Query 019399
Match_columns 341
No_of_seqs 220 out of 2011
Neff 10.7
Searched_HMMs 46136
Date Fri Mar 29 09:09:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019399.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019399hhsearch_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 6.3E-19 1.4E-23 172.9 22.6 187 6-293 193-382 (807)
2 TIGR02040 PpsR-CrtJ transcript 99.8 8.6E-19 1.9E-23 159.8 18.7 212 15-335 130-346 (442)
3 TIGR02040 PpsR-CrtJ transcript 99.8 5.7E-19 1.2E-23 161.0 15.1 202 24-315 2-205 (442)
4 PRK09776 putative diguanylate 99.8 1.9E-18 4.2E-23 174.7 19.5 212 15-326 280-493 (1092)
5 PRK09776 putative diguanylate 99.8 1.2E-17 2.6E-22 168.9 20.0 227 7-335 400-634 (1092)
6 TIGR02938 nifL_nitrog nitrogen 99.8 3.8E-18 8.2E-23 158.0 14.8 181 18-298 4-184 (494)
7 PRK13560 hypothetical protein; 99.8 8E-17 1.7E-21 158.1 20.4 219 17-336 66-299 (807)
8 PRK11359 cyclic-di-GMP phospho 99.7 4.8E-16 1E-20 152.4 20.2 210 19-334 13-230 (799)
9 PF13426 PAS_9: PAS domain; PD 99.7 1.1E-15 2.4E-20 110.3 13.3 104 28-135 1-104 (104)
10 PF08448 PAS_4: PAS fold; Int 99.6 1.3E-14 2.9E-19 105.7 11.6 110 24-138 1-110 (110)
11 PF00989 PAS: PAS fold; Inter 99.6 2.7E-14 5.8E-19 104.6 12.4 112 18-133 1-113 (113)
12 PRK11091 aerobic respiration c 99.5 9.2E-13 2E-17 128.8 14.5 124 15-142 152-275 (779)
13 PRK13559 hypothetical protein; 99.4 5E-12 1.1E-16 112.5 15.2 124 16-140 41-164 (361)
14 PRK13557 histidine kinase; Pro 99.4 1.6E-11 3.4E-16 115.3 15.0 127 15-142 27-153 (540)
15 PF00989 PAS: PAS fold; Inter 99.3 8.9E-12 1.9E-16 91.1 6.6 92 242-336 2-97 (113)
16 PF13426 PAS_9: PAS domain; PD 99.2 1.5E-11 3.2E-16 88.4 6.2 83 251-336 1-86 (104)
17 PRK13558 bacterio-opsin activa 99.2 1.6E-10 3.6E-15 111.1 15.2 124 19-143 149-272 (665)
18 PRK10060 RNase II stability mo 99.1 1E-09 2.2E-14 105.1 14.8 123 16-143 109-233 (663)
19 TIGR00229 sensory_box PAS doma 99.1 1.7E-09 3.6E-14 78.1 12.8 118 18-140 3-121 (124)
20 PF08447 PAS_3: PAS fold; Int 99.1 6.9E-10 1.5E-14 77.7 9.2 86 43-130 1-91 (91)
21 PRK11359 cyclic-di-GMP phospho 99.0 3.8E-09 8.3E-14 104.0 13.1 120 17-140 135-255 (799)
22 PF08448 PAS_4: PAS fold; Int 98.9 1.5E-09 3.2E-14 78.8 5.5 87 247-336 1-89 (110)
23 cd00130 PAS PAS domain; PAS mo 98.9 8.9E-08 1.9E-12 65.7 13.5 102 28-133 2-103 (103)
24 PF13596 PAS_10: PAS domain; P 98.9 2.6E-08 5.7E-13 71.9 10.4 106 20-134 1-106 (106)
25 PF12860 PAS_7: PAS fold 98.8 4.2E-08 9.2E-13 71.9 9.6 104 24-140 1-114 (115)
26 KOG3558 Hypoxia-inducible fact 98.8 6.9E-08 1.5E-12 87.3 12.5 69 263-331 283-351 (768)
27 PRK13557 histidine kinase; Pro 98.8 1.8E-08 3.8E-13 94.7 8.2 93 243-335 32-127 (540)
28 COG3829 RocR Transcriptional r 98.8 6.9E-08 1.5E-12 86.0 10.5 162 22-293 5-166 (560)
29 PRK11360 sensory histidine kin 98.7 2.8E-07 6E-12 87.7 14.4 121 16-143 260-381 (607)
30 TIGR02966 phoR_proteo phosphat 98.7 1.2E-07 2.7E-12 83.1 11.1 109 15-140 3-111 (333)
31 PRK11073 glnL nitrogen regulat 98.7 1.3E-07 2.7E-12 83.8 10.5 111 18-139 7-117 (348)
32 PRK10060 RNase II stability mo 98.7 5.4E-08 1.2E-12 93.3 8.6 81 243-326 113-194 (663)
33 PF14598 PAS_11: PAS domain; P 98.7 7.9E-07 1.7E-11 64.3 11.9 101 32-135 6-108 (111)
34 PRK13559 hypothetical protein; 98.6 1.1E-07 2.5E-12 84.5 8.2 93 243-335 45-140 (361)
35 KOG0501 K+-channel KCNQ [Inorg 98.6 4.8E-07 1E-11 80.5 10.1 121 18-139 14-139 (971)
36 PF08447 PAS_3: PAS fold; Int 98.5 1.2E-07 2.5E-12 66.3 3.7 64 266-330 1-69 (91)
37 COG3829 RocR Transcriptional r 98.5 7E-06 1.5E-10 73.6 15.2 112 15-139 114-225 (560)
38 COG5002 VicK Signal transducti 98.4 5.1E-06 1.1E-10 69.9 11.3 115 15-140 108-222 (459)
39 PF13188 PAS_8: PAS domain; PD 98.4 5.5E-07 1.2E-11 58.2 4.5 43 242-291 2-44 (64)
40 PRK11091 aerobic respiration c 98.3 1.7E-06 3.6E-11 85.1 6.7 90 243-335 157-249 (779)
41 PRK10820 DNA-binding transcrip 98.3 7E-06 1.5E-10 76.2 10.4 110 15-138 77-190 (520)
42 TIGR02938 nifL_nitrog nitrogen 98.2 1.1E-06 2.5E-11 81.4 5.1 90 242-334 5-97 (494)
43 PRK11006 phoR phosphate regulo 98.2 5.2E-06 1.1E-10 75.8 9.0 107 15-140 95-201 (430)
44 PF14598 PAS_11: PAS domain; P 98.2 1.8E-06 3.8E-11 62.5 4.8 65 263-327 11-77 (111)
45 TIGR00229 sensory_box PAS doma 98.2 5.7E-06 1.2E-10 59.1 7.6 65 243-310 5-69 (124)
46 PRK11073 glnL nitrogen regulat 98.2 2.9E-06 6.2E-11 75.1 6.8 88 243-335 9-99 (348)
47 PRK13558 bacterio-opsin activa 98.2 5.3E-06 1.1E-10 80.1 8.0 93 243-335 150-245 (665)
48 PRK11388 DNA-binding transcrip 98.2 5.4E-05 1.2E-09 72.5 14.5 49 243-294 205-253 (638)
49 TIGR02966 phoR_proteo phosphat 98.1 7.5E-06 1.6E-10 71.7 7.7 87 241-335 6-92 (333)
50 PF13188 PAS_8: PAS domain; PD 98.1 7.3E-06 1.6E-10 52.9 5.1 42 18-66 1-42 (64)
51 cd00130 PAS PAS domain; PAS mo 98.0 1.9E-05 4.1E-10 53.6 6.7 60 251-313 2-61 (103)
52 COG2202 AtoS FOG: PAS/PAC doma 98.0 0.00052 1.1E-08 54.2 14.6 119 16-139 110-231 (232)
53 PF13596 PAS_10: PAS domain; P 97.9 1.2E-05 2.5E-10 57.9 3.5 89 243-336 1-89 (106)
54 PRK11086 sensory histidine kin 97.9 0.00015 3.1E-09 68.4 11.2 110 16-141 219-331 (542)
55 PF12860 PAS_7: PAS fold 97.7 8.5E-05 1.8E-09 54.2 6.1 43 247-292 1-44 (115)
56 KOG1229 3'5'-cyclic nucleotide 97.7 1.3E-05 2.8E-10 69.3 1.7 74 243-319 159-233 (775)
57 smart00091 PAS PAS domain. PAS 97.7 0.00011 2.5E-09 45.4 5.5 61 243-306 3-63 (67)
58 PRK10820 DNA-binding transcrip 97.6 7.7E-05 1.7E-09 69.4 5.2 53 242-297 81-133 (520)
59 PRK11006 phoR phosphate regulo 97.5 7.4E-05 1.6E-09 68.2 3.8 51 243-296 100-150 (430)
60 KOG3559 Transcriptional regula 97.5 0.0015 3.2E-08 56.2 10.7 56 20-78 81-136 (598)
61 COG5000 NtrY Signal transducti 97.5 0.0012 2.7E-08 60.1 10.8 113 16-140 368-481 (712)
62 PRK09959 hybrid sensory histid 97.5 0.002 4.4E-08 66.7 13.6 42 15-59 573-614 (1197)
63 PRK11388 DNA-binding transcrip 97.5 0.0017 3.6E-08 62.5 12.0 108 19-138 204-311 (638)
64 KOG1229 3'5'-cyclic nucleotide 97.3 0.00012 2.7E-09 63.4 2.5 102 22-127 161-263 (775)
65 KOG3558 Hypoxia-inducible fact 97.3 0.00044 9.5E-09 63.4 5.9 91 41-131 284-374 (768)
66 COG2202 AtoS FOG: PAS/PAC doma 97.3 0.017 3.6E-07 45.3 14.8 49 243-294 114-162 (232)
67 PRK15053 dpiB sensor histidine 97.3 0.0013 2.8E-08 62.1 9.0 106 17-139 221-328 (545)
68 PRK11360 sensory histidine kin 97.3 0.00075 1.6E-08 64.3 7.4 66 243-313 264-329 (607)
69 COG3290 CitA Signal transducti 97.2 0.0015 3.3E-08 59.0 8.3 107 18-139 215-323 (537)
70 COG3852 NtrB Signal transducti 97.2 0.0037 7.9E-08 52.4 9.6 135 21-185 10-145 (363)
71 KOG0501 K+-channel KCNQ [Inorg 97.2 0.00034 7.3E-09 63.0 3.8 94 243-336 16-117 (971)
72 PF08670 MEKHLA: MEKHLA domain 97.2 0.016 3.5E-07 43.7 12.1 112 18-132 32-144 (148)
73 TIGR02373 photo_yellow photoac 97.2 0.0059 1.3E-07 44.0 9.1 67 22-91 20-87 (124)
74 smart00091 PAS PAS domain. PAS 97.0 0.0028 6E-08 38.7 6.0 52 20-74 3-54 (67)
75 COG2461 Uncharacterized conser 96.9 0.0051 1.1E-07 53.1 8.0 113 17-139 289-401 (409)
76 PF08670 MEKHLA: MEKHLA domain 96.7 0.0055 1.2E-07 46.2 6.2 71 243-314 33-103 (148)
77 PRK15053 dpiB sensor histidine 96.6 0.018 3.9E-07 54.4 10.4 51 243-296 224-276 (545)
78 COG3290 CitA Signal transducti 96.6 0.017 3.7E-07 52.4 9.4 53 243-298 217-271 (537)
79 TIGR02373 photo_yellow photoac 96.3 0.0075 1.6E-07 43.5 4.5 65 246-313 21-86 (124)
80 COG3283 TyrR Transcriptional r 95.9 0.016 3.4E-07 49.9 5.0 59 242-303 81-139 (511)
81 smart00086 PAC Motif C-termina 95.7 0.11 2.3E-06 27.8 6.9 40 95-135 3-42 (43)
82 PF08446 PAS_2: PAS fold; Int 95.4 0.033 7.1E-07 40.1 4.8 46 254-301 18-66 (110)
83 KOG3560 Aryl-hydrocarbon recep 95.4 0.071 1.5E-06 48.1 7.4 93 41-135 293-385 (712)
84 COG3852 NtrB Signal transducti 95.3 0.042 9.1E-07 46.3 5.5 87 245-336 11-100 (363)
85 COG5002 VicK Signal transducti 95.2 0.024 5.1E-07 48.5 4.0 56 243-301 113-168 (459)
86 PRK11086 sensory histidine kin 95.2 0.031 6.8E-07 52.6 5.2 49 243-294 223-274 (542)
87 COG3283 TyrR Transcriptional r 94.9 0.1 2.2E-06 45.2 6.8 56 15-73 77-132 (511)
88 KOG3561 Aryl-hydrocarbon recep 94.9 0.012 2.7E-07 56.2 1.7 55 246-303 100-154 (803)
89 KOG3560 Aryl-hydrocarbon recep 94.8 0.45 9.9E-06 43.2 10.8 59 22-83 115-173 (712)
90 PF07310 PAS_5: PAS domain; I 94.7 0.63 1.4E-05 34.9 10.2 86 41-130 51-136 (137)
91 KOG3753 Circadian clock protei 93.8 0.29 6.2E-06 47.0 7.7 51 262-312 339-389 (1114)
92 COG5000 NtrY Signal transducti 93.0 0.28 6.1E-06 45.5 6.2 48 243-293 372-419 (712)
93 PRK10841 hybrid sensory kinase 91.4 2.8 6E-05 42.5 11.8 42 15-58 331-372 (924)
94 KOG3561 Aryl-hydrocarbon recep 90.5 0.23 5.1E-06 47.9 3.1 68 262-329 380-448 (803)
95 KOG3559 Transcriptional regula 89.9 0.73 1.6E-05 40.3 5.3 85 30-117 227-311 (598)
96 PRK09959 hybrid sensory histid 87.8 0.81 1.8E-05 47.8 5.1 39 243-284 578-616 (1197)
97 KOG3753 Circadian clock protei 86.5 1.9 4.2E-05 41.7 6.1 91 39-129 339-432 (1114)
98 PF08446 PAS_2: PAS fold; Int 81.7 1.7 3.6E-05 31.2 3.0 42 30-73 17-61 (110)
99 COG3284 AcoR Transcriptional a 70.6 28 0.00062 33.0 8.3 41 249-292 230-271 (606)
100 PF08348 PAS_6: YheO-like PAS 70.2 23 0.00049 25.8 6.2 46 91-139 67-112 (118)
101 COG5388 Uncharacterized protei 68.1 45 0.00097 26.4 7.6 108 23-134 53-160 (209)
102 COG3887 Predicted signaling pr 67.5 13 0.00029 34.8 5.5 42 12-56 69-110 (655)
103 PRK13719 conjugal transfer tra 66.5 9.1 0.0002 31.1 3.8 37 242-281 20-56 (217)
104 PRK13719 conjugal transfer tra 65.8 11 0.00024 30.6 4.2 37 17-56 18-54 (217)
105 PRK10618 phosphotransfer inter 65.7 15 0.00032 37.2 6.0 40 15-56 340-379 (894)
106 COG2461 Uncharacterized conser 65.3 21 0.00045 31.7 5.9 68 241-314 290-357 (409)
107 PRK14538 putative bifunctional 63.8 9.2 0.0002 38.1 4.0 44 243-292 104-148 (838)
108 PF07310 PAS_5: PAS domain; I 63.0 21 0.00045 26.7 5.1 64 253-319 39-103 (137)
109 PF06785 UPF0242: Uncharacteri 62.9 21 0.00045 30.8 5.4 82 26-115 295-378 (401)
110 PRK14538 putative bifunctional 55.8 25 0.00053 35.2 5.4 46 17-68 101-147 (838)
111 PRK10618 phosphotransfer inter 52.5 17 0.00037 36.7 3.9 37 242-280 344-380 (894)
112 COG3887 Predicted signaling pr 46.4 30 0.00064 32.7 4.1 34 242-278 76-109 (655)
113 PF06785 UPF0242: Uncharacteri 46.0 12 0.00027 32.1 1.5 33 253-287 299-331 (401)
114 PF02743 Cache_1: Cache domain 35.5 95 0.0021 20.3 4.4 30 106-136 12-41 (81)
115 PF09884 DUF2111: Uncharacteri 24.6 2.3E+02 0.0049 19.1 6.0 47 82-134 37-83 (84)
116 COG4251 Bacteriophytochrome (l 23.6 1.3E+02 0.0027 29.1 4.2 39 254-294 32-70 (750)
117 COG4191 Signal transduction hi 23.4 6.8E+02 0.015 24.1 14.2 96 16-136 87-183 (603)
No 1
>PRK13560 hypothetical protein; Provisional
Probab=99.83 E-value=6.3e-19 Score=172.91 Aligned_cols=187 Identities=14% Similarity=0.133 Sum_probs=147.5
Q ss_pred hHHHHhhhhhhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHH
Q 019399 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREA 85 (341)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~ 85 (341)
+..++.+. +.+++++.++++++++++++|.+ |+++++|+++++++||++++++|+++..+.++.............
