Query 002210
Match_columns 953
No_of_seqs 694 out of 5030
Neff 8.3
Searched_HMMs 46136
Date Thu Mar 28 19:01:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002210hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4251 Bacteriophytochrome (l 100.0 6E-120 1E-124 996.2 42.6 480 68-579 17-503 (750)
2 PF00360 PHY: Phytochrome regi 100.0 8.6E-32 1.9E-36 271.7 13.2 170 409-580 5-179 (182)
3 PRK13560 hypothetical protein; 100.0 1.3E-28 2.9E-33 309.8 40.0 329 602-939 195-659 (807)
4 TIGR02938 nifL_nitrog nitrogen 99.9 3.2E-25 7E-30 262.4 25.0 310 611-939 4-333 (494)
5 PF08446 PAS_2: PAS fold; Int 99.9 2.5E-24 5.3E-29 199.3 8.2 109 67-182 2-110 (110)
6 PRK09776 putative diguanylate 99.9 4E-22 8.6E-27 259.4 29.3 263 602-880 274-537 (1092)
7 PRK11091 aerobic respiration c 99.9 5.9E-22 1.3E-26 248.2 24.6 211 722-950 138-349 (779)
8 PRK09776 putative diguanylate 99.9 7.1E-21 1.5E-25 247.7 30.5 262 602-878 401-665 (1092)
9 TIGR02040 PpsR-CrtJ transcript 99.9 1.6E-20 3.4E-25 219.7 28.8 242 603-871 125-368 (442)
10 PRK13560 hypothetical protein; 99.9 1.1E-19 2.4E-24 229.0 30.3 259 602-879 58-332 (807)
11 PRK11359 cyclic-di-GMP phospho 99.8 7.6E-18 1.6E-22 212.2 28.3 242 611-873 12-257 (799)
12 TIGR02040 PpsR-CrtJ transcript 99.8 1.5E-17 3.2E-22 194.7 22.5 232 617-873 2-249 (442)
13 PRK13557 histidine kinase; Pro 99.7 2.3E-15 5E-20 180.6 23.2 198 734-947 25-231 (540)
14 COG5002 VicK Signal transducti 99.7 1.8E-15 3.9E-20 158.4 17.7 197 721-949 92-292 (459)
15 PRK13559 hypothetical protein; 99.7 3.3E-15 7.1E-20 170.1 21.3 185 737-946 41-229 (361)
16 PRK11006 phoR phosphate regulo 99.6 1.3E-14 2.9E-19 169.2 18.9 191 720-950 79-271 (430)
17 PRK11360 sensory histidine kin 99.6 5.3E-14 1.2E-18 170.9 24.7 200 730-948 253-454 (607)
18 PRK11073 glnL nitrogen regulat 99.6 3.5E-14 7.7E-19 160.7 19.1 186 739-947 7-193 (348)
19 TIGR02966 phoR_proteo phosphat 99.6 3.5E-14 7.7E-19 158.9 17.3 177 735-949 2-181 (333)
20 PF08448 PAS_4: PAS fold; Int 99.4 2E-12 4.3E-17 119.6 13.6 110 617-729 1-110 (110)
21 PRK09959 hybrid sensory histid 99.4 4.3E-12 9.2E-17 166.9 22.1 217 720-950 557-779 (1197)
22 PF13426 PAS_9: PAS domain; PD 99.4 2.3E-12 5.1E-17 117.7 12.4 102 754-866 3-104 (104)
23 PRK10841 hybrid sensory kinase 99.4 2.4E-11 5.2E-16 153.5 24.2 182 732-950 327-513 (924)
24 PF13426 PAS_9: PAS domain; PD 99.4 4.4E-12 9.5E-17 115.9 12.4 104 621-726 1-104 (104)
25 PF00989 PAS: PAS fold; Inter 99.4 5.8E-12 1.3E-16 117.1 13.2 110 611-724 1-113 (113)
26 PF00989 PAS: PAS fold; Inter 99.4 1.2E-11 2.6E-16 115.0 13.9 112 739-864 1-113 (113)
27 PF01590 GAF: GAF domain; Int 99.3 7.7E-12 1.7E-16 123.5 11.4 153 215-390 1-154 (154)
28 PF08448 PAS_4: PAS fold; Int 99.3 1.6E-11 3.4E-16 113.5 11.8 109 746-869 2-110 (110)
29 PRK10618 phosphotransfer inter 99.3 6.2E-11 1.4E-15 147.8 19.4 177 730-950 334-516 (894)
30 COG3852 NtrB Signal transducti 99.3 1.6E-10 3.6E-15 120.2 16.6 176 743-940 11-187 (363)
31 PRK11086 sensory histidine kin 99.2 6.2E-10 1.3E-14 133.9 23.1 178 703-912 147-366 (542)
32 PRK11091 aerobic respiration c 99.2 3.2E-10 7E-15 142.5 20.7 137 601-739 145-281 (779)
33 PF00512 HisKA: His Kinase A ( 99.2 4.8E-11 1E-15 100.8 7.7 64 885-948 2-68 (68)
34 PRK10060 RNase II stability mo 99.1 1.4E-09 3.1E-14 133.4 18.7 167 694-879 71-238 (663)
35 PRK13559 hypothetical protein; 99.1 2.6E-09 5.6E-14 121.6 16.7 139 608-748 40-181 (361)
36 COG3829 RocR Transcriptional r 99.0 5.4E-09 1.2E-13 118.1 17.4 226 615-876 5-231 (560)
37 smart00065 GAF Domain present 99.0 9.8E-09 2.1E-13 98.3 16.0 139 215-392 1-141 (149)
38 PRK15053 dpiB sensor histidine 99.0 1.4E-07 3E-12 113.8 29.4 199 702-939 147-385 (545)
39 COG5000 NtrY Signal transducti 99.0 8.7E-09 1.9E-13 116.5 16.5 184 733-947 364-555 (712)
40 PRK13557 histidine kinase; Pro 99.0 5.5E-09 1.2E-13 125.5 15.9 130 606-737 25-157 (540)
41 PRK13558 bacterio-opsin activa 99.0 9.6E-09 2.1E-13 126.9 17.4 136 612-749 149-287 (665)
42 PRK13558 bacterio-opsin activa 98.9 2.5E-08 5.5E-13 123.1 19.0 124 741-878 150-276 (665)
43 TIGR00229 sensory_box PAS doma 98.9 1.7E-08 3.8E-13 90.9 12.5 120 611-733 3-123 (124)
44 TIGR02938 nifL_nitrog nitrogen 98.9 6.9E-09 1.5E-13 122.8 11.8 126 739-878 4-129 (494)
45 PRK10060 RNase II stability mo 98.9 3.3E-08 7.1E-13 121.5 17.9 161 606-770 106-283 (663)
46 TIGR00229 sensory_box PAS doma 98.8 4.3E-08 9.3E-13 88.3 13.0 119 739-872 3-122 (124)
47 PF13596 PAS_10: PAS domain; P 98.8 2.1E-08 4.6E-13 92.7 10.0 105 613-725 1-106 (106)
48 PRK11359 cyclic-di-GMP phospho 98.8 1.7E-07 3.7E-12 118.5 20.3 126 607-734 132-258 (799)
49 PF08447 PAS_3: PAS fold; Int 98.8 5.1E-08 1.1E-12 87.1 10.5 90 764-861 1-91 (91)
50 COG3290 CitA Signal transducti 98.8 2.3E-07 5.1E-12 105.1 18.0 191 703-927 141-371 (537)
51 PF08447 PAS_3: PAS fold; Int 98.6 3.8E-07 8.3E-12 81.4 10.4 86 633-721 1-91 (91)
52 COG2203 FhlA FOG: GAF domain [ 98.6 2.1E-07 4.5E-12 92.3 9.4 155 201-392 6-164 (175)
53 PF13492 GAF_3: GAF domain; PD 98.5 2E-06 4.4E-11 81.7 14.6 128 215-391 1-128 (129)
54 PRK11360 sensory histidine kin 98.5 1.6E-06 3.5E-11 105.3 16.9 129 605-738 256-385 (607)
55 KOG3558 Hypoxia-inducible fact 98.5 9.1E-07 2E-11 101.2 13.1 226 615-867 123-379 (768)
56 PRK11388 DNA-binding transcrip 98.5 9.8E-06 2.1E-10 99.4 21.7 225 613-869 64-311 (638)
57 cd00130 PAS PAS domain; PAS mo 98.4 4E-06 8.6E-11 71.4 12.9 103 620-724 1-103 (103)
58 PF12860 PAS_7: PAS fold 98.4 6.5E-07 1.4E-11 84.0 8.2 104 617-732 1-115 (115)
59 COG5002 VicK Signal transducti 98.4 4.8E-06 1E-10 88.6 15.3 124 604-736 104-227 (459)
60 COG2205 KdpD Osmosensitive K+ 98.4 1.1E-06 2.4E-11 103.4 11.1 67 883-949 658-728 (890)
61 TIGR02966 phoR_proteo phosphat 98.4 2.3E-06 5E-11 95.6 13.4 114 607-735 2-115 (333)
62 cd00130 PAS PAS domain; PAS mo 98.4 6E-06 1.3E-10 70.3 12.8 100 754-864 4-103 (103)
63 COG2202 AtoS FOG: PAS/PAC doma 98.4 5.2E-05 1.1E-09 75.3 21.3 228 624-869 2-230 (232)
64 PF13185 GAF_2: GAF domain; PD 98.3 9.8E-06 2.1E-10 79.0 13.7 136 215-390 3-147 (148)
65 TIGR01817 nifA Nif-specific re 98.3 5.8E-05 1.3E-09 90.5 23.0 219 199-458 5-232 (534)
66 PF13596 PAS_10: PAS domain; P 98.3 3.1E-06 6.7E-11 78.2 9.1 105 742-865 2-106 (106)
67 PRK11073 glnL nitrogen regulat 98.3 4.7E-06 1E-10 94.3 11.9 115 611-735 7-122 (348)
68 TIGR02956 TMAO_torS TMAO reduc 98.3 2.2E-06 4.8E-11 110.7 10.3 76 875-950 454-530 (968)
69 PRK15347 two component system 98.3 2.2E-06 4.7E-11 110.3 10.0 77 874-950 387-464 (921)
70 smart00388 HisKA His Kinase A 98.2 3.1E-06 6.8E-11 69.8 6.3 64 885-948 2-66 (66)
71 PRK05022 anaerobic nitric oxid 98.1 0.00028 6.1E-09 83.9 23.2 215 202-457 7-222 (509)
72 PRK11107 hybrid sensory histid 98.1 5.8E-06 1.3E-10 106.3 9.7 74 877-950 285-359 (919)
73 PF12860 PAS_7: PAS fold 98.1 9.9E-06 2.1E-10 76.0 8.6 111 746-871 2-114 (115)
74 COG3604 FhlA Transcriptional r 98.1 0.00012 2.5E-09 82.5 17.9 219 214-470 47-272 (550)
75 PRK11006 phoR phosphate regulo 98.1 2.2E-05 4.7E-10 91.8 12.3 117 602-735 89-205 (430)
76 PRK11086 sensory histidine kin 98.1 4.4E-05 9.5E-10 91.9 14.8 122 604-740 214-339 (542)
77 PRK11466 hybrid sensory histid 98.0 1.5E-05 3.3E-10 102.3 10.2 73 877-949 436-509 (914)
78 PRK10820 DNA-binding transcrip 98.0 0.0001 2.3E-09 87.6 16.1 111 605-729 74-190 (520)
79 PRK15429 formate hydrogenlyase 98.0 0.00064 1.4E-08 84.1 23.6 216 206-458 192-412 (686)
80 PF14598 PAS_11: PAS domain; P 97.9 0.00015 3.4E-09 67.4 11.9 101 755-866 5-108 (111)
81 PF14598 PAS_11: PAS domain; P 97.9 0.00022 4.8E-09 66.3 12.8 101 624-726 5-108 (111)
82 COG5000 NtrY Signal transducti 97.9 0.00032 7E-09 80.4 16.3 125 601-734 360-484 (712)
83 COG3829 RocR Transcriptional r 97.9 6E-05 1.3E-09 86.0 10.4 169 606-785 112-327 (560)
84 PRK09303 adaptive-response sen 97.8 6.4E-05 1.4E-09 86.3 9.6 69 882-950 148-224 (380)
85 PRK10820 DNA-binding transcrip 97.7 0.00027 6E-09 84.1 12.7 111 735-869 76-190 (520)
86 COG3290 CitA Signal transducti 97.7 0.00031 6.7E-09 80.3 12.3 120 603-736 207-329 (537)
87 PRK11061 fused phosphoenolpyru 97.7 0.0011 2.3E-08 81.9 18.1 149 203-391 7-155 (748)
88 KOG0501 K+-channel KCNQ [Inorg 97.7 0.00016 3.6E-09 81.1 9.6 100 761-869 39-138 (971)
89 cd00082 HisKA Histidine Kinase 97.6 0.00015 3.3E-09 59.1 6.9 60 885-944 4-65 (65)
90 PRK10490 sensor protein KdpD; 97.6 0.00045 9.7E-09 87.7 13.1 67 883-949 662-731 (895)
91 PRK15053 dpiB sensor histidine 97.5 0.0013 2.8E-08 79.4 15.6 122 603-739 214-337 (545)
92 KOG3560 Aryl-hydrocarbon recep 97.5 0.0007 1.5E-08 75.8 11.3 227 615-867 115-386 (712)
93 PF13188 PAS_8: PAS domain; PD 97.5 0.00014 3.1E-09 60.1 4.5 47 611-661 1-47 (64)
94 COG2202 AtoS FOG: PAS/PAC doma 97.4 0.0019 4.2E-08 63.7 13.1 125 603-730 104-231 (232)
95 COG4251 Bacteriophytochrome (l 97.4 0.00053 1.2E-08 78.8 9.4 71 877-947 516-590 (750)
96 COG4191 Signal transduction hi 97.4 0.017 3.7E-07 66.9 21.4 58 889-946 388-449 (603)
97 KOG3559 Transcriptional regula 97.4 0.0012 2.5E-08 71.3 11.2 205 615-851 83-313 (598)
98 PRK13837 two-component VirA-li 97.3 0.00084 1.8E-08 85.2 10.2 66 884-949 449-516 (828)
99 PRK15429 formate hydrogenlyase 97.3 0.084 1.8E-06 65.5 27.5 202 202-444 12-224 (686)
100 PRK11388 DNA-binding transcrip 97.0 0.031 6.8E-07 68.7 19.6 113 606-729 198-311 (638)
101 PF13188 PAS_8: PAS domain; PD 97.0 0.001 2.2E-08 55.0 4.4 42 739-787 1-42 (64)
102 KOG0501 K+-channel KCNQ [Inorg 96.9 0.003 6.4E-08 71.4 8.5 98 630-729 39-138 (971)
103 PRK09959 hybrid sensory histid 96.8 0.012 2.7E-07 78.0 15.6 131 602-737 567-701 (1197)
104 smart00091 PAS PAS domain. PAS 96.6 0.0067 1.4E-07 46.7 6.4 63 612-674 2-64 (67)
105 PRK10364 sensor protein ZraS; 96.5 0.01 2.2E-07 70.0 9.9 62 885-946 237-300 (457)
106 PRK10604 sensor protein RstB; 96.5 0.0059 1.3E-07 71.5 7.8 63 882-949 209-272 (433)
107 KOG1229 3'5'-cyclic nucleotide 96.5 0.0028 6E-08 69.2 4.4 115 731-859 150-264 (775)
108 PRK10815 sensor protein PhoQ; 96.3 0.011 2.5E-07 70.0 8.9 65 883-949 264-330 (485)
109 COG2461 Uncharacterized conser 96.1 0.013 2.8E-07 64.3 6.9 114 611-733 290-404 (409)
110 TIGR03785 marine_sort_HK prote 96.0 0.028 6.1E-07 69.8 10.4 68 882-949 482-550 (703)
111 COG4192 Signal transduction hi 95.9 0.03 6.6E-07 62.3 8.6 63 889-951 455-521 (673)
112 PF08670 MEKHLA: MEKHLA domain 95.5 0.16 3.4E-06 49.4 11.1 110 612-724 33-145 (148)
113 TIGR02916 PEP_his_kin putative 95.5 0.43 9.4E-06 59.3 18.2 151 202-392 308-459 (679)
114 PRK10337 sensor protein QseC; 95.5 0.05 1.1E-06 63.8 9.4 65 885-949 237-303 (449)
115 KOG3558 Hypoxia-inducible fact 95.4 0.027 5.8E-07 65.7 6.5 101 624-726 277-378 (768)
116 PF08670 MEKHLA: MEKHLA domain 95.3 0.36 7.7E-06 46.9 13.0 110 739-863 32-144 (148)
117 COG3852 NtrB Signal transducti 95.3 0.12 2.5E-06 55.4 10.2 107 615-731 11-120 (363)
118 TIGR02916 PEP_his_kin putative 95.3 0.12 2.6E-06 64.2 12.3 55 886-940 476-531 (679)
119 PRK09467 envZ osmolarity senso 95.2 0.062 1.3E-06 62.7 8.8 65 879-948 223-288 (435)
120 TIGR01386 cztS_silS_copS heavy 95.1 0.061 1.3E-06 63.0 8.7 67 883-949 239-307 (457)
121 PRK11100 sensory histidine kin 95.1 0.074 1.6E-06 62.6 9.4 65 885-949 256-321 (475)
122 PRK09835 sensor kinase CusS; P 95.0 0.07 1.5E-06 63.1 8.9 68 882-949 259-328 (482)
123 PRK10755 sensor protein BasS/P 94.8 0.077 1.7E-06 60.2 8.2 60 884-948 136-196 (356)
124 TIGR02373 photo_yellow photoac 94.6 0.17 3.7E-06 47.1 8.2 41 754-794 28-68 (124)
125 COG3283 TyrR Transcriptional r 94.5 0.12 2.7E-06 56.2 8.1 57 610-666 79-135 (511)
126 TIGR02373 photo_yellow photoac 94.4 0.27 5.9E-06 45.8 9.1 61 616-676 21-82 (124)
127 smart00086 PAC Motif C-termina 94.4 0.18 3.9E-06 34.3 6.5 40 827-866 3-42 (43)
128 PRK09470 cpxA two-component se 94.2 0.13 2.7E-06 60.5 8.5 63 883-948 241-304 (461)
129 PRK11644 sensory histidine kin 94.2 0.21 4.6E-06 59.4 10.3 60 883-942 300-361 (495)
130 TIGR02851 spore_V_T stage V sp 94.0 2.4 5.1E-05 43.0 15.6 126 214-390 52-179 (180)
131 PRK10549 signal transduction h 93.7 0.15 3.3E-06 60.0 7.8 67 882-949 237-304 (466)
132 smart00091 PAS PAS domain. PAS 93.4 0.25 5.3E-06 37.4 6.2 45 741-788 3-47 (67)
133 COG2461 Uncharacterized conser 93.1 0.24 5.3E-06 54.6 7.4 112 740-871 291-402 (409)
134 PRK10841 hybrid sensory kinase 92.8 1.6 3.5E-05 56.1 15.4 112 602-738 325-437 (924)
135 KOG1229 3'5'-cyclic nucleotide 92.3 0.11 2.4E-06 57.2 3.4 103 614-718 160-263 (775)
136 KOG3753 Circadian clock protei 91.9 0.35 7.5E-06 58.0 7.0 197 622-845 193-416 (1114)
137 COG0642 BaeS Signal transducti 91.9 0.66 1.4E-05 50.8 9.2 64 884-948 114-178 (336)
138 KOG3561 Aryl-hydrocarbon recep 88.7 0.5 1.1E-05 57.7 4.9 54 615-668 99-152 (803)
139 KOG0519 Sensory transduction h 88.6 0.073 1.6E-06 66.5 -2.3 70 879-950 213-285 (786)
140 COG3284 AcoR Transcriptional a 87.8 2.8 6.2E-05 49.7 10.1 173 606-787 69-268 (606)
141 smart00086 PAC Motif C-termina 86.9 2.3 4.9E-05 28.4 5.8 35 693-727 9-43 (43)
142 PRK10618 phosphotransfer inter 86.2 6.3 0.00014 50.4 12.8 44 603-646 335-379 (894)
143 COG3283 TyrR Transcriptional r 85.3 2.6 5.7E-05 46.3 7.5 46 740-788 81-126 (511)
144 PRK13837 two-component VirA-li 84.7 40 0.00086 43.1 19.2 132 215-391 293-426 (828)
145 COG3887 Predicted signaling pr 82.2 7.4 0.00016 45.7 9.8 100 609-736 73-172 (655)
146 PF14689 SPOB_a: Sensor_kinase 82.0 8.4 0.00018 31.6 7.6 47 887-937 14-60 (62)
147 PF08446 PAS_2: PAS fold; Int 80.9 3.4 7.4E-05 38.2 5.5 49 623-671 17-69 (110)
148 COG3605 PtsP Signal transducti 80.4 13 0.00028 43.7 10.8 146 201-390 5-154 (756)
149 PF07310 PAS_5: PAS domain; I 79.5 11 0.00024 36.3 8.9 87 630-721 50-136 (137)
150 PF08348 PAS_6: YheO-like PAS 78.6 8.8 0.00019 36.0 7.5 46 824-871 68-113 (118)
151 PF07310 PAS_5: PAS domain; I 77.7 22 0.00048 34.2 10.4 93 755-861 42-136 (137)
152 PRK10490 sensor protein KdpD; 76.0 1.1E+02 0.0023 39.5 18.8 48 332-392 596-644 (895)
153 KOG3559 Transcriptional regula 73.0 7.4 0.00016 43.0 6.1 87 621-709 225-311 (598)
154 COG1956 GAF domain-containing 73.0 1E+02 0.0022 30.4 15.1 107 230-387 48-157 (163)
155 KOG3560 Aryl-hydrocarbon recep 72.3 11 0.00024 43.4 7.4 94 630-726 292-385 (712)
156 PF04340 DUF484: Protein of un 71.6 65 0.0014 33.9 12.9 136 202-390 81-220 (225)
157 KOG3561 Aryl-hydrocarbon recep 67.3 4.9 0.00011 49.5 3.6 52 743-797 99-150 (803)
158 PF07568 HisKA_2: Histidine ki 66.8 19 0.00041 30.8 6.2 49 892-940 2-50 (76)
159 PRK10600 nitrate/nitrite senso 66.4 2.5E+02 0.0055 33.9 18.4 123 202-392 223-346 (569)
160 COG3920 Signal transduction hi 64.4 31 0.00066 36.3 8.6 58 862-926 2-59 (221)
161 PF02743 Cache_1: Cache domain 50.9 64 0.0014 27.5 7.0 56 697-766 11-67 (81)
162 PRK14538 putative bifunctional 50.3 90 0.002 39.6 10.6 46 611-659 102-148 (838)
163 PF03472 Autoind_bind: Autoind 45.6 1E+02 0.0022 29.3 8.4 111 223-367 8-123 (149)
164 COG3887 Predicted signaling pr 43.6 1.8E+02 0.0039 34.8 10.8 38 736-776 72-109 (655)
165 PF08348 PAS_6: YheO-like PAS 43.6 59 0.0013 30.5 5.9 42 691-734 75-116 (118)
166 PRK13719 conjugal transfer tra 39.4 41 0.0009 34.9 4.5 40 610-649 18-57 (217)
167 PF12282 H_kinase_N: Signal tr 38.4 1.7E+02 0.0038 28.4 8.5 112 603-729 17-132 (145)
168 PRK14538 putative bifunctional 35.2 5.6E+02 0.012 32.7 14.2 42 741-788 104-146 (838)
169 KOG0387 Transcription-coupled 32.7 25 0.00054 42.9 1.9 16 229-246 614-629 (923)
170 KOG3753 Circadian clock protei 29.6 73 0.0016 39.3 4.9 49 628-676 338-386 (1114)
171 COG1098 VacB Predicted RNA bin 29.5 35 0.00077 31.9 1.9 24 76-99 15-38 (129)
172 PF13192 Thioredoxin_3: Thiore 28.6 68 0.0015 27.2 3.5 24 441-464 52-75 (76)
173 COG5385 Uncharacterized protei 27.8 1.1E+02 0.0025 30.1 5.0 42 888-929 18-59 (214)
174 COG4191 Signal transduction hi 25.5 3.7E+02 0.0081 32.3 9.6 91 738-863 88-179 (603)
175 PRK10935 nitrate/nitrite senso 24.4 2.4E+02 0.0053 33.8 8.6 55 885-939 360-420 (565)
176 PRK13719 conjugal transfer tra 23.8 1.1E+02 0.0025 31.8 4.6 38 738-778 18-55 (217)
177 PRK13870 transcriptional regul 23.7 6.4E+02 0.014 26.6 10.6 113 213-364 15-131 (234)
178 PF09884 DUF2111: Uncharacteri 22.5 2.3E+02 0.005 24.6 5.3 48 671-725 36-83 (84)
179 PF02070 NMU: Neuromedin U; I 22.3 59 0.0013 21.2 1.3 17 69-85 5-21 (25)
180 COG3275 LytS Putative regulato 22.1 2.6E+02 0.0056 32.7 7.2 119 218-391 225-348 (557)
181 COG3284 AcoR Transcriptional a 21.1 4.9E+02 0.011 31.5 9.6 25 837-861 155-179 (606)
182 COG4564 Signal transduction hi 20.1 1.1E+03 0.024 26.3 11.1 63 741-824 82-146 (459)
183 PRK04158 transcriptional repre 20.1 9.1E+02 0.02 25.9 10.4 48 331-392 110-157 (256)
184 COG2205 KdpD Osmosensitive K+ 20.0 1.8E+03 0.04 27.9 17.7 128 203-393 514-641 (890)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=5.6e-120 Score=996.25 Aligned_cols=480 Identities=34% Similarity=0.618 Sum_probs=428.6
Q ss_pred hhcccCCCCCCccceEEEEecCCceEEEEccChhhhhCCCCCCCCCcccchhhccCCchhhccChhhHHHHHHHhccCCC
Q 002210 68 LQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEV 147 (953)
Q Consensus 68 ~~~i~~~g~iQ~~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 147 (953)
-+|||+||+||||||||++|+.++.|+|+|+||..+||+.|++ ++|+++.++|+..+...++.++..+..
T Consensus 17 ~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~----------l~~~tl~~vl~~~qv~~l~~~l~~~~~ 86 (750)
T COG4251 17 REPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPED----------LLGRTLGAVLTSEQVPPLQSALTVGGL 86 (750)
T ss_pred cCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhh----------hhcCCHHHhcchhhccHHHHhccccCc
Confidence 4799999999999999999999999999999999999999875 689999999999999999999999888
Q ss_pred CCCCceEEeecCCCceEEEEEEeeCCEEEEEEeeCCCCCCcchhhhhhHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHH
Q 002210 148 NLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLLCDVLVNEV 227 (953)
Q Consensus 148 ~~~~~~~~~~~~~~~~~~~~~h~~~~~~~ie~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~v~~v 227 (953)
...||..+..+. +..|++++||+++.+|+||||+...+.. ..+.+++++..++.+||+. .++.++|+.++++|
T Consensus 87 ~~~np~~~w~~~-~~~fDv~~HR~~~llIlEfEp~~t~e~~----~~l~f~h~~k~a~~~lq~a--~~l~~l~~~~tqeV 159 (750)
T COG4251 87 TTLNPTKMWTRK-GGSFDVSAHRSKELLILEFEPAGTGETA----SFLGFYHLAKLAMNRLQSA--ANLRDLLSRTTQEV 159 (750)
T ss_pred ccCCchhhhhhc-CCceeEEEEecCcEEEEEEecCcccccc----cccchHHHHHHHHHHHhcC--ccHHHHHHHHHHHH
Confidence 888885443232 3389999999999999999997544321 2345678888899999994 49999999999999
Q ss_pred HhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCCceeee--CCCCCC
Q 002210 228 SDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ--DKKLDQ 305 (953)
Q Consensus 228 r~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~~~l~~--~~~~~~ 305 (953)
|++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|.||||.| +|.++.
T Consensus 160 r~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavNp~t~~ 239 (750)
T COG4251 160 RRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNE 239 (750)
T ss_pred HHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccCcccCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998 688999
Q ss_pred ccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCCCChhHHHHHHHHHHH
Q 002210 306 PLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQV 385 (953)
Q Consensus 306 ~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~ 385 (953)
|+|||+|.|||+||||+|||+||||.||||||||++ |||||||+|||.|||++|+++|.+|||++|+
T Consensus 240 p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~-------------g~LWGLIACHH~sPk~ip~~vR~acef~gq~ 306 (750)
T COG4251 240 PLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD-------------GKLWGLIACHHQSPKVIPYEVRKACEFFGQV 306 (750)
T ss_pred cccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC-------------CeeEEeeeeccCCCccCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred HHHhhHHHHHHHHHHHHHHHH-HHHHHHHHhhccCCC-CccccCCcchhhhccCCeEEEEECCeEEEeCCCCCHHHHHHH
Q 002210 386 FGVQVNKEVELSAQLREKHIL-RTQTVLCDMLLRDSP-VGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDI 463 (953)
Q Consensus 386 ~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~l~~l~~~dg~a~~~~~~~~~~G~~p~~~~~~~l 463 (953)
+|++|+...+.+......... ....++..|...+++ .+++...+++++|++|||++++++|+|.++|.||+..++..|
T Consensus 307 ~s~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~L 386 (750)
T COG4251 307 LSMEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRL 386 (750)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHH
Confidence 999997654322211111111 222344455555554 678888999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCeEEEecccCcCCCCCccccccccceEEEEEeCC--CCEEEEeccCcccEEeccCCCCCCCC-CCCCccc
Q 002210 464 AEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITS--KDFLFWFRSHTAKEIKWGGAKHDSGG-KDGGRKM 540 (953)
Q Consensus 464 ~~~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~~~~~i~~--~~~l~wfR~e~~~~v~WaG~p~~~~~-~~dg~~l 540 (953)
+.||.+... ..+|.||+|+.. ||.++.|++.+|||+|++|+. ++|++|||+|..++|+|||+|+|++. +++|.|+
T Consensus 387 l~wl~~~~~-~~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL 464 (750)
T COG4251 387 LQWLAEREE-GDVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRL 464 (750)
T ss_pred HHHHhcCCc-ccEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCccc
Confidence 999988744 479999999985 999999999999999999997 89999999999999999999999987 4567899
Q ss_pred cccccccceeeeeeccccCchhhHHHHHHHHHHHHHHHh
Q 002210 541 HPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSL 579 (953)
Q Consensus 541 ~PR~SF~~w~e~v~g~s~pW~~~ei~aa~~L~~il~~~~ 579 (953)
+||+||+.|+|+|++++.||...|++++.+++..+.+..
T Consensus 465 ~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~iv 503 (750)
T COG4251 465 TPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIV 503 (750)
T ss_pred CCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999987655543
No 2
>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []. The protein undergoes reversible photochemical conversion between a biologically-inactive red light-absorbing form and the active far-red light-absorbing form. Phytochrome is a dimer of identical 124 kDa subunits, each of which contains a linear tetrapyrrole chromophore, covalently-attached via a Cys residue. This domain represents a region specific to phytochrome proteins.; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3C2W_G 3NHQ_B 3G6O_B 3IBR_A 2VEA_A 3ZQ5_A.
Probab=99.97 E-value=8.6e-32 Score=271.67 Aligned_cols=170 Identities=38% Similarity=0.716 Sum_probs=140.5
Q ss_pred HHHHHHhhcc-CC-CCccccCCcchhhhccCCeEEEEECCeEEEeCCCCCHHHHHHHHHHHHhhcCCCeEEEecccCcCC
Q 002210 409 QTVLCDMLLR-DS-PVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAG 486 (953)
Q Consensus 409 ~~~~~~~~~~-~~-~~~~~~~~~~l~~l~~~dg~a~~~~~~~~~~G~~p~~~~~~~l~~~l~~~~~~~~~~~t~~l~~~~ 486 (953)
++.|..++.. .. ..++..+.++|++|++|||+||+++|+++++|.+|+..++.+|++||.... +..+|+|++|.+.
T Consensus 5 ~~~L~~~~~~~~~~~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~-~~~v~~T~~L~~~- 82 (182)
T PF00360_consen 5 QQRLLEALSSSRDLLEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQA-DGEVFATDSLSED- 82 (182)
T ss_dssp HHHHHHHHHCSSSHHHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTT-T-SEEEESBGGGT-
T ss_pred HHHHHHHHccCCChhHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhC-CCccchhhhHhHh-
Confidence 3444444443 33 367888999999999999999999999999999999999999999999774 4479999999985
Q ss_pred CCCccccccccceEEEEEeCC--CCEEEEeccCcccEEeccCCCCCCCCCC-CCccccccccccceeeeeeccccCchhh
Q 002210 487 YPGALALGDAVCGIAAVKITS--KDFLFWFRSHTAKEIKWGGAKHDSGGKD-GGRKMHPRSSFKAFLEVVKQRSLPWEDV 563 (953)
Q Consensus 487 ~p~~~~~~~~~~g~~~~~i~~--~~~l~wfR~e~~~~v~WaG~p~~~~~~~-dg~~l~PR~SF~~w~e~v~g~s~pW~~~ 563 (953)
||++.++.+.+||||+++|+. ++|++|||+|+.++|+|||+|+|++..+ +|.+++||+||+.|+|.|+|+|.||...
T Consensus 83 ~p~~~~~~~~aaGvLai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~~~ 162 (182)
T PF00360_consen 83 YPDAAALAERAAGVLAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWSDA 162 (182)
T ss_dssp SGGGGGGCCCHSEEEEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---HH
T ss_pred ChhhhhhcccCCCcEEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCCHH
Confidence 999999999999999999985 6899999999999999999999998743 5789999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhH
Q 002210 564 EMDAIHSLQLILRGSLQ 580 (953)
Q Consensus 564 ei~aa~~L~~il~~~~~ 580 (953)
|+.++..++..+.....
T Consensus 163 d~~~A~~lr~~l~~~~~ 179 (182)
T PF00360_consen 163 DLEAAERLRRALLEVIL 179 (182)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999776665543
No 3
>PRK13560 hypothetical protein; Provisional
Probab=99.97 E-value=1.3e-28 Score=309.81 Aligned_cols=329 Identities=16% Similarity=0.140 Sum_probs=252.9
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccce
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN 681 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~ 681 (953)
++++|++++++++.+++++|++++++|.+|+++++|+++++++||+.++++|+++.++.++...+.........+..+..
T Consensus 195 ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 (807)
T PRK13560 195 AEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGS 274 (807)
T ss_pred HHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCc
Confidence 44568888999999999999999999999999999999999999999999999999988776665554444444433333
Q ss_pred EEEEEEEcccCCCCCEEEEEE--EEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeec
Q 002210 682 VEIKLRAFGPRETSGPVILVV--NACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTD 759 (953)
Q Consensus 682 ~e~~~~~~~~~~dG~~~~v~v--~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D 759 (953)
..++... .++||..+|+.+ +..|+.+.+|.+.|++++++|||++|++|++|++++++|+.++++++. +++.+|
T Consensus 275 ~~~e~~~--~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~---~i~~~d 349 (807)
T PRK13560 275 QIIEAEF--QNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPI---AAIGLD 349 (807)
T ss_pred eEEEEEE--EcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcc---cEEEEc
Confidence 3333332 466899886554 456678889999999999999999999999999999999999999987 899999
Q ss_pred CCccEEeh-hHHHHHHhCCChhhhhccccccccc---------------ccc----------------------------
Q 002210 760 EDGRCLEW-NDGMEKLSGLKREEAIERMLIGEVF---------------TVK---------------------------- 795 (953)
Q Consensus 760 ~~G~i~~~-N~a~~~l~G~~~eeliGk~~~~~~~---------------~~~---------------------------- 795 (953)
.+|+++++ |+++++++||+.++++|+++.+... +..
T Consensus 350 ~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 429 (807)
T PRK13560 350 ADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQEVLIE 429 (807)
T ss_pred CCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCceEEEE
Confidence 99999987 6788889999999999986532110 000
Q ss_pred ------------------cccc----------------------------------------------------------
Q 002210 796 ------------------NFGC---------------------------------------------------------- 799 (953)
Q Consensus 796 ------------------~~~~---------------------------------------------------------- 799 (953)
.++.
T Consensus 430 ~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~~~~~G~ 509 (807)
T PRK13560 430 REDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKNITQFGY 509 (807)
T ss_pred cCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecchhhhcCC
Confidence 0000
Q ss_pred -------------cccCcchHHHHHHHHHHHh-cCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEecc
Q 002210 800 -------------RVKNHDTLTKLRIVMNKVI-SGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVAS 865 (953)
Q Consensus 800 -------------~l~~~~~~~~~~~~l~~~~-~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DIT 865 (953)
.+.+++....+...+.... .+...+..++++.+++|.++|+.....|++|.+|++.+++++++|||
T Consensus 510 ~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~~~DIT 589 (807)
T PRK13560 510 EPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGIVIDIS 589 (807)
T ss_pred CHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEEEechH
Confidence 0000011111111111111 12234467888999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh
Q 002210 866 PELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD 939 (953)
Q Consensus 866 erK~~e~elq~~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D 939 (953)
++|++|+++++. ...+..|++.|||||||||++|.|+++++.....+++.+.++..+......|..+++.
T Consensus 590 erK~aE~~L~~a----~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 659 (807)
T PRK13560 590 ERKHAEEKIKAA----LTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAMALAHEK 659 (807)
T ss_pred HHHHHHHHHHHH----HHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999998776544 3457789999999999999999999999988777888888877776655566555554
No 4
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=99.94 E-value=3.2e-25 Score=262.41 Aligned_cols=310 Identities=13% Similarity=0.044 Sum_probs=223.8
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcc
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFG 690 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~ 690 (953)
+.|+.+++.++++++++|.+|+++++|+++++++||+.++++|++...+.++.........+...+..+..+..+...
