aligned_cols=31 Identities=10% Similarity=0.029 Sum_probs=28.0
Q ss_pred CCceeeehhh-hhhhccccceeccchhhHHHH
Q 022384 263 DMPMVYASDA-FLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 263 ~~~i~~~N~a-f~~itGys~eE~~G~~~~~~~ 293 (298)
+++|+++-+. ...++||.++|++|++..+|+
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~ 42 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFV 42 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGB
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCchHHhC
Confidence 9999999998 699999999999999999886
No 82
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=94.20 E-value=0.013 Score=41.11 Aligned_cols=44 Identities=14% Similarity=0.159 Sum_probs=32.6
Q ss_pred hhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHH
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTY 292 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~ 292 (298)
..++++..++++.|. +++|.|.|++..++++.+. ..+|++..++
T Consensus 3 ~il~s~~~~i~~vD~---~~~I~~~n~~a~~~f~~~~-~~iGr~l~~~ 46 (106)
T PF13596_consen 3 NILDSMPIGIIFVDR---NLRIRYFNPAAARLFNLSP-SDIGRPLFDI 46 (106)
T ss_dssp HHHHHSSSEEEEEET---TSBEEEE-SCGC-SS---G-GGTTSBCCCS
T ss_pred HHHhcCCCCEEEEcC---CCeEEEeChhHhhhcCCCh-HHCCCCHHHc
Confidence 456778889999999 9999999999999999775 4589876654
No 83
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=94.18 E-value=0.046 Score=50.37 Aligned_cols=48 Identities=13% Similarity=0.147 Sum_probs=39.7
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhcccc---ceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKG---KHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys---~eE~~G~~~~~~~ 293 (298)
....++++.++|+++|. +++|+++|+++++++||+ .++.+|+.+..+.
T Consensus 223 ~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~ 273 (542)
T PRK11086 223 RQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWM 273 (542)
T ss_pred HHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhC
Confidence 34577888999999999 999999999999999876 4577887765543
No 84
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=92.93 E-value=0.11 Score=49.17 Aligned_cols=56 Identities=18% Similarity=0.316 Sum_probs=47.4
Q ss_pred HHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHH
Q 022384 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR 77 (298)
Q Consensus 19 ~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~ 77 (298)
+-..+++++..-++++..+ |+|+||++....+|||..++++|.++..+.+|.+...
T Consensus 96 L~~LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~ 151 (803)
T KOG3561|consen 96 LTHLILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDK 151 (803)
T ss_pred HHHHHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCc
Confidence 3345678887788999999 9999999999999999999999999888877765443
No 85
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=92.90 E-value=0.065 Score=44.57 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=42.2
Q ss_pred hhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHh
Q 022384 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLK 294 (298)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~ 294 (298)
..++.+...+++.|. ++.|.|+|++++..+|-|..-+.|...+.++.
T Consensus 11 ~~Ln~~~~pVl~vd~---~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~ 57 (363)
T COG3852 11 AILNNLINPVLLVDD---ELAIHYANPAAEQLLAVSARRLAGTRLSELLP 57 (363)
T ss_pred hHHhccCCceEEEcC---CCcEEecCHHHHHHHHHHHHHHhcCChHHHcC
Confidence 567888889999999 99999999999999999999999988887764
No 86
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=92.71 E-value=3 Score=41.43 Aligned_cols=103 Identities=11% Similarity=0.077 Sum_probs=61.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEE
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (298)
..+++++.+++.+|.|+++++.. +|.++++|+.+..++|+...+. .. .+...+.... ...
