Query 002152
Match_columns 959
No_of_seqs 778 out of 3792
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 17:41:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002152.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002152hhsearch_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 3E-125 6E-130 1036.4 42.3 510 79-617 11-528 (750)
2 PF00360 PHY: Phytochrome regi 100.0 4.4E-33 9.6E-38 280.6 12.4 168 416-585 6-178 (182)
3 PRK13560 hypothetical protein; 100.0 1.1E-29 2.4E-34 319.9 38.2 329 606-946 192-659 (807)
4 TIGR02938 nifL_nitrog nitrogen 99.9 5.1E-25 1.1E-29 261.0 23.9 310 618-946 4-333 (494)
5 PF08446 PAS_2: PAS fold; Int 99.9 1.2E-24 2.6E-29 200.9 7.5 105 84-197 3-110 (110)
6 PRK09776 putative diguanylate 99.9 1.1E-22 2.3E-27 264.9 28.5 265 607-887 272-537 (1092)
7 PRK11091 aerobic respiration c 99.9 2.2E-22 4.7E-27 252.2 23.3 212 732-958 138-350 (779)
8 PRK09776 putative diguanylate 99.9 7.5E-22 1.6E-26 257.0 28.3 265 606-884 398-664 (1092)
9 PRK13560 hypothetical protein; 99.9 2.7E-20 5.8E-25 234.8 28.9 263 606-886 55-332 (807)
10 TIGR02040 PpsR-CrtJ transcript 99.9 1.8E-20 3.8E-25 219.3 24.9 242 610-878 125-368 (442)
11 PRK11359 cyclic-di-GMP phospho 99.8 4.8E-18 1E-22 214.1 27.5 242 618-880 12-257 (799)
12 TIGR02040 PpsR-CrtJ transcript 99.8 1.1E-17 2.4E-22 195.7 22.2 232 624-880 2-249 (442)
13 PRK13559 hypothetical protein; 99.7 2.9E-15 6.3E-20 170.6 21.3 186 746-953 40-229 (361)
14 COG5002 VicK Signal transducti 99.7 1.5E-15 3.3E-20 158.5 15.9 197 731-956 92-292 (459)
15 PRK13557 histidine kinase; Pro 99.6 4.3E-15 9.2E-20 178.5 21.2 198 743-953 24-230 (540)
16 PRK11006 phoR phosphate regulo 99.6 2.8E-14 6E-19 166.5 17.7 192 728-956 77-270 (430)
17 PRK11360 sensory histidine kin 99.6 1.4E-13 3.1E-18 167.3 23.7 200 740-955 253-454 (607)
18 PRK11073 glnL nitrogen regulat 99.5 1.4E-13 3.1E-18 155.8 18.5 185 749-953 7-192 (348)
19 TIGR02966 phoR_proteo phosphat 99.5 8.8E-14 1.9E-18 155.8 16.5 177 745-956 2-181 (333)
20 PRK09959 hybrid sensory histid 99.4 2.1E-12 4.6E-17 169.8 21.1 217 730-957 557-779 (1197)
21 PF13426 PAS_9: PAS domain; PD 99.4 1.4E-12 3E-17 119.2 11.9 104 628-736 1-104 (104)
22 PF08448 PAS_4: PAS fold; Int 99.4 1.4E-12 3E-17 120.6 11.7 110 624-739 1-110 (110)
23 PF01590 GAF: GAF domain; Int 99.4 2.3E-12 4.9E-17 127.3 13.3 153 230-396 1-154 (154)
24 PRK10841 hybrid sensory kinase 99.4 1.2E-11 2.6E-16 156.1 22.5 183 742-958 327-514 (924)
25 PF13426 PAS_9: PAS domain; PD 99.4 2E-12 4.3E-17 118.2 10.9 103 763-873 2-104 (104)