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-- 81 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLN-- 81 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceeec--
Confidence 467889999999999999999999999999999999999999998776665544444444444444333344333332
Q ss_pred cCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHH
Q 002210 691 PRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDG 770 (953)
Q Consensus 691 ~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a 770 (953)
.+++|..+|+.....|+++.+|.+.+++++++|||++|++++++++++..++.++++.+. +++++|.+|+++++|++
T Consensus 82 ~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~---~i~~~d~~~~i~~~N~~ 158 (494)
T TIGR02938 82 RRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPV---AFVLLDPTGRVILDNQE 158 (494)
T ss_pred cCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccc---eEEEEcCCCCEEEechh
Confidence 567899999999999999999999999999999999999999999999999999999987 89999999999999999
Q ss_pred HHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCC-EEEEEEEEEEeec
Q 002210 771 MEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGK-YVEALLSANKRTN 849 (953)
Q Consensus 771 ~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~-~~~v~~s~~pi~d 849 (953)
+++++|+...+..+..+...+.+. ....+...+. .+......+.++...+|. .+|+.....++.+
T Consensus 159 ~~~~~g~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (494)
T TIGR02938 159 YKKLATDLRVKEPAHTVLDLLREA-----------WREALAENWP---QQLAFSNREARFDRGGGRPARWLSCTGSVIGM 224 (494)
T ss_pred HHHhhchhhhhHHHHHHHHHhhHH-----------hhhhhhhcch---hhhccccceeeeccCCCceeeEEEecCceEEe
Confidence 999999998887776554322211 1111111111 111112234455555655 7899988888776
Q ss_pred CCCCE---------EEEEEEEEeccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCC
Q 002210 850 AEGKI---------SGILCFLHVASPELQYALQVQRISEQA-------AANSLNKLEYIRREIRKPLNGIAFMQNLMGTS 913 (953)
Q Consensus 850 ~~G~i---------~g~v~v~~DITerK~~e~elq~~ae~~-------~~~k~~fla~isHELrnPL~~I~g~~~LL~~~ 913 (953)
..|.. .+++++++|||++|+++++++..+.++ .+...++++.++|++||||++|.+++++|...
T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~~~al~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~i~~~~~~l~~~ 304 (494)
T TIGR02938 225 ESDCADSFFCAAEQPYLLLTIADISNLREEQERARLSALQALMAEEERLEAIRETLSAAIHRLQGPMNLISAAISVLQRR 304 (494)
T ss_pred ecchhhheeccCCCchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHhc
Confidence 66554 345668899999999887765433222 22334557788899999999999999999874
Q ss_pred CCC---HHHHHHHHHHHHHHHHHHhHhhh
Q 002210 914 DLS---EEQKQLLKTSVLCQEQLTNIVDD 939 (953)
Q Consensus 914 ~l~---e~~~~~l~~i~~~~~~L~~lI~D 939 (953)
..+ +.....+..+.....++...+++
T Consensus 305 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 333 (494)
T TIGR02938 305 GDDAGNPASAAMLQQALSAGREHMEALRQ 333 (494)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333 33444444443333344444444
No 5
>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=99.90 E-value=2.5e-24 Score=199.27 Aligned_cols=109 Identities=30% Similarity=0.502 Sum_probs=92.6
Q ss_pred hhhcccCCCCCCccceEEEEecCCceEEEEccChhhhhCCCCCCCCCcccchhhccCCchhhccChhhHHHHHHHhccCC
Q 002210 67 YLQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGE 146 (953)
Q Consensus 67 ~~~~i~~~g~iQ~~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 146 (953)
+-||||+||+|||||+|||+|+++++|+|||+|++++||++|. + +..++|+++.++|++...+.+++++....
T Consensus 2 ~~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~-~------~~~llG~~l~~ll~~~~~~~l~~~~~~~~ 74 (110)
T PF08446_consen 2 DREPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPE-L------PEELLGRPLSELLGAESAERLREALQSES 74 (110)
T ss_dssp GGS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS-----------HHHHTTCBHHHHSCCCCHHHHHHHCTCCC
T ss_pred CcccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccc-c------chhhcccCHHHHhCHHHHHHHHHhhhccC
Confidence 4689999999999999999999999999999999999999842 0 12479999999999999999999988887
Q ss_pred CCCCCceEEeecCCCceEEEEEEeeCCEEEEEEeeC
Q 002210 147 VNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPV 182 (953)
Q Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~ie~Ep~ 182 (953)
....+|+.+++..+++.|++++||+++++||||||+
T Consensus 75 ~~~~~~~~~~~~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 75 LSLSNPIALRLRIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCCEEEEEEEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred ccccCCeEEEeccCCeeEEEEEEEECCEEEEEEeeC
Confidence 777889988777778899999999999999999995
No 6
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.90 E-value=4e-22 Score=259.41 Aligned_cols=263 Identities=13% Similarity=0.105 Sum_probs=224.5
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh-cccc
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF-LEER 680 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l-~~~~ 680 (953)
..+++++++++++.++++++++|+.+|.+|+++++|+++++++||+.++++|+++.+++++++.+.....+.... +...
T Consensus 274 ~~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 353 (1092)
T PRK09776 274 ERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEIN 353 (1092)
T ss_pred HHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCcc
Confidence 345688899999999999999999999999999999999999999999999999999999988877766666666 3333
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecC
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDE 760 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~ 760 (953)
.+..+.+. .++||..+|+.++..++++.+|.+.+++++.+|||++|++|+++++++++++.+.+..+. ++|.+|.
T Consensus 354 ~~~~e~~~--~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~---~i~~~d~ 428 (1092)
T PRK09776 354 SYSMEKRY--YRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGI---GIWEWDL 428 (1092)
T ss_pred ceeeeeEE--EcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCc---eEEEEec
Confidence 44444443 567899999999999999999999999999999999999999999999999999999877 8999999
Q ss_pred CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEE
Q 002210 761 DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEA 840 (953)
Q Consensus 761 ~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v 840 (953)
+|++++||+++++++||+.++..+...+.. ..+++....+...+.....++.....+++++++|| .+|+
T Consensus 429 ~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~----------~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~w~ 497 (1092)
T PRK09776 429 KPNIISWDKRMFELYEIPPHIKPTWQVWYA----------CLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VRHI 497 (1092)
T ss_pred CCCeEeeCHHHHHHhCCCcccCCCHHHHHH----------hcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eEEE
Confidence 999999999999999999888444322211 12234444566667777788888889999999999 9999
Q ss_pred EEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHH
Q 002210 841 LLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQ 880 (953)
Q Consensus 841 ~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~ 880 (953)
.....++.|.+|++.+++++.+|||++|+.++++++..++
T Consensus 498 ~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~ 537 (1092)
T PRK09776 498 RALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKER 537 (1092)
T ss_pred EEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998887765543
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.89 E-value=5.9e-22 Score=248.17 Aligned_cols=211 Identities=20% Similarity=0.237 Sum_probs=185.6
Q ss_pred EecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccc
Q 002210 722 QDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRV 801 (953)
Q Consensus 722 ~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l 801 (953)
++|++++++++++++++..++.+++++++ +|+++|.+|+|+++|+++++++||+.++++|+++.+ +++.
T Consensus 138 ~~i~~r~~~~~~l~~~~~~l~~il~~~~~---~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~-l~~~------- 206 (779)
T PRK11091 138 NEIKEREETQIELEQQSSLLRSFLDASPD---LVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKD-VYSP------- 206 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcc---eEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHH-hCCH-------
Confidence 68999999999999999999999999988 899999999999999999999999999999998763 3322
Q ss_pred cCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHH
Q 002210 802 KNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQA 881 (953)
Q Consensus 802 ~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~ 881 (953)
+....+.........++....++..+.+++|+.+|+.++..|+.|.+|++.|++++++|||++|+++.++++ +
T Consensus 207 ---~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~----a 279 (779)
T PRK11091 207 ---EAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEK----A 279 (779)
T ss_pred ---HHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHH----H
Confidence 223334444555566666778888889999999999999999999999999999999999999988866543 3
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
.+.|.+|+++|+|||||||++|.|++++|....++++++++++.+..++++|..+++| +|++|++.|+.
T Consensus 280 ~~~~~~~~a~isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~ 349 (779)
T PRK11091 280 SRDKTTFISTISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKL 349 (779)
T ss_pred HHHHHHHHHHhhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCc
Confidence 4567899999999999999999999999998889999999999999999999999999 89999999863
No 8
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.88 E-value=7.1e-21 Score=247.71 Aligned_cols=262 Identities=12% Similarity=0.078 Sum_probs=215.4
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCC-ccccccCCcHHHHHHHHHHHhcccc
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTA-LVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~-~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
.++++++.+++++.+++..++++|.+|.++++++||+++.+++|++.++..+.. +.+.+++++.+.....+......+.
T Consensus 401 ~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~ 480 (1092)
T PRK09776 401 TEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRS 480 (1092)
T ss_pred HHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCC
Confidence 345678888899999999999999999999999999999999999988844432 3467788888888777877776666
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecC
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDE 760 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~ 760 (953)
.+..+++. .++|| .+|+.....++++.+|++.+++++.+|||++|++++++++.+++++.++++.++ +++.+|.
T Consensus 481 ~~~~e~r~--~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~---~i~~~D~ 554 (1092)
T PRK09776 481 PFKLEFRI--VVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGE---AVVCTDM 554 (1092)
T ss_pred CeeEEEEE--EcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhcccc---EEEEECC
Confidence 66666555 56789 999999999999999999999999999999999999999999999999999987 8999999
Q ss_pred CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCc--ceEEEEEEccCCCEE
Q 002210 761 DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDA--DKILFGFFDQQGKYV 838 (953)
Q Consensus 761 ~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~--~~~e~~~~~kdG~~~ 838 (953)
+|+++++|+++++++||+.++++|+++...+...+.+ .... ... +......... ...++.+.+++|+.+
T Consensus 555 ~g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~-----~~~~---~~~-~~~~~~~~~~~~~~~~~~~~~~~G~~~ 625 (1092)
T PRK09776 555 AMKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGD-----NGPL---MEN-IYSCLTSRSAAYLEQDVVLHCRSGGSY 625 (1092)
T ss_pred CCeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCC-----cchh---hHH-HHHHHhcCCCccccceEEEEeCCCcEE
Confidence 9999999999999999999999999875433222111 0111 111 3333333322 345677889999999
Q ss_pred EEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHH
Q 002210 839 EALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRIS 878 (953)
Q Consensus 839 ~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~a 878 (953)
|+..+..|+.|.+|++.|++++++|||++|+.++++++.+
T Consensus 626 ~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~L~~~a 665 (1092)
T PRK09776 626 DVHYSITPLSTLDGENIGSVLVIQDVTESRKMLRQLSYSA 665 (1092)
T ss_pred EEEEEeeeeecCCCCEEEEEEEEEecchHHHHHHHHHhhc
Confidence 9999999999999999999999999999999887776544
No 9
>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=99.87 E-value=1.6e-20 Score=219.69 Aligned_cols=242 Identities=17% Similarity=0.131 Sum_probs=184.5
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcC-CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccce
Q 002210 603 IDELRIITNEMVRLIETAAVPILAVDA-SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN 681 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle~~~~~I~~~D~-dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~ 681 (953)
..+|++.+++|+.++++++++|+++|. +|+|+++|+++++++||+.++++|+++.+++++++.+.+...+......+..
T Consensus 125 ~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~ 204 (442)
T TIGR02040 125 YWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSA 204 (442)
T ss_pred HHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCC
Confidence 346888899999999999999999998 8999999999999999999999999999999988888777777777644444
Q ss_pred EEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCC
Q 002210 682 VEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDED 761 (953)
Q Consensus 682 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~ 761 (953)
....+.. + +|+..| .+...++.. +|.. .+++...|||++++.++++. .+|+.+++++++ +|+++|.+
T Consensus 205 ~~~~~~~---~-~~~~~~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~~~---~~~~~l~e~~~d---~I~v~D~~ 271 (442)
T TIGR02040 205 APVRILL---R-RSQKRL-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDELS---ENLARLYHEAPD---AIVFSDAD 271 (442)
T ss_pred cceEEEE---c-CCCeEE-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHHHH---HHHHHHHHhCCc---eEEEEcCC
Confidence 3333332 2 233333 335555554 3333 56677899999998876653 379999999988 99999999
Q ss_pred ccEEehhHHHHHHhCCC-hhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEE
Q 002210 762 GRCLEWNDGMEKLSGLK-REEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEA 840 (953)
Q Consensus 762 G~i~~~N~a~~~l~G~~-~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v 840 (953)
|+|+++|+++++++||+ .++++|+++...+.+. ... +...+.....++....++..+.+++|+.+|+
T Consensus 272 G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~---------~~~---~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~v 339 (442)
T TIGR02040 272 GTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRG---------GVD---LRVLLSNVRRTGQVRLYATTLTGEFGAQTEV 339 (442)
T ss_pred CcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCC---------ccc---HHHHHHHHhhcCceEEEEEEEEcCCCCEEEE
Confidence 99999999999999997 5789999875332211 111 1222333334444456777889999999999
Q ss_pred EEEEEEeecCCCCEEEEEEEEEeccHHHHHH
Q 002210 841 LLSANKRTNAEGKISGILCFLHVASPELQYA 871 (953)
Q Consensus 841 ~~s~~pi~d~~G~i~g~v~v~~DITerK~~e 871 (953)
.+++.|+.+.++ ..++++++|||+||+.+
T Consensus 340 e~s~~~i~~~~~--~~~~~v~rDITeR~~~~ 368 (442)
T TIGR02040 340 EISAAWVDQGER--PLIVLVIRDISRRLTMR 368 (442)
T ss_pred EEEEEEeccCCc--eEEEEEEecchhhccCC
Confidence 999999986555 35788999999998664
No 10
>PRK13560 hypothetical protein; Provisional
Probab=99.85 E-value=1.1e-19 Score=228.98 Aligned_cols=259 Identities=14% Similarity=0.120 Sum_probs=195.0
Q ss_pred cHHHHHHHHHHH-HHHHHhcCccEEEEcCCCc----EEecCHHHHHHhCCCcchhcCC--CccccccCCcHHHHHH----
Q 002210 602 KIDELRIITNEM-VRLIETAAVPILAVDASGN----VNGWNSKAAELTGLTVDQAIGT--ALVDLVAGDSVDVVKN---- 670 (953)
Q Consensus 602 ~~~eL~~~~~~l-~~lle~~~~~I~~~D~dg~----i~~~N~a~~~l~G~~~~eliG~--~~~dl~~~~~~~~~~~---- 670 (953)
+..++++.++.+ +.+++++|.+++.++.+|. +.+++.+...++|+...++++. .+..++||++.+.+..
T Consensus 58 ~~~~l~~~~e~~~r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~ 137 (807)
T PRK13560 58 AEAEAQDCREQCERNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFR 137 (807)
T ss_pred HHHHHHHHHHHHHHHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhh
Confidence 456677777778 9999999999999887776 3336777778888887776653 2446788888775532
Q ss_pred ---HHHHHhcccceEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhC
Q 002210 671 ---MLSSAFLEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSS 747 (953)
Q Consensus 671 ---~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~ 747 (953)
.+..++......+++++. +++||. |+.+...|.++.+|.+ ++.++..|||++|++|++|++++.+|+.++++
T Consensus 138 ~~~~~~~~~~~~~~~~~e~r~--~~~dg~--~~~~~~~~~~~~~g~~-~~~g~~~DIT~rk~ae~~l~~~~~~l~~l~e~ 212 (807)
T PRK13560 138 SAETIAMALQSDDWQEEEGHF--RCGDGR--FIDCCLRFERHAHADD-QVDGFAEDITERKRAEERIDEALHFLQQLLDN 212 (807)
T ss_pred HHHHHHHHhccCcccceEEEE--EeCCcc--EEEEEeeeeecCCCce-EEEEEEEccchHHHHHHHHHHHHHHHHHHHhh
Confidence 222233333334444444 345674 5666778888877775 68899999999999999999999999999999
Q ss_pred CCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEE
Q 002210 748 PSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKIL 827 (953)
Q Consensus 748 ~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e 827 (953)
+++ +++++|.+|+++++|+++++++||+.++++|+++.+ +++.. ....+..........+....++
T Consensus 213 ~~~---~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~-~~~~~----------~~~~~~~~~~~~~~~~~~~~~e 278 (807)
T PRK13560 213 IAD---PAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHD-FAPAQ----------PADDYQEADAAKFDADGSQIIE 278 (807)
T ss_pred CCC---eEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchh-cCCcc----------hhHHHHHHHHHHhccCCceEEE
Confidence 988 899999999999999999999999999999998763 33321 1111222233334445556788
Q ss_pred EEEEccCCCEEEEEEE--EEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHH
Q 002210 828 FGFFDQQGKYVEALLS--ANKRTNAEGKISGILCFLHVASPELQYALQVQRISE 879 (953)
Q Consensus 828 ~~~~~kdG~~~~v~~s--~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae 879 (953)
.+++++||+.+|+.+. ..++.|.+|.+.|++++++|||++|+++.++++..+
T Consensus 279 ~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~ 332 (807)
T PRK13560 279 AEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKED 332 (807)
T ss_pred EEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHH
Confidence 8999999999966554 456789999999999999999999999988776544
No 11
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.80 E-value=7.6e-18 Score=212.19 Aligned_cols=242 Identities=12% Similarity=0.093 Sum_probs=186.5
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccc----eEEEEE
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER----NVEIKL 686 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~----~~e~~~ 686 (953)
..+..+++.++++++++|.+|+|++||+++++++||+.++++|+++.++++++........+......+. ....++
T Consensus 12 ~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 91 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSREL 91 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccceee
Confidence 4456788999999999999999999999999999999999999999998887766544444444442211 111222
Q ss_pred EEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEe
Q 002210 687 RAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLE 766 (953)
Q Consensus 687 ~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~ 766 (953)
+ ..++||..+|+.+...++. .+|.. +++++.+|||++++.+++. ..+..++++.+. +++.+|.+|++++
T Consensus 92 ~--~~~~dG~~~~v~~~~~~~~-~~g~~-~~~~~~~DiT~~~~~~~~~----~~~~~~~~~~~~---~i~~~d~~g~i~~ 160 (799)
T PRK11359 92 Q--LEKKDGSKIWTRFALSKVS-AEGKV-YYLALVRDASVEMAQKEQT----RQLIIAVDHLDR---PVIVLDPERRIVQ 160 (799)
T ss_pred E--EecCCcCEEEEEEEeeeec-cCCce-EEEEEEeeccchhhhHHHH----HHHHHHHhcCCC---cEEEEcCCCcEEE
Confidence 2 2466899999998887764 35554 5678889999988776654 445667888876 8999999999999
Q ss_pred hhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEE
Q 002210 767 WNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANK 846 (953)
Q Consensus 767 ~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~p 846 (953)
+|+++++++||+.++++|+.+...+.++. ........+.....+......++++.+++|..+|+..+..|
T Consensus 161 ~N~~~~~l~G~~~~e~~g~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~ 230 (799)
T PRK11359 161 CNRAFTEMFGYCISEASGMQPDTLLNIPE----------FPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISP 230 (799)
T ss_pred EChhhHhhhCCCHHHHCCCChHHhcCCCC----------CcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeee
Confidence 99999999999999999998754333221 11112333444555555667788889999999999999999
Q ss_pred eecCCCCEEEEEEEEEeccHHHHHHHH
Q 002210 847 RTNAEGKISGILCFLHVASPELQYALQ 873 (953)
Q Consensus 847 i~d~~G~i~g~v~v~~DITerK~~e~e 873 (953)
+.|.+|.+.|++++.+|||++|+.++.
T Consensus 231 v~d~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 231 VYDVLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred eecCCCceeEEEEEeehhhhHHHHHHH
Confidence 999999999999999999999976643
No 12
>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=99.77 E-value=1.5e-17 Score=194.70 Aligned_cols=232 Identities=18% Similarity=0.168 Sum_probs=169.5
Q ss_pred HHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhccc-ceEEEEEEEcccCCCC
Q 002210 617 IETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEE-RNVEIKLRAFGPRETS 695 (953)
Q Consensus 617 le~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~-~~~e~~~~~~~~~~dG 695 (953)
++.++++++++|.+|+|++||..+++++||+.++++|+++.+++++++.+.+...+......+ ..++.+ .....++|
T Consensus 2 ~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e--~~~~~~~g 79 (442)
T TIGR02040 2 LATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVE--LNHIDPSS 79 (442)
T ss_pred CcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEe--eccCCCCC
Confidence 578899999999999999999999999999999999999999999988777777776666333 233333 33344566
Q ss_pred CEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHH-----------HH---HHHHHHHHHHHHHhCCCCCCCCeEeecC-
Q 002210 696 GPVILVVNACCTQDTKENVIGVCFVGQDITGQKLV-----------MD---KYTRIQGDYVGIVSSPSALIPPIFMTDE- 760 (953)
Q Consensus 696 ~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~-----------E~---~L~~se~~~~~i~e~~~~li~~I~~~D~- 760 (953)
..+|+.++..+..+ + .+++++.+|||+++.. |+ ++++++++|+.+++++++ ++|++|.
T Consensus 80 ~~~~~~~~~~~~~~--~--~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l~~~e~r~~~l~e~~~~---~i~~~d~~ 152 (442)
T TIGR02040 80 FELPMRFILVRLGA--D--RGVLALGRDLRAVAELQQQLVAAQQAMERDYWTLREMETRYRVVLEVSSD---AVLLVDMS 152 (442)
T ss_pred CccCeEEEEEEeCC--C--CeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCc---eEEEEECC
Confidence 67777777777654 2 2667788999875543 33 567778899999999987 8999998
Q ss_pred CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEE
Q 002210 761 DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEA 840 (953)
Q Consensus 761 ~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v 840 (953)
+|+++++|+++++++||+.++++|+++...+. ++....+...+.....++.....+ +..++|...|
T Consensus 153 ~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~-----------~~~~~~~~~~l~~~~~~g~~~~~~--~~~~~~~~~~- 218 (442)
T TIGR02040 153 TGRIVEANSAAAALLGGVGQSLVGRAFPQEFE-----------GRRREELMLTLRNVRATGSAAPVR--ILLRRSQKRL- 218 (442)
T ss_pred CCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCC-----------HHHHHHHHHHHHHHHhcCCCcceE--EEEcCCCeEE-
Confidence 79999999999999999999999998764332 223334555566655555443433 4445555444
Q ss_pred EEEEEEeecCCCCEEEEEEEEEeccHHHHHHHH
Q 002210 841 LLSANKRTNAEGKISGILCFLHVASPELQYALQ 873 (953)
Q Consensus 841 ~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~e 873 (953)
.+...++.. +|.. ++++.+.|||++++.+.+
T Consensus 219 ~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~ 249 (442)
T TIGR02040 219 LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDE 249 (442)
T ss_pred EEEEEEEEe-CCce-EEEEEEcccchhhhhhHH
Confidence 345555543 3433 567889999999876644
No 13
>PRK13557 histidine kinase; Provisional
Probab=99.68 E-value=2.3e-15 Score=180.65 Aligned_cols=198 Identities=10% Similarity=0.009 Sum_probs=155.6
Q ss_pred HHHHHHHHHHHHhCCCCCCCCeEeecC---CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHH
Q 002210 734 YTRIQGDYVGIVSSPSALIPPIFMTDE---DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKL 810 (953)
Q Consensus 734 L~~se~~~~~i~e~~~~li~~I~~~D~---~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~ 810 (953)
....+..|+.++++++. +|+++|. +|+|+|+|+++++++||+.++++|+++...+.+.. ....
T Consensus 25 ~~~~~~~~~~~~~~~~~---~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~-----------~~~~ 90 (540)
T PRK13557 25 SDHRSDIFFAAVETTRM---PMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPET-----------DRAT 90 (540)
T ss_pred hhhhhHHHHHHHHhCcC---cEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCC-----------CHHH
Confidence 34457789999999887 8999995 78999999999999999999999998763332221 1112
Q ss_pred HHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002210 811 RIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLE 890 (953)
Q Consensus 811 ~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla 890 (953)
...+...+..+.....++...+++|+.+|+..+..|+.+.+|.+++++++.+|||++++++.++++..+. .....+++
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~~~--~~l~~~~~ 168 (540)
T PRK13557 91 VAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQKM--EALGQLTG 168 (540)
T ss_pred HHHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHHHH--HHhhhhhh
Confidence 3334444444555566777889999999999999999999999999999999999999887666543332 23456788
Q ss_pred HHHHHhhhHHHHHHHHHHhhcC-----CCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhc
Q 002210 891 YIRREIRKPLNGIAFMQNLMGT-----SDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEE 947 (953)
Q Consensus 891 ~isHELrnPL~~I~g~~~LL~~-----~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~ 947 (953)
.++|++||||+.|.+++++|.. ....+...+.++.+...++++..++++ +++++...
T Consensus 169 ~i~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~~~ 231 (540)
T PRK13557 169 GIAHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARKQR 231 (540)
T ss_pred hhhHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC
Confidence 9999999999999999998864 223456778899999999999999999 68877543
No 14
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.67 E-value=1.8e-15 Score=158.42 Aligned_cols=197 Identities=15% Similarity=0.219 Sum_probs=154.1
Q ss_pred EEecchhHHHH-HHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccc
Q 002210 721 GQDITGQKLVM-DKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGC 799 (953)
Q Consensus 721 ~~DITerk~~E-~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~ 799 (953)
+.|.|++.+.. .-++..+.++..++..+.+ |++..|..|+|+.+|..+.+++|.+.|+++|+.+.+.+-..
T Consensus 92 fn~Lt~~~~~aq~n~e~Er~kL~SvlayMtD---GViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~----- 163 (459)
T COG5002 92 FNDLTKRVQEAQANTEQERRKLDSVLAYMTD---GVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIE----- 163 (459)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHcC---ceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCc-----
Confidence 45677665433 3345556788899998887 99999999999999999999999999999999876433222
Q ss_pred cccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHH
Q 002210 800 RVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISE 879 (953)
Q Consensus 800 ~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae 879 (953)
+.+. +...+ ........ ...+ .++..-..++.+.+.-+.|-+.|++++++|+||+.+.|.|
T Consensus 164 -----d~y~-~~dL~----e~~~s~ll--d~~~-~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~E------ 224 (459)
T COG5002 164 -----DTYT-FEDLV----EKNDSLLL--DSSD-EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERE------ 224 (459)
T ss_pred -----ccee-HHHHH----hcCCcEEE--eecC-CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHH------
Confidence 1111 22222 22222222 2333 7778888888888888999999999999999998766643
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHH--HHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 880 QAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEE--QKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 880 ~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~--~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
+.+|.+++||||||||+++.++++-|+.....++ ..+++.......++|.+|++| |.+||+..++
T Consensus 225 -----rRefvanvSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~ 292 (459)
T COG5002 225 -----RREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNAR 292 (459)
T ss_pred -----HHHHHHhcchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchh
Confidence 5689999999999999999999999999554444 789999999999999999999 7999998765
No 15
>PRK13559 hypothetical protein; Provisional
Probab=99.66 E-value=3.3e-15 Score=170.13 Aligned_cols=185 Identities=11% Similarity=0.032 Sum_probs=145.0
Q ss_pred HHHHHHHHHhCCCCCCCCeEeecC---CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHH
Q 002210 737 IQGDYVGIVSSPSALIPPIFMTDE---DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIV 813 (953)
Q Consensus 737 se~~~~~i~e~~~~li~~I~~~D~---~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 813 (953)
++..|+.++++.++ +++++|. +|+++++|+++++++||+.++++|+.+. .+.+.. ........
T Consensus 41 ~~~~~~~~~e~~~~---~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~l~~~~----------~~~~~~~~ 106 (361)
T PRK13559 41 SGRLFEQAMEQTRM---AMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCR-FLQGAA----------TDPIAVAK 106 (361)
T ss_pred hhhHHHHHHHhCCC---cEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChh-hhcCCC----------CCHHHHHH
Confidence 45678889999887 8999997 5689999999999999999999999864 222211 11112334
Q ss_pred HHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002210 814 MNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIR 893 (953)
Q Consensus 814 l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~is 893 (953)
+...+.++..+..++...++||+.+|+..+..|+++.+|++.+++++++|||++|+.+.+. +.+.++++.++
T Consensus 107 ~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~--------~~~~~l~~~l~ 178 (361)
T PRK13559 107 IRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE--------AHERRLAREVD 178 (361)
T ss_pred HHHHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH--------HHHHHHHHHHH
Confidence 4555666666677888889999999999999999999999999999999999999765322 22346788999
Q ss_pred HHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchh
Q 002210 894 REIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIE 946 (953)
Q Consensus 894 HELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe 946 (953)
|++||||+.|.++.+++.. ..+..++++.+.....+|.+++++ |+.++.+
T Consensus 179 H~~~n~L~~i~~~~~l~~~---~~~~~~~~~~i~~~~~~l~~~~~~ll~~~~~~ 229 (361)
T PRK13559 179 HRSKNVFAVVDSIVRLTGR---ADDPSLYAAAIQERVQALARAHETLLDERGWE 229 (361)
T ss_pred HhhhhHHHHHHHHHHhhcc---CCCHHHHHHHHHHHHHHHHHHHHHHhccCCcC
Confidence 9999999999999999873 233456778888888899999988 6766543
No 16
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=99.61 E-value=1.3e-14 Score=169.17 Aligned_cols=191 Identities=14% Similarity=0.124 Sum_probs=144.9
Q ss_pred EEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccc
Q 002210 720 VGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGC 799 (953)
Q Consensus 720 v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~ 799 (953)
+.+++++.++.++++++.+++|+.+++++++ +++++|.+|+|+++|+++++++||+.++++|+++... +..
T Consensus 79 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~-~~~----- 149 (430)
T PRK11006 79 LYQMQLRNRKRRRELGNLIKRFRSGAESLPD---AVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNL-LRY----- 149 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---eEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHH-hcC-----
Confidence 4468888899999999999999999999988 9999999999999999999999999999999986532 211
Q ss_pred cccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHH
Q 002210 800 RVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISE 879 (953)
Q Consensus 800 ~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae 879 (953)
+. +...+... . ......+...+|.. +.+...|.. ++. ++.+.+|||++++.+.
T Consensus 150 -----~~---~~~~~~~~----~-~~~~~~~~~~~~~~--~~~~~~~~~--~~~---~~~~~~dit~~~~~e~------- 202 (430)
T PRK11006 150 -----PE---FTQYLKTR----D-FSRPLTLVLNNGRH--LEIRVMPYT--EGQ---LLMVARDVTQMHQLEG------- 202 (430)
T ss_pred -----HH---HHHHHHhc----c-cCCCeEEEcCCCCE--EEEEEEEcC--CCc---EEEEEehhhHHHHHHH-------
Confidence 11 11122111 1 11122334556654 445555543 232 4568899998876552
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCC-CCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 880 QAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSD-LSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 880 ~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
.+.+|++.++|||||||++|.+++++|.... .++...++++.+.+.+++|..++++ ++++|++.+..
T Consensus 203 ----~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~~~ 271 (430)
T PRK11006 203 ----ARRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAAPT 271 (430)
T ss_pred ----HHHHHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 2447999999999999999999999998744 4556778999999999999999999 79999998754
No 17
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.61 E-value=5.3e-14 Score=170.91 Aligned_cols=200 Identities=16% Similarity=0.212 Sum_probs=162.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHH
Q 002210 730 VMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTK 809 (953)
Q Consensus 730 ~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~ 809 (953)
+.+.++..+..++.++++.++ +++++|.+|+++++|+++++++|+++++++|+++. .+++... .
T Consensus 253 ~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~-~~~~~~~--------~---- 316 (607)
T PRK11360 253 LAQALRETRSLNELILESIAD---GVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYS-ELFPPNT--------P---- 316 (607)
T ss_pred HHHHHHHHHHHHHHHHHhccC---eEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHH-HHcCCch--------h----
Confidence 345667777888999999887 99999999999999999999999999999999875 3443211 1
Q ss_pred HHHHHHHHh-cCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHH
Q 002210 810 LRIVMNKVI-SGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNK 888 (953)
Q Consensus 810 ~~~~l~~~~-~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~f 888 (953)
+...+.... .+......++.+.+++|... +.++..|+.|.+|++.|++++++|||++|+.+.++++..+.+ ...++
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~~~--~l~~~ 393 (607)
T PRK11360 317 FASPLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQERLA--ALGEL 393 (607)
T ss_pred HHHHHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHHHH--HHHHH
Confidence 111222222 33344456778888899877 899999999999999999999999999999988877655433 35578
Q ss_pred HHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 889 LEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 889 la~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
++.++||++|||+.|.++++++.....+++..++++.+.+..++|..++++ +++++.+..
T Consensus 394 ~~~~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~~~ 454 (607)
T PRK11360 394 VAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPRES 454 (607)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcC
Confidence 999999999999999999999987767788899999999999999999999 788887653
No 18
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=99.59 E-value=3.5e-14 Score=160.70 Aligned_cols=186 Identities=15% Similarity=0.098 Sum_probs=139.0
Q ss_pred HHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHh
Q 002210 739 GDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI 818 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~ 818 (953)
..++.+++++++ +++++|.+|+|+++|+++++++||+.++++|+++.+. ++.. . .... .+...+
T Consensus 7 ~~~~~il~~~~~---gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~-~~~~----~----~~~~----~~~~~~ 70 (348)
T PRK11073 7 PDAGQILNSLIN---SILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPEL-LSYF----S----LNIE----LMRESL 70 (348)
T ss_pred chHHHHHhcCcC---eEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHH-cCcc----h----hhHH----HHHHHH
Confidence 356789999988 9999999999999999999999999999999987633 3321 0 1111 112222
Q ss_pred cCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 002210 819 SGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRK 898 (953)
Q Consensus 819 ~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrn 898 (953)
..+...........++|+.+|+.++..|+. + .+++..++|||++++.+.++.+.++. ....++++.++||+||
T Consensus 71 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~~~--~~~~~~~~~iaHelr~ 143 (348)
T PRK11073 71 QAGQGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHAQQ--VAARDLVRGLAHEIKN 143 (348)
T ss_pred HcCCcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHHHH--HHHHHHHHhhhHhhcC
Confidence 222222212223456999999999999986 2 23566789999998877665443332 3346789999999999
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhc
Q 002210 899 PLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEE 947 (953)
Q Consensus 899 PL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~ 947 (953)
||++|.+++++|.....+++.+++++.+...+++|.+++++ +++.+...
T Consensus 144 pL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~~~~ 193 (348)
T PRK11073 144 PLGGLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQRPGT 193 (348)
T ss_pred hHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCCC
Confidence 99999999999988666778899999999999999999999 67766544
No 19
>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=99.57 E-value=3.5e-14 Score=158.88 Aligned_cols=177 Identities=11% Similarity=0.104 Sum_probs=140.0
Q ss_pred HHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHH
Q 002210 735 TRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVM 814 (953)
Q Consensus 735 ~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l 814 (953)
++..++|+.++++.++ +++++|.+|++++||+++++++|+++++++|+.+.+..++ +. +...+
T Consensus 2 ~~~~~~l~~~~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~-----------~~---~~~~l 64 (333)
T TIGR02966 2 SALLSRFRAAAQALPD---AVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRH-----------PE---FVEYL 64 (333)
T ss_pred hhHHHHHHHHHHhCcC---cEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccC-----------HH---HHHHH
Confidence 3456789999999988 9999999999999999999999999999999987643322 11 23333
Q ss_pred HHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002210 815 NKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRR 894 (953)
Q Consensus 815 ~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isH 894 (953)
..... .....+..++|..+|+.+...|+.+.+ ++++++|||++++.+.. +.++++.++|
T Consensus 65 ~~~~~-----~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~-----------~~~~~~~l~h 123 (333)
T TIGR02966 65 AAGRF-----SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQM-----------RRDFVANVSH 123 (333)
T ss_pred Hhccc-----CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHH-----------HHHHHHhhhh
Confidence 32222 223456668899999999999987543 56788999988765422 3468999999
Q ss_pred HhhhHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 895 EIRKPLNGIAFMQNLMGTS--DLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 895 ELrnPL~~I~g~~~LL~~~--~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
++||||+.|.++.++|... ..++..+++++.+..+.++|..++++ +++++++.++
T Consensus 124 ~l~~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~~~ 181 (333)
T TIGR02966 124 ELRTPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRLESAA 181 (333)
T ss_pred hhcccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999999988753 45667888999999999999999999 7999998753
No 20
>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=99.43 E-value=2e-12 Score=119.64 Aligned_cols=110 Identities=23% Similarity=0.298 Sum_probs=98.7
Q ss_pred HHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCC
Q 002210 617 IETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSG 696 (953)
Q Consensus 617 le~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~ 696 (953)
++++|++++++|.+|+|+++|+++.+++|++.++++|+++.+++++...+.+...+.+++.++........... +|+
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~ 77 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR---DGE 77 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT---TSC
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee---cCC
Confidence 68999999999999999999999999999999999999999999998999999999999976666655544432 799
Q ss_pred EEEEEEEEEEeecCCCCEEEEEEEEEecchhHH
Q 002210 697 PVILVVNACCTQDTKENVIGVCFVGQDITGQKL 729 (953)
Q Consensus 697 ~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 729 (953)
.+|+.++..|+++.+|++.|++++++|||++|+
T Consensus 78 ~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 78 ERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp EEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred cEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 999999999999999999999999999999985
No 21
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.43 E-value=4.3e-12 Score=166.94 Aligned_cols=217 Identities=13% Similarity=0.116 Sum_probs=146.2
Q ss_pred EEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccc
Q 002210 720 VGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGC 799 (953)
Q Consensus 720 v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~ 799 (953)
..++++.++.++.++++.+..++.++++++. +|+++|.+|+|+++|+++++++|++.....+..... ...