T Consensus 193 k~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~ 268 (807)
T PRK13560 193 KRAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAK 268 (807)
T ss_pred HHHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHH
Confidence 34455555 56788999999999999999999 999999999999999999999999987776655444333344445
Q ss_pred HHcCCCcEEEEEEEcCCCCeEEEEEE--EEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhh
Q 019399 86 IREERPIEVNLLNYKKDGTPFWMLFK--MSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSC 163 (341)
Q Consensus 86 ~~~~~~~~~e~~~~~~dg~~~~~~~~--~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (341)
+..+.....+..+.++||..+|+.+. ..|+.+ .+|.+.+++++++|||++|++++++
T Consensus 269 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e~~L-------------------- 327 (807)
T PRK13560 269 FDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAEREL-------------------- 327 (807)
T ss_pred hccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHHHHH--------------------
Confidence 55666677888889999999976655 455667 7899999999999999999973332
Q ss_pred hhhhccchhhhhhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchH
Q 019399 164 RREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSL 243 (341)
Q Consensus 164 ~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (341)
+.. ...+
T Consensus 328 --------------------------------------~~s-----------------------------------e~~l 334 (807)
T PRK13560 328 --------------------------------------LEK-----------------------------------EDML 334 (807)
T ss_pred --------------------------------------HHH-----------------------------------HHHH
Confidence 000 0116
Q ss_pred HHHhhccCCceEEeCCCCCCCCEEEe-cHHHHHHhCCCcccccCCcccccc
Q 019399 244 YISLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGYDRNEVVGQNCRFLN 293 (341)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~d~~i~~~-N~~~~~~~Gy~~~e~~G~~~~~l~ 293 (341)
..++++++.+++++|.+ |.++++ |+++++++||+.++++|+++..+.
T Consensus 335 ~~l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~ 382 (807)
T PRK13560 335 RAIIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKPLPGMD 382 (807)
T ss_pred HHHHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCCccccC
Confidence 66889999999999999 999987 577888999999999999876553
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=99.82 E-value=8.6e-19 Score=159.82 Aligned_cols=212 Identities=17% Similarity=0.125 Sum_probs=146.0
Q ss_pred hhHHHHHHHHhhCCCeEEEEcC-CCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcE
Q 019399 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~-~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (341)
..+++++.++++++++++++|. + |+++++|+++++++||++++++|+++..+.++.+.......+......+....
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 4567899999999999999998 7 99999999999999999999999987777666655555556666665555544
Q ss_pred EEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhh
Q 019399 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (341)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 173 (341)
..+. .++|...| .+...++.. .|.. .+++...|||++++++.+.
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~~-~~l~~~~dit~~~~~e~~~------------------------------ 250 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGES-LFLCQLSPAGATQPVGDEL------------------------------ 250 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCce-EEEEEEcccchhhhhhHHH------------------------------
Confidence 4443 33443334 345556654 3333 5677889999987751110
Q ss_pred hhhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCc
Q 019399 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (341)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (341)
. ..+..++++++++
T Consensus 251 ----------------------------~--------------------------------------~~~~~l~e~~~d~ 264 (442)
T TIGR02040 251 ----------------------------S--------------------------------------ENLARLYHEAPDA 264 (442)
T ss_pred ----------------------------H--------------------------------------HHHHHHHHhCCce
Confidence 0 0166689999999
Q ss_pred eEEeCCCCCCCCEEEecHHHHHHhCCC-cccccCCccccccCCCChHHHHHHhhhhhccCcch--h-hhhcccccceeEE
Q 019399 254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR--A-SMHRRIKAHFGIF 329 (341)
Q Consensus 254 i~i~d~~~~d~~i~~~N~~~~~~~Gy~-~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~-~~~r~~~~~~~~~ 329 (341)
|+++|.+ |+|+++|++|++++||+ .++++|+++..+.+++.. .....+......+... . ...+++|...|+.
T Consensus 265 I~v~D~~---G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~ve 340 (442)
T TIGR02040 265 IVFSDAD---GTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRGGV-DLRVLLSNVRRTGQVRLYATTLTGEFGAQTEVE 340 (442)
T ss_pred EEEEcCC---CcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCCcc-cHHHHHHHHhhcCceEEEEEEEEcCCCCEEEEE
Confidence 9999998 99999999999999997 578999998766553322 1222222222233221 1 1245667777777
Q ss_pred EEEecc
Q 019399 330 FTYHPS 335 (341)
Q Consensus 330 ~~~~p~ 335 (341)
+..+|.
T Consensus 341 ~s~~~i 346 (442)
T TIGR02040 341 ISAAWV 346 (442)
T ss_pred EEEEEe
Confidence 666665
No 3
>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=5.7e-19 Score=160.98 Aligned_cols=202 Identities=13% Similarity=0.076 Sum_probs=145.1
Q ss_pred HhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCC-CcEEEEEEEcCC
Q 019399 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD 102 (341)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~d 102 (341)
+++++++++++|.+ |.++++|+.++.++||+.++++|+++..+.++++.......+......+. .+..+.....++
T Consensus 2 ~~~~~d~~~~~d~~---g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 78 (442)
T TIGR02040 2 LATAADVTLLLDAE---GVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPS 78 (442)
T ss_pred CcccCcEEEEECCC---CcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCC
Confidence 57889999999999 99999999999999999999999998888777665544445545555443 344555555566
Q ss_pred CCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhhhhhhhhccc
Q 019399 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD 182 (341)
Q Consensus 103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 182 (341)
|..+|+.++..++.+ + .+++++.+|||+.++.++++... +..
T Consensus 79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~~-----------------~~~---------------- 120 (442)
T TIGR02040 79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVAA-----------------QQA---------------- 120 (442)
T ss_pred CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHHH-----------------HHH----------------
Confidence 767777776666643 2 25678899999887742211000 000
Q ss_pred cCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCceEEeCC-CC
Q 019399 183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDP-HL 261 (341)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~d~-~~ 261 (341)
.+........ ....+..++++++++++++|. +
T Consensus 121 --------------~e~~~~~l~~--------------------------------~e~r~~~l~e~~~~~i~~~d~~~- 153 (442)
T TIGR02040 121 --------------MERDYWTLRE--------------------------------METRYRVVLEVSSDAVLLVDMST- 153 (442)
T ss_pred --------------HHHHHHHHHH--------------------------------HHHHHHHHHhhCCceEEEEECCC-
Confidence 0000000000 011277789999999999997 6
Q ss_pred CCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcch
Q 019399 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR 315 (341)
Q Consensus 262 ~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 315 (341)
|+|+++|+++++++||++++++|+++..+++|++.......+.....++...
T Consensus 154 --g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~ 205 (442)
T TIGR02040 154 --GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAA 205 (442)
T ss_pred --CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCc
Confidence 9999999999999999999999999988888888887777887777666544
No 4
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.80 E-value=1.9e-18 Score=174.66 Aligned_cols=212 Identities=12% Similarity=0.102 Sum_probs=172.6
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcC-CCcE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (341)
+.+++++.++++++.+++++|.+ |+++++|+++++++||++++++|++...+.++++.......+....... ..+.
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 56778999999999999999999 9999999999999999999999998877777776555544554444433 3356
Q ss_pred EEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhh
Q 019399 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (341)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 173 (341)
.+.+..++||+.+|+.....++.+ .+|.+.+++++.+|||++|++++++
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 788889999999999999999999 8999999999999999999973322
Q ss_pred hhhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCc
Q 019399 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (341)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 (341)
+... ..+..+++..+.+
T Consensus 406 ----------------------------~~~~-----------------------------------~~~~~~~~~~~~~ 422 (1092)
T PRK09776 406 ----------------------------ERLM-----------------------------------ERITLANEAGGIG 422 (1092)
T ss_pred ----------------------------HHHH-----------------------------------HHHHHHHHhcCce
Confidence 1100 1145577778899
Q ss_pred eEEeCCCCCCCCEEEecHHHHHHhCCCcccccCC-ccccccCCCChHHHHHHhhhhhccCcchhhhhcccccce
Q 019399 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ-NCRFLNGVDTDTTVLYQSSTDKGKHSNRASMHRRIKAHF 326 (341)
Q Consensus 254 i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~-~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~ 326 (341)
++.+|.+ +.++++|+++++++||+.++..+. .+....+|++.......+.+.+.++..+..++|..+++|
T Consensus 423 i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG 493 (1092)
T PRK09776 423 IWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG 493 (1092)
T ss_pred EEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc
Confidence 9999999 999999999999999999986553 345567899888888889899888888777777777777
No 5
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.78 E-value=1.2e-17 Score=168.94 Aligned_cols=227 Identities=15% Similarity=0.177 Sum_probs=168.3
Q ss_pred HHHHhhhhhhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCC-CCcccCCCCCHHHHHHHHHH
Q 019399 7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREA 85 (341)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~~ 85 (341)
..++.+. +..++++.+++..+.+++.+|.+ +.++++|+++++++|++.++..+.. +....++++.......+.+.
T Consensus 400 ~~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~ 475 (1092)
T PRK09776 400 RTEQVNE-RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDA 475 (1092)
T ss_pred HHHHHHH-HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHH
Confidence 3444444 56778889999999999999999 9999999999999999988743322 22334555555555667777
Q ss_pred HHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhh
Q 019399 86 IREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRR 165 (341)
Q Consensus 86 ~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (341)
...+..+..+++..++|| ..|+.....++.+ ++|.+.+++++.+|||++|++++++
T Consensus 476 ~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e~~L---------------------- 531 (1092)
T PRK09776 476 LQGRSPFKLEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLNEAL---------------------- 531 (1092)
T ss_pred HhcCCCeeEEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHHHHH----------------------
Confidence 778888889999999999 9999999999998 8999999999999999999973322
Q ss_pred hhccchhhhhhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHH
Q 019399 166 EVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYI 245 (341)
Q Consensus 166 e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (341)
+.. .++++.
T Consensus 532 ------------------------------------~~~-----------------------------------~~~l~~ 540 (1092)
T PRK09776 532 ------------------------------------FQE-----------------------------------KERLHI 540 (1092)
T ss_pred ------------------------------------HHH-----------------------------------HHHHHH
Confidence 000 011556
Q ss_pred HhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCC--ChHHHHHHhhhhhccCcc--hhh---h
Q 019399 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD--TDTTVLYQSSTDKGKHSN--RAS---M 318 (341)
Q Consensus 246 ~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~--~~~~~~~~~~~~~~~~~~--~~~---~ 318 (341)
++++++++|+++|.+ |+|+++|+++++++||+.+|++|+++..+.++. +.......+......... +.. .
T Consensus 541 ~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 617 (1092)
T PRK09776 541 TLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVL 617 (1092)
T ss_pred HHhccccEEEEECCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEE
Confidence 788899999999999 999999999999999999999999887665432 222222234444443333 111 3
Q ss_pred hcccccceeEEEEEecc
Q 019399 319 HRRIKAHFGIFFTYHPS 335 (341)
Q Consensus 319 ~r~~~~~~~~~~~~~p~ 335 (341)
.+++|...|+.+...|.
T Consensus 618 ~~~~G~~~~~~~~~~pi 634 (1092)
T PRK09776 618 HCRSGGSYDVHYSITPL 634 (1092)
T ss_pred EeCCCcEEEEEEEeeee
Confidence 35666667776666664
No 6
>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=99.78 E-value=3.8e-18 Score=158.02 Aligned_cols=181 Identities=22% Similarity=0.336 Sum_probs=147.4
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (341)
+.++.++++++.+++++|.+ |+++++|+++++++||++++++|+....+.++.........+...+..+..+..+..
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 56889999999999999999 999999999999999999999998866665555555555666666777777777777
Q ss_pred EEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhhhhhh
Q 019399 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (341)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ 177 (341)
..+++|..+|+.....|+.+ .+|.+.+++++++|||++|++++++
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~l---------------------------------- 125 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQVV---------------------------------- 125 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHHH----------------------------------
Confidence 78899999999999999998 8999999999999999999863221
Q ss_pred hhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCceEEe
Q 019399 178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI 257 (341)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~ 257 (341)
+... ..+..++++++.+++++
T Consensus 126 ------------------------~~~~-----------------------------------~~~~~~~~~~~~~i~~~ 146 (494)
T TIGR02938 126 ------------------------ANQK-----------------------------------LLIESVVDAAPVAFVLL 146 (494)
T ss_pred ------------------------HHHH-----------------------------------HHHHHHHhcccceEEEE
Confidence 0000 01566888899999999
Q ss_pred CCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCCh
Q 019399 258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298 (341)
Q Consensus 258 d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~ 298 (341)
|.+ ++++++|++|++++|+...+..+..+..+.+|+..