T Consensus 331 e~e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~~~~-------------~~----~~~~~~~~~~-~~~ 390 (924)
T PRK10841 331 EHEQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLTHED-------------RQ----RLTQIICGQQ-VNF 390 (924)
T ss_pred HHHHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCChhH-------------HH----HHHHHHhccc-cce
Confidence 45667889999999999999753 3999999999999887643211 01 1111111111 111
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhhhc
Q 022384 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (298)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee~l 143 (298)
......++....+ ...+... .+. ...+++..|||+++++|+++
T Consensus 391 -~~~~~~~~~~~~i--~~~~~~~--~~~-~~~i~~~~Dit~r~~~e~~L 433 (924)
T PRK10841 391 -VDVLTSNNTNLQI--SFVHSRY--RNE-NVAICVLVDVSARVKMEESL 433 (924)
T ss_pred -eeEEcCCCcEEEE--EEEeeee--cCc-eEEEEEEEEhhHHHHHHHHH
Confidence 1122334444333 3333332 222 24678899999999987776
No 87
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=89.94 E-value=0.19 Score=47.69 Aligned_cols=46 Identities=13% Similarity=0.114 Sum_probs=38.9
Q ss_pred hcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHhh
Q 022384 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLKL 295 (298)
Q Consensus 247 ~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~~ 295 (298)
+|....++++..- +|+|+||...-+.+.||..+|++|++.+++|+-
T Consensus 101 LeAlDGF~fvV~c---dG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp 146 (803)
T KOG3561|consen 101 LEALDGFLFVVNC---DGRIVYVSESVTSVLGYLQSDLMGQSLYDILHP 146 (803)
T ss_pred HHHhcCeEEEEec---CceEEEEecchHHhhCcCHHHHhcchHHHhcCc
Confidence 4555555666666 799999999999999999999999999999864
No 88
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=89.34 E-value=0.35 Score=41.47 Aligned_cols=48 Identities=15% Similarity=0.129 Sum_probs=43.4
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHH
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYL 293 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~ 293 (298)
+...++..++.+.-.|. .|.|.-+|||++.++|-+.+++.|...+.++
T Consensus 82 L~aLL~al~~pVlsvd~---kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l~ 129 (511)
T COG3283 82 LSALLEALPEPVLSVDM---KGKVDMANPAACQLFGRKEDRLRGHTAAQLI 129 (511)
T ss_pred HHHHHHhCCCceEEecc---cCceeecCHHHHHHhCCChhhhcCccHHHhc
Confidence 66778888999999999 9999999999999999999999999877665
No 89
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=88.95 E-value=0.93 Score=39.11 Aligned_cols=84 Identities=8% Similarity=0.050 Sum_probs=57.0
Q ss_pred EEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEccCCCEEEEE
Q 022384 30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (298)
Q Consensus 30 ~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (298)
-++....+ -.+++......+++||.+.+++++++...++..+.......-...+..|....--+++..+.|.+.|+.
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 889999999999999999999999876666655544443333334444444333456677888888876
Q ss_pred EEEEEee
Q 022384 110 FKMSLVF 116 (298)
Q Consensus 110 ~~~~p~~ 116 (298)
....-+.
T Consensus 304 syat~vH 310 (598)
T KOG3559|consen 304 SYATFVH 310 (598)
T ss_pred EeeEEEe
Confidence 5544443
No 90
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=88.03 E-value=0.28 Score=44.21 Aligned_cols=49 Identities=16% Similarity=0.076 Sum_probs=42.3
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhccccce--eccchhhHHHHh
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKH--SNRASMHSTYLK 294 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~e--E~~G~~~~~~~~ 294 (298)
....++++.+|++.+|+ .|.|.-+|.+.++|.|+... +.+|++..+++.
T Consensus 217 r~A~l~si~EGviAvd~---~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~ 267 (537)
T COG3290 217 RQAMLQSIKEGVIAVDK---KGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLP 267 (537)
T ss_pred HHHHHHHhhceEEEECC---CCeEeehhHHHHHHhcccCcCcccccccceEeec
Confidence 44578889999999999 99999999999999999986 689987766543
No 91
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=87.10 E-value=0.8 Score=41.09 Aligned_cols=59 Identities=12% Similarity=0.147 Sum_probs=51.6
Q ss_pred HHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHH
Q 022384 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (298)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~ 83 (298)
.++++++.-++++..+ |.|-|++...+..+|+...+++.++..++++.++.+.+.+.+.