T Consensus 557 l~~~i~~r~~~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~--~~~----- 626 (1197)
T PRK09959 557 LLRSVRRRKVIQGDLENQISFRKALSDSLPN---PTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLEN--SDS----- 626 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---cEEEEcCCCcEEEehHHHHHHhCccccccccccccc--ccC-----
Confidence 3478899999999999999999999999988 999999999999999999999998743332222110 000
Q ss_pred cccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEE-EEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHH
Q 002210 800 RVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSA-NKRTNAEGKISGILCFLHVASPELQYALQVQRIS 878 (953)
Q Consensus 800 ~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~-~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~a 878 (953)
.. .+..............+. ..+...+...+|...++.... .+.....+...++++..+|||++++.+.+++...
T Consensus 627 ~~--~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~ 702 (1197)
T PRK09959 627 PF--KDVFSNAHEVTAETKENR--TIYTQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVER 702 (1197)
T ss_pred ch--hhhHhHHHHHHHHHhhcc--ccceeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHH
Confidence 00 011100011111111111 112222333444332222211 2222233445668888999999998777666543
Q ss_pred H---HHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHH-HHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 879 E---QAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEE-QKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 879 e---~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~-~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
+ ++...+.+|++.|+|||||||++|.|++++|.....+++ ..++++.+..+.++|..+|++ ++++|+++|..
T Consensus 703 ~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~ 779 (1197)
T PRK09959 703 NKAINATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNY 779 (1197)
T ss_pred HHHHHHHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 3 345678889999999999999999999999987555544 557899999999999999999 89999998853
No 22
>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=99.40 E-value=2.3e-12 Score=117.70 Aligned_cols=102 Identities=23% Similarity=0.329 Sum_probs=85.6
Q ss_pred CeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEcc
Q 002210 754 PIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQ 833 (953)
Q Consensus 754 ~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~k 833 (953)
+++++|.+|+|+++|+++++++||++++++|+++. .+++.. ....+...+.+.+.++..+..++.+.++
T Consensus 3 ~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~~~~----------~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 71 (104)
T PF13426_consen 3 GIFILDPDGRILYVNPAFERLFGYSREELIGKSIS-DFFPEE----------DRPEFEEQIERALEEGGSWSGEVRLRRK 71 (104)
T ss_dssp EEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGG-GGCSTT----------SCHHHHHHHHHHHHHTSSEEEEEEEEET
T ss_pred EEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcc-cccCcc----------cchhhHHHHHHHHhcCCceeEEEEEEcC
Confidence 89999999999999999999999999999999985 344331 1223455666666666778889999999
Q ss_pred CCCEEEEEEEEEEeecCCCCEEEEEEEEEeccH
Q 002210 834 QGKYVEALLSANKRTNAEGKISGILCFLHVASP 866 (953)
Q Consensus 834 dG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITe 866 (953)
+|+.+|+.+++.|+.|.+|++.+++++++||||
T Consensus 72 ~g~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 72 DGETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp TSEEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred CCCEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 999999999999999999999999999999996
No 23
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=99.39 E-value=2.4e-11 Score=153.50 Aligned_cols=182 Identities=20% Similarity=0.235 Sum_probs=134.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCeEeec-CCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHH
Q 002210 732 DKYTRIQGDYVGIVSSPSALIPPIFMTD-EDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKL 810 (953)
Q Consensus 732 ~~L~~se~~~~~i~e~~~~li~~I~~~D-~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~ 810 (953)
.+++++++.++.++++++. ++++++ .+|.++..|+.+..++|+...+...+ +
T Consensus 327 ~~L~e~e~~~r~iv~~~p~---gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~~~~------------------------~ 379 (924)
T PRK10841 327 LRLEEHEQFNRKIVASAPV---GICILRTSDGTNILSNELAHNYLNMLTHEDRQR------------------------L 379 (924)
T ss_pred HHHHHHHHHHHHHHHhCCc---cEEEEEcCCCcEEEehHHHHHHhccCChhHHHH------------------------H
Confidence 4577788899999999987 888886 68999999999999988654322111 0
Q ss_pred HHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHH---HHHHHHHHHH
Q 002210 811 RIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRI---SEQAAANSLN 887 (953)
Q Consensus 811 ~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~---ae~~~~~k~~ 887 (953)
.. ......... ......++....+.+...... +.. ..++++.|||++++.+.++++. ++++++.|..
T Consensus 380 ~~----~~~~~~~~~--~~~~~~~~~~~~i~~~~~~~~---~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~a~~~k~~ 449 (924)
T PRK10841 380 TQ----IICGQQVNF--VDVLTSNNTNLQISFVHSRYR---NEN-VAICVLVDVSARVKMEESLQEMAQAAEQASQSKSM 449 (924)
T ss_pred HH----HHhccccce--eeEEcCCCcEEEEEEEeeeec---Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 111111111 122344555544444333322 233 3678999999999988877764 3455677888
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 888 KLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 888 fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
|++.|||||||||++|.|++++|....++++++++++.+..++++|.++|+| ||++|+++|+.
T Consensus 450 fla~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~ 513 (924)
T PRK10841 450 FLATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQL 513 (924)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 9999999999999999999999998888999999999999999999999999 89999999863
No 24
>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=99.38 E-value=4.4e-12 Score=115.88 Aligned_cols=104 Identities=19% Similarity=0.247 Sum_probs=87.8
Q ss_pred CccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEE
Q 002210 621 AVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVIL 700 (953)
Q Consensus 621 ~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v 700 (953)
|+|++++|.+|+|+++|+++++++|++.++++|+++.+++++.........+.+.+..+..+..++.. .+++|..+|+
T Consensus 1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~--~~~~g~~~~~ 78 (104)
T PF13426_consen 1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRL--RRKDGETFWV 78 (104)
T ss_dssp -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEE--EETTSEEEEE
T ss_pred CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEE--EcCCCCEEEE
Confidence 68999999999999999999999999999999999999998877777777787777544445444443 4568999999
Q ss_pred EEEEEEeecCCCCEEEEEEEEEecch
Q 002210 701 VVNACCTQDTKENVIGVCFVGQDITG 726 (953)
Q Consensus 701 ~v~~~pi~d~~g~v~gvv~v~~DITe 726 (953)
.+++.|+.+.+|++.+++++++|||+
T Consensus 79 ~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 79 EVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEECCCCCEEEEEEEEEECCC
Confidence 99999999999999999999999996
No 25
>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=99.37 E-value=5.8e-12 Score=117.08 Aligned_cols=110 Identities=24% Similarity=0.388 Sum_probs=91.6
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh-cc--cceEEEEEE
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF-LE--ERNVEIKLR 687 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l-~~--~~~~e~~~~ 687 (953)
++|+.+++++++|++++|.+|+|+++|++++++||++.++++|+++.+++++++.......+...+ .. .........
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFR 80 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEE
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEE
Confidence 468899999999999999999999999999999999999999999999999887665666666666 22 223333333
Q ss_pred EcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEec
Q 002210 688 AFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDI 724 (953)
Q Consensus 688 ~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DI 724 (953)
. ++|+.+|+.++..|+++.+|++.|++++++||
T Consensus 81 ~----~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 81 L----RDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp E----TTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred e----cCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 3 57999999999999999999999999999997
No 26
>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=99.35 E-value=1.2e-11 Score=114.98 Aligned_cols=112 Identities=27% Similarity=0.379 Sum_probs=88.8
Q ss_pred HHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHh
Q 002210 739 GDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI 818 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~ 818 (953)
++|+.+++++++ +++++|.+|+|+++|+++++++||+.++++|+++.+.+++++ .......+...+
T Consensus 1 e~~~~i~~~~~~---~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~-----------~~~~~~~~~~~~ 66 (113)
T PF00989_consen 1 ERYRAILENSPD---GIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPED-----------RRELRERLRQAL 66 (113)
T ss_dssp HHHHHHHHCSSS---EEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGG-----------HHHHHHHHHHHH
T ss_pred CHHHHHHhcCCc---eEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchh-----------hHHHHHHHHHHH
Confidence 478999999988 999999999999999999999999999999999875554431 112333444444
Q ss_pred cCCC-cceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEec
Q 002210 819 SGQD-ADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVA 864 (953)
Q Consensus 819 ~g~~-~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DI 864 (953)
.... ....+..+..++|+.+|+.++..|+++.+|++.|++++++||
T Consensus 67 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 67 SQGESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp HHCCHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred HcCCCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 3333 335566666689999999999999999999999999999997
No 27
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=99.33 E-value=7.7e-12 Score=123.46 Aligned_cols=153 Identities=18% Similarity=0.192 Sum_probs=112.4
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCC
Q 002210 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (953)
Q Consensus 215 ~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~ 294 (953)
|++++++.+++++++++|+||++||.+++++..-...-.....-.+..+..++.. -+ ...+....+..-.|+|+...|
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~i~d~~~~~ 78 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMD-ES-ICGQVLQSREPIVISDVAADP 78 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETT-SS-HHHHHHHHTSCEEESSSGGST
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccccccccccc-cc-HHHHHHhCCCeEeeccccccc
Confidence 6899999999999999999999999999999766444332221111122222111 11 256666777777888854443
Q ss_pred ceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCC-CCCCh
Q 002210 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSP-RFVPF 373 (953)
Q Consensus 295 ~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~~ 373 (953)
- ..+.......+++.++++.+|+..+|+++.|++||..+ |++||+|+++++.+ |.|+.
T Consensus 79 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~-------------g~~~G~l~l~~~~~~~~~~~ 137 (154)
T PF01590_consen 79 R--------FAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISG-------------GRLIGVLSLYRTRPGRPFTE 137 (154)
T ss_dssp T--------SSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEET-------------TEEEEEEEEEEESSSSS--H
T ss_pred c--------ccccccccccccccccccccccccccCceeeEeeeecc-------------cCcEEEEEEEECCCCCCcCH
Confidence 2 12223334557888999999999999999999998876 99999999999997 99999
Q ss_pred hHHHHHHHHHHHHHHhh
Q 002210 374 PLRYACEFLIQVFGVQV 390 (953)
Q Consensus 374 ~~r~~~~~l~~~~~~~l 390 (953)
.++.+++.+++++++.|
T Consensus 138 ~d~~ll~~~a~~~a~ai 154 (154)
T PF01590_consen 138 EDLALLESFAQQLAIAI 154 (154)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhC
Confidence 99999999999888754
No 28
>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=99.31 E-value=1.6e-11 Score=113.54 Aligned_cols=109 Identities=19% Similarity=0.303 Sum_probs=90.6
Q ss_pred hCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcce
Q 002210 746 SSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADK 825 (953)
Q Consensus 746 e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~ 825 (953)
+++++ +++++|.+|+++++|+++.+++|++.++++|+++. .++++ .....+...+.+++.++....
T Consensus 2 ~~~p~---~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~-~~~~~----------~~~~~~~~~~~~~~~~~~~~~ 67 (110)
T PF08448_consen 2 DSSPD---GIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLF-DLLPP----------EDREEFQAALRRALAGGEPVF 67 (110)
T ss_dssp HHCSS---EEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHH-HHSCC----------GCHHHHHHHHHHHHHHTSEEE
T ss_pred CCCCc---eeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccch-hcccc----------chhhhhHHHHHHhhccCceEE
Confidence 45555 89999999999999999999999999999999986 34443 244457778888888887665
Q ss_pred EEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHH
Q 002210 826 ILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQ 869 (953)
Q Consensus 826 ~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~ 869 (953)
.+..... +|..+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 68 ~~~~~~~-~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 68 FEEILLR-DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp EEEEECT-TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred EEEEEee-cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 5544444 999999999999999999999999999999999984
No 29
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.29 E-value=6.2e-11 Score=147.76 Aligned_cols=177 Identities=16% Similarity=0.113 Sum_probs=128.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCeEeec-CCccEEehhHHHHHHhCCChh-hhhcccccccccccccccccccCcchH
Q 002210 730 VMDKYTRIQGDYVGIVSSPSALIPPIFMTD-EDGRCLEWNDGMEKLSGLKRE-EAIERMLIGEVFTVKNFGCRVKNHDTL 807 (953)
Q Consensus 730 ~E~~L~~se~~~~~i~e~~~~li~~I~~~D-~~G~i~~~N~a~~~l~G~~~e-eliGk~~~~~~~~~~~~~~~l~~~~~~ 807 (953)
..++++..+..++.++++++. |++++| .+|+++.+|+++++++|...- .+.... . .
T Consensus 334 l~~~L~~~~~l~~~Ii~~lp~---Gilv~D~~~~~Ii~~N~aA~~ll~~~~l~~i~~~~-------~-----~------- 391 (894)
T PRK10618 334 MSHELRILRALNEEIVSNLPL---GLLVYDFESNRTVISNKIADHLLPHLNLQKITTMA-------E-----Q------- 391 (894)
T ss_pred HHHHHHHHHHHHHHHHHhCCc---eEEEEECCCCeEEEEhHHHHHHhCccchhhHHHHH-------H-----h-------
Confidence 334577788889999999987 899999 679999999999999985321 110000 0 0
Q ss_pred HHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHH---HHHHHHHH
Q 002210 808 TKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQR---ISEQAAAN 884 (953)
Q Consensus 808 ~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~---~ae~~~~~ 884 (953)
....+.. ..+++..++...... ....+++.+++|+++++..+.++++ ..+++.+.
T Consensus 392 --~~~~i~~---------------~i~~~~~eir~~~~~-----~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le~~~~~ 449 (894)
T PRK10618 392 --HQGVIQA---------------TINNELYEIRMFRSQ-----LAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQQA 449 (894)
T ss_pred --cchhhhh---------------hccCceeEEEEeecc-----ccCceEEEEEeehHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0000000 011222222221111 1223567789999988776666554 44555678
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
|.+|+++|||||||||++|.|++++|.....+++++++++.+..++++|.++|+| +|++|+|+|+.
T Consensus 450 k~~fla~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~ 516 (894)
T PRK10618 450 RKAFLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDW 516 (894)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Confidence 8999999999999999999999999988778899999999999999999999999 89999999864
No 30
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=99.25 E-value=1.6e-10 Score=120.22 Aligned_cols=176 Identities=15% Similarity=0.178 Sum_probs=128.3
Q ss_pred HHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCC
Q 002210 743 GIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQD 822 (953)
Q Consensus 743 ~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~ 822 (953)
.++++... +++++|.+|.|.|+|++++.+||.+...+.|..+. .+++... . ....+.+....+.
T Consensus 11 ~~Ln~~~~---pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~-~l~~~gs--------~----ll~ll~q~~~~~~ 74 (363)
T COG3852 11 AILNNLIN---PVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLS-ELLPFGS--------L----LLSLLDQVLERGQ 74 (363)
T ss_pred hHHhccCC---ceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChH-HHcCCCc--------H----HHHHHHHHHHhcC
Confidence 46666655 89999999999999999999999999999998875 4444321 1 3445555544443
Q ss_pred c-ceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 002210 823 A-DKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLN 901 (953)
Q Consensus 823 ~-~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrnPL~ 901 (953)
. .+++..+. .+|....+...+.|+-...|-+. ..++-+....+...++.+. ...++-....++++|||||||.
T Consensus 75 ~~~~~~v~l~-~~g~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~ridre~~q~--a~~~a~~~L~r~LAHEIKNPL~ 148 (363)
T COG3852 75 PVTEYEVTLV-ILGRSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRRLDREQTQH--AQQRAVKGLVRGLAHEIKNPLG 148 (363)
T ss_pred Ccccceeeee-ecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhHHHHHH--HHHHHHHHHHHHHHHHhcCccc
Confidence 3 35555555 78999999999999987666544 3344444333222221111 1123445678899999999999
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhhh
Q 002210 902 GIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDT 940 (953)
Q Consensus 902 ~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~DL 940 (953)
+|.|.+|||+..-.++..++|.+.|-+.++||..|++.|
T Consensus 149 GiRGAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRm 187 (363)
T COG3852 149 GIRGAAQLLERALPDEALRELTQLIIEEADRLRNLVDRL 187 (363)
T ss_pred chhhHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999988778889999999999999999999986
No 31
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=99.23 E-value=6.2e-10 Score=133.92 Aligned_cols=178 Identities=15% Similarity=0.170 Sum_probs=121.4
Q ss_pred EEEEeecCCCCEEEEEEEEEecchhHHHHHH--------------------------------------HHHHHHHHHHH
Q 002210 703 NACCTQDTKENVIGVCFVGQDITGQKLVMDK--------------------------------------YTRIQGDYVGI 744 (953)
Q Consensus 703 ~~~pi~d~~g~v~gvv~v~~DITerk~~E~~--------------------------------------L~~se~~~~~i 744 (953)
...|+++..|.++|++.+..++.+-...-.. +.+..+.++.+
T Consensus 147 ~~~p~~~~~~~~iG~v~vg~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~l~~l~~~ei~~l~~~~~~i 226 (542)
T PRK11086 147 VFTPVYDENGKQIGVVAVGISLSEVTEQINESRWSIYWSILFGALVGLIGTVILVRVLKRILFGLEPYEISTLFEQRQAM 226 (542)
T ss_pred EEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 5678888889999998777766544332211 12334556789
Q ss_pred HhCCCCCCCCeEeecCCccEEehhHHHHHHhCCCh---hhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCC
Q 002210 745 VSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKR---EEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQ 821 (953)
Q Consensus 745 ~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~---eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~ 821 (953)
++++++ +|+++|.+|+|+++|+++++++|++. ++.+|+.... +++ ... +...+..+
T Consensus 227 l~~~~~---gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~-~~~----------~~~-------~~~~~~~~ 285 (542)
T PRK11086 227 LQSIKE---GVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVES-WMP----------VSR-------LKEVLRTG 285 (542)
T ss_pred HHHhcC---cEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHH-hCC----------chh-------HHHHHhcC
Confidence 999987 99999999999999999999998763 3455554321 111 111 12222222
Q ss_pred Ccc-eEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 002210 822 DAD-KILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPL 900 (953)
Q Consensus 822 ~~~-~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrnPL 900 (953)
... ..+ ...+|. ++..+..|+.+ +|.+.|++++++|+|+.++.+.++.... ...++++.++||+||||
T Consensus 286 ~~~~~~~---~~~~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~-----~~~~~l~~~sHel~npL 354 (542)
T PRK11086 286 TPRRDEE---ININGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMV-----NYADALRAQSHEFMNKL 354 (542)
T ss_pred CCccceE---EEECCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHH-----HHHHHHHhhchhhcCHH
Confidence 222 222 222453 45566789987 8999999999999999887765544332 23456788999999999
Q ss_pred HHHHHHHHhhcC
Q 002210 901 NGIAFMQNLMGT 912 (953)
Q Consensus 901 ~~I~g~~~LL~~ 912 (953)
++|.|++++...
T Consensus 355 ~~I~g~~~~~~~ 366 (542)
T PRK11086 355 HVILGLLHLKSY 366 (542)
T ss_pred HHHHHHHHhCch
Confidence 999999987643
No 32
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.22 E-value=3.2e-10 Score=142.52 Aligned_cols=137 Identities=17% Similarity=0.163 Sum_probs=116.8
Q ss_pred ccHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 601 EKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 601 ~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
+..+++++.++.++.+++++|++|+++|.+|+|+++|+++++++|++.++++|+++.++++++....+.......+..+.
T Consensus 145 ~~~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~ 224 (779)
T PRK11091 145 ETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNV 224 (779)
T ss_pred HHHHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCC
Confidence 34677888899999999999999999999999999999999999999999999999999987766666666666665554
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHH
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQG 739 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~ 739 (953)
....+... ..++|..+|+.++..|+++.+|.+.|++++++|||++|++|+++++..+
T Consensus 225 ~~~~e~~~--~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~~ 281 (779)
T PRK11091 225 SLTYEQWL--DYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKASR 281 (779)
T ss_pred CeEEEEEE--EcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHHH
Confidence 55444433 4568999999999999999999999999999999999999998876544
No 33
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=99.19 E-value=4.8e-11 Score=100.76 Aligned_cols=64 Identities=30% Similarity=0.409 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcC-CCCCHHH-HHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGT-SDLSEEQ-KQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~-~~l~e~~-~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
|.+|++.++|||||||++|.+++++|.. ...++++ +++++.+..++++|.++|++ |+|+|+|+|
T Consensus 2 ~~~~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G 68 (68)
T PF00512_consen 2 KGEFLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 6789999999999999999999999999 8888988 99999999999999999999 899999998
No 34
>PRK10060 RNase II stability modulator; Provisional
Probab=99.11 E-value=1.4e-09 Score=133.38 Aligned_cols=167 Identities=13% Similarity=0.110 Sum_probs=120.8
Q ss_pred CCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHH
Q 002210 694 TSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEK 773 (953)
Q Consensus 694 dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~ 773 (953)
+|...|+.....++.. ....|......|++. ....+......++.+++.+++ +|+++|.+|+|+++|+++++
T Consensus 71 ~g~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~~~~~---gI~i~D~~g~I~~~N~a~~~ 142 (663)
T PRK10060 71 DGEPLSVHLVGRKINK--REWAGTASAWHDTPS---VARDLSHGLSFAEQVVSEANS---VIVILDSRGNIQRFNRLCEE 142 (663)
T ss_pred CCcEEEEEEeeeccCc--ccccchhhHHHHHHH---HHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEEcHHHHH
Confidence 6999998876666543 234444444455555 344455666678889999987 89999999999999999999
Q ss_pred HhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCC-
Q 002210 774 LSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEG- 852 (953)
Q Consensus 774 l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G- 852 (953)
++||+.++++|+++...+.++ +....+...+...+..+..+..++.+.+++|+.+|+.....+ .+.+|
T Consensus 143 l~Gy~~~eliG~~~~~l~~~~----------~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~~-~~~~g~ 211 (663)
T PRK10060 143 YTGLKEHDVIGQSVFKLFMSR----------REAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKFV-HSGSGK 211 (663)
T ss_pred HHCcCHHHHcCCCHHHHhCCh----------hhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeEE-EcCCCC
Confidence 999999999999876433332 111223444555556666678888999999999988765444 44444
Q ss_pred CEEEEEEEEEeccHHHHHHHHHHHHHH
Q 002210 853 KISGILCFLHVASPELQYALQVQRISE 879 (953)
Q Consensus 853 ~i~g~v~v~~DITerK~~e~elq~~ae 879 (953)
...+++++.+|||++|+.++++++.+.
T Consensus 212 ~~~~~i~~~~DITe~k~~e~~l~~~a~ 238 (663)
T PRK10060 212 NEIFLICSGTDITEERRAQERLRILAN 238 (663)
T ss_pred ceEEEEEEEEechHHHHHHHHHHHHhh
Confidence 446688899999999988877766543
No 35
>PRK13559 hypothetical protein; Provisional
Probab=99.06 E-value=2.6e-09 Score=121.64 Aligned_cols=139 Identities=12% Similarity=0.069 Sum_probs=108.0
Q ss_pred HHHHHHHHHHHhcCccEEEEcC---CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEE
Q 002210 608 IITNEMVRLIETAAVPILAVDA---SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEI 684 (953)
Q Consensus 608 ~~~~~l~~lle~~~~~I~~~D~---dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~ 684 (953)
.....+..+++.++++|+++|. +|.++++|+++++++||+.++++|+++..+.++.........+...+..+.....
T Consensus 40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (361)
T PRK13559 40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVV 119 (361)
T ss_pred hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEE
Confidence 3466788899999999999997 6789999999999999999999999988776655555455555556644444444
Q ss_pred EEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCC
Q 002210 685 KLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSP 748 (953)
Q Consensus 685 ~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~ 748 (953)
+... .+++|..+|+.++..|+++.+|.+.+++++++|||++|++++..++.+..++.+.+..
T Consensus 120 e~~~--~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~~~~~l~~~l~H~~ 181 (361)
T PRK13559 120 ELLN--YRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEAHERRLAREVDHRS 181 (361)
T ss_pred EEEE--EcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHHHHHHHHHHHHHhh
Confidence 4333 4568999999999999999999999999999999999998776555554444444433
No 36
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=99.04 E-value=5.4e-09 Score=118.08 Aligned_cols=226 Identities=18% Similarity=0.256 Sum_probs=157.8
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCC
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRET 694 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~d 694 (953)
.+++..+++++++|....+..+|..+..+++-....++|+++.+++++...+.+. -...+........ +
T Consensus 5 ~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~------~~~~~~~~~~~~~-----~ 73 (560)
T COG3829 5 GILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE------QSRDKELTERLKL-----K 73 (560)
T ss_pred hhhhhcccceEEEEcCCceeeechHHHHhhhcceEEEecccceeeccccCcceee------ccCccceeeeeec-----c
Confidence 4889999999999999999999999999999999999999988887765544222 0111111111111 1
Q ss_pred CCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHH-HHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHH
Q 002210 695 SGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKY-TRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEK 773 (953)
Q Consensus 695 G~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L-~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~ 773 (953)
....+.+..+| .+..++++|+..++.|+++....-+.. .+....|+.+++.+.+ +++++|.+|+++++|+++.+
T Consensus 74 -~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~---~l~vvD~~G~~i~~N~~~~~ 148 (560)
T COG3829 74 -VKRIVVVGKTP-VDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDD---GLLVVDEDGIIIYYNKAYAK 148 (560)
T ss_pred -ceeEEEcCCce-eecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhccC---ceEEEcCCCcEEEEcHHHHH
Confidence 23334434444 455899999999999999977666555 6667889999999987 99999999999999999999
Q ss_pred HhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCC
Q 002210 774 LSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGK 853 (953)
Q Consensus 774 l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~ 853 (953)
++|++.++++|+++.+.+ ....+ . .....+ ..+++... ......|... ..+..|++ .+|.
T Consensus 149 ~~gl~~e~~~gk~~~~v~-~~~~~--------s--~~l~vl---~~~kp~~~---~~~~~~~~~~--i~~~~pv~-~~g~ 208 (560)
T COG3829 149 LLGLSPEEVLGKHLLDVV-SAGED--------S--TLLEVL---RTGKPIRD---VVQTYNGNKI--IVNVAPVY-ADGQ 208 (560)
T ss_pred HhCCCHHHHcCCcHHHHH-hccCC--------c--eehhhh---hcCCccee---eeeeecCCce--eEeeccEe-cCCc
Confidence 999999999999876433 11100 0 011111 22332211 1233333333 45566666 6679
Q ss_pred EEEEEEEEEeccHHHHHHHHHHH
Q 002210 854 ISGILCFLHVASPELQYALQVQR 876 (953)
Q Consensus 854 i~g~v~v~~DITerK~~e~elq~ 876 (953)
++|.+++.+|+++-+....++++
T Consensus 209 l~G~v~~~~~~~~l~~l~~~~~~ 231 (560)
T COG3829 209 LIGVVGISKDVSELERLTRELEE 231 (560)
T ss_pred EEEEEEeecchHHHHHHHHHHHH
Confidence 99999999999988766655443
No 37
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=99.01 E-value=9.8e-09 Score=98.34 Aligned_cols=139 Identities=23% Similarity=0.335 Sum_probs=108.3
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCC
Q 002210 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (953)
Q Consensus 215 ~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~ 294 (953)
+++++++.+++.+.+++++||+.||.++++..+.....+..+...+..+..+|..+ .-.+.++..+....+.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999888887777665544445667787776 4566777778877777754333
Q ss_pred ceeeeCCCCCCccccCCccccCCChhHHHHhhhc-CCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecC-CCCCCC
Q 002210 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENM-GSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHT-SPRFVP 372 (953)
Q Consensus 295 ~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nm-gv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~-~pr~~~ 372 (953)
.+ . ..+...+ |+++.+++||..+ +++||+|.+.++ .++.|+
T Consensus 79 ~~-----------------------~-~~~~~~~~~~~s~~~~Pl~~~-------------~~~~G~l~~~~~~~~~~~~ 121 (149)
T smart00065 79 VF-----------------------A-LDLLGRYQGVRSFLAVPLVAD-------------GELVGVLALHNKDSPRPFT 121 (149)
T ss_pred cc-----------------------c-cccccceeceeeEEEeeeeec-------------CEEEEEEEEEecCCCCCCC
Confidence 11 0 1122223 4999999999987 899999999999 699999
Q ss_pred hhHHHHHHHHHHHHHHhhHH
Q 002210 373 FPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 373 ~~~r~~~~~l~~~~~~~l~~ 392 (953)
...+..++.+++.++..|..
T Consensus 122 ~~~~~~l~~~~~~i~~~l~~ 141 (149)
T smart00065 122 EEDEELLQALANQLAIALAN 141 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999988877753
No 38
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=99.00 E-value=1.4e-07 Score=113.82 Aligned_cols=199 Identities=14% Similarity=0.163 Sum_probs=127.2
Q ss_pred EEEEEeecCCCCEEEEEEEEEecchhHHHHH--------------------------------------HHHHHHHHHHH
Q 002210 702 VNACCTQDTKENVIGVCFVGQDITGQKLVMD--------------------------------------KYTRIQGDYVG 743 (953)
Q Consensus 702 v~~~pi~d~~g~v~gvv~v~~DITerk~~E~--------------------------------------~L~~se~~~~~ 743 (953)
..+.|+++.+|.++|++.+...+.+...... .+......++.
T Consensus 147 ~~a~PI~~~~g~~iGvi~v~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~~e~~~~~~~~~~~~~ 226 (545)
T PRK15053 147 RAKTPIFDDDGKVIGVVSIGYLVSKIDSWRLEFLLPMAGVFVVLLGILMLLSWFFAAHIRRQMMGMEPKQIARVVRQQEA 226 (545)
T ss_pred EEEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3789999889999999877765444322110 11122344567
Q ss_pred HHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCCh--hhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCC
Q 002210 744 IVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKR--EEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQ 821 (953)
Q Consensus 744 i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~--eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~ 821 (953)
++++..+ +++.+|.+|+|+++|+++++++|++. ++++|+++.+ +++.. .. + ..... .
T Consensus 227 il~~~~e---gii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~-~~~~~---------~~---~----~~~~~-~ 285 (545)
T PRK15053 227 LFSSVYE---GLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAE-VVRPA---------DF---F----TEQID-E 285 (545)
T ss_pred HHHHhCc---eEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHH-hCCCc---------hh---h----hhhcC-C
Confidence 8888877 99999999999999999999999975 5689988653 22221 00 0 00111 1
Q ss_pred CcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 002210 822 DADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLN 901 (953)
Q Consensus 822 ~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrnPL~ 901 (953)
...... ...+| ..+..+..|+.+ +|++.|++.+++|+|+.++.+.++.+..+ ..+.+..++||++|||+
T Consensus 286 ~~~~~~---~~~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~-----~~e~l~~~~he~~n~L~ 354 (545)
T PRK15053 286 KRQDVV---ANFNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQ-----YVESLRTLRHEHLNWMS 354 (545)
T ss_pred cccceE---EEECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhhHH
Confidence 111111 22344 344566777764 56788999999999998776655443322 23567789999999999
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh
Q 002210 902 GIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD 939 (953)
Q Consensus 902 ~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D 939 (953)
+|.|+.++-. ..+.++.+......+.+++++
T Consensus 355 ~i~g~l~~~~-------~~~~~~~i~~~s~~~~~l~~~ 385 (545)
T PRK15053 355 TLNGLLQMKE-------YDRVLEMVQGESQAQQQLIDS 385 (545)
T ss_pred HHHHHHhhch-------hhHHHHHHHHHHHHHHHHHHH
Confidence 9999887642 223444444444455555544
No 39
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=98.99 E-value=8.7e-09 Score=116.50 Aligned_cols=184 Identities=14% Similarity=0.153 Sum_probs=128.2
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHH
Q 002210 733 KYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRI 812 (953)
Q Consensus 733 ~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~ 812 (953)
++++.++.++.+++.... |++.+|.+|++.-+|++++.++|.+.++++|.++. .+-|+ +..
T Consensus 364 ~~e~rr~f~E~VLsgvta---GVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~ls-a~ap~---------------~~~ 424 (712)
T COG5000 364 ALEQRRRFLEAVLSGLTA---GVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLS-AIAPE---------------LEE 424 (712)
T ss_pred HHHHHHHHHHHHHhcCce---eEEEEcCCCeeEeecchHHHHhcCChhHhhcchhh-hhhhH---------------HHH
Confidence 344455566778888776 89999999999999999999999999999999864 22222 223
Q ss_pred HHHHHh-cCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002210 813 VMNKVI-SGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEY 891 (953)
Q Consensus 813 ~l~~~~-~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~ 891 (953)
++..+- .++.....+..+.+. |+.+...+.++... ++ +--|++.++.|||+-..++.. .+=.+-..-
T Consensus 425 vf~~~~a~~~~~~~~ev~~~r~-g~~rtl~Vq~t~~~-~d-~~~gyVvt~DDITdLV~AQRs---------~AW~dVArR 492 (712)
T COG5000 425 VFAEAGAAARTDKRVEVKLARE-GEERTLNVQATREP-ED-NGNGYVVTFDDITDLVIAQRS---------AAWGDVARR 492 (712)
T ss_pred HHHHhhhhcCCCccceeecccC-CCceeeeeeeeecc-cc-cCCceEEEecchHHHHHHHHH---------HHHHHHHHH
Confidence 333222 233334555555544 55555555555432 22 223578899999998755521 122345667
Q ss_pred HHHHhhhHHHHHHHHHHhhcC---CCCCHH---HHHHHHHHHHHHHHHHhHhhh-hcccchhc
Q 002210 892 IRREIRKPLNGIAFMQNLMGT---SDLSEE---QKQLLKTSVLCQEQLTNIVDD-TDIESIEE 947 (953)
Q Consensus 892 isHELrnPL~~I~g~~~LL~~---~~l~e~---~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~ 947 (953)
++|||||||+.|.-+++-|++ .+++++ -.+..++|.+.+..+.+++++ -+|+|.=+
T Consensus 493 IAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afARmP~ 555 (712)
T COG5000 493 IAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFARMPA 555 (712)
T ss_pred HHHHhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 899999999999999998877 455552 357788898989999999999 68888643
No 40
>PRK13557 histidine kinase; Provisional
Probab=98.98 E-value=5.5e-09 Score=125.50 Aligned_cols=130 Identities=13% Similarity=0.138 Sum_probs=106.2
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcC---CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceE
Q 002210 606 LRIITNEMVRLIETAAVPILAVDA---SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNV 682 (953)
Q Consensus 606 L~~~~~~l~~lle~~~~~I~~~D~---dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~ 682 (953)
....+..|..++++++++|+++|. +|+|+|+|+++++++||+.++++|+++..+++++........+...+..+...
T Consensus 25 ~~~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 104 (540)
T PRK13557 25 SDHRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREI 104 (540)
T ss_pred hhhhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCc
Confidence 445577889999999999999995 89999999999999999999999999998887766555555555555444344
Q ss_pred EEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHH
Q 002210 683 EIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRI 737 (953)
Q Consensus 683 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~s 737 (953)
..++.. .+++|..+|+.+...|+.+.+|.+++++++.+|||++++.++++.+.
T Consensus 105 ~~~~~~--~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~ 157 (540)
T PRK13557 105 ATEILN--YRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQA 157 (540)
T ss_pred eEEEEE--EeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHH
Confidence 333333 45689999999999999999999999999999999999998876543
No 41
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.96 E-value=9.6e-09 Score=126.87 Aligned_cols=136 Identities=21% Similarity=0.164 Sum_probs=112.3
Q ss_pred HHHHHHHhcCccEEEEcC---CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEE
Q 002210 612 EMVRLIETAAVPILAVDA---SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRA 688 (953)
Q Consensus 612 ~l~~lle~~~~~I~~~D~---dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~ 688 (953)
.++.+++.++.+++.+|. +|++++||+++++++||+.++++|+++..+.++.........+...+..+.....+++.
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 346789999999999984 79999999999999999999999999888877766555555555555444455555444
Q ss_pred cccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCC
Q 002210 689 FGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPS 749 (953)
Q Consensus 689 ~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~ 749 (953)
.+++|..+|+.++..|+.+.+|.+.+++++.+|||++|++|+++++.+..++.+++..+
T Consensus 229 --~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~ 287 (665)
T PRK13558 229 --YRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVE 287 (665)
T ss_pred --ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 56789999999999999999999999999999999999999999988887777766543
No 42
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.92 E-value=2.5e-08 Score=123.13 Aligned_cols=124 Identities=14% Similarity=0.166 Sum_probs=98.1
Q ss_pred HHHHHhCCCCCCCCeEeec---CCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHH
Q 002210 741 YVGIVSSPSALIPPIFMTD---EDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKV 817 (953)
Q Consensus 741 ~~~i~e~~~~li~~I~~~D---~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ 817 (953)
++.++++.+. +++..| .+|++++||+++++++||+.++++|+.+.. +++.+ ........+...
T Consensus 150 ~~~~~~~~~~---gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~-l~~~~----------~~~~~~~~~~~~ 215 (665)
T PRK13558 150 KERALDEAPV---GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRF-LQGED----------TNEERVAELREA 215 (665)
T ss_pred HHHHHhcCCc---cEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHH-hcCCC----------ccHHHHHHHHHH
Confidence 4567888776 888887 478999999999999999999999998642 22221 111123334445
Q ss_pred hcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHH
Q 002210 818 ISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRIS 878 (953)
Q Consensus 818 ~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~a 878 (953)
+.++.....++++++++|..+|+.++..|+.+.+|.+.+++++.+|||++|+.++++++..