T Consensus 147 d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 184 (494)
T TIGR02938 147 DPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWR 184 (494)
T ss_pred cCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhh
Confidence 998 99999999999999999888877766555554433
No 7
>PRK13560 hypothetical protein; Provisional
Probab=99.75 E-value=8e-17 Score=158.11 Aligned_cols=219 Identities=10% Similarity=0.050 Sum_probs=149.1
Q ss_pred HHHH-HHHHhhCCCeEEEEcCCCCCcc--EEEecHHHHHhcCCChhhhcCCC--CCcccCCCCCHHHH-------HHHHH
Q 019399 17 TLWV-HEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTI-------MEIRE 84 (341)
Q Consensus 17 ~~~~-~~~~~~~~~~i~~~d~~~~~~~--i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~-------~~~~~ 84 (341)
.+++ +.+++++|.+++.++.+ +++. +.++++++..++|+.+.++++.. +..+.+|++..... ..+..
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 4455 89999999999998876 1133 33477777788888777765532 33455666554332 12222
Q ss_pred HHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhh
Q 019399 85 AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCR 164 (341)
Q Consensus 85 ~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (341)
++..+.....++++.++||+ |+.+...|.++ .+|.. .+.|+..|||++|++++++
T Consensus 145 ~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae~~l--------------------- 199 (807)
T PRK13560 145 ALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAEERI--------------------- 199 (807)
T ss_pred HhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHHHHH---------------------
Confidence 33344556678888999996 56667778877 67765 6899999999999973332
Q ss_pred hhhccchhhhhhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHH
Q 019399 165 REVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLY 244 (341)
Q Consensus 165 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 244 (341)
+.. ...+.
T Consensus 200 -------------------------------------~~~-----------------------------------~~~l~ 207 (807)
T PRK13560 200 -------------------------------------DEA-----------------------------------LHFLQ 207 (807)
T ss_pred -------------------------------------HHH-----------------------------------HHHHH
Confidence 000 01166
Q ss_pred HHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhh---hhcc
Q 019399 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRAS---MHRR 321 (341)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~---~~r~ 321 (341)
.+++++++++++.|.+ |+++++|+++++++||+++|++|+++..+.++.............+..+..... ..++
T Consensus 208 ~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 284 (807)
T PRK13560 208 QLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNK 284 (807)
T ss_pred HHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcC
Confidence 7899999999999998 999999999999999999999999998887665544443444444444433322 3345
Q ss_pred cccceeEEEEEecce
Q 019399 322 IKAHFGIFFTYHPSV 336 (341)
Q Consensus 322 ~~~~~~~~~~~~p~~ 336 (341)
+|...|+++..++..
T Consensus 285 dG~~~~~~~~~~~~~ 299 (807)
T PRK13560 285 DGRTRPVDVIFNHAE 299 (807)
T ss_pred CCCEEEEEEEecceE
Confidence 666666666655543
No 8
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.72 E-value=4.8e-16 Score=152.43 Aligned_cols=210 Identities=20% Similarity=0.248 Sum_probs=152.7
Q ss_pred HHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCC----CcEE
Q 019399 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEV 94 (341)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~ 94 (341)
.+..+++.++.+++++|.+ |.++++|+++++++||++++++|++...+.++.........+......+. .+..
T Consensus 13 ~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (799)
T PRK11359 13 IFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSR 89 (799)
T ss_pred hHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccce
Confidence 4566889999999999999 99999999999999999999999987777666544333333333333222 2344
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhhh
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~ 174 (341)
+++..++||..+|+.+...++.. .|. .+++++.+|||++++.++..
T Consensus 90 e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~~~------------------------------- 135 (799)
T PRK11359 90 ELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKEQT------------------------------- 135 (799)
T ss_pred eeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHHHH-------------------------------
Confidence 77888999999999998888743 555 45788899999887641110
Q ss_pred hhhhhccccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCce
Q 019399 175 LDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSF 254 (341)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i 254 (341)
+. +..++++++.++
T Consensus 136 ---------------------------~~---------------------------------------~~~~~~~~~~~i 149 (799)
T PRK11359 136 ---------------------------RQ---------------------------------------LIIAVDHLDRPV 149 (799)
T ss_pred ---------------------------HH---------------------------------------HHHHHhcCCCcE
Confidence 00 334677889999
Q ss_pred EEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccC-CCChHHHHHHhhhhhccCcchhhhhc---ccccceeEEE
Q 019399 255 VLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG-VDTDTTVLYQSSTDKGKHSNRASMHR---RIKAHFGIFF 330 (341)
Q Consensus 255 ~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~~~r---~~~~~~~~~~ 330 (341)
+++|.+ |+++++|+++++++||+.++++|+++..+.+ +.+.......+...+..+..+...++ ++|...|+.+
T Consensus 150 ~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~ 226 (799)
T PRK11359 150 IVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKA 226 (799)
T ss_pred EEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEe
Confidence 999998 9999999999999999999999998876654 55555555666666666555544443 3444455555
Q ss_pred EEec
Q 019399 331 TYHP 334 (341)
Q Consensus 331 ~~~p 334 (341)
...|
T Consensus 227 ~~~~ 230 (799)
T PRK11359 227 SISP 230 (799)
T ss_pred eeee
Confidence 4444
No 9
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.68 E-value=1.1e-15 Score=110.28 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=94.6
Q ss_pred CCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEE
Q 019399 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (341)
Q Consensus 28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (341)
|++++++|.+ |.++++|+++++++|+++++++|+++..+.++.........+.+.+..+..+..+..+..++|..+|
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 6899999999 9999999999999999999999999888888777778888889999888889999999999999999
Q ss_pred EEEEEEEeecCCCCcEEEEEEEEecCch
Q 019399 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (341)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~Dite 135 (341)
+.+++.|+.+ ++|++.+++++++|||+
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 10
>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=99.60 E-value=1.3e-14 Score=105.73 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=96.5
Q ss_pred HhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCC
Q 019399 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (341)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg 103 (341)
|++++++++++|.+ ++++++|+++.+++|++..+++|+++..+.++.........+.+++.++........... +|
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 57899999999999 999999999999999999999999988877777667777888888888777666555544 89
Q ss_pred CeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhh
Q 019399 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (341)
Q Consensus 104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~ 138 (341)
...|+.+++.|+.+ .+|.+.+++++.+|||++|+
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 99999999999999 89999999999999999985
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=99.59 E-value=2.7e-14 Score=104.64 Aligned_cols=112 Identities=23% Similarity=0.366 Sum_probs=93.3
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcE-EEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL 96 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~ 96 (341)
++++.++++++++++++|.+ |+++++|+++++++|+++++++|++...+.++++.......+...+..+.... ...
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 99999999999999999999999998888776655456666777776665533 444
Q ss_pred EEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecC
Q 019399 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (341)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Di 133 (341)
....++|+.+|+.+...|+.+ .+|.+.+++++++||
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 445569999999999999999 888899999999997
No 12
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.46 E-value=9.2e-13 Score=128.77 Aligned_cols=124 Identities=15% Similarity=0.199 Sum_probs=106.3
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
+..++++.++++++++++++|.+ |+++++|+++++++|++.++++|+++..+.++.............+..+.....
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 45667889999999999999999 999999999999999999999999877776655444444455566667777888
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~ 142 (341)
+.....++|..+|+.++..|+.+ .+|...+++++++|||++|++++.
T Consensus 229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~ 275 (779)
T PRK11091 229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQDA 275 (779)
T ss_pred EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHHHH
Confidence 88888899999999999999998 899999999999999999997443
No 13
>PRK13559 hypothetical protein; Provisional
Probab=99.42 E-value=5e-12 Score=112.48 Aligned_cols=124 Identities=38% Similarity=0.683 Sum_probs=105.2
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEE
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (341)
....+..++++++++++++|.+..++.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..+
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 45668889999999999999742237899999999999999999999998777766555555566667777777777788
Q ss_pred EEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
....+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|+++
T Consensus 121 ~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e 164 (361)
T PRK13559 121 LLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVR 164 (361)
T ss_pred EEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhH
Confidence 8888999999999999999998 8999999999999999999863
No 14
>PRK13557 histidine kinase; Provisional
Probab=99.36 E-value=1.6e-11 Score=115.28 Aligned_cols=127 Identities=37% Similarity=0.688 Sum_probs=109.5
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
.....|..++++++.+++++|.+..+|+++|+|++|++++||+.++++|+++..+.++.........+...+..+..+..
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 45678899999999999999963223899999999999999999999999988777776666666777777777777778
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~ 142 (341)
+.+..+++|..+|+.+...|+.+ .+|.+.+++++..|||+++++++.
T Consensus 107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~ 153 (540)
T PRK13557 107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDA 153 (540)
T ss_pred EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHH
Confidence 88888899999999999999998 899999999999999999987543
No 15
>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=99.28 E-value=8.9e-12 Score=91.11 Aligned_cols=92 Identities=16% Similarity=0.124 Sum_probs=74.2
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhh---h
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRAS---M 318 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~---~ 318 (341)
+++.++++++++++++|.+ |+|+++|+++++++||++++++|+++..+.++++.......+...+..+..... .
T Consensus 2 ~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (113)
T PF00989_consen 2 RYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVR 78 (113)
T ss_dssp HHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEE
T ss_pred HHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEE
Confidence 4788999999999999998 999999999999999999999999999999888776677777777766554322 2
Q ss_pred hcc-cccceeEEEEEecce
Q 019399 319 HRR-IKAHFGIFFTYHPSV 336 (341)
Q Consensus 319 ~r~-~~~~~~~~~~~~p~~ 336 (341)
.+. +++..|+.+..+|..
T Consensus 79 ~~~~~g~~~~~~~~~~~~~ 97 (113)
T PF00989_consen 79 FRLRDGRPRWVEVRASPVR 97 (113)
T ss_dssp EEETTSCEEEEEEEEEEEE
T ss_pred EEecCCcEEEEEEEEEEEE
Confidence 333 677777777777764
No 16
>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=99.24 E-value=1.5e-11 Score=88.45 Aligned_cols=83 Identities=18% Similarity=0.296 Sum_probs=67.9
Q ss_pred CCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhh---hhccccccee
Q 019399 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRAS---MHRRIKAHFG 327 (341)
Q Consensus 251 ~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~---~~r~~~~~~~ 327 (341)
|+|++++|.+ |+|+++|++|++++||++++++|+++..+.+++........+.+++..+..+.. ..+++|...|
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 5799999998 999999999999999999999999999999988888889999999987776644 3456666777
Q ss_pred EEEEEecce
Q 019399 328 IFFTYHPSV 336 (341)
Q Consensus 328 ~~~~~~p~~ 336 (341)
+.++++|..
T Consensus 78 ~~~~~~~i~ 86 (104)
T PF13426_consen 78 VEVSASPIR 86 (104)
T ss_dssp EEEEEEEEE
T ss_pred EEEEEEEEE
Confidence 777776653
No 17
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.24 E-value=1.6e-10 Score=111.05 Aligned_cols=124 Identities=39% Similarity=0.703 Sum_probs=105.2
Q ss_pred HHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEE
Q 019399 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (341)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (341)
.++.+++.++.++++.|...+++.++++|+++++++||++++++|+++..+.++.........+...+..+.....+.+.
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 45678999999999998532238999999999999999999999998777766665555556666777777788888999
Q ss_pred EcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhccccc
Q 019399 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (341)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~ 143 (341)
.+++|..+|+.+...|+.+ ..|.+.+++++.+|||++|++++++
T Consensus 229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L 272 (665)
T PRK13558 229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELAL 272 (665)
T ss_pred ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHH
Confidence 9999999999999999998 8999999999999999999986554
No 18
>PRK10060 RNase II stability modulator; Provisional
Probab=99.14 E-value=1e-09 Score=105.07 Aligned_cols=123 Identities=14% Similarity=0.182 Sum_probs=95.9
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCccc-CCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
...+++.+++.++++++++|.+ |+++++|+++++++||+.++++|+++..+. ++.........+...+..+..+..
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 3456778999999999999999 999999999999999999999999865444 343334444556666777888888
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCc-EEEEEEEEecCchhhhccccc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGR-ATHFVAVQVPIVSRKHMRNSG 143 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~-~~~~~~~~~Dite~k~~~~~~ 143 (341)
+....+++|..+|+.....+ .. ..|. ..+++++.+|||+++++++++
T Consensus 186 e~~~~~~~G~~~~~~~~~~~-~~-~~g~~~~~~i~~~~DITe~k~~e~~l 233 (663)
T PRK10060 186 ERWIKTRKGQRLFLFRNKFV-HS-GSGKNEIFLICSGTDITEERRAQERL 233 (663)
T ss_pred EEEEEeCCCCEEEEEeeeEE-Ec-CCCCceEEEEEEEEechHHHHHHHHH
Confidence 98999999998887655443 33 3443 456788899999999886655
No 19
>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=99.14 E-value=1.7e-09 Score=78.07 Aligned_cols=118 Identities=21% Similarity=0.347 Sum_probs=90.2
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcC-CCcEEEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (341)
+.++.+++.++.+++++|.+ +.++++|+++.+++|++..+++|+....+.++.........+......+ .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 45678899999999999999 9999999999999999999999987666555554444444444444422 2233444
Q ss_pred EEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
.+...+|...|+.....|+.. +|...+++++..|||++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~ 121 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAE 121 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHH
Confidence 445788999999888888863 677888999999999998863
No 20
>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=99.11 E-value=6.9e-10 Score=77.75 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=71.0
Q ss_pred EEEecHHHHHhcCCChhhhcCCC----CCcccCCCCCHHHHHHHHH-HHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeec
Q 019399 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (341)
Q Consensus 43 i~~~N~~~~~~~G~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~ 117 (341)
++++|+.+++++||+++++ +.. +..+.+|++.......+.. ....+..+..++++++++|..+|+.....++.+
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 5799999999999999998 655 5567889988888888888 677777899999999999999999999999998
Q ss_pred CCCCcEEEEEEEE
Q 019399 118 KEDGRATHFVAVQ 130 (341)
Q Consensus 118 ~~~g~~~~~~~~~ 130 (341)
++|++..++|+.
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999998874
No 21
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.01 E-value=3.8e-09 Score=103.95 Aligned_cols=120 Identities=19% Similarity=0.307 Sum_probs=99.5
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccC-CCCCHHHHHHHHHHHHcCCCcEEE
Q 019399 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEVN 95 (341)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~e 95 (341)
.+.+..++++++.+++++|.+ |+++++|+++++++||+.++++|+....+.+ +.........+...+..+..+..+
T Consensus 135 ~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 211 (799)
T PRK11359 135 TRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDE 211 (799)
T ss_pred HHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence 445667899999999999999 9999999999999999999999998665543 444444444555666666667778
Q ss_pred EEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
.+..+++|..+|+.+...|+.+ .+|.+.+++++.+|||++++++
T Consensus 212 ~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e 255 (799)
T PRK11359 212 FLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIR 255 (799)
T ss_pred eEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHH
Confidence 8888999999999999999998 7899999999999999999874
No 22
>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=98.94 E-value=1.5e-09 Score=78.80 Aligned_cols=87 Identities=17% Similarity=0.103 Sum_probs=72.7
Q ss_pred hhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhh--ccccc
Q 019399 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMH--RRIKA 324 (341)
Q Consensus 247 ~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~--r~~~~ 324 (341)
+++++++++++|.+ ++|+++|+++++++|++.++++|+++.++.++.........+.+++.++....... ...+.