T Consensus 115 ~lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLh 173 (712)
T KOG3560|consen 115 LLLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLH 173 (712)
T ss_pred HHHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHh
Confidence 3577788888999999 9999999999999999999999999999999888887766554
No 92
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=86.63 E-value=7.6 Score=36.01 Aligned_cols=42 Identities=14% Similarity=0.135 Sum_probs=32.6
Q ss_pred ccccceEeeCCCCCCCceeeehhhhhhhcccc-ceeccchhhHHHH
Q 022384 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTDKG-KHSNRASMHSTYL 293 (298)
Q Consensus 249 ~~~~~i~i~d~~~~~~~i~~~N~af~~itGys-~eE~~G~~~~~~~ 293 (298)
...++.++.|. +++|+-.|++.-.+.+-+ ..-++|.++..++
T Consensus 230 ~~~~~~lavd~---~grvl~at~aA~~~La~~~~~~l~g~p~~~~~ 272 (606)
T COG3284 230 SQSEALLAVDQ---DGRVLGATRAARQLLALTDRQRLIGQPVEDFL 272 (606)
T ss_pred cccceeeeecC---cchhhhccHHHHHhhccchhhHhhcCCccccc
Confidence 34556678888 999999999999999888 5666666666554
No 93
>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=85.23 E-value=0.85 Score=32.29 Aligned_cols=43 Identities=26% Similarity=0.397 Sum_probs=34.2
Q ss_pred EEEEEeCCCCCCcEEEcchHHHHHhCCC---ccccCCCCCCCCcCCCC
Q 022384 30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPRT 74 (298)
Q Consensus 30 ~i~~~d~~~~~g~i~~~N~~~~~~~g~~---~~e~ig~~~~~l~~~~~ 74 (298)
.++++|.+ +++|+.++..+..++|.+ .++++|++...++++..
T Consensus 17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~ 62 (110)
T PF08446_consen 17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES 62 (110)
T ss_dssp EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence 35566654 489999999999999999 89999999887776543
No 94
>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=84.16 E-value=0.69 Score=32.74 Aligned_cols=39 Identities=23% Similarity=0.264 Sum_probs=32.2
Q ss_pred eEeeCCCCCCCceeeehhhhhhhcccc---ceeccchhhHHHHh
Q 022384 254 FVLIDPHLPDMPMVYASDAFLKLTDKG---KHSNRASMHSTYLK 294 (298)
Q Consensus 254 i~i~d~~~~~~~i~~~N~af~~itGys---~eE~~G~~~~~~~~ 294 (298)
++..|. ++.+|++++.....++|.+ .++++|++..+++.
T Consensus 18 LLa~d~--~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~ 59 (110)
T PF08446_consen 18 LLALDP--DDLRIVQASENIAELLGIPPELPEELLGRPLSELLG 59 (110)
T ss_dssp EEEEET--TTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSC
T ss_pred EEEEEC--CCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhC
Confidence 344554 3789999999999999999 99999999998875
No 95
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=79.95 E-value=4.7 Score=39.84 Aligned_cols=40 Identities=13% Similarity=0.075 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCC
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~ 56 (298)
...++.+.+++++|.|++++|.+ +|+++.+|+++.+++|+
T Consensus 340 ~~~~l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 340 ILRALNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCc
Confidence 45667889999999999999943 28999999999999975
No 96
>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=79.00 E-value=1.6 Score=32.58 Aligned_cols=44 Identities=16% Similarity=0.033 Sum_probs=33.5
Q ss_pred hhhhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchh
Q 022384 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASM 288 (298)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~ 288 (298)
...+-..+.+|+-.+. .++=..+|+|.+..+|++|+.+|++|-+
T Consensus 34 ~~~L~~ap~ailsh~~-~~dP~f~yaN~aaL~l~e~~w~el~~lP 77 (148)
T PF08670_consen 34 AKALWHAPFAILSHGT-KADPIFIYANQAALDLFETTWDELVGLP 77 (148)
T ss_pred HHHHHcCCCEEEEcCC-CCCCEEEehhHHHHHHhcCCHHHHhcCc
Confidence 3444445666666665 4566789999999999999999999843
No 97
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=78.01 E-value=8.5 Score=37.03 Aligned_cols=78 Identities=10% Similarity=0.152 Sum_probs=58.4
Q ss_pred EEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCC-C--EEEEEEEEccCCCEEE
Q 022384 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-P--IEVNLLNYKKDGTPFW 107 (298)
Q Consensus 31 i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~-~--~~~e~~~~~~dg~~~~ 107 (298)
++++... +++.+..+..++..++||-+.++||+++..++++.+...+.+....+++.+. + ....+++...+|..+.