T Consensus 216 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~ 276 (665)
T PRK13558 216 IDEERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRER 276 (665)
T ss_pred HhcCCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHH
Confidence 5566667888999999999999999999999999999999999999999999887766533
No 43
>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=98.90 E-value=1.7e-08 Score=90.87 Aligned_cols=120 Identities=20% Similarity=0.312 Sum_probs=94.9
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhccc-ceEEEEEEEc
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEE-RNVEIKLRAF 689 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~-~~~e~~~~~~ 689 (953)
+.++.+++.++.+++++|.+|+++++|+++.+++|++..+++|+.+.+++++.........+....... .........
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 81 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERRV- 81 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEeee-
Confidence 456778999999999999999999999999999999999999999988887776666555555555322 222222222
Q ss_pred ccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHH
Q 002210 690 GPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDK 733 (953)
Q Consensus 690 ~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~ 733 (953)
...+|..+|+.....|+. .+|...+++++..|||++++.+++
T Consensus 82 -~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 82 -RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred -EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhc
Confidence 244788999999999988 688899999999999999887654
No 44
>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=98.88 E-value=6.9e-09 Score=122.83 Aligned_cols=126 Identities=16% Similarity=0.096 Sum_probs=98.8
Q ss_pred HHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHh
Q 002210 739 GDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI 818 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~ 818 (953)
+.|+.++++++. +++++|.+|+++++|+++++++||++++++|+.... +.+.. .... ....+....
T Consensus 4 ~~~~~i~~~~~~---~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~-~~~~~------~~~~----~~~~~~~~~ 69 (494)
T TIGR02938 4 EAYRQTVDQAPL---AISITDLKANILYANDAFTRITGYTKEEIIGKNESV-LSNHT------TPPE----VYQALWGSL 69 (494)
T ss_pred HHHHHHHHhCCc---eEEEECCCCcEEEEchhheeecCCCHHHHhCCCchh-hcCCC------CCHH----HHHHHHHHH
Confidence 468899999987 899999999999999999999999999999987432 21110 1111 222333344
Q ss_pred cCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHH
Q 002210 819 SGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRIS 878 (953)
Q Consensus 819 ~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~a 878 (953)
..+..+..++...+++|+.+|+..+..|+.|.+|.+.+++++++|||++|+++.++++..
T Consensus 70 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~ 129 (494)
T TIGR02938 70 AEQKPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQK 129 (494)
T ss_pred HhCCcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHH
Confidence 445555667777899999999999999999999999999999999999999887766543
No 45
>PRK10060 RNase II stability modulator; Provisional
Probab=98.88 E-value=3.3e-08 Score=121.52 Aligned_cols=161 Identities=19% Similarity=0.208 Sum_probs=110.5
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCcccccc-CCcHHHHHHHHHHHhcccceEEE
Q 002210 606 LRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA-GDSVDVVKNMLSSAFLEERNVEI 684 (953)
Q Consensus 606 L~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~-~~~~~~~~~~l~~~l~~~~~~e~ 684 (953)
+......++.+++.++++|+++|.+|+|+++|+++++++||+.++++|+++.+++. +.+.......+...+..+..+..
T Consensus 106 ~~~~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (663)
T PRK10060 106 LSHGLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV 185 (663)
T ss_pred HHHHHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence 34445567789999999999999999999999999999999999999999887664 44444455556665644444444
Q ss_pred EEEEcccCCCCCEEEEEEEEEEeecCCC-CEEEEEEEEEecchhHHHHHHHHHH---------------HHHHHHHHhCC
Q 002210 685 KLRAFGPRETSGPVILVVNACCTQDTKE-NVIGVCFVGQDITGQKLVMDKYTRI---------------QGDYVGIVSSP 748 (953)
Q Consensus 685 ~~~~~~~~~dG~~~~v~v~~~pi~d~~g-~v~gvv~v~~DITerk~~E~~L~~s---------------e~~~~~i~e~~ 748 (953)
+... .+++|..+|+.... ++.+..| ...+++++.+|||++|+.++++++. .+++...+...
T Consensus 186 e~~~--~~~~G~~~~~~~~~-~~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~~l~~~l~~~ 262 (663)
T PRK10060 186 ERWI--KTRKGQRLFLFRNK-FVHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAINAA 262 (663)
T ss_pred EEEE--EeCCCCEEEEEeee-EEEcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHHHHHHHHHhC
Confidence 4433 55678888776444 4444344 4466788899999999999987663 34454444332
Q ss_pred CCCCCCeEeecCCccEEehhHH
Q 002210 749 SALIPPIFMTDEDGRCLEWNDG 770 (953)
Q Consensus 749 ~~li~~I~~~D~~G~i~~~N~a 770 (953)
.....+++.+|.++ +..+|..
T Consensus 263 ~~~~~~ll~idld~-fk~iNd~ 283 (663)
T PRK10060 263 DNNQVGIVYLDLDN-FKKVNDA 283 (663)
T ss_pred CCCcEEEEEEECcc-hhHHHHh
Confidence 21112477777764 3345544
No 46
>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=98.85 E-value=4.3e-08 Score=88.26 Aligned_cols=119 Identities=18% Similarity=0.233 Sum_probs=90.2
Q ss_pred HHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHh
Q 002210 739 GDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI 818 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~ 818 (953)
..++.++++.+. +++++|.+|+++++|+++.+++|++.++++|+.+.. +++. .....+...+....
T Consensus 3 ~~~~~~~~~~~~---~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~-~~~~----------~~~~~~~~~~~~~~ 68 (124)
T TIGR00229 3 ERYRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLE-LIPE----------EDREEVRERIERLL 68 (124)
T ss_pred hHHHHHHhhCCc---eEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhh-hcCh----------hhhHHHHHHHHHHH
Confidence 356778888876 899999999999999999999999999999988754 2222 11122333344444
Q ss_pred cCC-CcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHH
Q 002210 819 SGQ-DADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYAL 872 (953)
Q Consensus 819 ~g~-~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~ 872 (953)
.+. .....++.+..++|..+|+.....|+. .+|...+++++..|||++++.+.
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 69 EGEREPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred cCCCCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 433 233455666688999999999999988 78889999999999999886653
No 47
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.82 E-value=2.1e-08 Score=92.68 Aligned_cols=105 Identities=23% Similarity=0.278 Sum_probs=78.3
Q ss_pred HHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccc-eEEEEEEEccc
Q 002210 613 MVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER-NVEIKLRAFGP 691 (953)
Q Consensus 613 l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~-~~e~~~~~~~~ 691 (953)
+..++++++.+++++|.+++|.++|+++.++|++...+ +|+++.++.++...+.+...+..+..+.. ..+.....
T Consensus 1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~~i~~~~~~~~~~~~~~~~~--- 76 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKKIIEQVRSGKEEEFEIVIPN--- 76 (106)
T ss_dssp HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHHHHHHHHTTSBSEEEEEEEE---
T ss_pred ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHHHHHHHHcCCCceEEEEecC---
Confidence 46789999999999999999999999999999987665 89999999888777778888877774433 33333332
Q ss_pred CCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecc
Q 002210 692 RETSGPVILVVNACCTQDTKENVIGVCFVGQDIT 725 (953)
Q Consensus 692 ~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DIT 725 (953)
...|+.++..|+++.+|+..|++.++.|||
T Consensus 77 ----~~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 77 ----GGRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp ----TTEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred ----CCEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 245667799999999999999999999998
No 48
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.79 E-value=1.7e-07 Score=118.45 Aligned_cols=126 Identities=12% Similarity=0.133 Sum_probs=97.9
Q ss_pred HHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCcccccc-CCcHHHHHHHHHHHhcccceEEEE
Q 002210 607 RIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA-GDSVDVVKNMLSSAFLEERNVEIK 685 (953)
Q Consensus 607 ~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~-~~~~~~~~~~l~~~l~~~~~~e~~ 685 (953)
++.+..+..+++.++++++++|.+|+++++|+++++++||+.++++|+++.++++ +.........+............+
T Consensus 132 ~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 211 (799)
T PRK11359 132 KEQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDE 211 (799)
T ss_pred HHHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence 3344556678999999999999999999999999999999999999999887765 333333344444444333333333
Q ss_pred EEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHH
Q 002210 686 LRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKY 734 (953)
Q Consensus 686 ~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L 734 (953)
.+. .+++|..+|+.++..|+.+.+|.+.|++++.+|||++|++++..
T Consensus 212 ~~~--~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~ 258 (799)
T PRK11359 212 FLL--LTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLE 258 (799)
T ss_pred eEE--eCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHH
Confidence 333 45689999999999999999999999999999999999887653
No 49
>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=98.77 E-value=5.1e-08 Score=87.08 Aligned_cols=90 Identities=16% Similarity=0.248 Sum_probs=68.7
Q ss_pred EEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHH-HhcCCCcceEEEEEEccCCCEEEEEE
Q 002210 764 CLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNK-VISGQDADKILFGFFDQQGKYVEALL 842 (953)
Q Consensus 764 i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~-~~~g~~~~~~e~~~~~kdG~~~~v~~ 842 (953)
|++||+.+++++||+++++ +......+. ...++++...+...+.. ...++.....+++++++||+++|+..
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~-------~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~ 72 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWL-------ERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEV 72 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHH-------HHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHH-------hhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEE
Confidence 5899999999999999999 554111111 33345666778888888 67777788999999999999999999
Q ss_pred EEEEeecCCCCEEEEEEEE
Q 002210 843 SANKRTNAEGKISGILCFL 861 (953)
Q Consensus 843 s~~pi~d~~G~i~g~v~v~ 861 (953)
++.+++|.+|++++++|+.
T Consensus 73 ~~~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 73 RGRPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEEEETTTS-EEEEEEEE
T ss_pred EEEEEECCCCCEEEEEEEC
Confidence 9999999999999999874
No 50
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=98.77 E-value=2.3e-07 Score=105.07 Aligned_cols=191 Identities=16% Similarity=0.160 Sum_probs=131.2
Q ss_pred EEEEeecCCCCEEEEEEEEEecchhHHHHHH--------------------------------------HHHHHHHHHHH
Q 002210 703 NACCTQDTKENVIGVCFVGQDITGQKLVMDK--------------------------------------YTRIQGDYVGI 744 (953)
Q Consensus 703 ~~~pi~d~~g~v~gvv~v~~DITerk~~E~~--------------------------------------L~~se~~~~~i 744 (953)
...|++|.+|+++|++.+..-+++--..-.. +.++-+.-.++
T Consensus 141 ~~~PI~d~~g~~IGvVsVG~~l~~i~~~i~~~~~~l~~~~vl~lligl~ga~~la~~ikr~~~glEP~EIa~l~~er~A~ 220 (537)
T COG3290 141 AKVPIFDEDGKQIGVVSVGYLLSEIDDVILEFLRPLALIVVLGLLIGLLGAWILARHIKRQMLGLEPEEIATLLEERQAM 220 (537)
T ss_pred eecceECCCCCEEEEEEEeeEhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5689999999999999887766554322211 12222344567
Q ss_pred HhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChh--hhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCC
Q 002210 745 VSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKRE--EAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQD 822 (953)
Q Consensus 745 ~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~e--eliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~ 822 (953)
++++.. |++.+|..|.|+.+|.++++++|+... +.+|+++.+.+.| +.+ +...+.. ++.
T Consensus 221 l~si~E---GviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p-~~~------------l~~vl~~---~~~ 281 (537)
T COG3290 221 LQSIKE---GVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPP-DSD------------LPEVLET---GKP 281 (537)
T ss_pred HHHhhc---eEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeecc-ccC------------cHHHHhc---CCc
Confidence 777776 999999999999999999999999854 7889988744443 221 2222221 221
Q ss_pred cceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 002210 823 ADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNG 902 (953)
Q Consensus 823 ~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrnPL~~ 902 (953)
...-+ .+-+| .++.++..|+. .+|+++|++.+++|=||-++..++|... ++-.+-|...+||..|-|++
T Consensus 282 ~~~~e---~~~ng--~~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~v-----r~ya~aLRaq~HEfmNkLht 350 (537)
T COG3290 282 QHDEE---IRING--RLLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGV-----RQYAEALRAQSHEFMNKLHT 350 (537)
T ss_pred ccchh---hhcCC--eEEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHH-----HHHHHHHHHhhHHHHHHHHH
Confidence 11111 23334 36677778877 6899999999999999888666554332 23445678889999999999
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHH
Q 002210 903 IAFMQNLMGTSDLSEEQKQLLKTSV 927 (953)
Q Consensus 903 I~g~~~LL~~~~l~e~~~~~l~~i~ 927 (953)
|.|++++=+. ++..+|+..+.
T Consensus 351 I~GLlql~~y----d~a~~~I~~~~ 371 (537)
T COG3290 351 ILGLLQLGEY----DDALDYIQQES 371 (537)
T ss_pred HHHHHhhccH----HHHHHHHHHHH
Confidence 9999998653 44555655554
No 51
>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=98.58 E-value=3.8e-07 Score=81.36 Aligned_cols=86 Identities=17% Similarity=0.221 Sum_probs=71.5
Q ss_pred EEecCHHHHHHhCCCcchhcCCC----ccccccCCcHHHHHHHHHH-HhcccceEEEEEEEcccCCCCCEEEEEEEEEEe
Q 002210 633 VNGWNSKAAELTGLTVDQAIGTA----LVDLVAGDSVDVVKNMLSS-AFLEERNVEIKLRAFGPRETSGPVILVVNACCT 707 (953)
Q Consensus 633 i~~~N~a~~~l~G~~~~eliG~~----~~dl~~~~~~~~~~~~l~~-~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi 707 (953)
|++||+.+.+++||+++++ +.. +..++||++.+.+.+.+.. ....+..+..+++. .+++|+.+|+.+++.++
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~--~~~~G~~~wi~~~~~~~ 77 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRI--RRKDGEYRWIEVRGRPI 77 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEE--EGTTSTEEEEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEE--ECCCCCEEEEEEEEEEE
Confidence 6899999999999999998 777 7789999999999999999 66777788888777 56799999999999999
Q ss_pred ecCCCCEEEEEEEE
Q 002210 708 QDTKENVIGVCFVG 721 (953)
Q Consensus 708 ~d~~g~v~gvv~v~ 721 (953)
+|.+|++++++|+.
T Consensus 78 ~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 78 FDENGKPIRIIGVI 91 (91)
T ss_dssp ETTTS-EEEEEEEE
T ss_pred ECCCCCEEEEEEEC
Confidence 99999999998873
No 52
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.57 E-value=2.1e-07 Score=92.30 Aligned_cols=155 Identities=17% Similarity=0.235 Sum_probs=103.3
Q ss_pred HHHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCC--ceEEEeecCCCCCCccCCCCCCCCccH-HHHH
Q 002210 201 AAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEH--GEVVAECRRPDLEPYLGFHYPATDIPQ-ASRF 277 (953)
Q Consensus 201 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~--G~viaE~~~~~~~~~lg~~~pa~dip~-~ar~ 277 (953)
+..+...+.. +.+++++++.+++.+.+.+|+||..||++++|+. +.++++.......+...-.+.....|. ....
T Consensus 6 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (175)
T COG2203 6 LNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLVILPACLIGI 83 (175)
T ss_pred HHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhcccCcchhhhhh
Confidence 3445566666 5699999999999999999999999999999995 776666554430111110110000000 0111
Q ss_pred HHHhCCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCce
Q 002210 278 LIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKL 357 (953)
Q Consensus 278 ly~~n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~L 357 (953)
........++.|+...+.. ..+|..++... ++|.+++||+.+ +++
T Consensus 84 ~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~-i~~~l~vPl~~~-------------~~~ 128 (175)
T COG2203 84 ALREGRPVVVEDILQDPRF---------------------RDNPLVLLEPP-IRSYLGVPLIAQ-------------GEL 128 (175)
T ss_pred hhcCCceEEeeccccCccc---------------------ccCHHHHHHHH-HHHheeeeeeEC-------------CEe
Confidence 1122333344442222110 12566666655 899999999987 899
Q ss_pred eEEEeeecCCCC-CCChhHHHHHHHHHHHHHHhhHH
Q 002210 358 WGLVVCHHTSPR-FVPFPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 358 WGLi~~hh~~pr-~~~~~~r~~~~~l~~~~~~~l~~ 392 (953)
||.+++||+.++ .|+..++...+.+++.++..|..
T Consensus 129 ~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ai~~ 164 (175)
T COG2203 129 LGLLCVHDSEPRRQWSEEELELLEELAEQVAIAIER 164 (175)
T ss_pred eEEeeeeccCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 999999999966 69999999999999999888754
No 53
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.53 E-value=2e-06 Score=81.74 Aligned_cols=128 Identities=15% Similarity=0.146 Sum_probs=89.9
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCC
Q 002210 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (953)
Q Consensus 215 ~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~ 294 (953)
|++++++.+++.+++++|+|++.||.+++|..--.++... +..+-+.-.+| . -..-....+..+++..++|....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~--~~~~~~~~~l~-~-~~~~~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW--GGDPRLSESLP-E-DDPLIGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE--SS-GCGHHCEE-T-TSHHHHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe--CCCccccccCC-C-CccHHHHHHhhCCeEEeccccccc
Confidence 5799999999999999999999999999885444344333 22222222555 2 233444677777765555521110
Q ss_pred ceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCCCChh
Q 002210 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374 (953)
Q Consensus 295 ~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~ 374 (953)
..+.++.|++||..+ ++++|+|.+++..++.|+..
T Consensus 77 --------------------------------~~~~~s~~~vPl~~~-------------~~~~Gvl~~~~~~~~~~~~~ 111 (129)
T PF13492_consen 77 --------------------------------FLGIRSLLVVPLRSR-------------DRVIGVLCLDSREPEEFSDE 111 (129)
T ss_dssp --------------------------------TTTTCEEEEEEEEET-------------TEEEEEEEEEECTTCG-SHH
T ss_pred --------------------------------CCCCCEEEEEEEeEC-------------CEEEEEEEEEECCCCCCCHH
Confidence 046688899999987 79999999988888899999
Q ss_pred HHHHHHHHHHHHHHhhH
Q 002210 375 LRYACEFLIQVFGVQVN 391 (953)
Q Consensus 375 ~r~~~~~l~~~~~~~l~ 391 (953)
.....+.++..+|..|+
T Consensus 112 d~~~l~~~a~~~a~ale 128 (129)
T PF13492_consen 112 DLQLLESLANQLAIALE 128 (129)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999998887763
No 54
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.51 E-value=1.6e-06 Score=105.32 Aligned_cols=129 Identities=20% Similarity=0.308 Sum_probs=98.6
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcc-cceEE
Q 002210 605 ELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLE-ERNVE 683 (953)
Q Consensus 605 eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~-~~~~e 683 (953)
.++..+..++.++++++++++++|.+|+++++|+++++++|++.++++|+++.+++++... +...+...+.. .....
T Consensus 256 ~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 333 (607)
T PRK11360 256 ALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP--FASPLLDTLEHGTEHVD 333 (607)
T ss_pred HHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh--HHHHHHHHHhcCCCccc
Confidence 3555566778899999999999999999999999999999999999999999988775432 22233333322 21222
Q ss_pred EEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHH
Q 002210 684 IKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQ 738 (953)
Q Consensus 684 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se 738 (953)
..... ...+|... +.++..|+.+.+|++.|++++++|||++|++|+++++.+
T Consensus 334 ~~~~~--~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~ 385 (607)
T PRK11360 334 LEISF--PGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385 (607)
T ss_pred eEEEE--EcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHH
Confidence 22222 33456655 888999999999999999999999999999999887654
No 55
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.50 E-value=9.1e-07 Score=101.25 Aligned_cols=226 Identities=12% Similarity=0.151 Sum_probs=145.9
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhc-----------ccceEE
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFL-----------EERNVE 683 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~-----------~~~~~e 683 (953)
.++++....|++++.||.++|+.......+|++.-|+.|.++.|++||.|.+.+.+.+..... .+..+-
T Consensus 123 ~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRsFf 202 (768)
T KOG3558|consen 123 HILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERSFF 202 (768)
T ss_pred hHHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhccccCCCcccccccCccceeEE
Confidence 356777778899999999999999999999999999999999999999999988777654432 112233
Q ss_pred EEEEEcccCCCCCEEEE--------EEEEEE-eecCCCC----------EEEEEEEEEecchhHHHHHHHHHHHHHHHHH
Q 002210 684 IKLRAFGPRETSGPVIL--------VVNACC-TQDTKEN----------VIGVCFVGQDITGQKLVMDKYTRIQGDYVGI 744 (953)
Q Consensus 684 ~~~~~~~~~~dG~~~~v--------~v~~~p-i~d~~g~----------v~gvv~v~~DITerk~~E~~L~~se~~~~~i 744 (953)
++++.. ..+.|+...+ .++... +++..+. +.|.+.+..-|---+-.|--|
T Consensus 203 lRMKsT-LT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL---------- 271 (768)
T KOG3558|consen 203 LRMKST-LTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPL---------- 271 (768)
T ss_pred EEeeee-eccCCceeeeeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCccccccc----------
Confidence 333332 2233422221 111111 1111111 222232222222111111000
Q ss_pred HhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcc
Q 002210 745 VSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDAD 824 (953)
Q Consensus 745 ~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~ 824 (953)
+.-..+.....|-+|+|+.+.+.+++||.+++++|+.+.+.++..+ ...+.......+..+...
T Consensus 272 -----~~~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~D-----------s~~v~KSh~dL~~KGQv~ 335 (768)
T KOG3558|consen 272 -----DCHMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALD-----------SDRVRKSHHDLLTKGQVV 335 (768)
T ss_pred -----CCceeEEeeecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhh-----------hhHHHHHHHHHHhcCccc
Confidence 0000134456778999999999999999999999999876555543 233555555666666666
Q ss_pred eEEEEEEccCCCEEEEEEEEEEeecCC-CCEEEEEEEEEeccHH
Q 002210 825 KILFGFFDQQGKYVEALLSANKRTNAE-GKISGILCFLHVASPE 867 (953)
Q Consensus 825 ~~e~~~~~kdG~~~~v~~s~~pi~d~~-G~i~g~v~v~~DITer 867 (953)
...||+..|+|.++|+...++.+.+.. ++...++||-.-|+..
T Consensus 336 TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~~ 379 (768)
T KOG3558|consen 336 TGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSNI 379 (768)
T ss_pred hhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeeccc
Confidence 777899999999999999999888743 4556678877777644
No 56
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.46 E-value=9.8e-06 Score=99.35 Aligned_cols=225 Identities=17% Similarity=0.206 Sum_probs=127.8
Q ss_pred HHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCc-chhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEccc
Q 002210 613 MVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTV-DQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGP 691 (953)
Q Consensus 613 l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~-~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~ 691 (953)
+..++...+..+++.|.+|.++.++....-+..... .-..|..|.+-.-.. ..+-.++..+.++.+.-.-.+
T Consensus 64 l~~~l~~~~~~~~l~D~~G~vL~~~g~~~~~~~~~~~~~~~G~~w~E~~~GT------naig~al~~~~pv~v~g~EH~- 136 (638)
T PRK11388 64 AWEYMADRECALLILDETGCILSRNGDPQTLQQLSALGFNDGTYCAEGIIGT------NALSLAAISGQPVKTMGDQHF- 136 (638)
T ss_pred HHHHhcCCCcEEEEEcCCceEEEEeCCHHHHHHHHHcCCccCCccchhccCc------CHHHHHHhcCCceEEecHHHH-
Confidence 345566778899999999999987643322111000 111233333211111 123333433444333211110
Q ss_pred CCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchh------------HHHHHH---------HHHHHHHHHHHHhCCCC
Q 002210 692 RETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQ------------KLVMDK---------YTRIQGDYVGIVSSPSA 750 (953)
Q Consensus 692 ~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITer------------k~~E~~---------L~~se~~~~~i~e~~~~ 750 (953)
......+...+.|++|.+|+++|++.+..+.... +.+|.. +......+..++++.++
T Consensus 137 --~~~~~~~~c~aaPI~d~~G~liGvl~l~~~~~~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~~~~~~~~il~~~~~ 214 (638)
T PRK11388 137 --KQALHNWAFCATPVFDSKGRLTGTIALACPVEQTSAADLPLTLSIAREVGNLLLTDSLLAESNRHLNQLNALLESMDD 214 (638)
T ss_pred --HHhccCceEEeeEEEcCCCCEEEEEEEEecccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 1122234568999999999999998776643321 111111 12222334457788766
Q ss_pred CCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCC-cceEEEE
Q 002210 751 LIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQD-ADKILFG 829 (953)
Q Consensus 751 li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~-~~~~e~~ 829 (953)
+++++|.+|+|+++|+++++++|++.++++|+.+.+ +++.. .. + ...+..+. ....+..
T Consensus 215 ---gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~-l~~~~---------~~---l----~~vl~~~~~~~~~~~~ 274 (638)
T PRK11388 215 ---GVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITE-LLTLP---------AV---L----QQAIKQAHPLKHVEVT 274 (638)
T ss_pred ---cEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHH-Hhccc---------hH---H----HHHHhcCCceeeEEEE
Confidence 999999999999999999999999999999998753 33211 11 1 11222222 2222222
Q ss_pred EEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHH
Q 002210 830 FFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQ 869 (953)
Q Consensus 830 ~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~ 869 (953)
+ ..+|..+++.++..|+.+..|. +++.+++|++..++
T Consensus 275 l-~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 275 F-ESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred E-ecCCceEEEEEEEEeecccCce--EEEEEehhhHHHHH
Confidence 2 3457777889999998754443 35666778876543
No 57
>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=98.44 E-value=4e-06 Score=71.42 Aligned_cols=103 Identities=22% Similarity=0.342 Sum_probs=81.4
Q ss_pred cCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEE
Q 002210 620 AAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVI 699 (953)
Q Consensus 620 ~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~ 699 (953)
++++++++|.+|.++++|+++.+++|++..+++|+.+.+++++.+...+...+................ ...+|...|
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 78 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRL--RRKDGSVIW 78 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEE--EccCCCEEE
Confidence 367899999999999999999999999999999999988888877766666666655333333333333 234688899
Q ss_pred EEEEEEEeecCCCCEEEEEEEEEec
Q 002210 700 LVVNACCTQDTKENVIGVCFVGQDI 724 (953)
Q Consensus 700 v~v~~~pi~d~~g~v~gvv~v~~DI 724 (953)
+.+...++.+..|...+++++.+||
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 79 VLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999988888999999988886
No 58
>PF12860 PAS_7: PAS fold
Probab=98.43 E-value=6.5e-07 Score=84.03 Aligned_cols=104 Identities=21% Similarity=0.301 Sum_probs=71.1
Q ss_pred HHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchh-cCCCcccccc---------CCcHH-HHHHHHHHHhcccceEEEE
Q 002210 617 IETAAVPILAVDASGNVNGWNSKAAELTGLTVDQA-IGTALVDLVA---------GDSVD-VVKNMLSSAFLEERNVEIK 685 (953)
Q Consensus 617 le~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~el-iG~~~~dl~~---------~~~~~-~~~~~l~~~l~~~~~~e~~ 685 (953)
+++++.||+++|.+|++++||+++.+++|++.+.+ .|.++.+++. +.+.. .+...+.. ........++
T Consensus 1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 79 (115)
T PF12860_consen 1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLAR-LRRRQPRSFE 79 (115)
T ss_pred CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HhcCCCceeE
Confidence 47889999999999999999999999999999887 7888775542 12222 22222222 2222333333
Q ss_pred EEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHH
Q 002210 686 LRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMD 732 (953)
Q Consensus 686 ~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~ 732 (953)
... ..-+|+.++..|..+ | |++.++.|||++|++|+
T Consensus 80 ~~~------~dgr~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 80 LRL------PDGRWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred EEC------CCCEEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 333 234567778888754 3 57789999999998874
No 59
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.43 E-value=4.8e-06 Score=88.60 Aligned_cols=124 Identities=15% Similarity=0.210 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEE
Q 002210 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVE 683 (953)
Q Consensus 604 ~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e 683 (953)
+-++...+++.+++..+.+||+..|..|+|+.+|..+.+++|.+.++++|+++.+++.-++.-.+.+. ......+-
T Consensus 104 ~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL----~e~~~s~l 179 (459)
T COG5002 104 ANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDL----VEKNDSLL 179 (459)
T ss_pred HhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHH----HhcCCcEE
Confidence 34556677889999999999999999999999999999999999999999999988875554333333 32233333
Q ss_pred EEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHH
Q 002210 684 IKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTR 736 (953)
Q Consensus 684 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~ 736 (953)
..... .++...+.+++..++.+.|-+.|++.+..|+||+.+.|++.++
T Consensus 180 ld~~~-----~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRe 227 (459)
T COG5002 180 LDSSD-----EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERRE 227 (459)
T ss_pred EeecC-----CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHHH
Confidence 33222 4778888999999999999999999999999999999988654
No 60
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=98.41 E-value=1.1e-06 Score=103.41 Aligned_cols=67 Identities=24% Similarity=0.249 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcC--CCCCHH-HHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGT--SDLSEE-QKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~--~~l~e~-~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
+.++.+|+.+||||||||++|+|.++.|.. ..++++ +.+.+..|.+.+++|.+++++ ||++||++|-
T Consensus 658 ~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~ 728 (890)
T COG2205 658 RLRSALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGG 728 (890)
T ss_pred HHHHHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCC
Confidence 456778999999999999999999999988 556665 778999999999999999999 8999999994
No 61
>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=98.40 E-value=2.3e-06 Score=95.60 Aligned_cols=114 Identities=13% Similarity=0.224 Sum_probs=85.7
Q ss_pred HHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEE
Q 002210 607 RIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKL 686 (953)
Q Consensus 607 ~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~ 686 (953)
++..++++.++++++++|+++|.+|++++||++++++||++.++.+|+++.++.++++ +...+..... ... ..+
T Consensus 2 ~~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~---~~~~l~~~~~-~~~--~~~ 75 (333)
T TIGR02966 2 SALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE---FVEYLAAGRF-SEP--LEL 75 (333)
T ss_pred hhHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH---HHHHHHhccc-CCC--eEe
Confidence 3456778999999999999999999999999999999999999999999998876432 2222222211 222 222
Q ss_pred EEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHH
Q 002210 687 RAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYT 735 (953)
Q Consensus 687 ~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~ 735 (953)
. .++|..+|+.+...|+.+.. ++++++|||++++.++...
T Consensus 76 ~----~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~~ 115 (333)
T TIGR02966 76 P----SPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMRR 115 (333)
T ss_pred e----cCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHHH
Confidence 2 23578889999999987632 6678899999998876543
No 62
>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=98.39 E-value=6e-06 Score=70.30 Aligned_cols=100 Identities=23% Similarity=0.328 Sum_probs=79.1
Q ss_pred CeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEcc
Q 002210 754 PIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQ 833 (953)
Q Consensus 754 ~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~k 833 (953)
+++.+|.+|.+.++|+++.+++|++.++++|+.+...+.+. ....+...+.....+......++.+..+
T Consensus 4 ~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (103)
T cd00130 4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPE-----------DREELRERLENLLSGGEPVTLEVRLRRK 72 (103)
T ss_pred eEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCc-----------cchHHHHHHHHHHhcCcCeEEEEEEEcc
Confidence 78999999999999999999999999999998875333322 1112444455555544555677888889
Q ss_pred CCCEEEEEEEEEEeecCCCCEEEEEEEEEec
Q 002210 834 QGKYVEALLSANKRTNAEGKISGILCFLHVA 864 (953)
Q Consensus 834 dG~~~~v~~s~~pi~d~~G~i~g~v~v~~DI 864 (953)
+|..+|+.....++.+.+|...+++++.+||
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred CCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999999999999889999999998886
No 63
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.38 E-value=5.2e-05 Score=75.27 Aligned_cols=228 Identities=20% Similarity=0.248 Sum_probs=141.2
Q ss_pred EEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEEEEE
Q 002210 624 ILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVILVVN 703 (953)
Q Consensus 624 I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~ 703 (953)
++..+..+.+.+.|......+++......+ .............................. ......++...++...
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 77 (232)
T COG2202 2 ILVLDRDGRIIYANEAAEELLGYSAEELLG--LLLALHPEDRDRLRELLRRLLAGEELLSEE--LRLVRKDGEERWVELS 77 (232)
T ss_pred eEEEcccccEEEecccchhhcCCChHHhhh--hhhccCccchhhhHHHHHHHhccCCcchhh--HHhhhcCCcEEEEEec
Confidence 345677888888888888888887766555 111111111111111111111111110000 0011123444444433
Q ss_pred EEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhh
Q 002210 704 ACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAI 783 (953)
Q Consensus 704 ~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeli 783 (953)
........+........ .|++..+..++.+...+.+++.++++.+. +++..|.+|++.++|+++.+++|++..+..
T Consensus 78 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~ 153 (232)
T COG2202 78 AAPLRDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASPD---GIWVLDEDGRILYANPAAEELLGYSPEEEL 153 (232)
T ss_pred ceEEEcCCCCEEEEEee-eecchHHHHHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEeCHHHHHHhCCChHHhc
Confidence 33333334555555555 89999999999999999999999999987 899999999999999999999999988877
Q ss_pred cccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCE-EEEEEEEEEeecCCCCEEEEEEEEE
Q 002210 784 ERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKY-VEALLSANKRTNAEGKISGILCFLH 862 (953)
Q Consensus 784 Gk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~-~~v~~s~~pi~d~~G~i~g~v~v~~ 862 (953)
+............ +.. ..................++....++|.. .+......+..+ .|.+.++.+...
T Consensus 154 ~~~~~~~~~~~~~--------~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 223 (232)
T COG2202 154 GRGLSDLIHPEDE--------ERR-ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIAR 223 (232)
T ss_pred CCChhheEecCCC--------chh-hHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEe
Confidence 7665432222211 000 01111112222233457788889999996 888877777654 788999999999
Q ss_pred eccHHHH
Q 002210 863 VASPELQ 869 (953)
Q Consensus 863 DITerK~ 869 (953)
|+|++++
T Consensus 224 d~~~~~~ 230 (232)
T COG2202 224 DITERKQ 230 (232)
T ss_pred chHHHhh
Confidence 9998874
No 64
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=98.31 E-value=9.8e-06 Score=79.03 Aligned_cols=136 Identities=15% Similarity=0.157 Sum_probs=87.2
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCC--CCCC-ccHHHH------HHHHhCCce
Q 002210 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHY--PATD-IPQASR------FLIMKNKVR 285 (953)
Q Consensus 215 ~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~--pa~d-ip~~ar------~ly~~n~~r 285 (953)
+++++++.+++.+.+++|+|.+.||-+++++.=..++-+..+ ...++..+ |... .+.-.. .++..++..
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDP--SEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEPI 80 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSS--CTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-E
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCc--hhhhhhhcccCcccccccchhhhhHHHHHHhcCceE
Confidence 789999999999999999999999999877722222322222 22222221 1111 111110 114555555
Q ss_pred EeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeec
Q 002210 286 MICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHH 365 (953)
Q Consensus 286 ~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh 365 (953)
++. ..+ +.. +. .......|+++.+++||+.+ |++||.|...+
T Consensus 81 ~~~---~~~--------------------~~~-~~-~~~~~~~~~~s~l~vPl~~~-------------~~~~Gvl~l~~ 122 (148)
T PF13185_consen 81 IIN---DDD--------------------SSF-PP-WELARHPGIRSILCVPLRSG-------------GEVIGVLSLYS 122 (148)
T ss_dssp EES---CCC--------------------GGG-ST-THHHCCTT-SEEEEEEEEET-------------TEEEEEEEEEE
T ss_pred EEe---Ccc--------------------ccc-cc-hhhhccccCCEEEEEEEeEC-------------CEEEEEEEEee
Confidence 555 000 000 11 25688999999999999987 89999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHhh
Q 002210 366 TSPRFVPFPLRYACEFLIQVFGVQV 390 (953)
Q Consensus 366 ~~pr~~~~~~r~~~~~l~~~~~~~l 390 (953)
..++.++...+..++.++..+|..|
T Consensus 123 ~~~~~f~~~~~~~l~~la~~~a~ai 147 (148)
T PF13185_consen 123 KEPNAFSEEDLELLEALADQIAIAI 147 (148)
T ss_dssp SSTT---HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHh
Confidence 8899999999999999999888765
No 65
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=98.31 E-value=5.8e-05 Score=90.52 Aligned_cols=219 Identities=12% Similarity=0.099 Sum_probs=132.7
Q ss_pred HHHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHH
Q 002210 199 KLAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFL 278 (953)
Q Consensus 199 ~~~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~l 278 (953)
+.+.++...+.+ +.+++++++.+++.+.+++|+||..||-+++++...++ .+....-+..-...|+... --....