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLRDGE 77 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECTTSC
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEeecCC
Confidence 46789999999999 99999999999999999999999999999888889999999999999887665422 22556
Q ss_pred ceeEEEEEecce
Q 019399 325 HFGIFFTYHPSV 336 (341)
Q Consensus 325 ~~~~~~~~~p~~ 336 (341)
..|..+.++|..
T Consensus 78 ~~~~~~~~~Pi~ 89 (110)
T PF08448_consen 78 ERWFEVSISPIF 89 (110)
T ss_dssp EEEEEEEEEEEE
T ss_pred cEEEEEEEEEeE
Confidence 677777777763
No 23
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.91 E-value=8.9e-08 Score=65.67 Aligned_cols=102 Identities=21% Similarity=0.395 Sum_probs=81.6
Q ss_pred CCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEE
Q 019399 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (341)
Q Consensus 28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (341)
+.+++++|.+ +.++++|+.+++++|++..+++|.....+.++.........+......+.....+......+|...|
T Consensus 2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (103)
T cd00130 2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIW 78 (103)
T ss_pred CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEE
Confidence 5788999999 9999999999999999999999988666666665555555555555555556677777778899999
Q ss_pred EEEEEEEeecCCCCcEEEEEEEEecC
Q 019399 108 MLFKMSLVFGKEDGRATHFVAVQVPI 133 (341)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~Di 133 (341)
+.+...++.+ ..|...+++++..||
T Consensus 79 ~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 79 VLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEec-CCCCEEEEEEEEecC
Confidence 9999999887 677888888888875
No 24
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.89 E-value=2.6e-08 Score=71.86 Aligned_cols=106 Identities=21% Similarity=0.291 Sum_probs=71.7
Q ss_pred HHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEE
Q 019399 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (341)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (341)
+..++++++.++.++|.+ +++.++|+++.++++..+.+ +|++...+.++...+... .+.+.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~-~~i~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLK-KIIEQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHH-HHHHHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHH-HHHHHHHcCCCceEEEEe-
Confidence 357899999999999999 99999999999999987654 799987776543322333 333444555543333333
Q ss_pred cCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCc
Q 019399 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (341)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit 134 (341)
..+|. |+.+...|+++ ++|...|++.++.|||
T Consensus 75 ~~~~~--~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGGR--WYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETTE--EEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCCE--EEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 24444 67889999999 8999999999999997
No 25
>PF12860 PAS_7: PAS fold
Probab=98.82 E-value=4.2e-08 Score=71.91 Aligned_cols=104 Identities=21% Similarity=0.357 Sum_probs=70.2
Q ss_pred HhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhh-cCCCCCccc---------CCCCCHHHHHHHHHHHHcCCCcE
Q 019399 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (341)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (341)
+++++.|++++|.+ ++++++|+.|.+++|++.+.+ .|.+...+. .+.....................
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 999999999999999998876 676644332 11121222222222233333333
Q ss_pred EEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
.+ ....||. |+.+...|.. +| |++.++.|||+++++|
T Consensus 78 ~~--~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 78 FE--LRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred eE--EECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhc
Confidence 33 3456776 6677788883 45 6778999999999874
No 26
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.82 E-value=6.9e-08 Score=87.30 Aligned_cols=69 Identities=20% Similarity=0.254 Sum_probs=62.3
Q ss_pred CCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhhcccccceeEEEE
Q 019399 263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMHRRIKAHFGIFFT 331 (341)
Q Consensus 263 d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~ 331 (341)
|.+|+|+.+.+.++.||+++||+|+.+-+|+|+.|-..+.......+.+|......||..-+.|+..|.
T Consensus 283 DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWl 351 (768)
T KOG3558|consen 283 DMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWL 351 (768)
T ss_pred ceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEE
Confidence 489999999999999999999999999999999999999999999999999999999977766555444
No 27
>PRK13557 histidine kinase; Provisional
Probab=98.78 E-value=1.8e-08 Score=94.67 Aligned_cols=93 Identities=29% Similarity=0.580 Sum_probs=76.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhh---h
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASM---H 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 319 (341)
|..++++++.+|+++|.+..||+|+|+|++|++++||+.+|++|+++..+.+|++.......++..+..+..+... +
T Consensus 32 ~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 (540)
T PRK13557 32 FFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEILNY 111 (540)
T ss_pred HHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEE
Confidence 7889999999999999754569999999999999999999999999999988888888888888888777665443 4
Q ss_pred cccccceeEEEEEecc
Q 019399 320 RRIKAHFGIFFTYHPS 335 (341)
Q Consensus 320 r~~~~~~~~~~~~~p~ 335 (341)
+++|...|+.+...|.
T Consensus 112 ~~~G~~~~~~~~~~~i 127 (540)
T PRK13557 112 RKDGSSFWNALFVSPV 127 (540)
T ss_pred eCCCCEEEEEEEEEEe
Confidence 5566666666666554
No 28
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.76 E-value=6.9e-08 Score=86.04 Aligned_cols=162 Identities=20% Similarity=0.184 Sum_probs=116.1
Q ss_pred HHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcC
Q 019399 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKK 101 (341)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 101 (341)
.+++..++++++++.. ..+..+|..+..+.+-....++|+....+.++...+... .+...........+
T Consensus 5 ~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~~ 73 (560)
T COG3829 5 GILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKLK 73 (560)
T ss_pred hhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeecc
Confidence 4788999999999998 899999999999999888888898777665544332221 12222222222222
Q ss_pred CCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhhhhhhhhcc
Q 019399 102 DGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLAL 181 (341)
Q Consensus 102 dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~ 181 (341)
+ ...+.+...|+. +.++++|++.++.|+++....
T Consensus 74 -~-~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~------------------------------------------ 107 (560)
T COG3829 74 -V-KRIVVVGKTPVD--EQGRVVGVLEVFLDISEALEL------------------------------------------ 107 (560)
T ss_pred -c-eeEEEcCCceee--cCCceeeeehhhhhhHHHHHH------------------------------------------
Confidence 2 333334445554 588999999999999985542
Q ss_pred ccCCcCccccchhhhhhHHHHHHHhhhhchhheeecccccCCceEeeeecCCCCccchhchHHHHhhccCCceEEeCCCC
Q 019399 182 DSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHL 261 (341)
Q Consensus 182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~i~d~~~ 261 (341)
.+....... ..|..+++.+.++++++|.+
T Consensus 108 ---------------~~~~l~~~~-----------------------------------~~l~~il~~~~~~l~vvD~~- 136 (560)
T COG3829 108 ---------------IEENLRQLR-----------------------------------QRLEAILDSIDDGLLVVDED- 136 (560)
T ss_pred ---------------HHHHHHHHH-----------------------------------HHHHHHHhhccCceEEEcCC-
Confidence 000000000 11677889999999999999
Q ss_pred CCCCEEEecHHHHHHhCCCcccccCCcccccc
Q 019399 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (341)
Q Consensus 262 ~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~ 293 (341)
|.++++|+++.+++|++.++++|+++.++.
T Consensus 137 --G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~ 166 (560)
T COG3829 137 --GIIIYYNKAYAKLLGLSPEEVLGKHLLDVV 166 (560)
T ss_pred --CcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence 999999999999999999999999988776
No 29
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.72 E-value=2.8e-07 Score=87.70 Aligned_cols=121 Identities=14% Similarity=0.181 Sum_probs=94.4
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCC-cEE
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV 94 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~ 94 (341)
....++.++++++++++++|.+ +.++++|+++++++|+++++++|++...+.++.. .....+...+..+.. ...
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 3456778899999999999999 9999999999999999999999998776655432 223344444444433 334
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhccccc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~ 143 (341)
+.....++|... +.+...|+.+ .+|.+.+++++++|||+++++++++
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 566666777766 8889999998 8999999999999999999875443
No 30
>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=98.72 E-value=1.2e-07 Score=83.06 Aligned_cols=109 Identities=12% Similarity=0.076 Sum_probs=82.7
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
+..+.++.++++++++++++|.+ |+++++|+++++++|+++++.+|+++..+..+ .. +...+..+.. ..
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 45667889999999999999999 99999999999999999999999886665432 22 2333333222 22
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
......++|...|+.+...|+.+ . + +++++.|||++++++
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~~ 111 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRLE 111 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHHH
Confidence 34455578888899999999865 2 2 678889999998863
No 31
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.69 E-value=1.3e-07 Score=83.81 Aligned_cols=111 Identities=14% Similarity=0.136 Sum_probs=83.3
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (341)
..+..++++++++++++|.+ |+++++|+++++++|++.++++|+++..+.++.. .....+...+..+..+.....
T Consensus 7 ~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 81 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEV 81 (348)
T ss_pred chHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccce
Confidence 45678999999999999999 9999999999999999999999998776654332 112233444544444433333
Q ss_pred EEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
....+|..+|+.++..|+.. .+++..++|+|++++.
T Consensus 82 ~~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~ 117 (348)
T PRK11073 82 TLVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRL 117 (348)
T ss_pred EEEECCceEEEEEEEEEccC------ceeEEEEechhHHHHH
Confidence 44568999999999999853 2456778999998876
No 32
>PRK10060 RNase II stability modulator; Provisional
Probab=98.69 E-value=5.4e-08 Score=93.28 Aligned_cols=81 Identities=10% Similarity=-0.031 Sum_probs=62.8
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCcccccc-CCCChHHHHHHhhhhhccCcchhhhhcc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN-GVDTDTTVLYQSSTDKGKHSNRASMHRR 321 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 321 (341)
+..+++.++++|+++|.+ |+|+++|++|++++||+.++++|+++..++ +|++.......+...+..+..+..+++.
T Consensus 113 ~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 189 (663)
T PRK10060 113 AEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWI 189 (663)
T ss_pred HHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEE
Confidence 455788899999999999 999999999999999999999999986554 5555555566677777777766554444
Q ss_pred cccce
Q 019399 322 IKAHF 326 (341)
Q Consensus 322 ~~~~~ 326 (341)
.+++|
T Consensus 190 ~~~~G 194 (663)
T PRK10060 190 KTRKG 194 (663)
T ss_pred EeCCC
Confidence 44444
No 33
>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=98.66 E-value=7.9e-07 Score=64.33 Aligned_cols=101 Identities=17% Similarity=0.262 Sum_probs=82.3
Q ss_pred EEEcCCCCCccEEEecHH-HHHhcCCChhhhcCCCCCcccCCCCCHH-HHHHHHHHHHcCCCcEEEEEEEcCCCCeEEEE
Q 019399 32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (341)
Q Consensus 32 ~~~d~~~~~~~i~~~N~~-~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (341)
...+.+ |+++++.+. ...++||.++|++|+.+..+.+|++... ........+..|.....-+++..++|..+|+.
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 446677 999999999 5999999999999999999999998885 66777888888887777799999999999999
Q ss_pred EEEEEeecCCCCcEEEEEEEEecCch
Q 019399 110 FKMSLVFGKEDGRATHFVAVQVPIVS 135 (341)
Q Consensus 110 ~~~~~~~~~~~g~~~~~~~~~~Dite 135 (341)
..+.++.+|.++++..++++-.=|++
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 99999887456777777776655544
No 34
>PRK13559 hypothetical protein; Provisional
Probab=98.63 E-value=1.1e-07 Score=84.54 Aligned_cols=93 Identities=32% Similarity=0.549 Sum_probs=72.8
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhh---h
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASM---H 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 319 (341)
+..++++++++++++|.+.+++.|+++|++|++++||+.++++|+++..+.++.+.......+...+..+..+... .
T Consensus 45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 124 (361)
T PRK13559 45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNY 124 (361)
T ss_pred HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEE
Confidence 7778999999999999864458999999999999999999999999988877777777777777777777665443 3
Q ss_pred cccccceeEEEEEecc
Q 019399 320 RRIKAHFGIFFTYHPS 335 (341)
Q Consensus 320 r~~~~~~~~~~~~~p~ 335 (341)
+++|...|+.+...|.
T Consensus 125 ~~dG~~~~~~~~~~~i 140 (361)
T PRK13559 125 RKDGEPFWNALHLGPV 140 (361)
T ss_pred cCCCCEEEEEEEEEEE
Confidence 4555555665555554
No 35
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.57 E-value=4.8e-07 Score=80.50 Aligned_cols=121 Identities=26% Similarity=0.531 Sum_probs=95.4
Q ss_pred HHHHHHHhhCC--C-eEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCC--CCcccCCCCCHHHHHHHHHHHHcCCCc
Q 019399 18 LWVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPI 92 (341)
Q Consensus 18 ~~~~~~~~~~~--~-~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (341)
.+++.++..+. + .+++-+++.-|..++|+|+.||++.||.+.|++.++ +.+.++..........+.+.+..-..-
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 34455554443 3 344444443346789999999999999999999886 555666666666777788888776777
Q ss_pred EEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
.++.....++.+..|+.+.+.|+++ +...++-+++.+.|||..|+-
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 7888888999999999999999999 899999999999999999874
No 36
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=98.50 E-value=1.2e-07 Score=66.29 Aligned_cols=64 Identities=17% Similarity=0.121 Sum_probs=48.9
Q ss_pred EEEecHHHHHHhCCCcccccCCc----cccccCCCChHHHHHHhhh-hhccCcchhhhhcccccceeEEE
Q 019399 266 MVYASDAFLKLTGYDRNEVVGQN----CRFLNGVDTDTTVLYQSST-DKGKHSNRASMHRRIKAHFGIFF 330 (341)
Q Consensus 266 i~~~N~~~~~~~Gy~~~e~~G~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~r~~~~~~~~~~ 330 (341)
|+|+|+.+++|+||+++++ |.. +..++||++...+.+.+.. +...+..+..++|..+++|...|
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~w 69 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRW 69 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEE
Confidence 6899999999999999999 765 7789999999999999999 77778788777776666554433
No 37
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.48 E-value=7e-06 Score=73.60 Aligned_cols=112 Identities=17% Similarity=0.349 Sum_probs=83.0
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
...+.++.+++.+.++++++|.+ |.++++|.++..++|++.++++|++...+..... .....+++..+.+...