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 4444433 3477888999999999999999999998888888888877777777776553 2 2345777788887664
Q ss_pred EE
Q 022384 108 ML 109 (298)
Q Consensus 108 ~~ 109 (298)
+.
T Consensus 411 ld 412 (1114)
T KOG3753|consen 411 LD 412 (1114)
T ss_pred Ee
Confidence 43
No 98
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=77.91 E-value=1.7 Score=41.37 Aligned_cols=41 Identities=12% Similarity=0.101 Sum_probs=37.0
Q ss_pred eEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHHHhhhc
Q 022384 254 FVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTYLKLQE 297 (298)
Q Consensus 254 i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~~~~~~ 297 (298)
++|.+. +++|+|+.+.|+.+.||.++=+.|.+|.+||..|+
T Consensus 195 ~~vS~~---dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD 235 (1114)
T KOG3753|consen 195 VAVSFL---DGRILYISEQAALILGCKRDVLSSAKFVDFLAPQD 235 (1114)
T ss_pred EEEecc---CCcEEEeechhhhhccCchhhhccchhhhhcchhh
Confidence 456677 99999999999999999999999999999998765
No 99
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=76.81 E-value=2.2 Score=39.26 Aligned_cols=44 Identities=9% Similarity=-0.032 Sum_probs=38.1
Q ss_pred hhcccccceEeeCCCCCCCceeeehhhhhhhccccceeccchhhHHH
Q 022384 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTY 292 (298)
Q Consensus 246 ~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~ 292 (298)
++....-|++..|. +++|.-+||+.+.|+|.+.++++|++.+++
T Consensus 375 VLsgvtaGVi~~d~---~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ 418 (712)
T COG5000 375 VLSGLTAGVIGFDN---RGCITTVNPSAEQILGKPFDQLLGQSLSAI 418 (712)
T ss_pred HHhcCceeEEEEcC---CCeeEeecchHHHHhcCChhHhhcchhhhh
Confidence 44455668899999 999999999999999999999999887665
No 100
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=76.56 E-value=2.3 Score=43.54 Aligned_cols=36 Identities=6% Similarity=-0.042 Sum_probs=31.0
Q ss_pred hhhhcccccceEeeCCCCCCCceeeehhhhhhhccccce
Q 022384 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKGKH 282 (298)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys~e 282 (298)
...++.++.++++.|. +++|+++|++|++++|++..
T Consensus 579 ~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~ 614 (1197)
T PRK09959 579 KALSDSLPNPTYVVNW---QGNVISHNSAFEHYFTADYY 614 (1197)
T ss_pred HHHHhhCCCcEEEEcC---CCcEEEehHHHHHHhCcccc
Confidence 3445778899999999 99999999999999998743
No 101
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=67.10 E-value=14 Score=34.19 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=33.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCC
Q 022384 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (298)
Q Consensus 15 ~~~~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~ 56 (298)
+....+..++.++|.||++.+.+ +.+.|+||-...+++-
T Consensus 72 ~~~~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~~ 110 (655)
T COG3887 72 QAEKSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcCh
Confidence 44566778999999999999988 9999999999988864
No 102
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=65.82 E-value=13 Score=36.40 Aligned_cols=45 Identities=20% Similarity=0.097 Sum_probs=36.5
Q ss_pred HHHHHHHhhCCCEEEEEe-CCCCCCcEEEcchHHHHHhCCCccccCCCCCCC
Q 022384 18 LWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d-~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~ 68 (298)
.--+.++..+|.|++++| .+ |.+.|.|+.+..+++ .+ ++|++...