T Consensus 5 ~~L~~is~~l~~--~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~-aa~g~~~~~~~~~~~~~~~--gi~g~v 79 (534)
T TIGR01817 5 AALYEISKILSA--PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLV-AAIGWSEEGFAPIRYRVGE--GAIGQI 79 (534)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEE-EEeCCChhhcccccccCCc--cHHHHH
Confidence 344555566666 67999999999999999999999999999888754433 3322111111113343321 234566
Q ss_pred HHhCCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCcee
Q 002210 279 IMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLW 358 (953)
Q Consensus 279 y~~n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LW 358 (953)
+..+..-+|.|+...|-... +. -+...|++|.|++||..+ |+++
T Consensus 80 ~~~~~pvii~Dv~~d~~~~~---------------------~~--~~~~~~~~S~l~VPL~~~-------------g~vi 123 (534)
T TIGR01817 80 VATGNSLVVPDVAAEPLFLD---------------------RL--SLYDPGPVPFIGVPIKAD-------------SETI 123 (534)
T ss_pred HhcCCeEEecccccCchhhh---------------------cc--ccccCCcceEEEEEEcCC-------------CEEE
Confidence 77888888888655432110 00 023457899999999976 9999
Q ss_pred EEEeeecCC-CCCCChhHHHHHHHHHHHHHHhhHHHHHH--HHHHHHHHHHHHHHHHHHh---hcc---CCCCccccCCc
Q 002210 359 GLVVCHHTS-PRFVPFPLRYACEFLIQVFGVQVNKEVEL--SAQLREKHILRTQTVLCDM---LLR---DSPVGIVTQTP 429 (953)
Q Consensus 359 GLi~~hh~~-pr~~~~~~r~~~~~l~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~~---~~~---~~~~~~~~~~~ 429 (953)
|.|..++.. ++........+++.++..++..|...... ..++..+...+..+.+... ..+ .....++.+++
T Consensus 124 GvL~v~s~~~~~~ft~~d~~lL~~lA~~ia~aI~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~liG~s~ 203 (534)
T TIGR01817 124 GVLAADRDFRSRERLEEEVRFLEMVANLIGQTVRLHRLVAQRRERLIAEAVQLSKQLRDKAPEIARRRSGKEDGIIGKSP 203 (534)
T ss_pred EEEEEEeccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCccCceEECCH
Confidence 999999886 56778888899999999888887522111 1111111111111111110 000 12346778887
Q ss_pred chhhhccCCeEEEEECCeEEEeCCCCCHH
Q 002210 430 NVMDLVKCDGAALYYRGKLWLLGVTPTEE 458 (953)
Q Consensus 430 ~l~~l~~~dg~a~~~~~~~~~~G~~p~~~ 458 (953)
.+..+++--..+.-.+..+.+.|.+=+-.
T Consensus 204 ~~~~~~~~~~~~a~~~~pvli~Ge~GtGK 232 (534)
T TIGR01817 204 AMRQVVDQARVVARSNSTVLLRGESGTGK 232 (534)
T ss_pred HHHHHHHHHHHHhCcCCCEEEECCCCccH
Confidence 76666554333333455667777765533
No 66
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.29 E-value=3.1e-06 Score=78.17 Aligned_cols=105 Identities=18% Similarity=0.252 Sum_probs=72.9
Q ss_pred HHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCC
Q 002210 742 VGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQ 821 (953)
Q Consensus 742 ~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~ 821 (953)
+.++++++. ++..+|.+++|.++|+++.++|+....+ +|+++. .+.++.....+...+.....|+
T Consensus 2 ~~il~s~~~---~i~~vD~~~~I~~~n~~a~~~f~~~~~~-iGr~l~-----------~~~~~~~~~~l~~~i~~~~~~~ 66 (106)
T PF13596_consen 2 NNILDSMPI---GIIFVDRNLRIRYFNPAAARLFNLSPSD-IGRPLF-----------DIHPPLSYPNLKKIIEQVRSGK 66 (106)
T ss_dssp HHHHHHSSS---EEEEEETTSBEEEE-SCGC-SS---GGG-TTSBCC-----------CSS-HHHHHHHHHHHHHHHTTS
T ss_pred hHHHhcCCC---CEEEEcCCCeEEEeChhHhhhcCCChHH-CCCCHH-----------HcCCccchHHHHHHHHHHHcCC
Confidence 567788876 8999999999999999999999977544 699876 3333445556777777777777
Q ss_pred CcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEecc
Q 002210 822 DADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVAS 865 (953)
Q Consensus 822 ~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DIT 865 (953)
.. ..++.. ..+| .|+.++..|++|.+|+..|++.++.|||
T Consensus 67 ~~-~~~~~~-~~~~--~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 67 EE-EFEIVI-PNGG--RWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp BS-EEEEEE-EETT--EEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred Cc-eEEEEe-cCCC--EEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 53 233222 2444 5677899999999999999999999998
No 67
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.27 E-value=4.7e-06 Score=94.26 Aligned_cols=115 Identities=13% Similarity=0.117 Sum_probs=84.2
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEE-EEEEEc
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVE-IKLRAF 689 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e-~~~~~~ 689 (953)
..+..+++++++|++++|.+|+|+++|+++++++|++.++++|+++.++++..... ...+...+..+.... ....
T Consensus 7 ~~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-- 82 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLN--IELMRESLQAGQGFTDNEVT-- 82 (348)
T ss_pred chHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchhh--HHHHHHHHHcCCcccccceE--
Confidence 35678999999999999999999999999999999999999999999887654322 122333332222111 1111
Q ss_pred ccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHH
Q 002210 690 GPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYT 735 (953)
Q Consensus 690 ~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~ 735 (953)
...+|..+|+.++..|+.. .+++..++|+|++++.++++.
T Consensus 83 -~~~~g~~~~~~~~~~~~~~-----~~~~~~~~dit~~~~~~~~~~ 122 (348)
T PRK11073 83 -LVIDGRSHILSLTAQRLPE-----GMILLEMAPMDNQRRLSQEQL 122 (348)
T ss_pred -EEECCceEEEEEEEEEccC-----ceeEEEEechhHHHHHHHHHH
Confidence 1237899999999999872 345667899999998877654
No 68
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).
Probab=98.26 E-value=2.2e-06 Score=110.75 Aligned_cols=76 Identities=32% Similarity=0.376 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 875 QRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 875 q~~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
+..++++.+.|..|++.|||||||||++|.|++++|....++++++++++.+.+++++|..+|++ |+++|+|.|+.
T Consensus 454 ~~~~~~~~~~~~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~~~ 530 (968)
T TIGR02956 454 RAEAEEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGHL 530 (968)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34556677889999999999999999999999999999999999999999999999999999999 89999999853
No 69
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=98.26 E-value=2.2e-06 Score=110.26 Aligned_cols=77 Identities=31% Similarity=0.407 Sum_probs=70.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 874 VQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 874 lq~~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
.++.+++....+.+|++.++|||||||++|.|++++|....++++++++++.+..++.+|..+|++ ||++|+|+|+.
T Consensus 387 ~~~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~ 464 (921)
T PRK15347 387 AKQRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQM 464 (921)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 344556667788899999999999999999999999999999999999999999999999999999 89999999864
No 70
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=98.20 E-value=3.1e-06 Score=69.82 Aligned_cols=64 Identities=31% Similarity=0.466 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
+.++++.++||+||||++|.++++++.....+++..++++.+..+.+++..++++ +++++++.|
T Consensus 2 ~~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~ 66 (66)
T smart00388 2 KREFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIEAG 66 (66)
T ss_pred HHHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3568899999999999999999999988666777789999999999999999999 799998764
No 71
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=98.12 E-value=0.00028 Score=83.93 Aligned_cols=215 Identities=11% Similarity=0.047 Sum_probs=129.1
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHh
Q 002210 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMK 281 (953)
Q Consensus 202 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~ 281 (953)
.++...|-+ +.+++++++.+++.+.+++++|.+-|+.++++ .....+..+.-....+..|+..+-|.-...+ ..
T Consensus 7 ~eis~~L~~--s~d~~e~L~~vl~~l~~~l~~~~~~l~l~~~~---~l~~~as~gl~~~~~~~~~~~geGP~l~av~-~~ 80 (509)
T PRK05022 7 LPIALDLSR--GLPHQDRFQRLLTTLRQVLPCDASALLRLDGD---QLVPLAIDGLSPDVLGRRFALEEHPRLEAIL-RA 80 (509)
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC---cEEEEEEcCCChHhhCCccCCCcchHHHHHH-hc
Confidence 345555666 77999999999999999999999999999753 3222233332333456678777766433333 32
Q ss_pred CCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEE
Q 002210 282 NKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLV 361 (953)
Q Consensus 282 n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi 361 (953)
+++-.|+|....|-++ + |-... ...++|++|.|++||.++ |+.+|.|
T Consensus 81 g~~v~v~~~~~~p~~~----------~------~~~~~----~~~~~gi~S~l~vPL~~~-------------~~~~GvL 127 (509)
T PRK05022 81 GDPVRFPADSELPDPY----------D------GLIPG----VQESLPVHDCMGLPLFVD-------------GRLIGAL 127 (509)
T ss_pred CCeEEEecCCCCCccc----------c------ccccc----ccccCCcceEEEEEEEEC-------------CEEEEEE
Confidence 5444555432222111 0 00000 134579999999999988 8999999
Q ss_pred eeecCCCCCCChhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CCCccccCCcchhhhccCCeE
Q 002210 362 VCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRD-SPVGIVTQTPNVMDLVKCDGA 440 (953)
Q Consensus 362 ~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~l~~~dg~ 440 (953)
.+++..|..+.......++.++..++..|......+....+...+. ........+. .+..++.+++.+..+.+--..
T Consensus 128 ~l~~~~~~~f~~~~~~~l~~~a~~~a~Al~~a~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~iig~s~~~~~~~~~i~~ 205 (509)
T PRK05022 128 TLDALDPGQFDAFSDEELRALAALAAATLRNALLIEQLESQAELPQ--DVAEFLRQEALKEGEMIGQSPAMQQLKKEIEV 205 (509)
T ss_pred EEeeCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhhhccCCceeecCHHHHHHHHHHHH
Confidence 9999888778888788888888888888764433222211111111 1111111111 355677888766555443222
Q ss_pred EEEECCeEEEeCCCCCH
Q 002210 441 ALYYRGKLWLLGVTPTE 457 (953)
Q Consensus 441 a~~~~~~~~~~G~~p~~ 457 (953)
+--.+..+.+.|.+=+-
T Consensus 206 ~a~~~~pVlI~Ge~GtG 222 (509)
T PRK05022 206 VAASDLNVLILGETGVG 222 (509)
T ss_pred HhCCCCcEEEECCCCcc
Confidence 33335566677766553
No 72
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.12 E-value=5.8e-06 Score=106.26 Aligned_cols=74 Identities=24% Similarity=0.287 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 877 ISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 877 ~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
.++++.+.|.+|++.+||||||||++|.|++++|....++++++++++.+.+++++|..+|++ |+++|+|.|+.
T Consensus 285 ~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~ 359 (919)
T PRK11107 285 RAQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKL 359 (919)
T ss_pred HHHHHHHHHHHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 444556778899999999999999999999999988888999999999999999999999999 89999999864
No 73
>PF12860 PAS_7: PAS fold
Probab=98.12 E-value=9.9e-06 Score=75.96 Aligned_cols=111 Identities=15% Similarity=0.175 Sum_probs=68.1
Q ss_pred hCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhh-hcccccccccccccccccccCcch-HHHHHHHHHHHhcCCCc
Q 002210 746 SSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEA-IERMLIGEVFTVKNFGCRVKNHDT-LTKLRIVMNKVISGQDA 823 (953)
Q Consensus 746 e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eel-iGk~~~~~~~~~~~~~~~l~~~~~-~~~~~~~l~~~~~g~~~ 823 (953)
++++. ||+++|.+|++++||+++.+++|++.+.+ .|.++.+.+-..... ....+.. ...+...+... ....
T Consensus 2 d~l~~---Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~--g~~~~~~~~~~~~~~~~~~-~~~~- 74 (115)
T PF12860_consen 2 DSLPQ---GVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAER--GEFPPGDPEAWVRQRLARL-RRRQ- 74 (115)
T ss_pred CCcCc---eEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHc--CCCCCCCHHHHHHHHHHHH-hcCC-
Confidence 45555 99999999999999999999999999988 677664332211000 1111122 12222222222 2222
Q ss_pred ceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHH
Q 002210 824 DKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYA 871 (953)
Q Consensus 824 ~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e 871 (953)
...+.+...||+++ .++..|.- +| |++.++.|||++|++|
T Consensus 75 -~~~~~~~~~dgr~l--~~~~~~~~--~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 75 -PRSFELRLPDGRWL--EVRAQPLP--DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred -CceeEEECCCCEEE--EEEeEECC--CC---CEEEEEEeCCHHHHhc
Confidence 33344667888655 45556653 44 4567899999999776
No 74
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=98.11 E-value=0.00012 Score=82.50 Aligned_cols=219 Identities=17% Similarity=0.121 Sum_probs=131.5
Q ss_pred CCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHH--HHHHHHhCCceEe-ecC
Q 002210 214 GNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQA--SRFLIMKNKVRMI-CDC 290 (953)
Q Consensus 214 ~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~--ar~ly~~n~~r~i-~D~ 290 (953)
.+++.++..+++.+..+.|||+++++++|.+. .+..+.+.-..+.+|.+-+....|.+ .+-+=...+++++ .|+
T Consensus 47 ~~~e~ll~~v~~~l~~~~~~~~~~ll~~d~~~---l~~~~~~gl~~~~~~~~~~~~~~~~~~l~~i~~~~~p~~~~~~d~ 123 (550)
T COG3604 47 LRLERLLAEVAKELHSLFGCDASALLRLDSKN---LIPLATDGLSKDHLGREQRFVVEGHPLLEQILKAGRPLVFHPADS 123 (550)
T ss_pred hhHHHHHHHHHHHHHHHhcCCeeEEEEecccc---cchhhhhcccccccccccccccCcchHHHHHHhCCCcEEEecCCc
Confidence 58999999999999999999999999999887 44444444444556654333344433 3333333345441 221
Q ss_pred CCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCC
Q 002210 291 LAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRF 370 (953)
Q Consensus 291 ~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~ 370 (953)
. .+++..+ ++ --.+|+++-|.|.+||.++ +++||.+..-|+.|-.
T Consensus 124 ~------~~~~~~~---------l~-------~~~~~~~~~a~i~~PL~~~-------------~~~~G~Ltld~~~~~~ 168 (550)
T COG3604 124 L------FPDPYDG---------LL-------PDTEGNKKHACIGVPLKSG-------------DKLIGALTLDHTEPDQ 168 (550)
T ss_pred c------cCCcccc---------cc-------cCccCCcceeEEeeeeeeC-------------CeeeeeEEeeeecccc
Confidence 1 1111110 01 1156778899999999988 8999999999998877
Q ss_pred CChhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH-HHHHHHhhcc--CCCCccccCCcchhhhccCCeEEEEECCe
Q 002210 371 VPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRT-QTVLCDMLLR--DSPVGIVTQTPNVMDLVKCDGAALYYRGK 447 (953)
Q Consensus 371 ~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~l~~l~~~dg~a~~~~~~ 447 (953)
..+..-...++|+...++.+......+.-...++.+.. +..+..-+.. ....+|+.++|.++.+++.=-++--.+-.
T Consensus 169 f~~~~~~~lr~La~~a~la~~~~~l~~~l~~~~~~l~~e~~~~~~~~~~~~~~~~~iIG~S~am~~ll~~i~~VA~Sd~t 248 (550)
T COG3604 169 FDEDLDEELRFLAALAALAVANALLHRELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDST 248 (550)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccchhcccccceecCHHHHHHHHHHHHHhcCCCe
Confidence 77776777888888777666432211111111111111 1111111111 12457888898888887665555555666
Q ss_pred EEEeCCCCCHH-HHHHHHHHHHhh
Q 002210 448 LWLLGVTPTEE-QIKDIAEWLLEY 470 (953)
Q Consensus 448 ~~~~G~~p~~~-~~~~l~~~l~~~ 470 (953)
+.+.|.|=+=. -+...++.+...
T Consensus 249 VLi~GETGtGKElvAraIH~~S~R 272 (550)
T COG3604 249 VLIRGETGTGKELVARAIHQLSPR 272 (550)
T ss_pred EEEecCCCccHHHHHHHHHhhCcc
Confidence 77778776633 334445555544
No 75
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.07 E-value=2.2e-05 Score=91.79 Aligned_cols=117 Identities=15% Similarity=0.159 Sum_probs=82.3
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccce
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN 681 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~ 681 (953)
..+++++.+++++.+++++|++|+++|.+|+|+++|+++++++|++.++.+|+++.+++..++.. ..+... .....
T Consensus 89 ~~~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~~---~~~~~~-~~~~~ 164 (430)
T PRK11006 89 RRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEFT---QYLKTR-DFSRP 164 (430)
T ss_pred HHHHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHHH---HHHHhc-ccCCC
Confidence 34568888899999999999999999999999999999999999999999999988776543322 111111 11111
Q ss_pred EEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHH
Q 002210 682 VEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYT 735 (953)
Q Consensus 682 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~ 735 (953)
..... .++. ++.+...|..+ + +.+.+.+|||++++.+++.+
T Consensus 165 --~~~~~----~~~~--~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~~~ 205 (430)
T PRK11006 165 --LTLVL----NNGR--HLEIRVMPYTE--G---QLLMVARDVTQMHQLEGARR 205 (430)
T ss_pred --eEEEc----CCCC--EEEEEEEEcCC--C---cEEEEEehhhHHHHHHHHHH
Confidence 11221 1233 45556666543 2 24567899999998887644
No 76
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.05 E-value=4.4e-05 Score=91.88 Aligned_cols=122 Identities=16% Similarity=0.205 Sum_probs=88.8
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCC---cchhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLT---VDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 604 ~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~---~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
.|+....++++.+++++++||+++|.+|+|+++|+++++++|++ ..+.+|+.+.++.+... +..++..+.
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~ 286 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVSR-------LKEVLRTGT 286 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCchh-------HHHHHhcCC
Confidence 56777778889999999999999999999999999999999876 34567777666554322 233332222
Q ss_pred eEE-EEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHH
Q 002210 681 NVE-IKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGD 740 (953)
Q Consensus 681 ~~e-~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~ 740 (953)
... .+... +| .++.++..|+.+ +|.+.|++.+++|+|+.++.++++......
T Consensus 287 ~~~~~~~~~-----~g--~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~~~ 339 (542)
T PRK11086 287 PRRDEEINI-----NG--RLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMVNY 339 (542)
T ss_pred CccceEEEE-----CC--EEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHHHH
Confidence 221 12222 23 345567889998 899999999999999999998887665543
No 77
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.01 E-value=1.5e-05 Score=102.35 Aligned_cols=73 Identities=27% Similarity=0.292 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 877 ISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 877 ~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
..++..+.|..|++.|||||||||++|.|++++|.....+++++++++.+..++++|..+|++ ||+++++.|.
T Consensus 436 ~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~~ 509 (914)
T PRK11466 436 EAEKASQAKSAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGG 509 (914)
T ss_pred HHHHHHHHHHHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 344456778899999999999999999999999998888999999999999999999999999 8999999885
No 78
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.99 E-value=0.0001 Score=87.63 Aligned_cols=111 Identities=14% Similarity=0.164 Sum_probs=81.5
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccce--E
Q 002210 605 ELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN--V 682 (953)
Q Consensus 605 eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~--~ 682 (953)
.+++.+.++..+++++++||+++|.+|+|+++|++++++||++.++++|+++.++++.... ..++..... .
T Consensus 74 ~~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~l-------~~~le~~~~~~~ 146 (520)
T PRK10820 74 PSEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFNF-------LRWLESEPQDSH 146 (520)
T ss_pred hHHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcchH-------HHHHHcCCCccc
Confidence 3556677789999999999999999999999999999999999999999999998875432 223322211 1
Q ss_pred EEEEEEcccCCCCCEEEEEEEEEEee--cCCCCE--EEEEEEEEecchhHH
Q 002210 683 EIKLRAFGPRETSGPVILVVNACCTQ--DTKENV--IGVCFVGQDITGQKL 729 (953)
Q Consensus 683 e~~~~~~~~~~dG~~~~v~v~~~pi~--d~~g~v--~gvv~v~~DITerk~ 729 (953)
...+.. +|..+ .+...|+. +.+|.. .|++.+++|+++..+
T Consensus 147 ~~~v~~-----~g~~~--~v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 NEHVVI-----NGQDF--LMEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred eEEEEE-----CCEEE--EEEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 122222 35433 35678876 555554 899999999998643
No 79
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.99 E-value=0.00064 Score=84.05 Aligned_cols=216 Identities=8% Similarity=0.015 Sum_probs=127.0
Q ss_pred HHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeec--CCCCCCccCCCCCCCCccHHHHHHHHhCC
Q 002210 206 SRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECR--RPDLEPYLGFHYPATDIPQASRFLIMKNK 283 (953)
Q Consensus 206 ~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~--~~~~~~~lg~~~pa~dip~~ar~ly~~n~ 283 (953)
..+-+ ..+++++++.+++.+++++|+|++.|+-++++...-++.-+. ..+.....|...|... --+...+..+.
T Consensus 192 ~~l~s--~~dl~ell~~I~~~i~~~~~a~~~~I~L~d~~~~~L~~~aa~g~~~~~~~~~~~~~~~~~--~l~g~V~~~~~ 267 (686)
T PRK15429 192 NAVLS--RLDMDELVSEVAKEIHYYFDIDAISIVLRSHRKNKLNIYSTHYLDKQHPAHEQSEVDEAG--TLTERVFKSKE 267 (686)
T ss_pred HHHcc--CCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCcEEEEEecccChhhcccccccCCccc--chHHHHHhcCc
Confidence 33444 669999999999999999999999999998886554443222 1122222333333221 12345666777
Q ss_pred ceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEee
Q 002210 284 VRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVC 363 (953)
Q Consensus 284 ~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~ 363 (953)
..++.|....+...+ + ....+ +..-++++.+++|++.+ ++.=|.|..
T Consensus 268 p~lv~~~~~d~~~~~--~-----------------~~~~~-~~~~~~~s~l~vPL~~~-------------~~v~GvL~l 314 (686)
T PRK15429 268 MLLINLHERDDLAPY--E-----------------RMLFD-TWGNQIQTLCLLPLMSG-------------DTMLGVLKL 314 (686)
T ss_pred eEEEECccCcccchh--h-----------------hhhhh-cccccceEEEEEeEEEC-------------CEEEEEEEE
Confidence 777766443321100 0 00111 22336789999999987 899999999
Q ss_pred ecCCCCCCChhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH-HHHHHhhcc--CCCCccccCCcchhhhccCCeE
Q 002210 364 HHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQ-TVLCDMLLR--DSPVGIVTQTPNVMDLVKCDGA 440 (953)
Q Consensus 364 hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~l~~l~~~dg~ 440 (953)
.++.++.++......+..+++++++.|......+...+.+..+... ..+.+.+.. .....++..++.+..+++--..
T Consensus 315 ~~~~~~~F~~~dl~lL~~iA~~~A~Aie~a~~~~~~~~~~~~L~~e~~~lt~~L~~~n~~~~~liG~S~~~~~~~~~~~~ 394 (686)
T PRK15429 315 AQCEEKVFTTTNLKLLRQIAERVAIAVDNALAYQEIHRLKERLVDENLALTEQLNNVDSEFGEIIGRSEAMYSVLKQVEM 394 (686)
T ss_pred eeCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhhHHHHHHHhhhhccccccceeecCHHHHHHHHHHHH
Confidence 8888888888888999999998888886443322221111111110 011111111 1223577777766655433222
Q ss_pred EEEECCeEEEeCCCCCHH
Q 002210 441 ALYYRGKLWLLGVTPTEE 458 (953)
Q Consensus 441 a~~~~~~~~~~G~~p~~~ 458 (953)
+.-.+..+.+.|.+=+-.
T Consensus 395 ~a~~~~pVLI~GE~GTGK 412 (686)
T PRK15429 395 VAQSDSTVLILGETGTGK 412 (686)
T ss_pred HhCCCCCEEEECCCCcCH
Confidence 223344677777766544
No 80
>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=97.89 E-value=0.00015 Score=67.37 Aligned_cols=101 Identities=22% Similarity=0.188 Sum_probs=75.8
Q ss_pred eEeecCCccEEehhHH-HHHHhCCChhhhhcccccccccccccccccccCcchHHH-HHHHHHHHhcCCCcceEEEEEEc
Q 002210 755 IFMTDEDGRCLEWNDG-MEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTK-LRIVMNKVISGQDADKILFGFFD 832 (953)
Q Consensus 755 I~~~D~~G~i~~~N~a-~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~-~~~~l~~~~~g~~~~~~e~~~~~ 832 (953)
....+.+|+|+++-+. ...++||.++|++|+.+.+.++|+ +... +.......+..+......||++.
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~-----------D~~~~~~~~~~~~~~~g~~~~~~yR~~~ 73 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPD-----------DLQRVLKQHHREVLQKGQSVSPYYRFRT 73 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCC-----------THHHHHHHHHHHHHHHSSEEEEEEEEE-
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHh-----------hhhhHHHHHHHHHhhCCCcCcceEEEEe
Confidence 4567889999999999 699999999999999988655554 3333 44455555555556666799999
Q ss_pred cCCCEEEEEEEEEEeecCC-CCEEEEEEEEEeccH
Q 002210 833 QQGKYVEALLSANKRTNAE-GKISGILCFLHVASP 866 (953)
Q Consensus 833 kdG~~~~v~~s~~pi~d~~-G~i~g~v~v~~DITe 866 (953)
++|.++|+........+.. +++..++|+-.-|++
T Consensus 74 k~g~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 74 KNGGYVWVQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp TTSSEEEEEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred cCCcEEEEEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 9999999999999998744 566667777666664
No 81
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=97.88 E-value=0.00022 Score=66.33 Aligned_cols=101 Identities=14% Similarity=0.171 Sum_probs=79.6
Q ss_pred EEEEcCCCcEEecCHH-HHHHhCCCcchhcCCCccccccCCcHHH-HHHHHHHHhcccceEEEEEEEcccCCCCCEEEEE
Q 002210 624 ILAVDASGNVNGWNSK-AAELTGLTVDQAIGTALVDLVAGDSVDV-VKNMLSSAFLEERNVEIKLRAFGPRETSGPVILV 701 (953)
Q Consensus 624 I~~~D~dg~i~~~N~a-~~~l~G~~~~eliG~~~~dl~~~~~~~~-~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~ 701 (953)
+...+.+|+|+++-.+ ...++||.++|++|+++.+++|++|... +......++..+......++. ..++|..+|+.
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~--~~k~g~~vwvq 82 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRF--RTKNGGYVWVQ 82 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEE--E-TTSSEEEEE
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEE--EecCCcEEEEE
Confidence 4567899999999999 6999999999999999999999999996 888888888666555544444 55689999999
Q ss_pred EEEEEeecC-CCCEEEEEEEEEecch
Q 002210 702 VNACCTQDT-KENVIGVCFVGQDITG 726 (953)
Q Consensus 702 v~~~pi~d~-~g~v~gvv~v~~DITe 726 (953)
..+.++.+. .+++..++++-+=|++
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 999998874 4566667766555554
No 82
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.88 E-value=0.00032 Score=80.38 Aligned_cols=125 Identities=20% Similarity=0.225 Sum_probs=91.6
Q ss_pred ccHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 601 EKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 601 ~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
++.+++++..+.++.+++..+.|++.+|.+|+|..+|++++++||.+.++++|.++..+.+. .+.+........+..+
T Consensus 360 ~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap~--~~~vf~~~~a~~~~~~ 437 (712)
T COG5000 360 RAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSAIAPE--LEEVFAEAGAAARTDK 437 (712)
T ss_pred HHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhhhhhH--HHHHHHHhhhhcCCCc
Confidence 35667888888899999999999999999999999999999999999999999998766542 1222222222223444
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHH
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKY 734 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L 734 (953)
..++.+.. .|+.+.+.+..+....+ +--|++.++.|||+...++..-
T Consensus 438 ~~ev~~~r-----~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~AQRs~ 484 (712)
T COG5000 438 RVEVKLAR-----EGEERTLNVQATREPED--NGNGYVVTFDDITDLVIAQRSA 484 (712)
T ss_pred cceeeccc-----CCCceeeeeeeeecccc--cCCceEEEecchHHHHHHHHHH
Confidence 45554443 37777777776655443 2337888999999998887663
No 83
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.87 E-value=6e-05 Score=85.98 Aligned_cols=169 Identities=17% Similarity=0.305 Sum_probs=117.7
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEE
Q 002210 606 LRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIK 685 (953)
Q Consensus 606 L~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~ 685 (953)
|......|..+++.+.++++++|.+|+++++|+++..++|++.++++|+++.+++..... .....++..+++....
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~~~~ 187 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPIRDV 187 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCcceee
Confidence 456677889999999999999999999999999999999999999999999887611110 1233455555555444
Q ss_pred EEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHH--------HHHhCC---------
Q 002210 686 LRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYV--------GIVSSP--------- 748 (953)
Q Consensus 686 ~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~--------~i~e~~--------- 748 (953)
..+.. |... ..+..|++. +|.+.|.+++++|+++.+....++.+++...+ .|+-.+
T Consensus 188 ~~~~~----~~~~--i~~~~pv~~-~g~l~G~v~~~~~~~~l~~l~~~~~~~~~~~~~~a~y~f~~Iig~S~~m~~~~~~ 260 (560)
T COG3829 188 VQTYN----GNKI--IVNVAPVYA-DGQLIGVVGISKDVSELERLTRELEESEGLLRLKAKYTFDDIIGESPAMLRVLEL 260 (560)
T ss_pred eeeec----CCce--eEeeccEec-CCcEEEEEEeecchHHHHHHHHHHHHHhhhhccccccchhhhccCCHHHHHHHHH
Confidence 44431 2222 446667765 77999999999999999988888776664433 222111
Q ss_pred ----CCCCCCeEeecCCc-------------------cEEehhHHH-------HHHhCCChhhhhcc
Q 002210 749 ----SALIPPIFMTDEDG-------------------RCLEWNDGM-------EKLSGLKREEAIER 785 (953)
Q Consensus 749 ----~~li~~I~~~D~~G-------------------~i~~~N~a~-------~~l~G~~~eeliGk 785 (953)
......|.+..+.| .++.+|-|+ .++|||....+-|-
T Consensus 261 akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye~GAFTGA 327 (560)
T COG3829 261 AKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYEKGAFTGA 327 (560)
T ss_pred HHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCHHHHHHHHhCcCCcccccc
Confidence 00001466665543 577888764 57999988777663
No 84
>PRK09303 adaptive-response sensory kinase; Validated
Probab=97.80 E-value=6.4e-05 Score=86.28 Aligned_cols=69 Identities=12% Similarity=0.132 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCC-------HHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLS-------EEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~-------e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
.+.+.+++++++|||||||++|.+++++|.....+ +..+++++.+.++.++|.++|++ ++++|.+.+..
T Consensus 148 ~~~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~ 224 (380)
T PRK09303 148 LKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEAL 224 (380)
T ss_pred HHHHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 45578899999999999999999999999863322 34778999999999999999999 89999988754
No 85
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.69 E-value=0.00027 Score=84.08 Aligned_cols=111 Identities=11% Similarity=0.084 Sum_probs=76.5
Q ss_pred HHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHH
Q 002210 735 TRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVM 814 (953)
Q Consensus 735 ~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l 814 (953)
++.+..++++++++++ ||+.+|.+|+|+++|+++++++|++.++++|+++.+ +++. .. +...+
T Consensus 76 e~e~~~L~aIL~sm~e---GVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~e-li~~----------~~---l~~~l 138 (520)
T PRK10820 76 EREHRALSALLEALPE---PVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQ-LING----------FN---FLRWL 138 (520)
T ss_pred HHHHHHHHHHHHhCCC---cEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHH-HcCc----------ch---HHHHH
Confidence 3345568899999988 999999999999999999999999999999998863 3332 11 22222
Q ss_pred HHHhcCCCcceEEEEEEccCCCEEEEEEEEEEee--cCCCCE--EEEEEEEEeccHHHH
Q 002210 815 NKVISGQDADKILFGFFDQQGKYVEALLSANKRT--NAEGKI--SGILCFLHVASPELQ 869 (953)
Q Consensus 815 ~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~--d~~G~i--~g~v~v~~DITerK~ 869 (953)
. ........ .....+|..++ +...|+. |.+|.. .|.+.+++|+++..+
T Consensus 139 e----~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 139 E----SEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred H----cCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 2 22111111 12344576555 4556665 666664 899999999997543
No 86
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.68 E-value=0.00031 Score=80.27 Aligned_cols=120 Identities=23% Similarity=0.337 Sum_probs=90.5
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcc--hhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 603 IDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVD--QAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~--eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
-.|+...-++..++++++..||+.+|..|.|..+|.++++|+|+... +++|+++.++++|+. . +..++..++
T Consensus 207 P~EIa~l~~er~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~-~-----l~~vl~~~~ 280 (537)
T COG3290 207 PEEIATLLEERQAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDS-D-----LPEVLETGK 280 (537)
T ss_pred HHHHHHHHHHHHHHHHHhhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeecccc-C-----cHHHHhcCC
Confidence 46677777778899999999999999999999999999999999854 689999999998622 1 223332222
Q ss_pred eEE-EEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHH
Q 002210 681 NVE-IKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTR 736 (953)
Q Consensus 681 ~~e-~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~ 736 (953)
... -+++. +| .++.++..|++- +|+++|.+.+++|-|+-++.-++|..
T Consensus 281 ~~~~~e~~~-----ng--~~~i~nr~pI~~-~~~~~GaI~tFRdktei~~L~eqLt~ 329 (537)
T COG3290 281 PQHDEEIRI-----NG--RLLVANRVPIRS-GGQIVGAIITFRDKTEIKKLTEQLTG 329 (537)
T ss_pred cccchhhhc-----CC--eEEEEEeccEEE-CCEEeEEEEEEecHHHHHHHHHHHHH
Confidence 221 12222 12 345678899986 89999999999999999887777643
No 87
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=97.68 E-value=0.0011 Score=81.91 Aligned_cols=149 Identities=13% Similarity=0.044 Sum_probs=103.7
Q ss_pred HHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhC
Q 002210 203 KAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKN 282 (953)
Q Consensus 203 ~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n 282 (953)
++...+.+ +.+++++++.+++.+++++|+|++.||-+++|+..-+++-+...+-+..-..+||-..= -+...+..+
T Consensus 7 eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~geG--i~G~Va~tg 82 (748)
T PRK11061 7 EIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDEG--IVGLVGRLA 82 (748)
T ss_pred HHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCcc--hHHHHhccC
Confidence 34444555 56999999999999999999999999999998766555544332212222234443221 134455556
Q ss_pred CceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEe
Q 002210 283 KVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVV 362 (953)
Q Consensus 283 ~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~ 362 (953)
..-.|.|+...|--.. ...+...+++|.|++||+.+ |++=|.|.
T Consensus 83 ~pV~V~Dv~~dprf~~-----------------------~~~~~~~~~~S~L~VPL~~~-------------geVIGVL~ 126 (748)
T PRK11061 83 EPINLADAQKHPSFKY-----------------------IPSVKEERFRAFLGVPIIYR-------------RQLLGVLV 126 (748)
T ss_pred ceEEECCcccCccccc-----------------------CccccCccceEEEEEEEeeC-------------CEEEEEEE
Confidence 6667788654432100 00112458999999999976 89999999
Q ss_pred eecCCCCCCChhHHHHHHHHHHHHHHhhH
Q 002210 363 CHHTSPRFVPFPLRYACEFLIQVFGVQVN 391 (953)
Q Consensus 363 ~hh~~pr~~~~~~r~~~~~l~~~~~~~l~ 391 (953)
+++..|+.++......++.|+.+.+..|.
T Consensus 127 v~~~~~~~Fs~~d~~lL~~LA~~aAiAL~ 155 (748)
T PRK11061 127 VQQRELRQFDESEESFLVTLATQLAAILS 155 (748)
T ss_pred EeeCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999888888888887777664
No 88
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.67 E-value=0.00016 Score=81.15 Aligned_cols=100 Identities=20% Similarity=0.267 Sum_probs=80.8
Q ss_pred CccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEccCCCEEEE
Q 002210 761 DGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFDQQGKYVEA 840 (953)
Q Consensus 761 ~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v 840 (953)
|.-|+|+|..||++.||.+.|++.|...-.+... .+.+.+..+++...+ +..+...+|+-+..|+...+|.
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyG-----Eltdk~ti~k~~~t~----eN~~~~qfEillyKKN~TPvW~ 109 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYG-----ELTDKGTIEKVRQTL----ENYETNQFEILLYKKNRTPVWL 109 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeec-----cccchhhHHHHHHHH----HhhhhcceeeEeeecCCCceEE
Confidence 4679999999999999999999999764333332 233345555555544 4456678999999999999999
Q ss_pred EEEEEEeecCCCCEEEEEEEEEeccHHHH
Q 002210 841 LLSANKRTNAEGKISGILCFLHVASPELQ 869 (953)
Q Consensus 841 ~~s~~pi~d~~G~i~g~v~v~~DITerK~ 869 (953)
.+...|++++...++-++|.+.|||..||
T Consensus 110 ~vqiAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 110 LVQIAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred EEEeecccCCCceEEEEEeecccchhhcC
Confidence 99999999999999999999999998885
No 89
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=97.64 E-value=0.00015 Score=59.06 Aligned_cols=60 Identities=25% Similarity=0.308 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcCC-CCCHHHHHHHHHHHHHHHHHHhHhhh-hcccc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGTS-DLSEEQKQLLKTSVLCQEQLTNIVDD-TDIES 944 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~~-~l~e~~~~~l~~i~~~~~~L~~lI~D-Ldlsr 944 (953)
+.++.+.++||+||||++|.++++.+... ...++..++++.+..+..++..++++ ++++|
T Consensus 4 ~~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ 65 (65)
T cd00082 4 KGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLSR 65 (65)
T ss_pred HHHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 45688999999999999999999998773 33677889999999999999999999 67764
No 90
>PRK10490 sensor protein KdpD; Provisional
Probab=97.58 E-value=0.00045 Score=87.73 Aligned_cols=67 Identities=12% Similarity=0.080 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcCC--CCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGTS--DLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~~--~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
+.|..+++.++|||||||++|.|++++|... ....+..+.++.+.+...++.+++++ ++++|++.|.
T Consensus 662 ~lr~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~ 731 (895)
T PRK10490 662 QLRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGG 731 (895)
T ss_pred HHHHHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 4467789999999999999999999998652 23344556788888888999999999 8999999985
No 91
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.52 E-value=0.0013 Score=79.36 Aligned_cols=122 Identities=14% Similarity=0.231 Sum_probs=86.8
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCc--chhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 603 IDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTV--DQAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~--~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
..++.....++..++++.++|++++|.+|+|+++|+++++++|++. ++++|+++.+++++.... .......