T Consensus 114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~----~s~~l~vl~~~kp~~~ 186 (560)
T COG3829 114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGE----DSTLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccC----CceehhhhhcCCccee
Confidence 45678899999999999999999 9999999999999999999999998665541110 0123455666666554
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
.......+.. .....|+.. +|.+.|.+++.+|+++.+.+
T Consensus 187 ~~~~~~~~~~----i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l 225 (560)
T COG3829 187 VVQTYNGNKI----IVNVAPVYA--DGQLIGVVGISKDVSELERL 225 (560)
T ss_pred eeeeecCCce----eEeeccEec--CCcEEEEEEeecchHHHHHH
Confidence 4433322222 355667764 78999999999999998775
No 38
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.39 E-value=5.1e-06 Score=69.92 Aligned_cols=115 Identities=15% Similarity=0.241 Sum_probs=88.4
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
....++..++..+.+|++..|.. |+++.+|..+.+++|.+.++++|++...+..-.+.- .+.+.+....+...
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---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTY----TFEDLVEKNDSLLL 180 (459)
T ss_pred HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccce----eHHHHHhcCCcEEE
Confidence 44567888999999999999999 999999999999999999999999866554433322 23333444443333
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
+. ...++...+.+..+.++. ++|-+.|++.+..|+|++.+.|
T Consensus 181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~e 222 (459)
T COG5002 181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKVE 222 (459)
T ss_pred ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHHH
Confidence 32 236676777888888888 8999999999999999998863
No 39
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.38 E-value=5.5e-07 Score=58.24 Aligned_cols=43 Identities=21% Similarity=0.372 Sum_probs=35.4
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCcccc
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRF 291 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~ 291 (341)
.++.++++++.||+++| + ++|+++|+++++++||+ +.|+.+..
T Consensus 2 ~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~~ 44 (64)
T PF13188_consen 2 RYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIGQ 44 (64)
T ss_dssp HHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHHC
T ss_pred HHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHHH
Confidence 37889999999999999 8 89999999999999999 56665543
No 40
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.26 E-value=1.7e-06 Score=85.12 Aligned_cols=90 Identities=10% Similarity=-0.026 Sum_probs=72.1
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhh---h
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASM---H 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~---~ 319 (341)
+..++++++++|++.|.+ |+|+++|+++++++||+.++++|+++..+.+++............+..+..+... .
T Consensus 157 l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 233 (779)
T PRK11091 157 LRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLD 233 (779)
T ss_pred HHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEE
Confidence 778999999999999999 9999999999999999999999999999988877776666666676666554332 2
Q ss_pred cccccceeEEEEEecc
Q 019399 320 RRIKAHFGIFFTYHPS 335 (341)
Q Consensus 320 r~~~~~~~~~~~~~p~ 335 (341)
+++|...|+.+...|.
T Consensus 234 ~~~G~~~~~~~~~~pi 249 (779)
T PRK11091 234 YPDGRKACFELRKVPF 249 (779)
T ss_pred cCCCCEEEEEEEeeeE
Confidence 3456666666666654
No 41
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.26 E-value=7e-06 Score=76.18 Aligned_cols=110 Identities=14% Similarity=0.138 Sum_probs=78.4
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
+....+..++++++++++++|.+ |+++++|+++++++|++.++++|+++..+.+... +.+.+..+.....
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 45667889999999999999999 9999999999999999999999998777655432 2333444433111
Q ss_pred EEEEEcCCCCeEEEEEEEEEee--cCCCCc--EEEEEEEEecCchhhh
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRKH 138 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~--~~~~g~--~~~~~~~~~Dite~k~ 138 (341)
. .....+|..++ +...|+. + ++|. ..|.+.+++|+++..+
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 12234565544 5567775 4 4554 3799999999987643
No 42
>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=98.25 E-value=1.1e-06 Score=81.37 Aligned_cols=90 Identities=20% Similarity=0.280 Sum_probs=68.9
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhhc-
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMHR- 320 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~r- 320 (341)
.+..++++++.++++.|.+ ++++++|++|++++||++++++|++...+.++.........+...+..+..+...++
T Consensus 5 ~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (494)
T TIGR02938 5 AYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLN 81 (494)
T ss_pred HHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceeec
Confidence 3788999999999999999 999999999999999999999999887777776666667777777766666544333
Q ss_pred --ccccceeEEEEEec
Q 019399 321 --RIKAHFGIFFTYHP 334 (341)
Q Consensus 321 --~~~~~~~~~~~~~p 334 (341)
++|...|......|
T Consensus 82 ~~~~g~~~~~~~~~~~ 97 (494)
T TIGR02938 82 RRKDGELYLAELTVAP 97 (494)
T ss_pred cCCCccchhhheeeEE
Confidence 34444444444444
No 43
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.24 E-value=5.2e-06 Score=75.77 Aligned_cols=107 Identities=13% Similarity=0.148 Sum_probs=73.5
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
...++++.++++++++++++|.+ |+++++|+++++++|++.++..|+++..+..+. ..... +... ....
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 45678899999999999999999 999999999999999999999998865544322 11111 1111 1112
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
.......+|. ++.+...|..+ + ..+.+++|||++++++
T Consensus 164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e 201 (430)
T PRK11006 164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLE 201 (430)
T ss_pred CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHH
Confidence 2233344554 45556666643 2 2567889999998863
No 44
>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=98.24 E-value=1.8e-06 Score=62.50 Aligned_cols=65 Identities=18% Similarity=0.126 Sum_probs=55.1
Q ss_pred CCCEEEecHH-HHHHhCCCcccccCCccccccCCCChHH-HHHHhhhhhccCcchhhhhccccccee
Q 019399 263 DMPMVYASDA-FLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQSSTDKGKHSNRASMHRRIKAHFG 327 (341)
Q Consensus 263 d~~i~~~N~~-~~~~~Gy~~~e~~G~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~r~~~~~~~ 327 (341)
||+|+++.++ ...++||.++|++|+.+..++||+|... ..+..++++.+|......||...++|.
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~ 77 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGG 77 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSS
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCc
Confidence 3999999999 6999999999999999999999999997 777888998988876667887777643
No 45
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=98.24 E-value=5.7e-06 Score=59.08 Aligned_cols=65 Identities=18% Similarity=0.238 Sum_probs=55.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKG 310 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~ 310 (341)
+..++++++.+++++|.+ +.++++|+++++++|++..+++|.++..+.++.........+...+.
T Consensus 5 ~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (124)
T TIGR00229 5 YRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLE 69 (124)
T ss_pred HHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHc
Confidence 667889999999999998 99999999999999999999999988887777766666555666555
No 46
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.22 E-value=2.9e-06 Score=75.12 Aligned_cols=88 Identities=13% Similarity=-0.018 Sum_probs=65.8
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcch---hhhh
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR---ASMH 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~~~~ 319 (341)
+..+++++++|++++|.+ |+|+++|+++++++||+.++++|+++.++.++... ....+...+..+..+ ...+
T Consensus 9 ~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 83 (348)
T PRK11073 9 AGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSL--NIELMRESLQAGQGFTDNEVTL 83 (348)
T ss_pred HHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchh--hHHHHHHHHHcCCcccccceEE
Confidence 778999999999999999 99999999999999999999999999888754321 223344444444332 2244
Q ss_pred cccccceeEEEEEecc
Q 019399 320 RRIKAHFGIFFTYHPS 335 (341)
Q Consensus 320 r~~~~~~~~~~~~~p~ 335 (341)
.++|+..|+.++.+|.
T Consensus 84 ~~~g~~~~~~~~~~~~ 99 (348)
T PRK11073 84 VIDGRSHILSLTAQRL 99 (348)
T ss_pred EECCceEEEEEEEEEc
Confidence 5677777777777665
No 47
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.17 E-value=5.3e-06 Score=80.10 Aligned_cols=93 Identities=29% Similarity=0.480 Sum_probs=72.5
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhh---
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMH--- 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 319 (341)
+..+++.++.++++.|...+++.|+++|+++++++||++++++|+++..+.+++........+...+..+..+...+
T Consensus 150 ~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 229 (665)
T PRK13558 150 KERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNY 229 (665)
T ss_pred HHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEE
Confidence 45688899999999986545699999999999999999999999999888888777777777777777666654443
Q ss_pred cccccceeEEEEEecc
Q 019399 320 RRIKAHFGIFFTYHPS 335 (341)
Q Consensus 320 r~~~~~~~~~~~~~p~ 335 (341)
+++|...|+.+...|.
T Consensus 230 ~~dG~~~~~~~~~~pi 245 (665)
T PRK13558 230 RKDGSTFWNQVDIAPI 245 (665)
T ss_pred CCCCCEEEEEEEEEEE
Confidence 4555555666655554
No 48
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.16 E-value=5.4e-05 Score=72.53 Aligned_cols=49 Identities=14% Similarity=0.133 Sum_probs=43.8
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccC
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~ 294 (341)
+...++++.+||+++|.+ |+|+++|+++++++|++.++++|+++..++.
T Consensus 205 ~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~ 253 (638)
T PRK11388 205 LNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLT 253 (638)
T ss_pred HHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence 344777888999999999 9999999999999999999999999887764
No 49
>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=98.14 E-value=7.5e-06 Score=71.71 Aligned_cols=87 Identities=13% Similarity=0.098 Sum_probs=62.4
Q ss_pred chHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhhc
Q 019399 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMHR 320 (341)
Q Consensus 241 ~~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~r 320 (341)
..+..++++++++++++|.+ |+|+++|++|++++||++++++|+++..+.++++ ....+..... +.+.. ...
T Consensus 6 ~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~---~~~~l~~~~~-~~~~~-~~~ 77 (333)
T TIGR02966 6 SRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE---FVEYLAAGRF-SEPLE-LPS 77 (333)
T ss_pred HHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH---HHHHHHhccc-CCCeE-eec
Confidence 34788999999999999999 9999999999999999999999999888776532 2222222222 22211 222
Q ss_pred ccccceeEEEEEecc
Q 019399 321 RIKAHFGIFFTYHPS 335 (341)
Q Consensus 321 ~~~~~~~~~~~~~p~ 335 (341)
+.+...|+.+...|.
T Consensus 78 ~~~~~~~~~~~~~p~ 92 (333)
T TIGR02966 78 PINSERVLEIRIAPY 92 (333)
T ss_pred CCCCceEEEEEEEEc
Confidence 455667777776664
No 50
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.10 E-value=7.3e-06 Score=52.90 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.3
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCC
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~ 66 (341)
++++.++++++.+++++| + ++++++|+++++++||+ ..|+..
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence 468899999999999999 8 89999999999999998 455554
No 51
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.04 E-value=1.9e-05 Score=53.64 Aligned_cols=60 Identities=17% Similarity=0.205 Sum_probs=49.6
Q ss_pred CCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCc
Q 019399 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHS 313 (341)
Q Consensus 251 ~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~ 313 (341)
+.+++++|.+ +.++++|+++++++|++.++++|.++..+.++++.......+......+.
T Consensus 2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (103)
T cd00130 2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGE 61 (103)
T ss_pred CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCc
Confidence 4688999988 99999999999999999999999998888888777666666666655433
No 52
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.95 E-value=0.00052 Score=54.18 Aligned_cols=119 Identities=24% Similarity=0.359 Sum_probs=83.9
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHH-HHHHHHHH-HHcCCCcE
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREA-IREERPIE 93 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~-~~~~~~~~ 93 (341)
...++..+++..+.+++.+|.+ +.+.++|+.+.+++|++..+..+.....+........ ........ ........
T Consensus 110 ~~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 186 (232)
T COG2202 110 SEERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLE 186 (232)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcc
Confidence 3444788999999999999999 9999999999999999987777766444333222211 11111222 22233466
Q ss_pred EEEEEEcCCCCe-EEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 94 VNLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 94 ~e~~~~~~dg~~-~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
.+.....++|.. .+......+... .|.+..+.....|+++++++
T Consensus 187 ~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 187 IEYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred eEEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence 777888899985 777666666643 68888889999999988764
No 53
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.89 E-value=1.2e-05 Score=57.91 Aligned_cols=89 Identities=10% Similarity=0.089 Sum_probs=57.5
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhhccc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMHRRI 322 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~ 322 (341)
|..++++++.+++++|.+ ++|.+.|+++.++++..+.+ +|+++..+.++...+.....+..+..++........ .
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~-~ 75 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKKIIEQVRSGKEEEFEIVI-P 75 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHHHHHHHHTTSBSEEEEEE-E
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHHHHHHHHcCCCceEEEEe-c
Confidence 356889999999999999 99999999999999987644 799999998765555555555555555543222222 2
Q ss_pred ccceeEEEEEecce
Q 019399 323 KAHFGIFFTYHPSV 336 (341)
Q Consensus 323 ~~~~~~~~~~~p~~ 336 (341)
....++...+.|..
T Consensus 76 ~~~~~~~~~~~P~~ 89 (106)
T PF13596_consen 76 NGGRWYLVRYRPYR 89 (106)
T ss_dssp ETTEEEEEEEEEEE
T ss_pred CCCEEEEEEEEEEE
Confidence 33445556666643
No 54
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=97.85 E-value=0.00015 Score=68.36 Aligned_cols=110 Identities=10% Similarity=0.151 Sum_probs=75.1
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCCh---hhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCc
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (341)
..+.++.++++++++++++|.+ |+++++|+++++++|++. .+.+|.....+.+. ..+...+..+...
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 3455678999999999999999 999999999999998753 34455543333221 1233444444443
Q ss_pred EEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhccc
Q 019399 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (341)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~ 141 (341)
..... ..+|. ++.+...|+.+ +|.+.|++.+++|+|+.+++++
T Consensus 289 ~~~~~--~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~ 331 (542)
T PRK11086 289 RDEEI--NINGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQ 331 (542)
T ss_pred cceEE--EECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHH
Confidence 22211 12343 44566788876 7889999999999999887643
No 55
>PF12860 PAS_7: PAS fold
Probab=97.75 E-value=8.5e-05 Score=54.24 Aligned_cols=43 Identities=23% Similarity=0.347 Sum_probs=38.2
Q ss_pred hhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccc-cCCccccc
Q 019399 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV-VGQNCRFL 292 (341)
Q Consensus 247 ~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~-~G~~~~~l 292 (341)
+++++.||++.|.+ ++++++|++|.+++|++++.+ .|.++..+
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l 44 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDL 44 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHH
Confidence 46789999999999 999999999999999999998 78877544
No 56
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=97.73 E-value=1.3e-05 Score=69.25 Aligned_cols=74 Identities=18% Similarity=0.256 Sum_probs=63.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCC-CChHHHHHHhhhhhccCcchhhhh
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV-DTDTTVLYQSSTDKGKHSNRASMH 319 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 319 (341)
+-.+++...++|-|+|.+ ..|.|||++|++|+||-..|++|+...++... ..+......+..++++|..+.+++
T Consensus 159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~ 233 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEE 233 (775)
T ss_pred HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchH
Confidence 455677888999999988 89999999999999999999999998887653 357788899999999998887744
No 57
>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=97.70 E-value=0.00011 Score=45.39 Aligned_cols=61 Identities=21% Similarity=0.264 Sum_probs=49.9
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhh
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSS 306 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~ 306 (341)
+..+++.++.++++++.. +.+.++|+.+.+++|++..++.|..+..+.++.+.......+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQ 63 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHH
Confidence 455777888999999988 9999999999999999999999988877777777655544443
No 58
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.62 E-value=7.7e-05 Score=69.37 Aligned_cols=53 Identities=17% Similarity=0.096 Sum_probs=48.5
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCC
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT 297 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~ 297 (341)
.+..+++++++||+++|.+ |+|+++|+++++++|++.++++|+++..+++...