26 PF00989 PAS: PAS fold; Inter 99.3 6.9E-12 1.5E-16 116.6 11.8 112 618-734 1-113 (113)
27 PRK11091 aerobic respiration c 99.3 2.5E-11 5.3E-16 152.6 18.5 144 602-750 139-282 (779)
28 PF00989 PAS: PAS fold; Inter 99.3 2.4E-11 5.3E-16 112.8 13.2 112 749-871 1-113 (113)
29 PRK10618 phosphotransfer inter 99.3 5E-11 1.1E-15 148.5 19.7 179 740-958 334-517 (894)
30 PF08448 PAS_4: PAS fold; Int 99.3 1.5E-11 3.3E-16 113.6 11.3 110 755-876 1-110 (110)
31 PF00512 HisKA: His Kinase A ( 99.2 1.9E-11 4.1E-16 103.1 7.0 65 891-955 1-68 (68)
32 PRK11086 sensory histidine kin 99.2 1.6E-09 3.4E-14 130.5 22.3 202 712-946 146-390 (542)
33 COG3852 NtrB Signal transducti 99.1 1.1E-09 2.3E-14 114.0 16.0 176 753-947 11-187 (363)
34 smart00065 GAF Domain present 99.1 2E-09 4.3E-14 103.4 16.6 140 230-399 1-142 (149)
35 PRK10060 RNase II stability mo 99.1 1.9E-09 4.2E-14 132.3 19.9 169 702-885 69-237 (663)
36 PRK13559 hypothetical protein; 99.1 1.5E-09 3.3E-14 123.5 16.2 132 616-752 41-175 (361)
37 PRK13558 bacterio-opsin activa 99.0 3.1E-09 6.7E-14 131.3 17.4 137 618-759 148-287 (665)
38 COG5000 NtrY Signal transducti 99.0 6E-09 1.3E-13 117.5 17.0 187 743-957 364-558 (712)
39 PRK13557 histidine kinase; Pro 99.0 3.4E-09 7.5E-14 127.3 16.1 131 613-748 25-158 (540)
40 TIGR00229 sensory_box PAS doma 98.9 9.9E-09 2.1E-13 92.7 12.6 120 618-743 3-123 (124)
41 COG3829 RocR Transcriptional r 98.9 1.9E-08 4.2E-13 113.5 17.1 224 621-880 4-228 (560)
42 PRK10060 RNase II stability mo 98.9 1.2E-08 2.6E-13 125.3 16.9 129 613-747 106-236 (663)
43 PF08447 PAS_3: PAS fold; Int 98.9 5.1E-09 1.1E-13 93.5 9.9 90 774-868 1-91 (91)
44 PRK11359 cyclic-di-GMP phospho 98.9 2.6E-08 5.7E-13 125.9 19.3 125 615-744 133-258 (799)
45 PRK13558 bacterio-opsin activa 98.9 3.8E-08 8.3E-13 121.6 17.6 123 751-884 150-275 (665)
46 PRK15053 dpiB sensor histidine 98.8 5E-07 1.1E-11 109.0 24.3 199 712-946 147-385 (545)
47 TIGR02938 nifL_nitrog nitrogen 98.8 1.5E-08 3.2E-13 120.1 10.6 125 749-884 4-128 (494)
48 TIGR00229 sensory_box PAS doma 98.8 5.2E-08 1.1E-12 87.9 11.8 119 749-879 3-122 (124)
49 PF08447 PAS_3: PAS fold; Int 98.8 3.8E-08 8.3E-13 87.8 9.4 86 640-731 1-91 (91)
50 COG3290 CitA Signal transducti 98.7 2.1E-06 4.5E-11 97.4 24.4 199 705-934 133-371 (537)
51 PF13596 PAS_10: PAS domain; P 98.7 3.8E-08 8.3E-13 90.8 8.6 106 620-735 1-106 (106)
52 KOG3558 Hypoxia-inducible fact 98.7 1.5E-07 3.3E-12 107.3 14.7 226 621-873 122-378 (768)
53 COG2203 FhlA FOG: GAF domain [ 98.7 6.8E-08 1.5E-12 95.9 10.3 153 216-399 6-165 (175)
54 PF13492 GAF_3: GAF domain; PD 98.6 7.3E-07 1.6E-11 84.8 15.0 128 230-397 1-128 (129)