T Consensus 214 ~~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~~------~~~~~~~- 286 (545)
T PRK15053 214 PKQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADFF------TEQIDEK- 286 (545)
T ss_pred HHHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchhh------hhhcCCc-
Confidence 3455566677888999999999999999999999999999999975 468999988877643211 1111111
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHH
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQG 739 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~ 739 (953)
........ +| ..+.++..|+.. +|++.|++.+++|+|+.++.+.++...+.
T Consensus 287 ~~~~~~~~-----~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~ 337 (545)
T PRK15053 287 RQDVVANF-----NG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQ 337 (545)
T ss_pred ccceEEEE-----CC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHH
Confidence 11111111 23 334467788776 67788999999999999888887765543
No 92
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=97.49 E-value=0.0007 Score=75.76 Aligned_cols=227 Identities=12% Similarity=0.092 Sum_probs=139.7
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceE---EEEEEE---
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNV---EIKLRA--- 688 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~---e~~~~~--- 688 (953)
-++++.+..++++..+|.|.|++...+..+|+-..+++.+++.+++|.+|++.+...+.-++.-.... ....++
T Consensus 115 ~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~~ppq~~~s~q~~~e~~~~ 194 (712)
T KOG3560|consen 115 LLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAMDPPQVVFSQQPPLETGDD 194 (712)
T ss_pred HHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhccCCchhhccCCCccccccc
Confidence 47888899999999999999999999999999999999999999999999998887766544111000 000000
Q ss_pred ----cccCCCCC--------EEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHH--------------H--------
Q 002210 689 ----FGPRETSG--------PVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDK--------------Y-------- 734 (953)
Q Consensus 689 ----~~~~~dG~--------~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~--------------L-------- 734 (953)
.....|+. .+.+.++...+.|...... ..|+-.+-+.--- |
T Consensus 195 ~~~~~~~~~d~~ppens~yleRcficR~RCLLDnTsGFL-----amdfqGklk~LhGqkkk~~~g~~lpP~LaLf~iatP 269 (712)
T KOG3560|consen 195 AILRAQEWGDGTPPENSAYLERCFICRFRCLLDNTSGFL-----AMDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIATP 269 (712)
T ss_pred cceeeeccCccCCcccchHHhhhheeeEEEeecCCccee-----eeecccceeeecCCcccCCCCccCCCceeEEEEecC
Confidence 00001111 1234445555666443322 2454433111000 0
Q ss_pred ----HHHHHHH-HHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHH
Q 002210 735 ----TRIQGDY-VGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTK 809 (953)
Q Consensus 735 ----~~se~~~-~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~ 809 (953)
..+|-.. ..|+.+-.- .|+..+.+......++||...|+.|......++.+ +..-
T Consensus 270 ~~pPS~lEi~~k~~i~rtKhk---------lDfa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~-----------D~~y 329 (712)
T KOG3560|consen 270 FLPPSALEIKMKSAILRTKHK---------LDFALVSMDAKVKATLGYCEAELHGMPGYNLVHVE-----------DKVY 329 (712)
T ss_pred CCCchhhhhhhhhhhhhcccc---------cccceeccchhhhhhhccchhhccCCCccceeehh-----------hhhh
Confidence 0000000 011111111 13344455666777899999999986655444433 3323
Q ss_pred HHHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHH
Q 002210 810 LRIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPE 867 (953)
Q Consensus 810 ~~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITer 867 (953)
+...-...++.+++.-+.||..+|+|+|.|+..++.-++ .+|+.-.+++.-+-.+++
T Consensus 330 ~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~thr~l~De 386 (712)
T KOG3560|consen 330 MAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTHRGLGDE 386 (712)
T ss_pred hhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee-ecCCCCEEEecCCCccch
Confidence 444556677788888889999999999999999888776 677777667766666653
No 93
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.47 E-value=0.00014 Score=60.14 Aligned_cols=47 Identities=23% Similarity=0.300 Sum_probs=38.3
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCcccccc
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA 661 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~ 661 (953)
++|+.+++++|+||+++| +++|+++|+++++++||+ ..|+.+..+++
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~~~~~ 47 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIGQLFP 47 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHHCTST
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHHHhCc
Confidence 468899999999999999 889999999999999998 56666654443
No 94
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.43 E-value=0.0019 Score=63.72 Aligned_cols=125 Identities=22% Similarity=0.299 Sum_probs=85.3
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHH-HHHHHHHHh-cccc
Q 002210 603 IDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDV-VKNMLSSAF-LEER 680 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~-~~~~l~~~l-~~~~ 680 (953)
..++.....++..+++..+++++.+|.+|.+.++|+++.+++|++..+..+....++........ ......... ....
T Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (232)
T COG2202 104 EEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGG 183 (232)
T ss_pred HHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCC
Confidence 34455566668999999999999999999999999999999999988777877765554333221 111222222 2222
Q ss_pred eEEEEEEEcccCCCCCE-EEEEEEEEEeecCCCCEEEEEEEEEecchhHHH
Q 002210 681 NVEIKLRAFGPRETSGP-VILVVNACCTQDTKENVIGVCFVGQDITGQKLV 730 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~-~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~ 730 (953)
........ ..++|.. .+......+... .|.+.++.....|++++++.
T Consensus 184 ~~~~~~~~--~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 184 PLEIEYRV--RRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred CcceEEEE--EecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 23333222 3346775 666666666554 78889999999999998764
No 95
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=97.41 E-value=0.00053 Score=78.83 Aligned_cols=71 Identities=17% Similarity=0.224 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcC---CCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhc
Q 002210 877 ISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGT---SDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEE 947 (953)
Q Consensus 877 ~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~---~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~ 947 (953)
..|+.+..-.+|...+||++|+||+.|.+++++|.+ ..++++.++++..+.+....|.+||+| +.+|++..
T Consensus 516 ~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~~ 590 (750)
T COG4251 516 ELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLGL 590 (750)
T ss_pred HHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Confidence 335566666667777799999999999999999988 578999999999999999999999999 79998764
No 96
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=97.41 E-value=0.017 Score=66.94 Aligned_cols=58 Identities=19% Similarity=0.236 Sum_probs=49.5
Q ss_pred HHHHHHHhhhHHHHHHHHHH---hhcCCCCCHHHHHHHHHHHHHHHHHHhHhhhh-cccchh
Q 002210 889 LEYIRREIRKPLNGIAFMQN---LMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDT-DIESIE 946 (953)
Q Consensus 889 la~isHELrnPL~~I~g~~~---LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~DL-dlsrIe 946 (953)
.+.++||||+||.+|..+.+ +|.+....++.++.+..|..-.++|.+|.++| .|+|--
T Consensus 388 SA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FArk~ 449 (603)
T COG4191 388 SAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFARKS 449 (603)
T ss_pred HHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 57789999999999999887 44457778999999999999999999999996 676643
No 97
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.40 E-value=0.0012 Score=71.33 Aligned_cols=205 Identities=21% Similarity=0.263 Sum_probs=126.6
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh-----cccceEEEE----
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF-----LEERNVEIK---- 685 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l-----~~~~~~e~~---- 685 (953)
.++++....|++++++|+|.|++..+.-.+|++.-|+.|..+.+.+|+.|.+.+...+...- .-++.+-+.
T Consensus 83 hlLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~H~qeyeIErsfflrmkCv 162 (598)
T KOG3559|consen 83 HLLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQHLQEYEIERSFFLRMKCV 162 (598)
T ss_pred hHHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHhhhhhhhhhhhhhhhhhhhhhh
Confidence 46778888899999999999999999999999999999999999999999886665543221 001111111
Q ss_pred --EEEcccCCCCCEE-----EEEEEEEEeecCCC----CEEEEEEEEEe-----cchhHHHHHHHHHHHHHHHHHHhCCC
Q 002210 686 --LRAFGPRETSGPV-----ILVVNACCTQDTKE----NVIGVCFVGQD-----ITGQKLVMDKYTRIQGDYVGIVSSPS 749 (953)
Q Consensus 686 --~~~~~~~~dG~~~-----~v~v~~~pi~d~~g----~v~gvv~v~~D-----ITerk~~E~~L~~se~~~~~i~e~~~ 749 (953)
.+..+.+..|... ++.+...++.-... ..+|++.+..- ||+-|. -.|+
T Consensus 163 lakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteikl---------------~sNm- 226 (598)
T KOG3559|consen 163 LAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIKL---------------HSNM- 226 (598)
T ss_pred heeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEEe---------------ccce-
Confidence 1111111112111 11222222221111 34566666443 333321 1222
Q ss_pred CCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHH-hcCCCcceEEE
Q 002210 750 ALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKV-ISGQDADKILF 828 (953)
Q Consensus 750 ~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~-~~g~~~~~~e~ 828 (953)
.+|....|-++++....+.+++||++.+++++++...++..+.. . +...-... ..|+.. .--|
T Consensus 227 ----FmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~--------~---lr~~H~~ll~kGqvt-TkYY 290 (598)
T KOG3559|consen 227 ----FMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSF--------H---LRCAHHLLLVKGQVT-TKYY 290 (598)
T ss_pred ----EEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHH--------H---HHHHHHHHHhccccc-cHHH
Confidence 57788889999999999999999999999999986544443211 1 11111111 223322 2236
Q ss_pred EEEccCCCEEEEEEEEEEeecCC
Q 002210 829 GFFDQQGKYVEALLSANKRTNAE 851 (953)
Q Consensus 829 ~~~~kdG~~~~v~~s~~pi~d~~ 851 (953)
|+..+.|.++|+.-...-+.+.-
T Consensus 291 R~l~k~ggwvwvqsyat~vHnSr 313 (598)
T KOG3559|consen 291 RFLLKQGGWVWVQSYATFVHNSR 313 (598)
T ss_pred HHHHcCCceEEEEEeeEEEeccc
Confidence 78889999999998887776543
No 98
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=97.28 E-value=0.00084 Score=85.17 Aligned_cols=66 Identities=9% Similarity=-0.008 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhhcC-CCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 884 NSLNKLEYIRREIRKPLNGIAFMQNLMGT-SDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 884 ~k~~fla~isHELrnPL~~I~g~~~LL~~-~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
...+|++.++|||||||++|.++.+++.. ...+++.+++++.+..+++++..+|++ ++++|.+.+.
T Consensus 449 ~l~~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~~~~~ 516 (828)
T PRK13837 449 AVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRKGERN 516 (828)
T ss_pred HHHHHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 44578999999999999999999999876 445567889999999999999999999 8999977654
No 99
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.27 E-value=0.084 Score=65.48 Aligned_cols=202 Identities=11% Similarity=0.063 Sum_probs=115.5
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHh
Q 002210 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMK 281 (953)
Q Consensus 202 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~ 281 (953)
.++...+-+ ..+++++++.+-..++++.-+|||-|.-+|+.. +.+.-=....+-++. .| + .......
T Consensus 12 ~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~---~~----~---~~~~~~~ 78 (686)
T PRK15429 12 FDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV---KY----E---DETVLAH 78 (686)
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch---hc----c---chhhhcc
Confidence 334444445 459999999999999999999999999999976 555321111111110 00 0 0111222
Q ss_pred CCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHH--HHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeE
Q 002210 282 NKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHA--RYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWG 359 (953)
Q Consensus 282 n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~--~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWG 359 (953)
+++.++- .+++|+-+++...+-..|--. .+...| ++-+.|||.+. |+..|
T Consensus 79 g~~g~vl-------------~~~~~l~~~~~~~~~~~~~l~~~~~~~~~--~~~lgvPl~~~-------------~~v~G 130 (686)
T PRK15429 79 GPVRRIL-------------SRPDTLHCSYEEFCETWPQLAAGGLYPKF--GHYCLMPLAAE-------------GHIFG 130 (686)
T ss_pred CcceEEe-------------ecCceEEEchHHhhhccHHHhhcccccCc--cceEEeceeeC-------------CeeEE
Confidence 2222222 124555444433333222111 122344 55888999988 99999
Q ss_pred EEeeecCCCCCCChhHHHHHHHHHHHHHHhhHHHHHH-HHHHHHHHHH---HHHHHHHHhhc----cCCCCccc-cCCcc
Q 002210 360 LVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVEL-SAQLREKHIL---RTQTVLCDMLL----RDSPVGIV-TQTPN 430 (953)
Q Consensus 360 Li~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~~~-~~~~~~~~~~---~~~~~~~~~~~----~~~~~~~~-~~~~~ 430 (953)
-|..-.+.+..++.+....+.+|+++.+..|+..... +.+.++.... ..+..+.++.. ...+..+. .-...
T Consensus 131 ~l~l~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~eIs~~l~s~~dl~ell~~I~~~ 210 (686)
T PRK15429 131 GCEFIRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVAITNAVLSRLDMDELVSEVAKE 210 (686)
T ss_pred EEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCCHHHHHHHHHHH
Confidence 9999888889999999999999999999988643221 1111111110 11223333321 12222222 22356
Q ss_pred hhhhccCCeEEEEE
Q 002210 431 VMDLVKCDGAALYY 444 (953)
Q Consensus 431 l~~l~~~dg~a~~~ 444 (953)
+..++++|.+.|+.
T Consensus 211 i~~~~~a~~~~I~L 224 (686)
T PRK15429 211 IHYYFDIDAISIVL 224 (686)
T ss_pred HHHHhCCCEEEEEE
Confidence 78889999977765
No 100
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=96.98 E-value=0.031 Score=68.73 Aligned_cols=113 Identities=16% Similarity=0.194 Sum_probs=77.1
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEE-E
Q 002210 606 LRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVE-I 684 (953)
Q Consensus 606 L~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e-~ 684 (953)
+......+..++++.++||+++|.+|+|+++|+++++++|++.++++|+++.++++... .+..++..+.... .
T Consensus 198 ~~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~~------~l~~vl~~~~~~~~~ 271 (638)
T PRK11388 198 SNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLTLPA------VLQQAIKQAHPLKHV 271 (638)
T ss_pred HHHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhccch------HHHHHHhcCCceeeE
Confidence 33444555678999999999999999999999999999999999999999988875321 1233332233221 1
Q ss_pred EEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHH
Q 002210 685 KLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKL 729 (953)
Q Consensus 685 ~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 729 (953)
+... ..+|..+++.+...|+.+..| .+++.+..|++..++
T Consensus 272 ~~~l---~~~g~~~~~~v~~~Pi~~~~g--~~~v~~l~~~~~~~~ 311 (638)
T PRK11388 272 EVTF---ESQGQFIDAVITLKPIIEGQG--TSFILLLHPVEQMRQ 311 (638)
T ss_pred EEEE---ecCCceEEEEEEEEeecccCc--eEEEEEehhhHHHHH
Confidence 1111 123666678888889865334 335556788887554
No 101
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=96.96 E-value=0.001 Score=54.95 Aligned_cols=42 Identities=21% Similarity=0.336 Sum_probs=34.9
Q ss_pred HHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccc
Q 002210 739 GDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERML 787 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~ 787 (953)
++|+.++++++. +|+++| +++|+++|+++++++||+ ..|+..
T Consensus 1 e~~~~l~~~~~~---~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPD---GILIID-GGRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSS---EEEEEE-TSBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCcc---ceEEEE-CCChHHhhHHHHHHhCCC---CCCCCH
Confidence 478999999988 999999 889999999999999998 555544
No 102
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=96.89 E-value=0.003 Score=71.43 Aligned_cols=98 Identities=15% Similarity=0.171 Sum_probs=72.0
Q ss_pred CCcEEecCHHHHHHhCCCcchhcCCCcc-ccccCCcHH-HHHHHHHHHhcccceEEEEEEEcccCCCCCEEEEEEEEEEe
Q 002210 630 SGNVNGWNSKAAELTGLTVDQAIGTALV-DLVAGDSVD-VVKNMLSSAFLEERNVEIKLRAFGPRETSGPVILVVNACCT 707 (953)
Q Consensus 630 dg~i~~~N~a~~~l~G~~~~eliG~~~~-dl~~~~~~~-~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi 707 (953)
|.-|+|+|+.|+++.||.+.|++.++.. .+.+.+-.+ ...+.++..++..+.-.+++-. .+++..++|+.+...|+
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEill--yKKN~TPvW~~vqiAPI 116 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILL--YKKNRTPVWLLVQIAPI 116 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEe--eecCCCceEEEEEeecc
Confidence 6779999999999999999999988765 344433211 1222334444333333444433 45678999999999999
Q ss_pred ecCCCCEEEEEEEEEecchhHH
Q 002210 708 QDTKENVIGVCFVGQDITGQKL 729 (953)
Q Consensus 708 ~d~~g~v~gvv~v~~DITerk~ 729 (953)
+++...++-+++.+.|||..|+
T Consensus 117 rNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 117 RNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred cCCCceEEEEEeecccchhhcC
Confidence 9999999999999999999875
No 103
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=96.85 E-value=0.012 Score=78.04 Aligned_cols=131 Identities=13% Similarity=-0.051 Sum_probs=73.6
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh---cc
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF---LE 678 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l---~~ 678 (953)
...+++..+..++.+++++|++|+++|.+|+|+++|++++++||+......+.+.....++ ..+.+........ ..
T Consensus 567 ~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 645 (1197)
T PRK09959 567 IQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSDSP-FKDVFSNAHEVTAETKEN 645 (1197)
T ss_pred HHHHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccccccccccCc-hhhhHhHHHHHHHHHhhc
Confidence 3456777788889999999999999999999999999999999987443333222211111 1111111111111 11
Q ss_pred cceEEEEEEEcccCCCCCEEE-EEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHH
Q 002210 679 ERNVEIKLRAFGPRETSGPVI-LVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRI 737 (953)
Q Consensus 679 ~~~~e~~~~~~~~~~dG~~~~-v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~s 737 (953)
...+...... .+|.... +.....+.....+...++++.++|||++++.+++++..
T Consensus 646 ~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~ 701 (1197)
T PRK09959 646 RTIYTQVFEI----DNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVE 701 (1197)
T ss_pred cccceeeEee----ecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHH
Confidence 1111111111 1222221 11112222223444567778889999999888776543
No 104
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=96.58 E-value=0.0067 Score=46.70 Aligned_cols=63 Identities=24% Similarity=0.400 Sum_probs=53.0
Q ss_pred HHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHH
Q 002210 612 EMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSS 674 (953)
Q Consensus 612 ~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~ 674 (953)
+++.+++..+++++.+|.++.+.++|+.+.+++|++..++.|..+.+++++.+...+...+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (67)
T smart00091 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQR 64 (67)
T ss_pred hHHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHH
Confidence 356688999999999999999999999999999999999999988888887776655554443
No 105
>PRK10364 sensor protein ZraS; Provisional
Probab=96.49 E-value=0.01 Score=70.00 Aligned_cols=62 Identities=18% Similarity=0.227 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcC-CCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchh
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGT-SDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIE 946 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~-~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe 946 (953)
..++.+.++||+||||++|.++++++.. ...+++.+++++.+.+..+++..++++ ++++|..
T Consensus 237 ~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~~ 300 (457)
T PRK10364 237 LGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKPT 300 (457)
T ss_pred HHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC
Confidence 4467889999999999999999999877 444567788899999999999999999 7888743
No 106
>PRK10604 sensor protein RstB; Provisional
Probab=96.49 E-value=0.0059 Score=71.45 Aligned_cols=63 Identities=16% Similarity=0.196 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
...+.++++.++|||||||+.|.+.++++... +++.++. +.+..++|.+++++ +.++|++.+.
T Consensus 209 ~~~~~~l~~~vsHeLrtPL~~i~~~l~~l~~~--~~~~~~~---i~~~~~~l~~li~~ll~~~rl~~~~ 272 (433)
T PRK10604 209 IASKKQLIDGIAHELRTPLVRLRYRLEMSDNL--SAAESQA---LNRDIGQLEALIEELLTYARLDRPQ 272 (433)
T ss_pred HHHHHHHHHHhhHhhcChHHHHHHHHHHhcCC--CcHHHHH---HHHHHHHHHHHHHHHHHHHhccCCC
Confidence 34567789999999999999999999998742 2333332 66677899999999 7999999875
No 107
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.46 E-value=0.0028 Score=69.24 Aligned_cols=115 Identities=14% Similarity=0.070 Sum_probs=87.5
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHH
Q 002210 731 MDKYTRIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKL 810 (953)
Q Consensus 731 E~~L~~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~ 810 (953)
.-+++.....|..+-+.- . +|-+.|.+..|.|+|+++++++||-+.|++|+...+. ... ......+
T Consensus 150 afkiRAcnalFaaLD~c~-e---AiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adl-pkk---------dknradl 215 (775)
T KOG1229|consen 150 AFKIRACNALFAALDECD-E---AIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADL-PKK---------DKNRADL 215 (775)
T ss_pred HHHHhhhHHHHHHHhhhh-h---hheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhc-ccc---------ccchhhh
Confidence 344555665665554443 3 6888999999999999999999999999999986421 111 1222336
Q ss_pred HHHHHHHhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEE
Q 002210 811 RIVMNKVISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILC 859 (953)
Q Consensus 811 ~~~l~~~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~ 859 (953)
...++..+..+..+..++.-++|.|......+..+|+.+.+|++..++.
T Consensus 216 ldtintcikkgke~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfvs 264 (775)
T KOG1229|consen 216 LDTINTCIKKGKEAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFVS 264 (775)
T ss_pred hhhhhHhhhcCccccchHHHhhccCCcccceEEEeeecCCCCceeeehh
Confidence 6778888888888888888899999988888999999999999987764
No 108
>PRK10815 sensor protein PhoQ; Provisional
Probab=96.30 E-value=0.011 Score=70.03 Aligned_cols=65 Identities=11% Similarity=0.075 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCC-CCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGTSD-LSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
....+|++.++|||||||++|.++++.|.... .+.+ +....+.+...++.+++++ ++.++.+++.
T Consensus 264 ~~~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~~--~~~~~~~~~i~ri~~~i~~ll~~~~~~~~~ 330 (485)
T PRK10815 264 TKYRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSVE--QAEPIMLEQISRISQQIGYYLHRASMRSEH 330 (485)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 34456899999999999999999999997643 3332 2334455566788888888 7888877653
No 109
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.08 E-value=0.013 Score=64.30 Aligned_cols=114 Identities=21% Similarity=0.179 Sum_probs=85.5
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh-cccceEEEEEEEc
Q 002210 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF-LEERNVEIKLRAF 689 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l-~~~~~~e~~~~~~ 689 (953)
+++.+++++.|.-|-.+|.++++.+.|+. .++|-.+... +|+++...-+|.+...+...+...- +.....++- .
T Consensus 290 ~e~naif~~lP~Ditfvdk~diV~ffs~~-~rif~rt~sv-iGr~v~~chpPksv~iv~ki~~~fksG~kd~~efw--~- 364 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKNDIVRFFSGG-ERIFPRTPSV-IGRRVQLCHPPKSVHIVEKILKDFKSGEKDFAEFW--I- 364 (409)
T ss_pred HHHHHHHhhCCCceEEecccceEEecCCc-ceecccChHh-hCCcccCCCCCchHHHHHHHHHHhhcCCcchHHHh--c-
Confidence 45678999999989999999999999988 8888887765 8999997767767666665555544 222222222 1
Q ss_pred ccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHH
Q 002210 690 GPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDK 733 (953)
Q Consensus 690 ~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~ 733 (953)
+ ....++.++..+++|.+|+..|++-+.+|||.-|..+-+
T Consensus 365 --~--~~~~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ge 404 (409)
T COG2461 365 --N--MGDKFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELEGE 404 (409)
T ss_pred --c--CCCceEEEEEEEEEcCCCceeeeehhhhhhHHHHhccch
Confidence 1 223456678999999999999999999999998776543
No 110
>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase. This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase.
Probab=95.97 E-value=0.028 Score=69.78 Aligned_cols=68 Identities=16% Similarity=0.229 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
......+.+.++||+||||+.|.+.++.+.....+++..++++.+....++|..++++ ++++|+|.+.
T Consensus 482 ~~~l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~~~ 550 (703)
T TIGR03785 482 THYLENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQAI 550 (703)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence 3445568899999999999999999999988888888899999999999999999999 6899988763
No 111
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=95.85 E-value=0.03 Score=62.31 Aligned_cols=63 Identities=16% Similarity=0.156 Sum_probs=53.5
Q ss_pred HHHHHHHhhhHHHHHHHHHHhhcC---CCCCHHHHHHHHHHHHHHHHHHhHhhhh-cccchhccccc
Q 002210 889 LEYIRREIRKPLNGIAFMQNLMGT---SDLSEEQKQLLKTSVLCQEQLTNIVDDT-DIESIEEWYDC 951 (953)
Q Consensus 889 la~isHELrnPL~~I~g~~~LL~~---~~l~e~~~~~l~~i~~~~~~L~~lI~DL-dlsrIe~G~~~ 951 (953)
+..++|||+.|||++..|+--... ...++....+++.|..-.++|..|++.| .|+|=.+|+.+
T Consensus 455 mTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~~~ 521 (673)
T COG4192 455 MTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDES 521 (673)
T ss_pred HHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 667899999999999887765444 6667788999999999999999999996 99998888754
No 112
>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=95.48 E-value=0.16 Score=49.37 Aligned_cols=110 Identities=14% Similarity=0.003 Sum_probs=78.8
Q ss_pred HHHHHHHhcCccEEEEcC--CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEc
Q 002210 612 EMVRLIETAAVPILAVDA--SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAF 689 (953)
Q Consensus 612 ~l~~lle~~~~~I~~~D~--dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~ 689 (953)
..+.+++ .|.+|+..+. +=.++|.|.++.+||+++-+++++.+..-...+..++.....+.++...+-.... ...
T Consensus 33 ~~~~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 33 LAKALWH-APFAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNY--SGI 109 (148)
T ss_pred HHHHHHc-CCCEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCC--CeE
Confidence 3445566 9999998866 5689999999999999999999999988767777777777788777743322111 111
Q ss_pred ccCCCCCEEEEE-EEEEEeecCCCCEEEEEEEEEec
Q 002210 690 GPRETSGPVILV-VNACCTQDTKENVIGVCFVGQDI 724 (953)
Q Consensus 690 ~~~~dG~~~~v~-v~~~pi~d~~g~v~gvv~v~~DI 724 (953)
...+.|+.+++. ..+-.+.|.+|+..|...++.+-
T Consensus 110 Riss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~W 145 (148)
T PF08670_consen 110 RISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSNW 145 (148)
T ss_pred EEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEeee
Confidence 123457777765 23344778899999988887664
No 113
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=95.48 E-value=0.43 Score=59.29 Aligned_cols=151 Identities=12% Similarity=0.054 Sum_probs=88.5
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHh
Q 002210 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMK 281 (953)
Q Consensus 202 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~ 281 (953)
.+.+++|.+ +.+.+++++.+++.+.+++++++..+|-.++|+ +....... .+++ ..+...|. +.|- .+.+-..
T Consensus 308 l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~~-~~~~~~~~-~~~~-~~~~~~~~-~~~~-~~~~~~~ 380 (679)
T TIGR02916 308 LRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGND-GLYRPAAR-WNQP-LAQAFEPS-DSAF-CQFLQES 380 (679)
T ss_pred HHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCCC-CEEeeehh-cCCC-CcccCCCC-CCHH-HHHHHhC
Confidence 456777777 568999999999999999999999999665544 43433321 1111 11212222 2221 1122223
Q ss_pred CCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEE
Q 002210 282 NKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLV 361 (953)
Q Consensus 282 n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi 361 (953)
+++--+.+....|.. ...+. .|. ..+..-++.+.+||..+ +++.|.+
T Consensus 381 ~~v~~~~~~~~~~~~-------~~~~~---------~~~----~~~~~~~~~l~vPL~~~-------------~~~~G~l 427 (679)
T TIGR02916 381 GWIINLEEARSEPDH-------YSGLV---------LPE----WLREIPNAWLIVPLISG-------------EELVGFV 427 (679)
T ss_pred CCcccchhhcCCccc-------ccccc---------cch----hhhcCCCceEEEEeccC-------------CEEEEEE
Confidence 333111111111100 00000 021 12223356899999977 8999999
Q ss_pred eeecC-CCCCCChhHHHHHHHHHHHHHHhhHH
Q 002210 362 VCHHT-SPRFVPFPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 362 ~~hh~-~pr~~~~~~r~~~~~l~~~~~~~l~~ 392 (953)
.+.+. .++.++.+.+...+.++.+++..+..
T Consensus 428 ~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~~ 459 (679)
T TIGR02916 428 VLARPRTAGEFNWEVRDLLKTAGRQAASYLAQ 459 (679)
T ss_pred EEecCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 88766 46778889999999999988887754
No 114
>PRK10337 sensor protein QseC; Provisional
Probab=95.45 E-value=0.05 Score=63.80 Aligned_cols=65 Identities=17% Similarity=0.189 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCH-HHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSE-EQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e-~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
..+|++.++||+||||+.+.+..+.+.....++ ...++++.+....+++.+++++ ++++|++.+.
T Consensus 237 ~~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~~~ 303 (449)
T PRK10337 237 ERRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDSLD 303 (449)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 446899999999999999999999887644444 4567899998889999999999 7999988753
No 115
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=95.40 E-value=0.027 Score=65.69 Aligned_cols=101 Identities=14% Similarity=0.137 Sum_probs=79.1
Q ss_pred EEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEEEEE
Q 002210 624 ILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVILVVN 703 (953)
Q Consensus 624 I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~ 703 (953)
+.....|.+|+||.+++.+++||.+++++|+++.+++|..|.+.+.+.....+..++.+.-.++. ..+.|+.+|+...
T Consensus 277 vtRhs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~--lak~GGyvWlQTq 354 (768)
T KOG3558|consen 277 VTRHSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRL--LAKNGGYVWLQTQ 354 (768)
T ss_pred EEeeecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHH--HHhcCCeEEEEee
Confidence 34457799999999999999999999999999999999999999998888888777666555444 4568999999999
Q ss_pred EEEeecCC-CCEEEEEEEEEecch
Q 002210 704 ACCTQDTK-ENVIGVCFVGQDITG 726 (953)
Q Consensus 704 ~~pi~d~~-g~v~gvv~v~~DITe 726 (953)
++.+.+.. ++...++++-.=|+.
T Consensus 355 ATVi~~tkn~q~q~IicVnYVlS~ 378 (768)
T KOG3558|consen 355 ATVIYNTKNPQEQNIICVNYVLSN 378 (768)
T ss_pred eEEEecCCCCCcceEEEEEeeecc
Confidence 88887643 233445554444443
No 116
>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=95.33 E-value=0.36 Score=46.95 Aligned_cols=110 Identities=8% Similarity=-0.031 Sum_probs=73.4
Q ss_pred HHHHHHHhCCCCCCCCeEeecCC--ccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHH
Q 002210 739 GDYVGIVSSPSALIPPIFMTDED--GRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNK 816 (953)
Q Consensus 739 ~~~~~i~e~~~~li~~I~~~D~~--G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~ 816 (953)
..++.+.+ .+. +|+..|.+ -.++|.|.++.++|+++-+++.+.+.. .... +.........+.+
T Consensus 32 ~~~~~L~~-ap~---ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr-~sae----------~~~r~er~~lL~~ 96 (148)
T PF08670_consen 32 ELAKALWH-APF---AILSHGTKADPIFIYANQAALDLFETTWDELVGLPSR-LSAE----------EPERKERQSLLAQ 96 (148)
T ss_pred HHHHHHHc-CCC---EEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHh-hccC----------hhhHHHHHHHHHH
Confidence 34566666 444 56665544 589999999999999999999998864 2221 1222334445555
Q ss_pred HhcCCCcceEEEEEEccCCCEEEEE-EEEEEeecCCCCEEEEEEEEEe
Q 002210 817 VISGQDADKILFGFFDQQGKYVEAL-LSANKRTNAEGKISGILCFLHV 863 (953)
Q Consensus 817 ~~~g~~~~~~e~~~~~kdG~~~~v~-~s~~pi~d~~G~i~g~v~v~~D 863 (953)
+...+-...+.---..+.|+.+++. ..+..+.|++|...|...++.+
T Consensus 97 v~~qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 97 VMQQGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSN 144 (148)
T ss_pred HHHhCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEee
Confidence 5554433333323357889888775 5677999999999987776654
No 117
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=95.29 E-value=0.12 Score=55.39 Aligned_cols=107 Identities=17% Similarity=0.175 Sum_probs=77.0
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccce---EEEEEEEccc
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN---VEIKLRAFGP 691 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~---~e~~~~~~~~ 691 (953)
.++++.+.+++++|.+|.|.|+|++++.+||.+...+.|.++.++++..+. ....+.++...+.. ++..+.
T Consensus 11 ~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs~--ll~ll~q~~~~~~~~~~~~v~l~---- 84 (363)
T COG3852 11 AILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPFGSL--LLSLLDQVLERGQPVTEYEVTLV---- 84 (363)
T ss_pred hHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCcH--HHHHHHHHHHhcCCcccceeeee----
Confidence 578999999999999999999999999999999999999999998876543 34455555533322 233333
Q ss_pred CCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHH
Q 002210 692 RETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVM 731 (953)
Q Consensus 692 ~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E 731 (953)
.+|....+.....|+....|-+ +..++-+....+..
T Consensus 85 -~~g~~~~v~~~v~~v~~~~G~v---lle~~~~~~~~rid 120 (363)
T COG3852 85 -ILGRSHIVDLTVAPVPEEPGSV---LLEFHPRDMQRRLD 120 (363)
T ss_pred -ecCccceEEEEEeeccCCCCeE---EEEechhHHHhHhh
Confidence 2588888999999987655543 33444444444333
No 118
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=95.26 E-value=0.12 Score=64.19 Aligned_cols=55 Identities=7% Similarity=0.154 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHhhcCCCCC-HHHHHHHHHHHHHHHHHHhHhhhh
Q 002210 886 LNKLEYIRREIRKPLNGIAFMQNLMGTSDLS-EEQKQLLKTSVLCQEQLTNIVDDT 940 (953)
Q Consensus 886 ~~fla~isHELrnPL~~I~g~~~LL~~~~l~-e~~~~~l~~i~~~~~~L~~lI~DL 940 (953)
.++.+.++||+|||++.+..+.+.++....+ +...++++.+.++.++|.+++++|
T Consensus 476 ~~~~a~i~HdLrn~l~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l 531 (679)
T TIGR02916 476 NRMSAFVVHDLKNLVAQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQL 531 (679)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467889999999999999988887664444 456778899999999999999885
No 119
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=95.15 E-value=0.062 Score=62.71 Aligned_cols=65 Identities=15% Similarity=0.199 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 879 EQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 879 e~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
++..+.+..+++.++|||||||+.|.++.+++... .....+.+....++|..++++ +++.|.+.+
T Consensus 223 ~~~~~~~~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~~~ 288 (435)
T PRK09467 223 KQLEDDRTLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTGQE 288 (435)
T ss_pred HHHHHHHHHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 33445677789999999999999999999887532 233445666777899999999 788886654
No 120
>TIGR01386 cztS_silS_copS heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.
Probab=95.11 E-value=0.061 Score=63.03 Aligned_cols=67 Identities=16% Similarity=0.188 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCC-CCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGTSD-LSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
.....+.+.++||+||||+.+.+..+.+.... ..++..++++.+....+++.+++++ |++++++.+.
T Consensus 239 ~~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~ 307 (457)
T TIGR01386 239 QRLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQ 307 (457)
T ss_pred HHHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 34456789999999999999999999876533 3455667888888888999999999 7999998864
No 121
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=95.10 E-value=0.074 Score=62.63 Aligned_cols=65 Identities=14% Similarity=0.274 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
..++++.++||+|||++.+.+..++|......++..++++.+....+++..++++ +++++++.++
T Consensus 256 ~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~ 321 (475)
T PRK11100 256 VEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQRQ 321 (475)
T ss_pred HHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 4567899999999999999999999988666777889999999999999999999 7999888754
No 122
>PRK09835 sensor kinase CusS; Provisional
Probab=95.01 E-value=0.07 Score=63.12 Aligned_cols=68 Identities=15% Similarity=0.169 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCC-CCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTS-DLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~-~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
...+.++++.++|||||||+.|.+..+.+... ....+..+.+..+.....++..++++ ++++|++.++
T Consensus 259 ~~~~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~~~ 328 (482)
T PRK09835 259 FTRQSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADNNQ 328 (482)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34466789999999999999999999987653 33445566777777777899999999 7999988765
No 123
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=94.82 E-value=0.077 Score=60.15 Aligned_cols=60 Identities=15% Similarity=0.206 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 884 NSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 884 ~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
.+.++++.++||+||||++|.++.+++..... ++... +....+++..++++ ++++|.+..
T Consensus 136 ~~~~~~~~~sHelrtPL~~i~~~~e~l~~~~~-~~~~~----~~~~~~~l~~~i~~ll~~~r~~~~ 196 (356)
T PRK10755 136 QERLFTADVAHELRTPLAGIRLHLELLEKQHH-IDVAP----LIARLDQMMHTVEQLLQLARAGQS 196 (356)
T ss_pred HHHHHHHHhhHhhcChHHHHHHHHHHHHhccc-hhHHH----HHHHHHHHHHHHHHHHHHHHcccc
Confidence 34468999999999999999999999865322 22222 22334677777888 688776543
No 124
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=94.64 E-value=0.17 Score=47.13 Aligned_cols=41 Identities=24% Similarity=0.338 Sum_probs=37.8
Q ss_pred CeEeecCCccEEehhHHHHHHhCCChhhhhccccccccccc
Q 002210 754 PIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTV 794 (953)
Q Consensus 754 ~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~ 794 (953)
|++-+|.+|+|+..|.+-.++.|++++.++|+++..++-|.