T Consensus 81 ~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~ 133 (520)
T PRK10820 81 ALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN 133 (520)
T ss_pred HHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch
Confidence 3778999999999999999 9999999999999999999999999998876544
No 59
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.53 E-value=7.4e-05 Score=68.22 Aligned_cols=51 Identities=18% Similarity=0.151 Sum_probs=46.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCC
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~ 296 (341)
++.++++++++|+++|.+ |+|+++|+++++++||+.++++|+++..+..++
T Consensus 100 ~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~ 150 (430)
T PRK11006 100 FRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP 150 (430)
T ss_pred HHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH
Confidence 777899999999999998 999999999999999999999999987766443
No 60
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.50 E-value=0.0015 Score=56.18 Aligned_cols=56 Identities=18% Similarity=0.240 Sum_probs=46.1
Q ss_pred HHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHH
Q 019399 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78 (341)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~ 78 (341)
-..++.....-+++++++ |+|+|+++.+.-.+|++.-|+.|....+.+++.+....
T Consensus 81 gshlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~dem 136 (598)
T KOG3559|consen 81 GSHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEM 136 (598)
T ss_pred HHhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHHH
Confidence 345666677778899999 99999999999999999999999887777777765543
No 61
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.50 E-value=0.0012 Score=60.11 Aligned_cols=113 Identities=12% Similarity=0.041 Sum_probs=76.2
Q ss_pred hHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCC-CcEE
Q 019399 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEV 94 (341)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~ 94 (341)
..+.++.+++....|++..|.+ |.+.-+|+++++|+|.+..+++|++...+.+ .+...+...-..+. ....
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 3456778999999999999999 9999999999999999999999988554322 12222222222222 2223
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~ 140 (341)
+.. ....|+...+.+..+.... + .-.+++.++.|||+...++
T Consensus 440 ev~-~~r~g~~rtl~Vq~t~~~~-d--~~~gyVvt~DDITdLV~AQ 481 (712)
T COG5000 440 EVK-LAREGEERTLNVQATREPE-D--NGNGYVVTFDDITDLVIAQ 481 (712)
T ss_pred eee-cccCCCceeeeeeeeeccc-c--cCCceEEEecchHHHHHHH
Confidence 333 3345566666666665543 2 2236889999999988863
No 62
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.46 E-value=0.002 Score=66.74 Aligned_cols=42 Identities=10% Similarity=0.055 Sum_probs=37.0
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChh
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA 59 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~ 59 (341)
....+++.++++++.+++++|.+ |+++++|+++++++|.+..
T Consensus 573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~ 614 (1197)
T PRK09959 573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYY 614 (1197)
T ss_pred HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccc
Confidence 34566788999999999999999 9999999999999998643
No 63
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.46 E-value=0.0017 Score=62.46 Aligned_cols=108 Identities=12% Similarity=0.228 Sum_probs=74.8
Q ss_pred HHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEE
Q 019399 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (341)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (341)
.+..++++..++++++|.+ |+++++|+++++++|++..+++|++...+.+.. ..+..++..+.........
T Consensus 204 ~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~~ 274 (638)
T PRK11388 204 QLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEVT 274 (638)
T ss_pred HHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEEE
Confidence 3455889999999999999 999999999999999999999999866654321 1223444555544332223
Q ss_pred EcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhh
Q 019399 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (341)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~ 138 (341)
...+|..+++.+...|+.+ ..|. +++.++.|++..++
T Consensus 275 l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 275 FESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 3345666678888889865 3443 35556678776544
No 64
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=97.33 E-value=0.00012 Score=63.40 Aligned_cols=102 Identities=24% Similarity=0.377 Sum_probs=82.9
Q ss_pred HHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCC-CHHHHHHHHHHHHcCCCcEEEEEEEc
Q 019399 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT-NRRTIMEIREAIREERPIEVNLLNYK 100 (341)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (341)
..++....++-+.|.+ ..+.|+|++|++|+|+-+.|++|+...++...+. ...+...+..+++.|..++++...++
T Consensus 161 aaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~aRR 237 (775)
T KOG1229|consen 161 AALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEARR 237 (775)
T ss_pred HHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHHhh
Confidence 4577888888889888 8889999999999999999999999877765443 34556777888889999999888888
Q ss_pred CCCCeEEEEEEEEEeecCCCCcEEEEE
Q 019399 101 KDGTPFWMLFKMSLVFGKEDGRATHFV 127 (341)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~ 127 (341)
+.|......+-.+|+.. ..|++..++
T Consensus 238 ksgdS~dqh~~itP~~g-qggkirhfv 263 (775)
T KOG1229|consen 238 KSGDSCDQHFIITPFAG-QGGKIRHFV 263 (775)
T ss_pred ccCCcccceEEEeeecC-CCCceeeeh
Confidence 88887777778889887 667776654
No 65
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.32 E-value=0.00044 Score=63.44 Aligned_cols=91 Identities=11% Similarity=0.269 Sum_probs=77.0
Q ss_pred ccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCC
Q 019399 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (341)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (341)
.+|.|+.+.+..++||.+++++|+.+..++++.+...+.......+..|...+..+++..+.|...|+...++.+.+..+
T Consensus 284 mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn 363 (768)
T KOG3558|consen 284 MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKN 363 (768)
T ss_pred eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCC
Confidence 78999999999999999999999999999999988888888899999999999999999999999999998888865223
Q ss_pred CcEEEEEEEEe
Q 019399 121 GRATHFVAVQV 131 (341)
Q Consensus 121 g~~~~~~~~~~ 131 (341)
++...+++|--
T Consensus 364 ~q~q~IicVnY 374 (768)
T KOG3558|consen 364 PQEQNIICVNY 374 (768)
T ss_pred CCcceEEEEEe
Confidence 33344444443
No 66
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.32 E-value=0.017 Score=45.32 Aligned_cols=49 Identities=24% Similarity=0.276 Sum_probs=41.2
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccC
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~ 294 (341)
+..++++.+.++++.|.+ +.+.++|+++++++||+..+..+.....+..
T Consensus 114 ~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~ 162 (232)
T COG2202 114 LRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIH 162 (232)
T ss_pred HHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEe
Confidence 455788888999999998 9999999999999999988888777655443
No 67
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.28 E-value=0.0013 Score=62.09 Aligned_cols=106 Identities=14% Similarity=0.108 Sum_probs=71.9
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCCh--hhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
...++.++++..++++++|.+ |+++++|+++++++|++. .+.+|++...+.++... . ..... ......
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~---~---~~~~~-~~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF---F---TEQID-EKRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh---h---hhhcC-Ccccce
Confidence 345677899999999999999 999999999999999965 46888876555433211 0 11111 111111
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
. ...+| ..+.+...|+.. .+.+.|.+.+++|+|+.+..
T Consensus 291 ~---~~~~~--~~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l 328 (545)
T PRK15053 291 V---ANFNG--LSVIANREAIRS--GDDLLGAIISFRSKDEISTL 328 (545)
T ss_pred E---EEECC--EEEEEEeeeEEE--CCeEEEEEEEEEchHHHHHH
Confidence 1 11234 234466778875 67788999999999998775
No 68
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=97.27 E-value=0.00075 Score=64.25 Aligned_cols=66 Identities=20% Similarity=0.142 Sum_probs=52.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHS 313 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~ 313 (341)
+..++++++++++++|.+ ++++++|+++++++||++++++|+++..+.++... ....+.+.+..+.
T Consensus 264 ~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~ 329 (607)
T PRK11360 264 NELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP--FASPLLDTLEHGT 329 (607)
T ss_pred HHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh--HHHHHHHHHhcCC
Confidence 566788999999999998 99999999999999999999999999888765432 2334444444433
No 69
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.24 E-value=0.0015 Score=58.96 Aligned_cols=107 Identities=13% Similarity=0.178 Sum_probs=78.4
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChh--hhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (341)
+....+++++..|++.+|.. |.+..+|.++++|+|+... +.+|++...+.+|+.. +...+..+.+...+
T Consensus 215 ~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~~~ 285 (537)
T COG3290 215 EERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQHDE 285 (537)
T ss_pred HHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCcccch
Confidence 34467899999999999999 9999999999999999764 6788887776665321 12223344432222
Q ss_pred EEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
. ..-+|. ++.+...|+.. .|+++|++..++|-|+-++.
T Consensus 286 e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L 323 (537)
T COG3290 286 E--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKL 323 (537)
T ss_pred h--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHH
Confidence 1 122344 56678889986 89999999999999998876
No 70
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=97.21 E-value=0.0037 Score=52.36 Aligned_cols=135 Identities=13% Similarity=0.122 Sum_probs=91.5
Q ss_pred HHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcE-EEEEEE
Q 019399 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY 99 (341)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~ 99 (341)
..++++...+++++|.+ +.+.|+|++++.+||.+...+.|...+.+.+... .....+.+....+..+. +++.+.
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs--~ll~ll~q~~~~~~~~~~~~v~l~ 84 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFGS--LLLSLLDQVLERGQPVTEYEVTLV 84 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCc--HHHHHHHHHHHhcCCcccceeeee
Confidence 46889999999999999 9999999999999999999998888776655432 33445556666655544 333333
Q ss_pred cCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhcccccccccccCCCCcchhhhhhhhhhhhccchhhhhhhhh
Q 019399 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVL 179 (341)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~ 179 (341)
.+|....+...+.|+.. ..|. ++..++-+....+..+. ...-....++..++.+.
T Consensus 85 -~~g~~~~v~~~v~~v~~-~~G~---vlle~~~~~~~~ridre--------------------~~q~a~~~a~~~L~r~L 139 (363)
T COG3852 85 -ILGRSHIVDLTVAPVPE-EPGS---VLLEFHPRDMQRRLDRE--------------------QTQHAQQRAVKGLVRGL 139 (363)
T ss_pred -ecCccceEEEEEeeccC-CCCe---EEEEechhHHHhHhhHH--------------------HHHHHHHHHHHHHHHHH
Confidence 78888889999999976 5553 34555555544432000 00111334566777888
Q ss_pred ccccCC
Q 019399 180 ALDSDD 185 (341)
Q Consensus 180 ~~~~~~ 185 (341)
+|++-+
T Consensus 140 AHEIKN 145 (363)
T COG3852 140 AHEIKN 145 (363)
T ss_pred HHHhcC
Confidence 888844
No 71
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.20 E-value=0.00034 Score=62.98 Aligned_cols=94 Identities=26% Similarity=0.449 Sum_probs=70.9
Q ss_pred HHHHhhccC---CceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCcc--ccccCCCChHHHHHHhhhhhccCcch--
Q 019399 243 LYISLGRIK---QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQSSTDKGKHSNR-- 315 (341)
Q Consensus 243 ~~~~~~~~~---~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~-- 315 (341)
+..++..+. ..+++.+++..|..|+|.|+.||++.||.+.|+.-+++ .+..+.-.+....++++.+++.-+.-
T Consensus 16 LENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qf 95 (971)
T KOG0501|consen 16 LENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQF 95 (971)
T ss_pred HHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcce
Confidence 344444333 45777888888999999999999999999999998755 55555556777788888888755432
Q ss_pred h-hhhcccccceeEEEEEecce
Q 019399 316 A-SMHRRIKAHFGIFFTYHPSV 336 (341)
Q Consensus 316 ~-~~~r~~~~~~~~~~~~~p~~ 336 (341)
+ ..|.+.+..-|..+.+.|++
T Consensus 96 EillyKKN~TPvW~~vqiAPIr 117 (971)
T KOG0501|consen 96 EILLYKKNRTPVWLLVQIAPIR 117 (971)
T ss_pred eeEeeecCCCceEEEEEeeccc
Confidence 2 26777788899999998874
No 72
>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=97.19 E-value=0.016 Score=43.68 Aligned_cols=112 Identities=11% Similarity=0.102 Sum_probs=75.6
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEE
Q 019399 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (341)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (341)
..++.+++ .|.+|+-.+.+ ++-.++|.|.++.++++++-+++.+.+.+.-..+.........+.++...|-.....-.
T Consensus 32 ~~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~Gi 109 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGI 109 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence 44555555 88888877654 33578999999999999999999998866544444445555566666666654433334
Q ss_pred EEcCCCCeEEEEE-EEEEeecCCCCcEEEEEEEEec
Q 019399 98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVP 132 (341)
Q Consensus 98 ~~~~dg~~~~~~~-~~~~~~~~~~g~~~~~~~~~~D 132 (341)
-+.+.|+.+++.- .+--+.+ ++|...|.-..+.+
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 4567888877653 2334556 68887776665554
No 73
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=97.17 E-value=0.0059 Score=44.03 Aligned_cols=67 Identities=18% Similarity=0.063 Sum_probs=54.0
Q ss_pred HHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCC-cccCCCCCHHHHHHHHHHHHcCCC
Q 019399 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREERP 91 (341)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~~ 91 (341)
.-++..|-|++-+|.+ |.++..|.+-.++.|++++..+|++.. ++-|....+.+...+.+....|..
T Consensus 20 eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~L 87 (124)
T TIGR02373 20 AQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGTL 87 (124)
T ss_pred hHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCCC
Confidence 4588999999999999 999999999999999999999999854 444445555577777776665543
No 74
>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=97.02 E-value=0.0028 Score=38.73 Aligned_cols=52 Identities=25% Similarity=0.441 Sum_probs=42.9
Q ss_pred HHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCC
Q 019399 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74 (341)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~ 74 (341)
++.+++..+.++++++.. +.+.++|+.+..++|++..++.|..+..+.++.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 54 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPED 54 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCccc
Confidence 456788899999999998 9999999999999999988888876555544444
No 75
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.90 E-value=0.0051 Score=53.07 Aligned_cols=113 Identities=16% Similarity=0.179 Sum_probs=86.2
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEE
Q 019399 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (341)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (341)
.+.+..++++.|.-+-.+|.+ +.+.+.|+. .++|..++.. +|+... +.+|+........+.+.+++|..-..+.
T Consensus 289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~sv-iGr~v~-~chpPksv~iv~ki~~~fksG~kd~~ef 362 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPSV-IGRRVQ-LCHPPKSVHIVEKILKDFKSGEKDFAEF 362 (409)
T ss_pred HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChHh-hCCccc-CCCCCchHHHHHHHHHHhhcCCcchHHH
Confidence 466888999999888888998 999999987 8888777654 788754 4555555566667777778776655554
Q ss_pred EEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
. ....+. .+.++..++++ ++|...|.+-+.+|||.-+..