T Consensus 102 ~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~ 147 (838)
T PRK14538 102 QIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQ 147 (838)
T ss_pred HHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHH
Confidence 344567889999999999 68 999999999999987 23 78887654
No 103
>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=65.23 E-value=29 Score=24.87 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=36.7
Q ss_pred EEEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhhhh
Q 022384 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (298)
Q Consensus 92 ~~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DITe~k~~ee 141 (298)
+...+....++|+. ++.+...+++ ++|.+.+++|+-.|+|....+++
T Consensus 68 ~~~nY~~~~~~Gk~--lrSsT~~Ird-~~g~~iG~LCIN~D~s~~~~~~~ 114 (118)
T PF08348_consen 68 YIINYKTKTKDGKI--LRSSTFFIRD-ENGKLIGALCINFDISALEQAQN 114 (118)
T ss_pred ccccccccCCCCCE--EEEEEEEEEC-CCCCEEEEEEEEeccHHHHHHHH
Confidence 44455566778864 5677788888 88999999999999999888743
No 104
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=63.26 E-value=16 Score=29.20 Aligned_cols=38 Identities=18% Similarity=0.065 Sum_probs=33.2
Q ss_pred HHHHHHHhhCCCEEEEEeCCCCCCcEEEcchHHHHHhCCCc
Q 022384 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (298)
Q Consensus 18 ~~l~~~~~~~~~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~ 58 (298)
+.+..+++..|.++.+-+.+ |.+++.|.+|.+.+.-.-
T Consensus 19 ~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhcC
Confidence 35667899999999999999 999999999999987543
No 105
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=57.51 E-value=19 Score=30.62 Aligned_cols=90 Identities=13% Similarity=0.272 Sum_probs=53.1
Q ss_pred HHHHHhhCC----CEEEEEeCCCCCCcEEEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEE
Q 022384 20 VHEALDELP----DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (298)
Q Consensus 20 l~~~~~~~~----~~i~~~d~~~~~g~i~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (298)
+++++|++. .++++..+. +.+.+|+|..+...+||+.++.+......+.. . -..+...+. .. ......+.
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV~e-G-l~qW~~dL~-~~-s~~E~~gr 358 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIVQE-G-LAQWETDLQ-LL-SRQERSGR 358 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHHHh-h-HHHHHHHHH-hh-hhhhhhce
Confidence 445555543 345555543 47899999999999999999887543221111 1 111111121 11 22334566
Q ss_pred EEEEccCCCEEEEEEEEEEe
Q 022384 96 LLNYKKDGTPFWMLFKMSLV 115 (298)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~p~ 115 (298)
+....++|...++......+
T Consensus 359 lviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 359 LVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred EEEEecCCCceeeEEEEeec
Confidence 77788898888776666655
No 106
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.26 E-value=89 Score=24.51 Aligned_cols=105 Identities=16% Similarity=0.223 Sum_probs=66.7
Q ss_pred HHhhCCCEEEEEeCCCCCCcE--EEcchHHHHHhCCCccccCCCCCCCCcCCCCCHHHHHHHHHHHHhCCCEEEEEEEEc
Q 022384 23 ALDELPDSFTITDPSISGHPI--VFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (298)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~g~i--~~~N~~~~~~~g~~~~e~ig~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (298)
+-..+++.++. ..+ ++|.+ ..+-...|.++|. |+-|.+...+..+.+.......+..+.+...+.-.......