T Consensus 28 GvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC 68 (124)
T TIGR02373 28 GAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPC 68 (124)
T ss_pred ceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccc
Confidence 89999999999999999999999999999999987666653
No 125
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=94.51 E-value=0.12 Score=56.23 Aligned_cols=57 Identities=28% Similarity=0.371 Sum_probs=51.4
Q ss_pred HHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHH
Q 002210 610 TNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVD 666 (953)
Q Consensus 610 ~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~ 666 (953)
.-.+.+++++.|++++.+|..|.+..+|++++++||.+.+++.|.++..++......
T Consensus 79 hl~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~ 135 (511)
T COG3283 79 HLALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL 135 (511)
T ss_pred hHHHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHH
Confidence 345678999999999999999999999999999999999999999999888766544
No 126
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=94.44 E-value=0.27 Score=45.79 Aligned_cols=61 Identities=13% Similarity=0.291 Sum_probs=49.9
Q ss_pred HHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCcc-ccccCCcHHHHHHHHHHHh
Q 002210 616 LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALV-DLVAGDSVDVVKNMLSSAF 676 (953)
Q Consensus 616 lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~-dl~~~~~~~~~~~~l~~~l 676 (953)
-++..|.|++-+|.+|.|+..|.+-.++.|++++.++|+++. ++.|-.....+...+....
T Consensus 21 elD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~ 82 (124)
T TIGR02373 21 QFDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGV 82 (124)
T ss_pred HhhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhh
Confidence 478999999999999999999999999999999999999987 5555444444555555544
No 127
>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=94.37 E-value=0.18 Score=34.31 Aligned_cols=40 Identities=23% Similarity=0.435 Sum_probs=34.9
Q ss_pred EEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccH
Q 002210 827 LFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASP 866 (953)
Q Consensus 827 e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITe 866 (953)
++.+...+|...|+.....++.+..|.+.+++++..|||+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 4556788999999999999999888999999999999985
No 128
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=94.23 E-value=0.13 Score=60.49 Aligned_cols=63 Identities=16% Similarity=0.234 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
..+.++++.++||+||||+.|.+..+++.......+ .+..+....++|.+++++ ++++|.+.+
T Consensus 241 ~~~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~~---~~~~i~~~~~~l~~~i~~l~~~~~~~~~ 304 (461)
T PRK09470 241 TSQQRLLSDISHELRTPLTRLQLATALLRRRQGESK---ELERIETEAQRLDSMINDLLVLSRNQQK 304 (461)
T ss_pred HHHHHHHHhhhHhhCCHHHHHHHHHHHHhhccCChH---HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 445578999999999999999999999876443332 456677778899999999 799987654
No 129
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=94.23 E-value=0.21 Score=59.39 Aligned_cols=60 Identities=10% Similarity=-0.001 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCC-CCHHHHHHHHHHHHHHHHHHhHhhh-hcc
Q 002210 883 ANSLNKLEYIRREIRKPLNGIAFMQNLMGTSD-LSEEQKQLLKTSVLCQEQLTNIVDD-TDI 942 (953)
Q Consensus 883 ~~k~~fla~isHELrnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~~L~~lI~D-Ldl 942 (953)
..+.+..+.++||++|||++|.+..+++++.. .+++.++..+.+.+.+.++.+.+++ ++.
T Consensus 300 ~~r~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~ 361 (495)
T PRK11644 300 SVRRDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGR 361 (495)
T ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34556778889999999999999999997733 3455667888888888888888887 543
No 130
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=93.96 E-value=2.4 Score=42.99 Aligned_cols=126 Identities=13% Similarity=0.143 Sum_probs=90.6
Q ss_pred CCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCC
Q 002210 214 GNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP 293 (953)
Q Consensus 214 ~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~ 293 (953)
.++....+.+++-+.+.||+ -|+|- +.-.|+|=+-.+ - ..|-|.+ +.+..++.+..+++.+..+.+.+
T Consensus 52 ~~~~~~A~~~aeII~~~t~~-aVaIT-----Dr~~ILA~~G~g-~----d~~~~~~-is~~t~~~i~~gk~~~~~~~~~~ 119 (180)
T TIGR02851 52 GELGDFAKEYAESLYQSLGH-IVLIT-----DRDTVIAVAGVS-K----KEYLNKP-ISDELEDTMEERKTVILSDTKDG 119 (180)
T ss_pred cchHHHHHHHHHHHHHHhCC-EEEEE-----CCCcEEEEECCC-h----hhcCCCc-cCHHHHHHHHcCCEEEecCCccc
Confidence 35677777788889999999 88886 344677755332 2 2344554 99999999999999888873321
Q ss_pred CceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCC--CC
Q 002210 294 PVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPR--FV 371 (953)
Q Consensus 294 ~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr--~~ 371 (953)
.++... -.+....+.+++||+.+ |+.=|.|.-. ...+ .+
T Consensus 120 ~i~c~~-------------------------~~~~~l~s~ii~Pl~~~-------------g~viGtLkly-~k~~~~~~ 160 (180)
T TIGR02851 120 PIEIID-------------------------GQEFEYTSQVIAPIIAE-------------GDPIGAVIIF-SKEPGEKL 160 (180)
T ss_pred eecccc-------------------------CCCCCcceEEEEEEEEC-------------CeEEEEEEEE-ECCccCCC
Confidence 122110 01122478999999987 8899977776 6666 78
Q ss_pred ChhHHHHHHHHHHHHHHhh
Q 002210 372 PFPLRYACEFLIQVFGVQV 390 (953)
Q Consensus 372 ~~~~r~~~~~l~~~~~~~l 390 (953)
+..++.+.+-|++.||.||
T Consensus 161 ~~~e~~la~glA~lLS~QL 179 (180)
T TIGR02851 161 GEVEQKAAETAAAFLGKQM 179 (180)
T ss_pred CHHHHHHHHHHHHHHHHhh
Confidence 8899999999999999887
No 131
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=93.73 E-value=0.15 Score=60.01 Aligned_cols=67 Identities=16% Similarity=0.109 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhccc
Q 002210 882 AANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWY 949 (953)
Q Consensus 882 ~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~ 949 (953)
...+.++++.++||++|||+.|.+.++.+.... .+...+.+..+....++|.+++++ +++++.+.|.
T Consensus 237 ~~~~~~~~~~~shel~~pL~~i~~~~~~l~~~~-~~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~ 304 (466)
T PRK10549 237 EQMRRDFMADISHELRTPLAVLRGELEAIQDGV-RKFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGA 304 (466)
T ss_pred HHHHHHHHHHHhHHhCChHHHHHHHHHHHHhcc-ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Confidence 445667899999999999999999999997632 223345677777778899999999 6888888774
No 132
>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=93.42 E-value=0.25 Score=37.41 Aligned_cols=45 Identities=38% Similarity=0.456 Sum_probs=38.6
Q ss_pred HHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhccccc
Q 002210 741 YVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLI 788 (953)
Q Consensus 741 ~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~ 788 (953)
++.+++..+. +++.+|.++.+.++|+.+.+++|++..++.|+.+.
T Consensus 3 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (67)
T smart00091 3 LRAILESLPD---GIFVLDLDGRILYANPAAEELLGYSPEELIGKSLL 47 (67)
T ss_pred HHHHHhhCCc---eEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHH
Confidence 5567777766 89999999999999999999999999988887654
No 133
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=93.15 E-value=0.24 Score=54.63 Aligned_cols=112 Identities=14% Similarity=0.135 Sum_probs=78.1
Q ss_pred HHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhc
Q 002210 740 DYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVIS 819 (953)
Q Consensus 740 ~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~ 819 (953)
.+.+++...|- -|-.+|.++++.+.|+. .++|-+++.. +|+... .. +++.....+...+....+
T Consensus 291 e~naif~~lP~---Ditfvdk~diV~ffs~~-~rif~rt~sv-iGr~v~-~c----------hpPksv~iv~ki~~~fks 354 (409)
T COG2461 291 ELNAIFKHLPV---DITFVDKNDIVRFFSGG-ERIFPRTPSV-IGRRVQ-LC----------HPPKSVHIVEKILKDFKS 354 (409)
T ss_pred HHHHHHhhCCC---ceEEecccceEEecCCc-ceecccChHh-hCCccc-CC----------CCCchHHHHHHHHHHhhc
Confidence 46788888863 47889999999999998 8888887764 588764 22 233444445555555555
Q ss_pred CCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHH
Q 002210 820 GQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYA 871 (953)
Q Consensus 820 g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e 871 (953)
|.. ...++. ....+. .+.++..+++|++|+..|++-+++|||.-|..+
T Consensus 355 G~k-d~~efw-~~~~~~--~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 355 GEK-DFAEFW-INMGDK--FIHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred CCc-chHHHh-ccCCCc--eEEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 543 344444 233333 456677888999999999999999999877544
No 134
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=92.77 E-value=1.6 Score=56.14 Aligned_cols=112 Identities=8% Similarity=0.042 Sum_probs=68.4
Q ss_pred cHHHHHHHHHHHHHHHHhcCccEEEEc-CCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccc
Q 002210 602 KIDELRIITNEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEER 680 (953)
Q Consensus 602 ~~~eL~~~~~~l~~lle~~~~~I~~~D-~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~ 680 (953)
...++++.++.++.+++++|+++++++ .+|.++..|+.+..++|+...+ +..... .......
T Consensus 325 ~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~-------------~~~~~~----~~~~~~~ 387 (924)
T PRK10841 325 NALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHE-------------DRQRLT----QIICGQQ 387 (924)
T ss_pred HHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChh-------------HHHHHH----HHHhccc
Confidence 445688888899999999999999997 6999999999999998864322 111111 1111111
Q ss_pred eEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHH
Q 002210 681 NVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQ 738 (953)
Q Consensus 681 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se 738 (953)
........ .++... .+.....+. .+.. ..++++.|||+++++|+++++..
T Consensus 388 ~~~~~~~~----~~~~~~--~i~~~~~~~-~~~~-~~i~~~~Dit~r~~~e~~L~~~~ 437 (924)
T PRK10841 388 VNFVDVLT----SNNTNL--QISFVHSRY-RNEN-VAICVLVDVSARVKMEESLQEMA 437 (924)
T ss_pred cceeeEEc----CCCcEE--EEEEEeeee-cCce-EEEEEEEEhhHHHHHHHHHHHHH
Confidence 11111111 123333 333333332 2333 35677899999999998876544
No 135
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=92.30 E-value=0.11 Score=57.21 Aligned_cols=103 Identities=10% Similarity=0.049 Sum_probs=73.5
Q ss_pred HHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCC-cHHHHHHHHHHHhcccceEEEEEEEcccC
Q 002210 614 VRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGD-SVDVVKNMLSSAFLEERNVEIKLRAFGPR 692 (953)
Q Consensus 614 ~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~-~~~~~~~~l~~~l~~~~~~e~~~~~~~~~ 692 (953)
-..++....+|-+.|.+..|.|+|++++.++|+-..|++|++..++-..+ .+..+...+...+..++..+-+. ..++
T Consensus 160 FaaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~--~aRR 237 (775)
T KOG1229|consen 160 FAALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEE--EARR 237 (775)
T ss_pred HHHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchH--HHhh
Confidence 35678888899999999999999999999999999999999998876533 23344455555554444333322 2245
Q ss_pred CCCCEEEEEEEEEEeecCCCCEEEEE
Q 002210 693 ETSGPVILVVNACCTQDTKENVIGVC 718 (953)
Q Consensus 693 ~dG~~~~v~v~~~pi~d~~g~v~gvv 718 (953)
+.|......+..+|+....|++-.++
T Consensus 238 ksgdS~dqh~~itP~~gqggkirhfv 263 (775)
T KOG1229|consen 238 KSGDSCDQHFIITPFAGQGGKIRHFV 263 (775)
T ss_pred ccCCcccceEEEeeecCCCCceeeeh
Confidence 56766666677888888677765543
No 136
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=91.91 E-value=0.35 Score=57.99 Aligned_cols=197 Identities=18% Similarity=0.137 Sum_probs=106.6
Q ss_pred ccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceE---------------EEEE
Q 002210 622 VPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNV---------------EIKL 686 (953)
Q Consensus 622 ~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~---------------e~~~ 686 (953)
..+++-+.+|+|+|+...+..++|+.++-+.|..+.|++++.|...+...+....-..+.. .+..
T Consensus 193 F~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~vF~sfta~~~lp~ws~~s~~ds~~~~c~~~ks~fc 272 (1114)
T KOG3753|consen 193 FVVAVSFLDGRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGVFYSFTARYKLPLWSMGSSADSFTQECAEEKSFFC 272 (1114)
T ss_pred eEEEEeccCCcEEEeechhhhhccCchhhhccchhhhhcchhhhhhhhhccccccCccccccccccchhhhhhhhcceee
Confidence 3556667899999999999999999999999999999999988876655544332111100 0011
Q ss_pred EEcc-cCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHH------HHHHHHHHHHHhCCCCCCCCeEee-
Q 002210 687 RAFG-PRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKY------TRIQGDYVGIVSSPSALIPPIFMT- 758 (953)
Q Consensus 687 ~~~~-~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L------~~se~~~~~i~e~~~~li~~I~~~- 758 (953)
+..+ .......++--++.+| .+..+-++..++.+. .++..-|++= +..++- -||.+
T Consensus 273 Risgr~~~~~~~~y~PFRl~p-------------yl~ev~~~~~~~s~~ccLllaerihSgYeAP-rIps~K--riFtT~ 336 (1114)
T KOG3753|consen 273 RISGRKDRENEIRYHPFRLTP-------------YLVEVRDQQGAESQPCCLLLAERIHSGYEAP-RIPSNK--RIFTTT 336 (1114)
T ss_pred eeecccCCcCccccCcccccc-------------eeEEeccccccCcCcceeehhhhhhcccccC-cCCccc--ceeEec
Confidence 1110 0000111111111111 111121111111110 1111112111 111110 14544
Q ss_pred -cCCccEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHh-cCCCc--ceEEEEEEccC
Q 002210 759 -DEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI-SGQDA--DKILFGFFDQQ 834 (953)
Q Consensus 759 -D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~-~g~~~--~~~e~~~~~kd 834 (953)
...+-+..+..++.-++||-+.++||+.+...+++++ +.-+...-.+.+ .++.. ..-.+||...+
T Consensus 337 HTptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eD-----------r~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqN 405 (1114)
T KOG3753|consen 337 HTPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPED-----------RHVMVQIHQKVLQSGGKPVFSHSPIRFCAQN 405 (1114)
T ss_pred cCCcceeeecchhhhhhhccCchhhhccchhhhhcCCc-----------hHHHHHHHHHHHHhCCCCcccccceeeeecC
Confidence 3456788899999999999999999999876555542 111222222222 22222 35568999999
Q ss_pred CCEEEEEEEEE
Q 002210 835 GKYVEALLSAN 845 (953)
Q Consensus 835 G~~~~v~~s~~ 845 (953)
|.++.+....+
T Consensus 406 G~yv~ldTeWS 416 (1114)
T KOG3753|consen 406 GSYVRLDTEWS 416 (1114)
T ss_pred CcEEEEechhh
Confidence 99987765443
No 137
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=91.86 E-value=0.66 Score=50.82 Aligned_cols=64 Identities=28% Similarity=0.350 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcc
Q 002210 884 NSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEW 948 (953)
Q Consensus 884 ~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G 948 (953)
.+..+++.++||+|||++.+.++.+++..... +..++++..+....+++..++++ +++++++.+
T Consensus 114 ~~~~~~~~~~hel~~pl~~i~~~~~~~~~~~~-~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~ 178 (336)
T COG0642 114 AKREFLANISHELRTPLTAIRGLLELLLEGLL-DPQRELLEIIEEEAERLLRLVNDLLDLSRLEAG 178 (336)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHhccCCc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 36788999999999999999999996665522 22788888888788999999999 899999875
No 138
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=88.72 E-value=0.5 Score=57.70 Aligned_cols=54 Identities=15% Similarity=0.210 Sum_probs=48.6
Q ss_pred HHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHH
Q 002210 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVV 668 (953)
Q Consensus 615 ~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~ 668 (953)
.+++++...++++..+|+|+|+.+....++||..+|++|+++.+++|+.+.+..
T Consensus 99 LmLeAlDGF~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~ 152 (803)
T KOG3561|consen 99 LILEALDGFLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKP 152 (803)
T ss_pred HHHHHhcCeEEEEecCceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcc
Confidence 367888888899999999999999999999999999999999999998775543
No 139
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=88.59 E-value=0.073 Score=66.55 Aligned_cols=70 Identities=29% Similarity=0.415 Sum_probs=61.1
Q ss_pred HHHHHHHHH--HHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhh-hcccchhcccc
Q 002210 879 EQAAANSLN--KLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDD-TDIESIEEWYD 950 (953)
Q Consensus 879 e~~~~~k~~--fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~D-LdlsrIe~G~~ 950 (953)
+++...+.+ +++.++||||+|+++ |+...+..+..+.+++.+++....++..+..+++| +|.+++++|+.
T Consensus 213 e~~~~~~sq~~~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g~~ 285 (786)
T KOG0519|consen 213 EAAVWSPSQKGFLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESGKG 285 (786)
T ss_pred hhcccCccchhhcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccccc
Confidence 344444555 899999999999999 77788888999999999999999999999999999 89999999863
No 140
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=87.77 E-value=2.8 Score=49.66 Aligned_cols=173 Identities=20% Similarity=0.255 Sum_probs=92.6
Q ss_pred HHHHHHHHHHHH---HhcCccEEEEcCCCcEEecCHHHHHHhCCCc-chhcCCCccccccCCcHHHHHHHHHHHhcccce
Q 002210 606 LRIITNEMVRLI---ETAAVPILAVDASGNVNGWNSKAAELTGLTV-DQAIGTALVDLVAGDSVDVVKNMLSSAFLEERN 681 (953)
Q Consensus 606 L~~~~~~l~~ll---e~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~-~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~ 681 (953)
|......|..++ ...+..+++.|.+|.++..+-......++.. .-..|..|.+-... .+.+-.++.+++.
T Consensus 69 L~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WSE~~~G------TNgIGTcLve~~a 142 (606)
T COG3284 69 LTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWSEPREG------TNGIGTCLVEGEA 142 (606)
T ss_pred HHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecChhhhhhhhhhcccccccccccccc------ccchhhhhccCcc
Confidence 333444455554 4467789999999999987654322222211 11123333321111 1123334444445
Q ss_pred EEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEE---EecchhHHH------HHHHHHHH---------HHHHH
Q 002210 682 VEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVG---QDITGQKLV------MDKYTRIQ---------GDYVG 743 (953)
Q Consensus 682 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~---~DITerk~~------E~~L~~se---------~~~~~ 743 (953)
+.+.-.- |-......+.+++.|++|.+|+++|++-+. .|+++.-.. ...-+..| ..+..
T Consensus 143 VtI~~~q---HF~~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~~~~~~s~~~~~~iV~~~ar~IE~~~~~~~~~~~~~l 219 (606)
T COG3284 143 VTIHGDQ---HFIQAHHGLSCSAAPIFDEQGELVGVLDISSCRSDLSEASQPLTLAIVTDAARRIEAELFLAAFEGHWLL 219 (606)
T ss_pred eEEehhh---hHhhcccCceeeeeccccCCCcEEEEEEeccCCcchhhhhhHHHHHHHHHHHHHHHHHHHHHhcCcchHH
Confidence 5443221 222444567789999999999999986554 233332210 00111111 11111
Q ss_pred HHhCCCCC----CCCeEeecCCccEEehhHHHHHHhCCC-hhhhhcccc
Q 002210 744 IVSSPSAL----IPPIFMTDEDGRCLEWNDGMEKLSGLK-REEAIERML 787 (953)
Q Consensus 744 i~e~~~~l----i~~I~~~D~~G~i~~~N~a~~~l~G~~-~eeliGk~~ 787 (953)
.+...+++ -.+.+.+|.+|+++-.|+++..+++.+ ..-++|.+.
T Consensus 220 r~~~~p~~~d~~~~~~lavd~~grvl~at~aA~~~La~~~~~~l~g~p~ 268 (606)
T COG3284 220 RIALAPDYLDSQSEALLAVDQDGRVLGATRAARQLLALTDRQRLIGQPV 268 (606)
T ss_pred HHhcCccccCcccceeeeecCcchhhhccHHHHHhhccchhhHhhcCCc
Confidence 22222211 125889999999999999999999988 455556554
No 141
>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=86.88 E-value=2.3 Score=28.38 Aligned_cols=35 Identities=26% Similarity=0.295 Sum_probs=29.6
Q ss_pred CCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchh
Q 002210 693 ETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQ 727 (953)
Q Consensus 693 ~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITer 727 (953)
.+|...|+.....++.+..|.+.+++++..|||++
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 9 KDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 (43)
T ss_pred cCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence 36788888888888888888999999999999863
No 142
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=86.15 E-value=6.3 Score=50.37 Aligned_cols=44 Identities=23% Similarity=0.180 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEc-CCCcEEecCHHHHHHhCC
Q 002210 603 IDELRIITNEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGL 646 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle~~~~~I~~~D-~dg~i~~~N~a~~~l~G~ 646 (953)
.+++++.+...+.+++++|+|++++| .+|+|+.+|+++.+++|.
T Consensus 335 ~~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 335 SHELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHHHHhCc
Confidence 45788888899999999999999999 689999999999999975
No 143
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=85.27 E-value=2.6 Score=46.34 Aligned_cols=46 Identities=15% Similarity=0.181 Sum_probs=42.4
Q ss_pred HHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhccccc
Q 002210 740 DYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLI 788 (953)
Q Consensus 740 ~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~ 788 (953)
.+.+++++.++ +++.+|..|.+...|+|++++||.+.+++.|++..
T Consensus 81 ~L~aLL~al~~---pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~ 126 (511)
T COG3283 81 ALSALLEALPE---PVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA 126 (511)
T ss_pred HHHHHHHhCCC---ceEEecccCceeecCHHHHHHhCCChhhhcCccHH
Confidence 46788899887 99999999999999999999999999999999875
No 144
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=84.69 E-value=40 Score=43.08 Aligned_cols=132 Identities=11% Similarity=0.077 Sum_probs=78.7
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCC
Q 002210 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (953)
Q Consensus 215 ~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~ 294 (953)
.++..++.+.+.+..++|.+++.++-|+.++...+... . |. .|..+.+...+.+-.. +...+
T Consensus 293 ~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---~------~~-~~~~~~~~~~~~~~~~--------~~~~~ 354 (828)
T PRK13837 293 ELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---P------GL-TPDPVWPDRLRALAST--------VKAAE 354 (828)
T ss_pred hhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---C------cc-CCCCCchHHHHHHHHH--------HhccC
Confidence 45689999999999999999999999988765443221 1 11 1233344433333111 00000
Q ss_pred -ceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCC-CCCC
Q 002210 295 -VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSP-RFVP 372 (953)
Q Consensus 295 -~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~ 372 (953)
..++.. +...+....++...+....+++|+..+ +++.|++.+....+ ..++
T Consensus 355 ~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~g~l~~~~~~~~~~~~ 407 (828)
T PRK13837 355 RDVVFVD--------------RNGPVRKRSCLTRRGPALWACLAFKSG-------------DRIVALLGLGRQRYGLRPP 407 (828)
T ss_pred CceEEee--------------cccchhhhcccccCCcceEEEEEeccC-------------CceEEEEEecccccCCCCC
Confidence 001100 111122333444668889999999876 89999999877653 3344
Q ss_pred hhHHHHHHHHHHHHHHhhH
Q 002210 373 FPLRYACEFLIQVFGVQVN 391 (953)
Q Consensus 373 ~~~r~~~~~l~~~~~~~l~ 391 (953)
..+...++.++..++..+.
T Consensus 408 ~~~~~~l~~~~~~~~~~~~ 426 (828)
T PRK13837 408 AGELQLLELALDCLAHAIE 426 (828)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 5666777777777766654
No 145
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=82.18 E-value=7.4 Score=45.75 Aligned_cols=100 Identities=17% Similarity=0.251 Sum_probs=60.6
Q ss_pred HHHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEE
Q 002210 609 ITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRA 688 (953)
Q Consensus 609 ~~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~ 688 (953)
.+..+..++.+.|.||+.+|.++.+.|+||-+..+|+ ++.+|....++. .+.+...........+. .
T Consensus 73 ~~~~~~~al~nmPiGii~~~e~~~veW~Npf~~~if~---~~~~~~~~~~~~--------~~il~~~~~~~~~~~~~--i 139 (655)
T COG3887 73 AEKSLEEALTNMPIGIILFNETNKVEWVNPFASKIFN---KNEIGESLSELI--------PEILKQLARNDEKQYIK--I 139 (655)
T ss_pred HHHHHHHHHHhCCceEEEEcCCCceEEecHHHHHhcC---hhhhhhhHHHHh--------HHHHHHHhcCCcceEEE--E
Confidence 3555678899999999999999999999999999997 333443333322 23333333222221222 1
Q ss_pred cccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHH
Q 002210 689 FGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTR 736 (953)
Q Consensus 689 ~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~ 736 (953)
++..+.. ..+.+.+++ .+-|+|++.+.++.++.
T Consensus 140 ------~e~~y~~-----~~~~~~~li----Yf~DvT~~~~~~~~~~~ 172 (655)
T COG3887 140 ------NEKKYDV-----YFDSDKRLI----YFFDVTEEEAIEEEYEN 172 (655)
T ss_pred ------cceEEEE-----EEecCCCEE----EEEeccHHHHHHHHHhc
Confidence 2222211 233444443 45899999888777543
No 146
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=81.98 E-value=8.4 Score=31.58 Aligned_cols=47 Identities=21% Similarity=0.164 Sum_probs=37.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHh
Q 002210 887 NKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIV 937 (953)
Q Consensus 887 ~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI 937 (953)
+.+....||+.|-|..|.|++++=+ .++.++|+..+....+....++
T Consensus 14 ~~lR~~RHD~~NhLqvI~gllqlg~----~~~a~eYi~~~~~~~~~~s~l~ 60 (62)
T PF14689_consen 14 DSLRAQRHDFLNHLQVIYGLLQLGK----YEEAKEYIKELSKDLQQESELL 60 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHHHHHHHHHHHH
Confidence 4467779999999999999998754 4778889988877777776654
No 147
>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=80.86 E-value=3.4 Score=38.24 Aligned_cols=49 Identities=22% Similarity=0.424 Sum_probs=39.7
Q ss_pred cEEEEcC-CCcEEecCHHHHHHhCCC---cchhcCCCccccccCCcHHHHHHH
Q 002210 623 PILAVDA-SGNVNGWNSKAAELTGLT---VDQAIGTALVDLVAGDSVDVVKNM 671 (953)
Q Consensus 623 ~I~~~D~-dg~i~~~N~a~~~l~G~~---~~eliG~~~~dl~~~~~~~~~~~~ 671 (953)
.++++|. +++|+.++..+.+++|.+ .++++|+++.+++.+.....+.+.
T Consensus 17 ~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~~ 69 (110)
T PF08446_consen 17 ALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLREA 69 (110)
T ss_dssp EEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHHH
T ss_pred EEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHHh
Confidence 3456765 699999999999999999 999999999999988776644443
No 148
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=80.39 E-value=13 Score=43.71 Aligned_cols=146 Identities=18% Similarity=0.241 Sum_probs=99.8
Q ss_pred HHHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCC-ceEEEeecCCCCCCccCCCCCCCCccHHHHHHH
Q 002210 201 AAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEH-GEVVAECRRPDLEPYLGFHYPATDIPQASRFLI 279 (953)
Q Consensus 201 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~-G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly 279 (953)
+.++.+.+.+ ..++.+-++.+|++|..-...+=+-||--+.|++ =+..| .. ||.=|+-
T Consensus 5 Lr~i~E~va~--~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~A---Te------GLnk~av---------- 63 (756)
T COG3605 5 LRRIVEKVAS--ALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELMA---TE------GLNKPAV---------- 63 (756)
T ss_pred HHHHHHHHhc--ccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEe---cc------ccCcccc----------
Confidence 3455667777 6699999999999999999999999999999883 44444 12 3332211
Q ss_pred HhCCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcC---CeeEEEEEEEEeCCcccccccccCCCc
Q 002210 280 MKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMG---SIASLVMSVTINEAEDELDNDQEQGRK 356 (953)
Q Consensus 280 ~~n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmg---v~asl~~~i~~~~~~~~~~~~~~~~~~ 356 (953)
..+++-.| ..=|.++ ....+||+|+.+ +-||.. .|+..-| ..|-|-+||+.. |+
T Consensus 64 --~~~~l~~~--eGLVG~v--~~~aePlNLsdA---qsHPsF-~Y~petgEE~Y~sFLGvPIi~~-------------~r 120 (756)
T COG3605 64 --HLVQLAFG--EGLVGLV--GRSAEPLNLADA---QSHPSF-KYLPETGEERYHSFLGVPIIRR-------------GR 120 (756)
T ss_pred --ceEEecCC--Cchhhhh--hhccCCCChhhh---hhCCcc-ccccccchHHHHHhhccceeec-------------Cc
Confidence 12222222 1112222 345688999776 344543 3666555 367889999977 99
Q ss_pred eeEEEeeecCCCCCCChhHHHHHHHHHHHHHHhh
Q 002210 357 LWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQV 390 (953)
Q Consensus 357 LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~~~~l 390 (953)
+-|.++.++.++|.....+..+.+.++.+++.-+
T Consensus 121 ~lGVLVVQqk~~R~y~E~Eve~L~T~A~~lA~iv 154 (756)
T COG3605 121 LLGVLVVQQRELRQYDEDEVEFLVTLAMQLAEIV 154 (756)
T ss_pred eeEEEEEecccccccchHHHHHHHHHHHHHHHHH
Confidence 9999999999999999888777777666555443
No 149
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=79.52 E-value=11 Score=36.27 Aligned_cols=87 Identities=13% Similarity=-0.003 Sum_probs=68.3
Q ss_pred CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEEEEEEEEeec
Q 002210 630 SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVILVVNACCTQD 709 (953)
Q Consensus 630 dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d 709 (953)
+.++-.+-...++++|. ++.|+++.+++.+.....+...+..+.......-..... ...+|....++.-..|+.+
T Consensus 50 ~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~--~~~~g~~~~~e~l~LPL~~ 124 (137)
T PF07310_consen 50 DFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRA--EDADGRYLEYERLLLPLRS 124 (137)
T ss_pred ceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEE--ecCCCCeeEEEEEEcccCC
Confidence 34566688999999995 567999999999999988888888888777666555444 3446778888888999999
Q ss_pred CCCCEEEEEEEE
Q 002210 710 TKENVIGVCFVG 721 (953)
Q Consensus 710 ~~g~v~gvv~v~ 721 (953)
.+|.+..++|+.
T Consensus 125 ~~~~v~rilG~~ 136 (137)
T PF07310_consen 125 DGGTVDRILGAL 136 (137)
T ss_pred CCCCccEEEEec
Confidence 888887777653
No 150
>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=78.64 E-value=8.8 Score=36.00 Aligned_cols=46 Identities=24% Similarity=0.140 Sum_probs=36.5
Q ss_pred ceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEeccHHHHHH
Q 002210 824 DKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHVASPELQYA 871 (953)
Q Consensus 824 ~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~DITerK~~e 871 (953)
....|....++|+ .+..+...++|++|+++|++|+-.|+|.-.++.
T Consensus 68 ~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~ 113 (118)
T PF08348_consen 68 YIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQAQ 113 (118)
T ss_pred ccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHHH
Confidence 3455667788895 456677888999999999999999999876544
No 151
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=77.74 E-value=22 Score=34.18 Aligned_cols=93 Identities=20% Similarity=0.190 Sum_probs=67.6
Q ss_pred eEeecCCc--cEEehhHHHHHHhCCChhhhhcccccccccccccccccccCcchHHHHHHHHHHHhcCCCcceEEEEEEc
Q 002210 755 IFMTDEDG--RCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVISGQDADKILFGFFD 832 (953)
Q Consensus 755 I~~~D~~G--~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~g~~~~~~e~~~~~ 832 (953)
|+..+.+| ++-.+-...++++|+ |+.|+.+.+. +. ++....+...+........+.........
T Consensus 42 ile~~~~~~~r~RLaGt~i~~~~G~---d~tG~~~~el-~~----------~~~~~~~~~~~~~v~~~~~p~~~~~~~~~ 107 (137)
T PF07310_consen 42 ILEVDDPGDFRYRLAGTRIVELFGR---DLTGRRLSEL-FP----------PEDRERVRRAYRAVVERPAPVRARGRAED 107 (137)
T ss_pred EEEEeCCCceEEEEecHHHHHHhCC---CCCCCCHHHh-cC----------hHhHHHHHHHHHHHHcCCceEEEEEEEec
Confidence 44444444 555677888888887 4457776532 22 23344567778888888877777778888
Q ss_pred cCCCEEEEEEEEEEeecCCCCEEEEEEEE
Q 002210 833 QQGKYVEALLSANKRTNAEGKISGILCFL 861 (953)
Q Consensus 833 kdG~~~~v~~s~~pi~d~~G~i~g~v~v~ 861 (953)
.+|+...++...-|+.+.+|.+..++|.+
T Consensus 108 ~~g~~~~~e~l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 108 ADGRYLEYERLLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred CCCCeeEEEEEEcccCCCCCCccEEEEec
Confidence 99999999999999999999998888864
No 152
>PRK10490 sensor protein KdpD; Provisional
Probab=76.00 E-value=1.1e+02 Score=39.53 Aligned_cols=48 Identities=8% Similarity=0.146 Sum_probs=36.3
Q ss_pred eEEEEEEEEeCCcccccccccCCCceeEEEeeecCCC-CCCChhHHHHHHHHHHHHHHhhHH
Q 002210 332 ASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSP-RFVPFPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 332 asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~~~~r~~~~~l~~~~~~~l~~ 392 (953)
+.+.+|+... ++++|.+.+..+.+ +.+..+.+...+.++.+++..+..
T Consensus 596 ~~~~lPl~~~-------------~~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler 644 (895)
T PRK10490 596 PYQILPLKSA-------------QKTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALER 644 (895)
T ss_pred ceEEEEEEEC-------------CEEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 4567999877 89999999877664 456777777888877777766653
No 153
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=73.01 E-value=7.4 Score=43.02 Aligned_cols=87 Identities=13% Similarity=0.062 Sum_probs=60.7
Q ss_pred CccEEEEcCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEE
Q 002210 621 AVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVIL 700 (953)
Q Consensus 621 ~~~I~~~D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v 700 (953)
+..++....|.++++...++.+++||++.+++++.+...++..|...+..+-...+..+....--++. ..+.|++.|+
T Consensus 225 NmFmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~--l~k~ggwvwv 302 (598)
T KOG3559|consen 225 NMFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRF--LLKQGGWVWV 302 (598)
T ss_pred ceEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHH--HHcCCceEEE
Confidence 34567778899999999999999999999999999999998888776665555555322211111111 2345888888
Q ss_pred EEEEEEeec
Q 002210 701 VVNACCTQD 709 (953)
Q Consensus 701 ~v~~~pi~d 709 (953)
.-.+.-+.+
T Consensus 303 qsyat~vHn 311 (598)
T KOG3559|consen 303 QSYATFVHN 311 (598)
T ss_pred EEeeEEEec
Confidence 766655544
No 154
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=72.96 E-value=1e+02 Score=30.44 Aligned_cols=107 Identities=20% Similarity=0.200 Sum_probs=75.3
Q ss_pred hhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccH---HHHHHHHhCCceEeecCCCCCceeeeCCCCCCc
Q 002210 230 LTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQ---ASRFLIMKNKVRMICDCLAPPVKVIQDKKLDQP 306 (953)
Q Consensus 230 ~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~---~ar~ly~~n~~r~i~D~~~~~~~l~~~~~~~~~ 306 (953)
+..+|=|=.|.++ +++-|- .||-|. -+=.+||- -...--.+|++-.|.||++-|=-|-=++
T Consensus 48 l~~~nW~GFYl~~---~~~LvL-------gPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~ghiaCD~----- 111 (163)
T COG1956 48 LPDVNWVGFYLLE---GDELVL-------GPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHAFPGHIACDA----- 111 (163)
T ss_pred ccCCceEEEEEec---CCeEEE-------ecccCC-cceEEeccCcchhHHHHhcCCeEEecccccCCCcccccc-----
Confidence 3447777778777 556654 488886 45566773 1233456799999999888775432222
Q ss_pred cccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCCCChhHHHHHHHHHHHH
Q 002210 307 LSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVF 386 (953)
Q Consensus 307 ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~ 386 (953)
-++|-+++||+++ ||+-|.|=.-..+|-+.+...+..++.++..+
T Consensus 112 ----------------------as~SEIVvPi~~~-------------g~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~~l 156 (163)
T COG1956 112 ----------------------ASNSEIVVPIFKD-------------GKLIGVLDIDSPTPGRFDEEDEAGLEKLAALL 156 (163)
T ss_pred ----------------------ccCceEEEEEEEC-------------CEEEEEEecCCCCcccCCHHHHHHHHHHHHHH
Confidence 3488999999988 99999999888887777777776666665544
Q ss_pred H
Q 002210 387 G 387 (953)
Q Consensus 387 ~ 387 (953)
.