T Consensus 363 w-~~~~~~--~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l 401 (409)
T COG2461 363 W-INMGDK--FIHIRYFAVKD-EEGEYLGTLEVVQDITRIKEL 401 (409)
T ss_pred h-ccCCCc--eEEEEEEEEEc-CCCceeeeehhhhhhHHHHhc
Confidence 4 222222 46688999999 899999999999999998875
No 76
>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=96.73 E-value=0.0055 Score=46.17 Aligned_cols=71 Identities=17% Similarity=0.069 Sum_probs=58.3
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN 314 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 314 (341)
....+-+.+.+|+-.+.. +|-.++|.|.++.+|++|+.+|++|.+.+.-..+..+......+.++..+|-.
T Consensus 33 ~~~~L~~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~ 103 (148)
T PF08670_consen 33 LAKALWHAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYI 103 (148)
T ss_pred HHHHHHcCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCc
Confidence 444555588888888776 77899999999999999999999999887766777787778888888777753
No 77
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=96.61 E-value=0.018 Score=54.40 Aligned_cols=51 Identities=12% Similarity=0.152 Sum_probs=44.3
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCc--ccccCCccccccCCC
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVD 296 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~--~e~~G~~~~~l~~~~ 296 (341)
+..+++++.+|++++|.+ |+|+++|+++++++|++. ++++|+++..+.++.
T Consensus 224 ~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~ 276 (545)
T PRK15053 224 QEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPA 276 (545)
T ss_pred HHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCc
Confidence 566888899999999999 999999999999999975 469999988776543
No 78
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=96.60 E-value=0.017 Score=52.42 Aligned_cols=53 Identities=21% Similarity=0.238 Sum_probs=46.1
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcc--cccCCccccccCCCCh
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN--EVVGQNCRFLNGVDTD 298 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~--e~~G~~~~~l~~~~~~ 298 (341)
...+++++.+||+.+|.. |.|+.+|.++++|+|+... +.+|++...+..|+.+
T Consensus 217 r~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~ 271 (537)
T COG3290 217 RQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD 271 (537)
T ss_pred HHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC
Confidence 455788899999999999 9999999999999999765 6999999988887433
No 79
>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=96.33 E-value=0.0075 Score=43.52 Aligned_cols=65 Identities=12% Similarity=0.059 Sum_probs=53.5
Q ss_pred HhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccc-cccCCCChHHHHHHhhhhhccCc
Q 019399 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR-FLNGVDTDTTVLYQSSTDKGKHS 313 (341)
Q Consensus 246 ~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~-~l~~~~~~~~~~~~~~~~~~~~~ 313 (341)
-++..+-|++-.|.+ |.|+..|.+-..+.|++++.++|+++. ++-+=...+.+...+.+....+.
T Consensus 21 elD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 21 QFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred HhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 467788999999999 999999999999999999999999985 45444455667778877666554
No 80
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=95.86 E-value=0.016 Score=49.94 Aligned_cols=59 Identities=17% Similarity=0.073 Sum_probs=52.3
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHH
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY 303 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~ 303 (341)
.+..++++.+++|+-+|.. |.+..+|+|+++++|-+++++.|++...++...+...+..
T Consensus 81 ~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~~~l~ 139 (511)
T COG3283 81 ALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFLRWLE 139 (511)
T ss_pred HHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHHHHHh
Confidence 3788999999999999999 9999999999999999999999999999887766555443
No 81
>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=95.67 E-value=0.11 Score=27.77 Aligned_cols=40 Identities=28% Similarity=0.420 Sum_probs=32.7
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCch
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite 135 (341)
+......+|...|+.....++.+ ..+.+.+++++..|+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccC
Confidence 34456678888899888888887 78888899999999986
No 82
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=95.45 E-value=0.033 Score=40.10 Aligned_cols=46 Identities=26% Similarity=0.484 Sum_probs=36.2
Q ss_pred eEEeCCCCCCCCEEEecHHHHHHhCCC---cccccCCccccccCCCChHHH
Q 019399 254 FVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNGVDTDTTV 301 (341)
Q Consensus 254 i~i~d~~~~d~~i~~~N~~~~~~~Gy~---~~e~~G~~~~~l~~~~~~~~~ 301 (341)
+++.|.+ +++|++++....+++|.+ .++++|+++..+..+......
T Consensus 18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l 66 (110)
T PF08446_consen 18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERL 66 (110)
T ss_dssp EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHH
T ss_pred EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHH
Confidence 4555543 599999999999999999 999999999999876654433
No 83
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=95.37 E-value=0.071 Score=48.05 Aligned_cols=93 Identities=14% Similarity=0.162 Sum_probs=75.4
Q ss_pred ccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCC
Q 019399 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (341)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (341)
+..+.+......++||...|+.|.....+++.++.........+.+++|.+...-++...++|++.|+..++..+.. +
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 55677788889999999999999887888887776666677788889998888888999999999999877766664 8
Q ss_pred CcEEEEEEEEecCch
Q 019399 121 GRATHFVAVQVPIVS 135 (341)
Q Consensus 121 g~~~~~~~~~~Dite 135 (341)
|+.-.++...+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 888777766665554
No 84
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=95.31 E-value=0.042 Score=46.27 Aligned_cols=87 Identities=14% Similarity=0.100 Sum_probs=61.7
Q ss_pred HHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhh---hhcc
Q 019399 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRAS---MHRR 321 (341)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~---~~r~ 321 (341)
.+++++..+|++.|.+ +.|.|+|++++.++|-+..-+.|..+..+.+... ....-+.++...+.++.. ..-.
T Consensus 11 ~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs--~ll~ll~q~~~~~~~~~~~~v~l~~ 85 (363)
T COG3852 11 AILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFGS--LLLSLLDQVLERGQPVTEYEVTLVI 85 (363)
T ss_pred hHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCc--HHHHHHHHHHHhcCCcccceeeeee
Confidence 4788889999999999 9999999999999999999999999988775433 344556666665554322 1124
Q ss_pred cccceeEEEEEecce
Q 019399 322 IKAHFGIFFTYHPSV 336 (341)
Q Consensus 322 ~~~~~~~~~~~~p~~ 336 (341)
.|..-.+...++|..
T Consensus 86 ~g~~~~v~~~v~~v~ 100 (363)
T COG3852 86 LGRSHIVDLTVAPVP 100 (363)
T ss_pred cCccceEEEEEeecc
Confidence 455444444555443
No 85
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=95.25 E-value=0.024 Score=48.53 Aligned_cols=56 Identities=16% Similarity=0.252 Sum_probs=48.7
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHH
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTV 301 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~ 301 (341)
|..++.-+.+||+-+|.. |+|+.+|+.+.+|+|.+.++++|++..++..-++.-.+
T Consensus 113 L~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~ 168 (459)
T COG5002 113 LDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTF 168 (459)
T ss_pred HHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeH
Confidence 677788888999999999 99999999999999999999999998887765554443
No 86
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=95.18 E-value=0.031 Score=52.61 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=41.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCC---cccccCCccccccC
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNG 294 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~---~~e~~G~~~~~l~~ 294 (341)
+..+++++++||+++|.+ |+|+++|+++++++|++ ..+.+|+.+..+.+
T Consensus 223 ~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~ 274 (542)
T PRK11086 223 RQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMP 274 (542)
T ss_pred HHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCC
Confidence 677899999999999999 99999999999999875 35677777766554
No 87
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=94.95 E-value=0.1 Score=45.20 Aligned_cols=56 Identities=16% Similarity=0.183 Sum_probs=48.3
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCC
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR 73 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~ 73 (341)
|.+-.+..++++.+++++-+|.. |.+..+|++++.++|.+.+.+.|.+...+....
T Consensus 77 R~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~ 132 (511)
T COG3283 77 REHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGF 132 (511)
T ss_pred hHhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcC
Confidence 34556788999999999999999 999999999999999999999998866665443
No 88
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=94.94 E-value=0.012 Score=56.24 Aligned_cols=55 Identities=15% Similarity=0.190 Sum_probs=44.6
Q ss_pred HhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHH
Q 019399 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY 303 (341)
Q Consensus 246 ~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~ 303 (341)
+++....-++++..+ |+|+||+++...++||..+|+.|+++..+.||++.....+
T Consensus 100 mLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ 154 (803)
T KOG3561|consen 100 ILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPRE 154 (803)
T ss_pred HHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcccc
Confidence 445444445667776 9999999999999999999999999999989887655444
No 89
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=94.82 E-value=0.45 Score=43.15 Aligned_cols=59 Identities=12% Similarity=0.147 Sum_probs=50.6
Q ss_pred HHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHH
Q 019399 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (341)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~ 83 (341)
.++.+.+.-++++..+ |.|.|++.....++|+-..+++.++..++++.++..++.+++.
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 4566777778888888 9999999999999999999999999999999888877766654
No 90
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=94.71 E-value=0.63 Score=34.94 Aligned_cols=86 Identities=13% Similarity=0.156 Sum_probs=67.7
Q ss_pred ccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCC
Q 019399 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (341)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (341)
.++..+-...++++|+ ++.|+....+..+.........+..++....+..........+|....+..-.-|+.+ +.
T Consensus 51 ~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~ 126 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG 126 (137)
T ss_pred eEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence 4566788999999998 5678887777777766666677777777777777777777788888888888899988 77
Q ss_pred CcEEEEEEEE
Q 019399 121 GRATHFVAVQ 130 (341)
Q Consensus 121 g~~~~~~~~~ 130 (341)
|.+..++|..
T Consensus 127 ~~v~rilG~~ 136 (137)
T PF07310_consen 127 GTVDRILGAL 136 (137)
T ss_pred CCccEEEEec
Confidence 8888888764
No 91
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=93.78 E-value=0.29 Score=46.97 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=43.6
Q ss_pred CCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccC
Q 019399 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKH 312 (341)
Q Consensus 262 ~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~ 312 (341)
+.+.|..|..++..++||-+.++||+.+..++|++|+.-..+.-..+++.+
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~ 389 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSG 389 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhC
Confidence 558889999999999999999999999999999999887777666666644
No 92
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=93.00 E-value=0.28 Score=45.48 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=43.4
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCcccccc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~ 293 (341)
+...++....||+..|.+ |+|.-+|+++++|+|.+-++++|++.+.+.
T Consensus 372 ~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~a 419 (712)
T COG5000 372 LEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIA 419 (712)
T ss_pred HHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhh
Confidence 566788889999999999 999999999999999999999999977664
No 93
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=91.44 E-value=2.8 Score=42.55 Aligned_cols=42 Identities=7% Similarity=0.025 Sum_probs=34.9
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCCh
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~ 58 (341)
+.++..+.+++.+|.++++++.. +|.++..|+.+..++|+..
T Consensus 331 e~e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~ 372 (924)
T PRK10841 331 EHEQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLT 372 (924)
T ss_pred HHHHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCC
Confidence 45667889999999999999854 3999999999999888643
No 94
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=90.51 E-value=0.23 Score=47.90 Aligned_cols=68 Identities=10% Similarity=0.103 Sum_probs=51.4
Q ss_pred CCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcch-hhhhcccccceeEE
Q 019399 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR-ASMHRRIKAHFGIF 329 (341)
Q Consensus 262 ~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~r~~~~~~~~~ 329 (341)
.+|.++++-.....+.||...+++|+.+..+.|+++.......++.+....+.. ...||...+++...
T Consensus 380 ~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~ 448 (803)
T KOG3561|consen 380 SDGSFTFVDQRASAILGYQPQELLGRSSYESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSI 448 (803)
T ss_pred cCCceeccccccccccccCchhhcCcccccccCccccchhhchHHHHHHhcccccccccccccCCCCcc
Confidence 569999999999999999999999999988889988877777666555543333 33566555555443
No 95
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=89.93 E-value=0.73 Score=40.26 Aligned_cols=85 Identities=8% Similarity=0.051 Sum_probs=57.8
Q ss_pred eEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCCCCeEEEE
Q 019399 30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (341)
Q Consensus 30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (341)
-++....+ ..+++......+++||.+.+++++++...++..+...........+..|..-+--++++.+.|.+.|+.
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 34455566 789999999999999999999999876666655554444333334444443333456677888888887
Q ss_pred EEEEEeec
Q 019399 110 FKMSLVFG 117 (341)
Q Consensus 110 ~~~~~~~~ 117 (341)
-....+.+
T Consensus 304 syat~vHn 311 (598)
T KOG3559|consen 304 SYATFVHN 311 (598)
T ss_pred EeeEEEec
Confidence 66555543
No 96
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=87.81 E-value=0.81 Score=47.85 Aligned_cols=39 Identities=8% Similarity=-0.039 Sum_probs=34.3
Q ss_pred HHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccc
Q 019399 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV 284 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~ 284 (341)
+..++++++.+|+++|.+ |+|+++|+++++++|++....
T Consensus 578 ~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~ 616 (1197)
T PRK09959 578 RKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKN 616 (1197)
T ss_pred HHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccc
Confidence 566789999999999999 999999999999999875443
No 97
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=86.53 E-value=1.9 Score=41.72 Aligned_cols=91 Identities=10% Similarity=0.116 Sum_probs=64.4
Q ss_pred CCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCC-C--cEEEEEEEcCCCCeEEEEEEEEEe
Q 019399 39 SGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-P--IEVNLLNYKKDGTPFWMLFKMSLV 115 (341)
Q Consensus 39 ~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~--~~~e~~~~~~dg~~~~~~~~~~~~ 115 (341)
+++.+..|..++.-++||-+.++||+.+..++++.+.....+....++..++ . ....+++...+|.++.+...+..+
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTeWSsF 418 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTEWSSF 418 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEechhhhc
Confidence 3477888999999999999999999998888888876666555555555443 3 234678888999988777665555
Q ss_pred ecCCCCcEEEEEEE
Q 019399 116 FGKEDGRATHFVAV 129 (341)
Q Consensus 116 ~~~~~g~~~~~~~~ 129 (341)
.+|-..++.++||-
T Consensus 419 VNPWSRKieFVvGR 432 (1114)
T KOG3753|consen 419 VNPWSRKIEFVVGR 432 (1114)
T ss_pred cChhhhheeeeeee
Confidence 44334455554443
No 98
>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=81.74 E-value=1.7 Score=31.22 Aligned_cols=42 Identities=26% Similarity=0.394 Sum_probs=33.4
Q ss_pred eEEEEcCCCCCccEEEecHHHHHhcCCC---hhhhcCCCCCcccCCC
Q 019399 30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPR 73 (341)
Q Consensus 30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~---~~e~~g~~~~~l~~~~ 73 (341)
.++++|.+ +++++.++.++..++|.+ .++++|++...+..+.