T Consensus 53 l~slL~d~FiL-~~~-~~G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s 127 (209)
T COG5388 53 LKSLLPDVFIL-ERD-GRGKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRS 127 (209)
T ss_pred HHhhcCceEEE-ecc-CCCCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhh
Confidence 44556665443 333 11443 4455667777774 67787776676666666666666666666666555555556
Q ss_pred cCCCEEEEEEEEEEeecCCCCcEEEEEEEEecC
Q 022384 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (298)
Q Consensus 101 ~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DI 133 (298)
..|...-+++-..|+.. ..|....++|...-+
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 67777778888999988 677756677766544
No 107
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=41.65 E-value=1e+02 Score=20.41 Aligned_cols=47 Identities=15% Similarity=0.169 Sum_probs=29.8
Q ss_pred HHHHHHhCCCEEEEEEEEccCCCEEEEEEEEEEeecCCCCcEEEEEEEEecCc
Q 022384 82 IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (298)
Q Consensus 82 ~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~p~~~~~~g~~~~~~~~~~DIT 134 (298)
+.+++..++... .....|...-+-+.+.|+.+ .+|.+.+.+++. |+|
T Consensus 37 Le~vl~~g~v~r----~~P~~G~Y~G~PViV~PI~~-~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 37 LEEVLETGKVIR----VTPIEGPYKGVPVIVAPIKD-EDGEVIAAIGVV-DLT 83 (84)
T ss_pred HHHHHHcCCEEE----eccCCcccCCeeEEEEEEEc-CCCCEEEEEEEE-Ecc
Confidence 345566655332 22334544445577899998 779999888875 665
No 108
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=35.67 E-value=37 Score=33.40 Aligned_cols=43 Identities=12% Similarity=0.049 Sum_probs=33.7
Q ss_pred hhhhcccccceEeeC-CCCCCCceeeehhhhhhhccccceeccchhhHHH
Q 022384 244 YISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTDKGKHSNRASMHSTY 292 (298)
Q Consensus 244 ~~~~~~~~~~i~i~d-~~~~~~~i~~~N~af~~itGys~eE~~G~~~~~~ 292 (298)
..++...+-++++.| . ++.|+++||.|..++| .+ ++|++..++
T Consensus 105 ~~~l~~~p~gi~~~~~~---~~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 105 EEVLNELPIGIVLIDIS---SKEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HHHHHhCCceEEEEeCC---CCEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 345566677888999 6 7899999999999988 33 899877663
No 109
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=32.79 E-value=37 Score=33.81 Aligned_cols=36 Identities=8% Similarity=-0.069 Sum_probs=30.3
Q ss_pred hhhhhcccccceEeeCCCCCCCceeeehhhhhhhcccc
Q 022384 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTDKG 280 (298)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~~~~i~~~N~af~~itGys 280 (298)
....+++++.|+++.|. .+++|+.+|+++.+++|+.
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 44567888999999994 2789999999999999974
No 110
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=32.29 E-value=14 Score=31.28 Aligned_cols=25 Identities=12% Similarity=0.159 Sum_probs=21.8
Q ss_pred CCCceeeehhhhhhhccccceeccc
Q 022384 262 PDMPMVYASDAFLKLTDKGKHSNRA 286 (298)
Q Consensus 262 ~~~~i~~~N~af~~itGys~eE~~G 286 (298)
.+.+.+|+|.-|..+|||+.|..+-
T Consensus 306 k~qRllFAN~~fk~wtGy~~edFl~ 330 (401)
T PF06785_consen 306 KSQRLLFANSQFKTWTGYSSEDFLK 330 (401)
T ss_pred hhhHHHHhHHHHHHHhccCHHHHHh
Confidence 4778999999999999999887653
No 111
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.78 E-value=23 Score=23.83 Aligned_cols=17 Identities=24% Similarity=0.114 Sum_probs=13.3
Q ss_pred eehhhhhhhccccceec
Q 022384 268 YASDAFLKLTDKGKHSN 284 (298)
Q Consensus 268 ~~N~af~~itGys~eE~ 284 (298)
..|+-.+++|||++.|=
T Consensus 73 tyndflekltgytakEr 89 (96)
T COG4004 73 TYNDFLEKLTGYTAKER 89 (96)
T ss_pred HHHHHHHHHhchhHHHH
Confidence 34777899999998773
No 112
>PF15660 Imm49: Immunity protein 49
Probab=21.11 E-value=59 Score=20.11 Aligned_cols=23 Identities=13% Similarity=0.255 Sum_probs=16.6
Q ss_pred cceEeeCCCCCCCceeeehhhhh
Q 022384 252 QSFVLIDPHLPDMPMVYASDAFL 274 (298)
Q Consensus 252 ~~i~i~d~~~~~~~i~~~N~af~ 274 (298)
+-+++|...-...+.+|.||-|.
T Consensus 32 drlmvttsvgeearlvyfnpdfa 54 (84)
T PF15660_consen 32 DRLMVTTSVGEEARLVYFNPDFA 54 (84)
T ss_pred ceEEEEeccCceeEEEEeCCCcC
Confidence 45566666455678999999875
Done!