T Consensus 157 ~ 157 (163)
T COG1956 157 E 157 (163)
T ss_pred H
Confidence 3
No 155
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=72.33 E-value=11 Score=43.45 Aligned_cols=94 Identities=10% Similarity=-0.044 Sum_probs=67.7
Q ss_pred CCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHhcccceEEEEEEEcccCCCCCEEEEEEEEEEeec
Q 002210 630 SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLEERNVEIKLRAFGPRETSGPVILVVNACCTQD 709 (953)
Q Consensus 630 dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d 709 (953)
|+..+.+..+...++||...|+.|.+-.+++|-+|.--+.+...+.++.+..--+-++. .+++|++.|+..++..++-
T Consensus 292 Dfa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~--qtk~grw~wvqssarllyk 369 (712)
T KOG3560|consen 292 DFALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYRE--QTKAGRWAWVQSSARLLYK 369 (712)
T ss_pred ccceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEE--eecCCcEEEeeccceeeee
Confidence 45556667778889999999999999999999888765555666666444433333332 5668999999977766654
Q ss_pred CCCCEEEEEEEEEecch
Q 002210 710 TKENVIGVCFVGQDITG 726 (953)
Q Consensus 710 ~~g~v~gvv~v~~DITe 726 (953)
+|+.-.++.+-+-.++
T Consensus 370 -ngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 370 -NGKPDLVIDTHRGLGD 385 (712)
T ss_pred -cCCCCEEEecCCCccc
Confidence 7777777776666666
No 156
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=71.60 E-value=65 Score=33.90 Aligned_cols=136 Identities=15% Similarity=0.097 Sum_probs=71.6
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHh
Q 002210 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMK 281 (953)
Q Consensus 202 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~ 281 (953)
.++.-+|-. +.+++++++++...+++..+.|-|-+--|++++.- +++.. .++..+ .....-...
T Consensus 81 ~~l~l~LL~--a~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~~---~~~~~--------~~~~~~---~~~~~~~~~ 144 (225)
T PF04340_consen 81 HRLVLALLA--ARSLQELLQALDDGLREDFDVDAVRLRLFDDDAAP---GPSLT--------DHVWLS---RDAFAQVFI 144 (225)
T ss_dssp HHHHHHHHC----SHHHHHHHHHHHHHHTS--SEEEEEEE-SS------SEE--------------E----HHHHHHHHC
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHhcCCCeEEEEeecccccc---ccchh--------hccccc---HHHHHHHHH
Confidence 344555555 56999999999999999999999999999987662 11110 111111 111111000
Q ss_pred CCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHH-Hhh--hcCCeeEEEEEEEEeCCcccccccccCCCcee
Q 002210 282 NKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHAR-YME--NMGSIASLVMSVTINEAEDELDNDQEQGRKLW 358 (953)
Q Consensus 282 n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~-yl~--nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LW 358 (953)
..+ . .+.|.+- -.+..-.. .+- .-+|+|...+|+. . ++.+
T Consensus 145 ~~l---~--------------~~~p~~G------~~~~~~~~~lF~~~~~~v~S~AlipL~-~-------------~~~~ 187 (225)
T PF04340_consen 145 DLL---G--------------LQQPYCG------RLSEEEAALLFGDEAAQVGSVALIPLG-S-------------GRPI 187 (225)
T ss_dssp CCH---T--------------T---CCC------S--HHHHHHHHHHCHCC-SEEEEEEEE-S-------------SSEE
T ss_pred HHh---C--------------CCCceeC------CCCcchhHHhcCCCCccccchheeecc-C-------------CCce
Confidence 100 0 0111111 01111111 221 2468898999997 5 7999
Q ss_pred EEEeeecCC-CCCCChhHHHHHHHHHHHHHHhh
Q 002210 359 GLVVCHHTS-PRFVPFPLRYACEFLIQVFGVQV 390 (953)
Q Consensus 359 GLi~~hh~~-pr~~~~~~r~~~~~l~~~~~~~l 390 (953)
|+|+-=... -|+-|----...++|+.+++..|
T Consensus 188 G~LalGS~D~~rF~p~mgT~fL~~La~vv~~~L 220 (225)
T PF04340_consen 188 GLLALGSRDPDRFQPDMGTDFLEQLAEVVSAAL 220 (225)
T ss_dssp EEEEEEESSTTCCCSTTTTHHHHHHHHHHHHHG
T ss_pred EEEEecCCChhhCCCCccHHHHHHHHHHHHHHH
Confidence 999886665 45555555678888888887665
No 157
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=67.30 E-value=4.9 Score=49.47 Aligned_cols=52 Identities=15% Similarity=0.249 Sum_probs=44.1
Q ss_pred HHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCChhhhhcccccccccccccc
Q 002210 743 GIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLKREEAIERMLIGEVFTVKNF 797 (953)
Q Consensus 743 ~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~~eeliGk~~~~~~~~~~~~ 797 (953)
.|++.+.. .+|++..+|+|+||+.....++||..+|++|+.+.+.+++.+.+
T Consensus 99 LmLeAlDG---F~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~ 150 (803)
T KOG3561|consen 99 LILEALDG---FLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDND 150 (803)
T ss_pred HHHHHhcC---eEEEEecCceEEEEecchHHhhCcCHHHHhcchHHHhcCccccC
Confidence 45666644 58889999999999999999999999999999998888776544
No 158
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=66.80 E-value=19 Score=30.84 Aligned_cols=49 Identities=10% Similarity=0.169 Sum_probs=39.2
Q ss_pred HHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHhHhhhh
Q 002210 892 IRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLCQEQLTNIVDDT 940 (953)
Q Consensus 892 isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~~L~~lI~DL 940 (953)
+.|.++|.|..|.+++.+-.....+++.++.+..+..-..-|..+-+.|
T Consensus 2 ~~HRVkNnLq~i~sll~lq~~~~~~~e~~~~L~~~~~RI~aia~vh~~L 50 (76)
T PF07568_consen 2 LHHRVKNNLQIISSLLRLQARRSEDPEAREALEDAQNRIQAIALVHEQL 50 (76)
T ss_pred hHHhHHhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6799999999999999999888888888888888766655555554444
No 159
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=66.40 E-value=2.5e+02 Score=33.94 Aligned_cols=123 Identities=15% Similarity=0.217 Sum_probs=74.9
Q ss_pred HHHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEE-eecCCCCCCccCCCCCCCCccHHHHHHHH
Q 002210 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVA-ECRRPDLEPYLGFHYPATDIPQASRFLIM 280 (953)
Q Consensus 202 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~via-E~~~~~~~~~lg~~~pa~dip~~ar~ly~ 280 (953)
..+..+|.. +..+...|+.+.+++..++|.+.+.+.-+++++...... .+. ++ .+.++
T Consensus 223 y~~~~~l~~--~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-~~------~~~~~------------ 281 (569)
T PRK10600 223 WQANRRLHS--RAPLCERLSPVLNGLQNLTLLRDIELRVYETDDEENHQEFTCQ-SD------MTCDD------------ 281 (569)
T ss_pred HHHHHHHhc--CcchHHHHHHHHHHHHHhcCCCceEEEEeccccccceeeccCC-Cc------cCccc------------
Confidence 334456666 557888999999999999999999998877655542221 111 00 00000
Q ss_pred hCCceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEE
Q 002210 281 KNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGL 360 (953)
Q Consensus 281 ~n~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGL 360 (953)
..|...+... .|-.. + ...+.+||..+ ++.-|.
T Consensus 282 -------~~~~~~~~~~-------~~~~~---------~-----------~~~~~~~l~~~-------------~~~~G~ 314 (569)
T PRK10600 282 -------KGCQLCPRGV-------LPVGD---------R-----------GTTLKWRLSDK-------------HGQYGI 314 (569)
T ss_pred -------cccccccccC-------CCcCC---------C-----------CceEEEEeecC-------------CcceEE
Confidence 0011111000 00000 0 25667899766 788898
Q ss_pred EeeecCCCCCCChhHHHHHHHHHHHHHHhhHH
Q 002210 361 VVCHHTSPRFVPFPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 361 i~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~ 392 (953)
+..+-..++.++++.+.+++.++..++..+..
T Consensus 315 ~~~~~~~~~~l~~~~~~ll~~l~~~l~~~l~~ 346 (569)
T PRK10600 315 LLATLPQGRHLSHDQQQLVDTLVEQLTATLAL 346 (569)
T ss_pred EEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 87654446778888899999988888776643
No 160
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=64.41 E-value=31 Score=36.30 Aligned_cols=58 Identities=14% Similarity=0.090 Sum_probs=40.2
Q ss_pred EeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 002210 862 HVASPELQYALQVQRISEQAAANSLNKLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTS 926 (953)
Q Consensus 862 ~DITerK~~e~elq~~ae~~~~~k~~fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i 926 (953)
.|+|+++..+..+... .+.-.+.-+.|.++|.|..|.+.+.+-.+...++ .++++...
T Consensus 2 ~~~~~~~~~e~~~~~~------~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~ 59 (221)
T COG3920 2 LLTTARKETEERLAES------EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRES 59 (221)
T ss_pred chHHHHHHHHHHHHHH------HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHH
Confidence 3567777655443322 3556788899999999999999999988866564 44444444
No 161
>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=50.85 E-value=64 Score=27.48 Aligned_cols=56 Identities=16% Similarity=0.181 Sum_probs=35.6
Q ss_pred EEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHHHHHHHHHHHHHhCCCCCCC-CeEeecCCccEEe
Q 002210 697 PVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKYTRIQGDYVGIVSSPSALIP-PIFMTDEDGRCLE 766 (953)
Q Consensus 697 ~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L~~se~~~~~i~e~~~~li~-~I~~~D~~G~i~~ 766 (953)
..++..-+.|+++.+|+++|++++-.++.. +..++......-. -++++|.+|.++.
T Consensus 11 ~~~vi~~s~pi~~~~g~~~Gvv~~di~l~~--------------l~~~i~~~~~~~~g~~~ivd~~G~ii~ 67 (81)
T PF02743_consen 11 GQPVITISVPIYDDDGKIIGVVGIDISLDQ--------------LSEIISNIKFGNNGYAFIVDKNGTIIA 67 (81)
T ss_dssp TEEEEEEEEEEEETTTEEEEEEEEEEEHHH--------------HHHHHTTSBBTTTBEEEEEETTSBBCE
T ss_pred CcEEEEEEEEEECCCCCEEEEEEEEeccce--------------eeeEEEeeEECCCEEEEEEECCCCEEE
Confidence 344556789999989999999887555433 2233333222111 2788999998864
No 162
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=50.31 E-value=90 Score=39.57 Aligned_cols=46 Identities=17% Similarity=0.193 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCccEEEEc-CCCcEEecCHHHHHHhCCCcchhcCCCcccc
Q 002210 611 NEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGLTVDQAIGTALVDL 659 (953)
Q Consensus 611 ~~l~~lle~~~~~I~~~D-~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl 659 (953)
.-...++...|.|++++| .+|.|.|+|+.+.+++| .+ ++|+++.++
T Consensus 102 ~~~~~~l~~~p~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 102 QIGEEVLNELPIGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HHHHHHHHhCCceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 334567899999999999 79999999999999988 33 799988864
No 163
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=45.56 E-value=1e+02 Score=29.25 Aligned_cols=111 Identities=13% Similarity=0.119 Sum_probs=58.5
Q ss_pred HHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCCCCceeee-CC
Q 002210 223 LVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ-DK 301 (953)
Q Consensus 223 ~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~~~~~l~~-~~ 301 (953)
++..+.+.+|||++++.....+..+ .-.. .++ +..|....+.|.++....+. | ++. ..
T Consensus 8 ~l~~~~~~~Gf~~~~~~~~~~~~~~-~~~~-------~~~------~~~p~~w~~~Y~~~~~~~~D-----P--v~~~~~ 66 (149)
T PF03472_consen 8 LLERLAARLGFDRFAYGAPSPDPRG-DSDF-------LLI------SNYPDEWLEHYEERGYFRID-----P--VVRHAR 66 (149)
T ss_dssp HHHHHHHCTTTSEEEEEEEETTSCE-CEEE-------EEE------ESS-HHHHHHHHHTTGGGT------H--HHHHHC
T ss_pred HHHHHHHHcCCCEEEEEeccCCCCC-CccE-------EEE------ecCCHHHHHHHHHcCCcCCC-----H--HHHHHH
Confidence 3445668899999999922222211 1111 112 23566888888888742211 1 111 01
Q ss_pred CCCCccccCCccccCC-Ch---hHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCC
Q 002210 302 KLDQPLSLCGSTLRAP-HG---CHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTS 367 (953)
Q Consensus 302 ~~~~~ldl~~s~lr~~-s~---~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~ 367 (953)
....|+.=+....+.- +| ...+..+.+|+++-+++|+.-. +|.. |+|+.....
T Consensus 67 ~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~~~p~~~~------------~g~~-~~~s~~~~~ 123 (149)
T PF03472_consen 67 RSSGPFFWSDLFERDALSPEQRRFFDEARDFGLRSGVSVPLHGP------------DGRF-GALSFAGDE 123 (149)
T ss_dssp HTSSEEEEECHCTSSSSSHHHHHHHHHHHHTTTSEEEEEEEEEC------------CGCE-EEEEEEESS
T ss_pred hCCCCEEEccchhhhhhhHHHHHHHHHHHHcCCCceEEEEeEcC------------CCCE-EEEEEECCC
Confidence 1122332222222211 34 3456788999999999999754 2566 888664333
No 164
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=43.63 E-value=1.8e+02 Score=34.83 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhC
Q 002210 736 RIQGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSG 776 (953)
Q Consensus 736 ~se~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G 776 (953)
+.+.-.+.++.++|- ||+.+|.++++.|+||-+...|+
T Consensus 72 ~~~~~~~~al~nmPi---Gii~~~e~~~veW~Npf~~~if~ 109 (655)
T COG3887 72 QAEKSLEEALTNMPI---GIILFNETNKVEWVNPFASKIFN 109 (655)
T ss_pred HHHHHHHHHHHhCCc---eEEEEcCCCceEEecHHHHHhcC
Confidence 344556777888876 99999999999999999999986
No 165
>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=43.60 E-value=59 Score=30.52 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=33.2
Q ss_pred cCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHHHHHHH
Q 002210 691 PRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKLVMDKY 734 (953)
Q Consensus 691 ~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~~E~~L 734 (953)
..++|+ .+..+...++|.+|+++|++++-.|+|....+.+.|
T Consensus 75 ~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~~~L 116 (118)
T PF08348_consen 75 KTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQAQNFL 116 (118)
T ss_pred cCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHHHHHH
Confidence 344664 455678889999999999999999999987776554
No 166
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=39.44 E-value=41 Score=34.95 Aligned_cols=40 Identities=13% Similarity=0.087 Sum_probs=35.1
Q ss_pred HHHHHHHHHhcCccEEEEcCCCcEEecCHHHHHHhCCCcc
Q 002210 610 TNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVD 649 (953)
Q Consensus 610 ~~~l~~lle~~~~~I~~~D~dg~i~~~N~a~~~l~G~~~~ 649 (953)
.+.+..+++..|.|+++-+.+|.++++|.++.++|.-...
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~~ 57 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQ 57 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcCC
Confidence 3467889999999999999999999999999999975543
No 167
>PF12282 H_kinase_N: Signal transduction histidine kinase; InterPro: IPR022066 This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with PF07568 from PFAM, PF08448 from PFAM, PF02518 from PFAM. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this. ; PDB: 2YKH_B 2YKF_A.
Probab=38.39 E-value=1.7e+02 Score=28.43 Aligned_cols=112 Identities=17% Similarity=0.148 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHH--hcCccEEEEcCCCcEEecCHHHHHHhCCC--cchhcCCCccccccCCcHHHHHHHHHHHhcc
Q 002210 603 IDELRIITNEMVRLIE--TAAVPILAVDASGNVNGWNSKAAELTGLT--VDQAIGTALVDLVAGDSVDVVKNMLSSAFLE 678 (953)
Q Consensus 603 ~~eL~~~~~~l~~lle--~~~~~I~~~D~dg~i~~~N~a~~~l~G~~--~~eliG~~~~dl~~~~~~~~~~~~l~~~l~~ 678 (953)
.+.|......++-+-+ .+...+|+.+.+|.++-+- .+.--++.+ .++++|+.... ...+ .+.+++..
T Consensus 17 i~~L~~l~~~wql~ADLs~aDl~l~v~~~~~~~vvvA-~~rP~t~~t~y~~dvVG~~~~~----~~ep----~v~~a~~t 87 (145)
T PF12282_consen 17 IEWLQRLVADWQLLADLSFADLFLWVPTKDGNAVVVA-QARPSTAPTLYPDDVVGKVALR----ENEP----AVDRALET 87 (145)
T ss_dssp HHHHHHHHHHTHHHHHHHTSEEEEEEE-TTS-EEEEE-EE--SSS--S--S--TT-EE-G----GGSH----HHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHhhcCCEEEEEEcCCCCEEEEE-EeCCCCCCCCCCCCCCCCccCc----cccH----HHHHHHHh
Confidence 4456666666655544 4555777778888643331 112223322 45567765432 2223 44455543
Q ss_pred cceEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecchhHH
Q 002210 679 ERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDITGQKL 729 (953)
Q Consensus 679 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 729 (953)
+......-.. ..+...+..+..|+++ +|+++|++..-.++...+.
T Consensus 88 g~~~~~~~~~-----~~~~~~v~~~~~PI~~-~~~vIaVl~~~~~~~~~~~ 132 (145)
T PF12282_consen 88 GRPVRGGRAV-----WQGGVPVRQEVVPIRR-NGRVIAVLIRETNLSASRT 132 (145)
T ss_dssp ----------------------EEEEEEEEE-TTEEEEEEEEE--GGGS--
T ss_pred CCceecCCcc-----ccCCceeEEEEEEEEE-CCEEEEEEEEEcccccccC
Confidence 4333221111 1233367789999999 5699998886667766554
No 168
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=35.22 E-value=5.6e+02 Score=32.71 Aligned_cols=42 Identities=12% Similarity=-0.004 Sum_probs=32.6
Q ss_pred HHHHHhCCCCCCCCeEeec-CCccEEehhHHHHHHhCCChhhhhccccc
Q 002210 741 YVGIVSSPSALIPPIFMTD-EDGRCLEWNDGMEKLSGLKREEAIERMLI 788 (953)
Q Consensus 741 ~~~i~e~~~~li~~I~~~D-~~G~i~~~N~a~~~l~G~~~eeliGk~~~ 788 (953)
-+.++...|- |++++| .+|.|.|.|+.+.+++| .+ ++|+++.
T Consensus 104 ~~~~l~~~p~---gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 104 GEEVLNELPI---GIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHHhCCc---eEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 3445566655 899999 78999999999999987 23 7888765
No 169
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=32.73 E-value=25 Score=42.94 Aligned_cols=16 Identities=44% Similarity=0.781 Sum_probs=14.3
Q ss_pred hhhCCCeEEEEeecCCCC
Q 002210 229 DLTGYDRVMVYKFHEDEH 246 (953)
Q Consensus 229 ~~~g~DRVmiY~F~~d~~ 246 (953)
.|||++||+| ||||||
T Consensus 614 NLTgAnRVII--fDPdWN 629 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN 629 (923)
T ss_pred ccccCceEEE--ECCCCC
Confidence 5899999999 589997
No 170
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=29.61 E-value=73 Score=39.31 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=43.7
Q ss_pred cCCCcEEecCHHHHHHhCCCcchhcCCCccccccCCcHHHHHHHHHHHh
Q 002210 628 DASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (953)
Q Consensus 628 D~dg~i~~~N~a~~~l~G~~~~eliG~~~~dl~~~~~~~~~~~~l~~~l 676 (953)
...+.+..+..++..++||-+.++||+++..++|++|+..+.+....++
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~ 386 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVL 386 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHH
Confidence 3466778888999999999999999999999999999998888888887
No 171
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=29.48 E-value=35 Score=31.89 Aligned_cols=24 Identities=21% Similarity=0.401 Sum_probs=19.4
Q ss_pred CCCccceEEEEecCCceEEEEccC
Q 002210 76 LIQPFGCMIAVDEQNFTVLGYSEN 99 (953)
Q Consensus 76 ~iQ~~G~ll~~~~~~~~i~~~S~N 99 (953)
-|||||+.+.++..+-=.+|+||=
T Consensus 15 gI~~yGAFV~l~~g~tGLVHISEI 38 (129)
T COG1098 15 GITPYGAFVELEGGKTGLVHISEI 38 (129)
T ss_pred eeEecceEEEecCCCcceEEehHh
Confidence 489999999999854447889973
No 172
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=28.62 E-value=68 Score=27.16 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=18.4
Q ss_pred EEEECCeEEEeCCCCCHHHHHHHH
Q 002210 441 ALYYRGKLWLLGVTPTEEQIKDIA 464 (953)
Q Consensus 441 a~~~~~~~~~~G~~p~~~~~~~l~ 464 (953)
+++.||++...|..|+.++++.++
T Consensus 52 alvIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 52 ALVINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EEEETTEEEEESS--HHHHHHHHH
T ss_pred EEEECCEEEEEecCCCHHHHHHHh
Confidence 468899999999999999877654
No 173
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.84 E-value=1.1e+02 Score=30.07 Aligned_cols=42 Identities=14% Similarity=0.224 Sum_probs=34.1
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Q 002210 888 KLEYIRREIRKPLNGIAFMQNLMGTSDLSEEQKQLLKTSVLC 929 (953)
Q Consensus 888 fla~isHELrnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~ 929 (953)
+.+.+.|++-.|..+|..-++||++..-+++....+....++
T Consensus 18 LcsRvCHDiISPvgAInnGLeLLdeg~addDAm~LIrsSArn 59 (214)
T COG5385 18 LCSRVCHDIISPVGAINNGLELLDEGGADDDAMDLIRSSARN 59 (214)
T ss_pred HHHHHHhhccCcHHHhhchhhhhccCCccHHHHHHHHHHhhh
Confidence 356789999999999999999999977777776666665444
No 174
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=25.54 E-value=3.7e+02 Score=32.28 Aligned_cols=91 Identities=15% Similarity=0.234 Sum_probs=52.7
Q ss_pred HHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCC-hhhhhcccccccccccccccccccCcchHHHHHHHHHH
Q 002210 738 QGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLK-REEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNK 816 (953)
Q Consensus 738 e~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~-~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~ 816 (953)
+..++.+-..+.. ..++++|++|..+-.+. |. +..++|.++. |...+..
T Consensus 88 n~~L~~in~~a~s--s~iYlid~~G~~iaASN-------w~~p~SFVG~nya---------------------fRpYf~~ 137 (603)
T COG4191 88 NRYLEQINEAAGS--SAIYLIDPTGLTLAASN-------WNLPTSFVGRNYA---------------------FRPYFQD 137 (603)
T ss_pred HHHHHHHHhhccC--CeEEEECCCCcEEeecc-------CCCCCcccccCcc---------------------cHHHHHH
Confidence 3344555555443 27999999998876542 22 4445565542 5667888
Q ss_pred HhcCCCcceEEEEEEccCCCEEEEEEEEEEeecCCCCEEEEEEEEEe
Q 002210 817 VISGQDADKILFGFFDQQGKYVEALLSANKRTNAEGKISGILCFLHV 863 (953)
Q Consensus 817 ~~~g~~~~~~e~~~~~kdG~~~~v~~s~~pi~d~~G~i~g~v~v~~D 863 (953)
++.|+....+-... -.|+ +-..-..|+++.+| ++|++++--|
T Consensus 138 Am~gg~~r~yalGt--ts~~--pGyy~a~pV~~~~~-ilGvivvKvd 179 (603)
T COG4191 138 AMAGGSGRFYALGT--TSGR--PGYYLAAPVDDGGG-ILGVIVVKVD 179 (603)
T ss_pred HHhcCCceeEeecc--ccCC--CceeEeeeeccCCc-eeEEEEEEEe
Confidence 88888654443222 2222 22334567665444 8888876655
No 175
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=24.38 E-value=2.4e+02 Score=33.79 Aligned_cols=55 Identities=7% Similarity=0.123 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHh----hcC--CCCCHHHHHHHHHHHHHHHHHHhHhhh
Q 002210 885 SLNKLEYIRREIRKPLNGIAFMQNL----MGT--SDLSEEQKQLLKTSVLCQEQLTNIVDD 939 (953)
Q Consensus 885 k~~fla~isHELrnPL~~I~g~~~L----L~~--~~l~e~~~~~l~~i~~~~~~L~~lI~D 939 (953)
+.+....++||+++|++.+..+..+ +.. ....++..+.+..+.....++.+.+.+
T Consensus 360 ~~~~~~~la~el~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~ 420 (565)
T PRK10935 360 LMEERATIARELHDSLAQVLSYLKIQLTLLKRSLDEDNAKAQSIIAEFDQALSDAYRQLRE 420 (565)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455667899999999888777654 333 233455566676666666666666665
No 176
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.80 E-value=1.1e+02 Score=31.78 Aligned_cols=38 Identities=16% Similarity=0.148 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCCCCCCCeEeecCCccEEehhHHHHHHhCCC
Q 002210 738 QGDYVGIVSSPSALIPPIFMTDEDGRCLEWNDGMEKLSGLK 778 (953)
Q Consensus 738 e~~~~~i~e~~~~li~~I~~~D~~G~i~~~N~a~~~l~G~~ 778 (953)
.+.+.+++...+. |+++-+.+|.+++.|.+|.++|.-.
T Consensus 18 ~~~~~~~i~~~~~---P~CiR~~~g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 18 PESLTAFIDDYSY---PACIRNESGKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHHHcCCC---CeEEECCCCCeeecchHHHHHHHhc
Confidence 3456778888776 8999999999999999999999754
No 177
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.74 E-value=6.4e+02 Score=26.58 Aligned_cols=113 Identities=11% Similarity=0.152 Sum_probs=68.1
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhCCceEeecCCC
Q 002210 213 SGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLA 292 (953)
Q Consensus 213 ~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~D~~~ 292 (953)
+++.+.+++.+.. +.+.+|||.+.+-.... ...+..+..|...++.|..+..-.+ |
T Consensus 15 ~~~~~~~~~~l~~-~~~~~Gf~~~~y~~~~~-------------------~~~~~~~nyP~~W~~~Y~~~~y~~~-D--- 70 (234)
T PRK13870 15 EGDECILKTGLAD-IADHFGFTGYAYLHIQH-------------------RHITAVTNYHREWQSVYFDKKFDAL-D--- 70 (234)
T ss_pred hCCHHHHHHHHHH-HHHHcCCCcEEEEecCC-------------------CCeeEeCCCCHHHHHHHHHCCCccc-C---
Confidence 5677777775544 44556999996543311 1123356789999999999997444 2
Q ss_pred CCceeeeCCCCCCccccCCcc-ccCCChhHH---HHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeee
Q 002210 293 PPVKVIQDKKLDQPLSLCGST-LRAPHGCHA---RYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCH 364 (953)
Q Consensus 293 ~~~~l~~~~~~~~~ldl~~s~-lr~~s~~h~---~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~h 364 (953)
||--. ......|+.=+... ....++... +..+.+|++.=+++||.-. +.-+|++++=
T Consensus 71 -Pvv~~-~~~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~tiPi~~~-------------~g~~~~lS~~ 131 (234)
T PRK13870 71 -PVVKR-ARSRKHIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTA-------------NGSMSMFTLA 131 (234)
T ss_pred -hHHHH-HhcCCCCeecCcccccccCCHHHHHHHHHHHHcCCCCceEEEEECC-------------CCCEEEEEEe
Confidence 32211 11122344443221 123345555 4567889999999999733 3468888863
No 178
>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=22.55 E-value=2.3e+02 Score=24.62 Aligned_cols=48 Identities=17% Similarity=0.101 Sum_probs=0.0
Q ss_pred HHHHHhcccceEEEEEEEcccCCCCCEEEEEEEEEEeecCCCCEEEEEEEEEecc
Q 002210 671 MLSSAFLEERNVEIKLRAFGPRETSGPVILVVNACCTQDTKENVIGVCFVGQDIT 725 (953)
Q Consensus 671 ~l~~~l~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DIT 725 (953)
.+++++..++.....-.. |...=+-+...|+++.+|++++.+++ -|+|
T Consensus 36 VLe~vl~~g~v~r~~P~~------G~Y~G~PViV~PI~~~~g~viaAiGv-VD~t 83 (84)
T PF09884_consen 36 VLEEVLETGKVIRVTPIE------GPYKGVPVIVAPIKDEDGEVIAAIGV-VDLT 83 (84)
T ss_pred HHHHHHHcCCEEEeccCC------cccCCeeEEEEEEEcCCCCEEEEEEE-EEcc
No 179
>PF02070 NMU: Neuromedin U; InterPro: IPR008199 Neuromedin U (NmU) [, ] is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved.; GO: 0006940 regulation of smooth muscle contraction
Probab=22.33 E-value=59 Score=21.15 Aligned_cols=17 Identities=24% Similarity=0.178 Sum_probs=13.9
Q ss_pred hcccCCCCCCccceEEE
Q 002210 69 QRVQRGRLIQPFGCMIA 85 (953)
Q Consensus 69 ~~i~~~g~iQ~~G~ll~ 85 (953)
+..|-||.||+-|..|.
T Consensus 5 ee~QgP~~~qsrgyFlf 21 (25)
T PF02070_consen 5 EEFQGPGGIQSRGYFLF 21 (25)
T ss_pred hhccCCcccccccEEEe
Confidence 45688999999998874
No 180
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=22.06 E-value=2.6e+02 Score=32.69 Aligned_cols=119 Identities=18% Similarity=0.211 Sum_probs=78.5
Q ss_pred HHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccC----CCCCCCCccHHH-HHHHHhCCceEeecCCC
Q 002210 218 LLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLG----FHYPATDIPQAS-RFLIMKNKVRMICDCLA 292 (953)
Q Consensus 218 ~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg----~~~pa~dip~~a-r~ly~~n~~r~i~D~~~ 292 (953)
+=+..+++-|.+.+|.+=|.+ --+..+-.|.| +|.|-.+|-... |.--..|.+ +..|-..
T Consensus 225 es~~~va~Ii~~~~~~~AVai--------------Td~e~ilA~vg~g~dhhi~g~~i~s~~t~~ai~~g~v-v~~~~~e 289 (557)
T COG3275 225 ESLMKVAEIIYEELGAGAVAI--------------TDREKLLAFVGIGDDHHIPGKPIISSLTRKAIKTGEV-VYADGNE 289 (557)
T ss_pred hhHHHHHHHHHHHhCCCeEEe--------------cCHHHHHHhhcccccccCCCCeeccHHHHHHHhhCCE-EEEccch
Confidence 345567777888888887654 33333333433 577877765443 333344443 3333221
Q ss_pred CCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCCCC
Q 002210 293 PPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVP 372 (953)
Q Consensus 293 ~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~ 372 (953)
. |. |. -.-| .+.|.+++|+--+ |+.=|-|--.-+.|+.++
T Consensus 290 ~----~~------------cs---h~~c--------~l~s~lViPL~~~-------------g~ViGTiK~y~~~~~lis 329 (557)
T COG3275 290 V----YE------------CS---HPTC--------KLGSALVIPLRGK-------------GRVIGTIKLYEAKARLIS 329 (557)
T ss_pred h----hc------------cC---CCCC--------CcCCceEeecccC-------------CceeeeEEEEeccHhHhh
Confidence 1 10 00 0023 4588999999644 889999999999999999
Q ss_pred hhHHHHHHHHHHHHHHhhH
Q 002210 373 FPLRYACEFLIQVFGVQVN 391 (953)
Q Consensus 373 ~~~r~~~~~l~~~~~~~l~ 391 (953)
.-.|.+.+-++|.+|.|+.
T Consensus 330 ~~~r~la~Gia~l~SaQie 348 (557)
T COG3275 330 SINRELAEGIAQLLSAQIE 348 (557)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999986
No 181
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=21.14 E-value=4.9e+02 Score=31.55 Aligned_cols=25 Identities=20% Similarity=0.165 Sum_probs=19.8
Q ss_pred EEEEEEEEEEeecCCCCEEEEEEEE
Q 002210 837 YVEALLSANKRTNAEGKISGILCFL 861 (953)
Q Consensus 837 ~~~v~~s~~pi~d~~G~i~g~v~v~ 861 (953)
...+..++.|++|.+|+++|++-+.
T Consensus 155 ~~~lsCsAaPI~D~qG~L~gVLDIS 179 (606)
T COG3284 155 HHGLSCSAAPIFDEQGELVGVLDIS 179 (606)
T ss_pred ccCceeeeeccccCCCcEEEEEEec
Confidence 3456778999999999999877443
No 182
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=20.11 E-value=1.1e+03 Score=26.32 Aligned_cols=63 Identities=14% Similarity=0.148 Sum_probs=35.3
Q ss_pred HHHHHhCCCCCCCC-eEeecCCccEEehhHHHHHHhCCC-hhhhhcccccccccccccccccccCcchHHHHHHHHHHHh
Q 002210 741 YVGIVSSPSALIPP-IFMTDEDGRCLEWNDGMEKLSGLK-REEAIERMLIGEVFTVKNFGCRVKNHDTLTKLRIVMNKVI 818 (953)
Q Consensus 741 ~~~i~e~~~~li~~-I~~~D~~G~i~~~N~a~~~l~G~~-~eeliGk~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~ 818 (953)
.++++.+..-..+| +|++|.+|+=+ . .+ .-+..|+++| ++.+++.-.-+...+.++.
T Consensus 82 vk~iLt~ldyG~DGYFF~YD~~G~Nl---------v-HPrQpelvG~nlw-----------~L~D~rGd~~Iq~Li~kAq 140 (459)
T COG4564 82 VKAILTNLDYGSDGYFFVYDYQGTNL---------V-HPRQPELVGQNLW-----------QLTDPRGDRVIQALIAKAQ 140 (459)
T ss_pred HHHHHhhcccCCCceEEEEecCCccc---------c-CCCCccccccchh-----------hccCCCcChHHHHHHHHHH
Confidence 44555554332234 67778887532 1 22 3467788887 3333333334666777787
Q ss_pred cCCCcc
Q 002210 819 SGQDAD 824 (953)
Q Consensus 819 ~g~~~~ 824 (953)
+|+...
T Consensus 141 ~GGG~~ 146 (459)
T COG4564 141 EGGGLH 146 (459)
T ss_pred hCCCeE
Confidence 877543
No 183
>PRK04158 transcriptional repressor CodY; Validated
Probab=20.09 E-value=9.1e+02 Score=25.93 Aligned_cols=48 Identities=8% Similarity=0.104 Sum_probs=36.5
Q ss_pred eeEEEEEEEEeCCcccccccccCCCceeEEEeeecCCCCCCChhHHHHHHHHHHHHHHhhHH
Q 002210 331 IASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNK 392 (953)
Q Consensus 331 ~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~ 392 (953)
+=.+++||..+ |..-|-|+.-.+... ...+...++|..+-+.+++|-.
T Consensus 110 ~~~tIvPI~gg-------------GeRLGTLvl~r~~~~-f~~dDliL~EyaATVVgLEIlR 157 (256)
T PRK04158 110 KLTTIVPIIGG-------------GERLGTLILARFDKE-FTDDDLILAEYAATVVGMEILR 157 (256)
T ss_pred ceEEEEEEecC-------------CeEEEEEEEEecCCC-CCHHHHHHHHHHHHHHHHHHHH
Confidence 34678999977 888888888776632 3455678999999999998854
No 184
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=20.05 E-value=1.8e+03 Score=27.94 Aligned_cols=128 Identities=11% Similarity=0.111 Sum_probs=73.2
Q ss_pred HHHHHhccCCCCCHHHHHHHHHHHHHhhhCCCeEEEEeecCCCCceEEEeecCCCCCCccCCCCCCCCccHHHHHHHHhC
Q 002210 203 KAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKN 282 (953)
Q Consensus 203 ~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~DRVmiY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n 282 (953)
.+-.+|.. +.+.++++.++.+.|.++++- ||.+|=-++++.- ..+.+|.. +++.-+..-..-
T Consensus 514 e~s~~L~~--a~t~~~vl~~~~~qi~~~~~~-~v~i~l~~~~~~~--------------~~~~~~~~-l~~~d~aaa~W~ 575 (890)
T COG2205 514 EFSKKLAG--ARTREDILAAAGQQIASLLNQ-RVVILLPDDNGKL--------------QPLGNPDG-LSADDRAAAQWA 575 (890)
T ss_pred HHHHHHHh--cCCHHHHHHHHHHHHHHHhCC-ceEEEEecCCccc--------------ccccCCcc-ccHHHHHHhhch
Confidence 34455666 679999999999999999986 5666655544322 12233332 444433321110
Q ss_pred CceEeecCCCCCceeeeCCCCCCccccCCccccCCChhHHHHhhhcCCeeEEEEEEEEeCCcccccccccCCCceeEEEe
Q 002210 283 KVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVV 362 (953)
Q Consensus 283 ~~r~i~D~~~~~~~l~~~~~~~~~ldl~~s~lr~~s~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~LWGLi~ 362 (953)
+ ..+++=-.+-.||. |++ .+-+||-.. ++--|++.
T Consensus 576 ~------------------~~~~~AG~gTdTlp-------------g~~-~~~lPl~~~-------------~~~~gvlg 610 (890)
T COG2205 576 F------------------ENGKPAGAGTDTLP-------------GAK-YLYLPLKSG-------------GKVLGVLG 610 (890)
T ss_pred h------------------hCCCccccCCCCCC-------------CCc-eeEeecccC-------------CceEEEEE
Confidence 0 01111111112232 222 345799766 78888888
Q ss_pred eecCCCCCCChhHHHHHHHHHHHHHHhhHHH
Q 002210 363 CHHTSPRFVPFPLRYACEFLIQVFGVQVNKE 393 (953)
Q Consensus 363 ~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~ 393 (953)
.+....-...++.|...+.++...++.|...
T Consensus 611 v~~~~~~ll~p~~~rlL~a~~~q~AlAler~ 641 (890)
T COG2205 611 VEPGLSPLLAPEQRRLLDAVLTQIALALERV 641 (890)
T ss_pred ecCCCCccCChHHHHHHHHHHHHHHHHHHHH
Confidence 8776433455666777777777788887643
Done!