T Consensus 17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~ 61 (110)
T PF08446_consen 17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAE 61 (110)
T ss_dssp EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCC
T ss_pred EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHH
Confidence 35567654 489999999999999999 8999999987776544
No 99
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=70.60 E-value=28 Score=32.99 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=32.3
Q ss_pred ccCCceEEeCCCCCCCCEEEecHHHHHHhCCC-cccccCCccccc
Q 019399 249 RIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFL 292 (341)
Q Consensus 249 ~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~-~~e~~G~~~~~l 292 (341)
..+++.+++|.+ ++|+..|++...+.+.+ ..-++|++...+
T Consensus 230 ~~~~~~lavd~~---grvl~at~aA~~~La~~~~~~l~g~p~~~~ 271 (606)
T COG3284 230 SQSEALLAVDQD---GRVLGATRAARQLLALTDRQRLIGQPVEDF 271 (606)
T ss_pred cccceeeeecCc---chhhhccHHHHHhhccchhhHhhcCCcccc
Confidence 345678899988 99999999999999987 555667766544
No 100
>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=70.16 E-value=23 Score=25.79 Aligned_cols=46 Identities=15% Similarity=0.199 Sum_probs=36.2
Q ss_pred CcEEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchhhhc
Q 019399 91 PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (341)
Q Consensus 91 ~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~k~~ 139 (341)
.....+....++|+ .+..+...+++ ++|.++|++++-.|+|....+
T Consensus 67 ~~~~nY~~~~~~Gk--~lrSsT~~Ird-~~g~~iG~LCIN~D~s~~~~~ 112 (118)
T PF08348_consen 67 DYIINYKTKTKDGK--ILRSSTFFIRD-ENGKLIGALCINFDISALEQA 112 (118)
T ss_pred CccccccccCCCCC--EEEEEEEEEEC-CCCCEEEEEEEEeccHHHHHH
Confidence 34455566778886 45667788898 899999999999999988765
No 101
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.07 E-value=45 Score=26.43 Aligned_cols=108 Identities=17% Similarity=0.218 Sum_probs=68.6
Q ss_pred HHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEEEEEEEcCC
Q 019399 23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKD 102 (341)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~d 102 (341)
+-+..++.+++.+...+.-.+..+-...|.+||- |+-|..+..+..+.+.......+..+.+...++-.........
T Consensus 53 l~slL~d~FiL~~~~~G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s~~ 129 (209)
T COG5388 53 LKSLLPDVFILERDGRGKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRSHG 129 (209)
T ss_pred HHhhcCceEEEeccCCCCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhhcc
Confidence 4556677665544331112244566667888874 6777765555555555555555555556666665555556677
Q ss_pred CCeEEEEEEEEEeecCCCCcEEEEEEEEecCc
Q 019399 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (341)
Q Consensus 103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit 134 (341)
|....+++-..|+.. ..|....++|...-+.
T Consensus 130 G~sl~fEmLl~PL~~-~~g~~~R~LGais~~~ 160 (209)
T COG5388 130 GRSLGFEMLLAPLQG-ASGETDRFLGAISPIA 160 (209)
T ss_pred CcccceeeeeecccC-CCCCccchhhhccccc
Confidence 877888999999988 7787666777766554
No 102
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=67.48 E-value=13 Score=34.80 Aligned_cols=42 Identities=12% Similarity=0.125 Sum_probs=35.3
Q ss_pred hhhhhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCC
Q 019399 12 FNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (341)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~ 56 (341)
+..+.+.....++.+.|.|+++++.+ +.+.|+||-+..+|+-
T Consensus 69 ls~~~~~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~~ 110 (655)
T COG3887 69 LSYQAEKSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcCh
Confidence 34455666778899999999999988 9999999999998863
No 103
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=66.51 E-value=9.1 Score=31.06 Aligned_cols=37 Identities=14% Similarity=0.036 Sum_probs=32.5
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCc
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR 281 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~ 281 (341)
++..++...+.+++|-+.+ |.+++.|.+|.+.++-+-
T Consensus 20 ~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 20 SLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhcC
Confidence 4677899999999999999 999999999999887543
No 104
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=65.83 E-value=11 Score=30.58 Aligned_cols=37 Identities=19% Similarity=0.086 Sum_probs=32.9
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCC
Q 019399 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (341)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~ 56 (341)
.+.+..++...+.++++-+.+ |.+++.|.+|.+.+.-
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~ 54 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLG 54 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHh
Confidence 446777999999999999999 9999999999998864
No 105
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=65.71 E-value=15 Score=37.24 Aligned_cols=40 Identities=13% Similarity=0.075 Sum_probs=34.2
Q ss_pred hhHHHHHHHHhhCCCeEEEEcCCCCCccEEEecHHHHHhcCC
Q 019399 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (341)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~ 56 (341)
...+..+.+++++|.|++++|.. +++++.+|+++.+++|.
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 45667789999999999999954 38999999999999875
No 106
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=65.29 E-value=21 Score=31.69 Aligned_cols=68 Identities=10% Similarity=0.130 Sum_probs=53.6
Q ss_pred chHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcc
Q 019399 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN 314 (341)
Q Consensus 241 ~~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 314 (341)
..+..++...|.-+-.+|.+ +++.+.|+. .++|-.++. ++|++.. ++||......+..+-+...+|+.
T Consensus 290 ~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~-~chpPksv~iv~ki~~~fksG~k 357 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQ-LCHPPKSVHIVEKILKDFKSGEK 357 (409)
T ss_pred HHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCccc-CCCCCchHHHHHHHHHHhhcCCc
Confidence 34788899999888888888 899999998 888877765 5788765 56777777888888888877764
No 107
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=63.80 E-value=9.2 Score=38.12 Aligned_cols=44 Identities=11% Similarity=0.018 Sum_probs=37.3
Q ss_pred HHHHhhccCCceEEeC-CCCCCCCEEEecHHHHHHhCCCcccccCCccccc
Q 019399 243 LYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL 292 (341)
Q Consensus 243 ~~~~~~~~~~~i~i~d-~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l 292 (341)
-..++...|-|+++.| .+ |.|+|+|+.|.+++| .+ ++|++...+
T Consensus 104 ~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 104 GEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 5667888999999999 57 999999999999988 33 899988764
No 108
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=62.98 E-value=21 Score=26.72 Aligned_cols=64 Identities=13% Similarity=0.089 Sum_probs=48.9
Q ss_pred ceEEeCCCC-CCCCEEEecHHHHHHhCCCcccccCCccccccCCCChHHHHHHhhhhhccCcchhhhh
Q 019399 253 SFVLIDPHL-PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNRASMH 319 (341)
Q Consensus 253 ~i~i~d~~~-~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 319 (341)
.++|++... .+.++..+=...++++|++ +.|+++.++..++........+..++....+.....
T Consensus 39 ~i~ile~~~~~~~r~RLaGt~i~~~~G~d---~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~ 103 (137)
T PF07310_consen 39 HIFILEVDDPGDFRYRLAGTRIVELFGRD---LTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARG 103 (137)
T ss_pred CeEEEEEeCCCceEEEEecHHHHHHhCCC---CCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEE
Confidence 344444432 1456778899999999985 779999999999999888999999998888765433
No 109
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=62.88 E-value=21 Score=30.77 Aligned_cols=82 Identities=13% Similarity=0.283 Sum_probs=51.8
Q ss_pred hCCCeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHH--cCCCcEEEEEEEcCCC
Q 019399 26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR--EERPIEVNLLNYKKDG 103 (341)
Q Consensus 26 ~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~~e~~~~~~dg 103 (341)
....++++..+. +.+.+++|.-+..++||+.++.+......+. .....+...+. ......+.+.+.++.|
T Consensus 295 EnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV~------eGl~qW~~dL~~~s~~E~~grlviKTK~~ 366 (401)
T PF06785_consen 295 ENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIVQ------EGLAQWETDLQLLSRQERSGRLVIKTKNG 366 (401)
T ss_pred cccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHHH------hhHHHHHHHHHhhhhhhhhceEEEEecCC
Confidence 334467777776 4778999999999999999987654322111 11223332222 2233456677788888
Q ss_pred CeEEEEEEEEEe
Q 019399 104 TPFWMLFKMSLV 115 (341)
Q Consensus 104 ~~~~~~~~~~~~ 115 (341)
...++......+
T Consensus 367 g~ipf~ycL~ii 378 (401)
T PF06785_consen 367 GNIPFYYCLGII 378 (401)
T ss_pred CceeeEEEEeec
Confidence 888777666555
No 110
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=55.82 E-value=25 Score=35.24 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=36.6
Q ss_pred HHHHHHHHhhCCCeEEEEc-CCCCCccEEEecHHHHHhcCCChhhhcCCCCCc
Q 019399 17 TLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68 (341)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d-~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~ 68 (341)
......++...|.|++++| .+ |.+.|+|+.|..++| .. .+|++...
T Consensus 101 ~~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~ 147 (838)
T PRK14538 101 SQIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQ 147 (838)
T ss_pred hHHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHH
Confidence 3444567899999999999 67 999999999999987 22 68887554
No 111
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=52.52 E-value=17 Score=36.75 Aligned_cols=37 Identities=8% Similarity=-0.107 Sum_probs=31.9
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhCCC
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~Gy~ 280 (341)
..+.++++++.|+++.|.+ +++|+++|+++.+++|+.
T Consensus 344 l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 344 LNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCcc
Confidence 3677899999999999954 389999999999999864
No 112
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=46.43 E-value=30 Score=32.65 Aligned_cols=34 Identities=15% Similarity=0.147 Sum_probs=30.8
Q ss_pred hHHHHhhccCCceEEeCCCCCCCCEEEecHHHHHHhC
Q 019399 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (341)
Q Consensus 242 ~~~~~~~~~~~~i~i~d~~~~d~~i~~~N~~~~~~~G 278 (341)
.+..++.+.|.||++.|.+ +.+.|+||-...+++
T Consensus 76 ~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~ 109 (655)
T COG3887 76 SLEEALTNMPIGIILFNET---NKVEWVNPFASKIFN 109 (655)
T ss_pred HHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcC
Confidence 3777899999999999987 999999999999886
No 113
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=45.96 E-value=12 Score=32.10 Aligned_cols=33 Identities=18% Similarity=0.498 Sum_probs=26.6
Q ss_pred ceEEeCCCCCCCCEEEecHHHHHHhCCCcccccCC
Q 019399 253 SFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ 287 (341)
Q Consensus 253 ~i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~ 287 (341)
+++|..+. +.+.+++|.-+..++||+.++.+-.
T Consensus 299 mlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~ 331 (401)
T PF06785_consen 299 MLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKD 331 (401)
T ss_pred eEEEecch--hhHHHHhHHHHHHHhccCHHHHHhc
Confidence 45565554 4789999999999999999998743
No 114
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=35.50 E-value=95 Score=20.29 Aligned_cols=30 Identities=10% Similarity=0.217 Sum_probs=22.7
Q ss_pred EEEEEEEEEeecCCCCcEEEEEEEEecCchh
Q 019399 106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (341)
Q Consensus 106 ~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~ 136 (341)
.++..-..|+.+ .+|++.|++++-.++...
T Consensus 12 ~~vi~~s~pi~~-~~g~~~Gvv~~di~l~~l 41 (81)
T PF02743_consen 12 QPVITISVPIYD-DDGKIIGVVGIDISLDQL 41 (81)
T ss_dssp EEEEEEEEEEEE-TTTEEEEEEEEEEEHHHH
T ss_pred cEEEEEEEEEEC-CCCCEEEEEEEEecccee
Confidence 356667889998 799999999876665544
No 115
>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=24.64 E-value=2.3e+02 Score=19.11 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=30.7
Q ss_pred HHHHHHcCCCcEEEEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCc
Q 019399 82 IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (341)
Q Consensus 82 ~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dit 134 (341)
+.+++..+.. .+.....|.+.-+-+.+.|+++ .+|.+++.+|+. |+|
T Consensus 37 Le~vl~~g~v----~r~~P~~G~Y~G~PViV~PI~~-~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 37 LEEVLETGKV----IRVTPIEGPYKGVPVIVAPIKD-EDGEVIAAIGVV-DLT 83 (84)
T ss_pred HHHHHHcCCE----EEeccCCcccCCeeEEEEEEEc-CCCCEEEEEEEE-Ecc
Confidence 3455555543 2333456666556678899998 789999998864 443
No 116
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=23.58 E-value=1.3e+02 Score=29.07 Aligned_cols=39 Identities=15% Similarity=0.363 Sum_probs=32.1
Q ss_pred eEEeCCCCCCCCEEEecHHHHHHhCCCcccccCCccccccC
Q 019399 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (341)
Q Consensus 254 i~i~d~~~~d~~i~~~N~~~~~~~Gy~~~e~~G~~~~~l~~ 294 (341)
+++++. +|+.|+.++..+..++|..+++++|+++..+..
T Consensus 32 Llvl~~--~~~~Vlq~S~N~~~~LG~~~e~l~~~tl~~vl~ 70 (750)
T COG4251 32 LLVLDE--ADLMVLQASENCANILGREPEDLLGRTLGAVLT 70 (750)
T ss_pred EEEeec--CCchhhhhhhhHHHHhCCChhhhhcCCHHHhcc
Confidence 444542 359999999999999999999999999877664
No 117
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=23.37 E-value=6.8e+02 Score=24.14 Aligned_cols=96 Identities=16% Similarity=0.135 Sum_probs=51.1
Q ss_pred hHHHHHHHHhhCC-CeEEEEcCCCCCccEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCHHHHHHHHHHHHcCCCcEE
Q 019399 16 YTLWVHEALDELP-DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (341)
Q Consensus 16 ~~~~~~~~~~~~~-~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (341)
.++.++.+-..+. ..+|++|+. |..+-++.. + -+...+|.+.. +...+.++..++....+
T Consensus 87 ~n~~L~~in~~a~ss~iYlid~~---G~~iaASNw-----~-~p~SFVG~nya----------fRpYf~~Am~gg~~r~y 147 (603)
T COG4191 87 ANRYLEQINEAAGSSAIYLIDPT---GLTLAASNW-----N-LPTSFVGRNYA----------FRPYFQDAMAGGSGRFY 147 (603)
T ss_pred HHHHHHHHHhhccCCeEEEECCC---CcEEeeccC-----C-CCCcccccCcc----------cHHHHHHHHhcCCceeE
Confidence 3444444444333 478999999 887765421 1 12334554432 23455666665543322
Q ss_pred EEEEEcCCCCeEEEEEEEEEeecCCCCcEEEEEEEEecCchh
Q 019399 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (341)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~Dite~ 136 (341)
-+= ...|..-+ .-..|+.. .|+++|.+.+-.|+...
T Consensus 148 alG--tts~~pGy--y~a~pV~~--~~~ilGvivvKvdl~~l 183 (603)
T COG4191 148 ALG--TTSGRPGY--YLAAPVDD--GGGILGVIVVKVDLDRL 183 (603)
T ss_pred eec--cccCCCce--eEeeeecc--CCceeEEEEEEEehHHH
Confidence 221 11122211 23567876 66699999988886643
Done!