55 PRK11360 sensory histidine kin 98.6 4.6E-07 1E-11 110.3 15.2 132 611-749 255-386 (607)
56 PF13185 GAF_2: GAF domain; PD 98.5 1.6E-06 3.5E-11 84.6 14.5 137 230-397 3-148 (148)
57 cd00130 PAS PAS domain; PAS mo 98.5 1.3E-06 2.9E-11 74.6 12.2 103 627-734 1-103 (103)
58 TIGR02966 phoR_proteo phosphat 98.5 1.1E-06 2.5E-11 98.1 12.7 114 614-745 2-115 (333)
59 PF12860 PAS_7: PAS fold 98.4 6.5E-07 1.4E-11 84.0 8.3 104 624-742 1-115 (115)
60 TIGR01817 nifA Nif-specific re 98.4 2.2E-05 4.7E-10 94.1 23.2 153 214-398 5-158 (534)
61 cd00130 PAS PAS domain; PAS mo 98.4 3.7E-06 8E-11 71.8 12.0 100 764-871 4-103 (103)
62 COG2202 AtoS FOG: PAS/PAC doma 98.4 3.8E-05 8.3E-10 76.4 20.3 226 632-876 3-230 (232)
63 TIGR02956 TMAO_torS TMAO reduc 98.4 6.6E-07 1.4E-11 115.7 8.6 77 882-958 454-531 (968)
64 COG5002 VicK Signal transducti 98.4 2.1E-06 4.6E-11 91.0 10.6 130 606-747 99-228 (459)
65 PF13596 PAS_10: PAS domain; P 98.3 3.3E-06 7.2E-11 77.9 10.1 106 751-872 1-106 (106)
66 PRK11073 glnL nitrogen regulat 98.3 3.7E-06 8E-11 95.2 12.6 116 619-747 8-124 (348)
67 PRK15347 two component system 98.3 8.3E-07 1.8E-11 114.1 8.1 77 882-958 388-465 (921)
68 PRK11388 DNA-binding transcrip 98.2 1.4E-05 3E-10 98.0 16.2 220 619-874 63-309 (638)
69 COG2205 KdpD Osmosensitive K+ 98.2 1.4E-06 3.1E-11 102.3 7.1 69 890-958 658-730 (890)
70 smart00388 HisKA His Kinase A 98.2 1.8E-06 4E-11 71.2 5.8 64 892-955 2-66 (66)
71 PRK11107 hybrid sensory histid 98.2 2.2E-06 4.8E-11 110.2 8.3 77 882-958 283-360 (919)
72 PRK05022 anaerobic nitric oxid 98.2 0.00018 4E-09 85.4 23.3 214 217-462 7-221 (509)
73 PRK15429 formate hydrogenlyase 98.2 0.00019 4E-09 88.7 24.2 147 228-400 197-345 (686)
74 PRK11006 phoR phosphate regulo 98.2 1.2E-05 2.6E-10 93.9 12.5 118 608-745 88-205 (430)
75 PF14598 PAS_11: PAS domain; P 98.1 2.6E-05 5.7E-10 72.4 11.7 102 765-874 5-109 (111)
76 COG3604 FhlA Transcriptional r 98.1 0.00013 2.8E-09 82.0 18.1 205 229-462 47-257 (550)
77 PRK11061 fused phosphoenolpyru 98.1 8.6E-05 1.9E-09 91.4 17.9 151 217-398 6-156 (748)
78 PRK10820 DNA-binding transcrip 98.1 7.2E-05 1.6E-09 88.9 16.3 112 613-739 75-190 (520)
79 PRK11466 hybrid sensory histid 98.0 9.6E-06 2.1E-10 104.3 9.2 73 884-956 436-509 (914)
80 PF14598 PAS_11: PAS domain; P 98.0 5.6E-05 1.2E-09 70.2 10.6 101 631-736 5-108 (111)
81 PF12860 PAS_7: PAS fold 98.0 2.4E-05 5.2E-10 73.2 8.1 110 756-878 2-114 (115)
82 PRK11086 sensory histidine kin 98.0 7.4E-05 1.6E-09 90.0 14.5 121 611-749 214-338 (542)
83 PRK09303 adaptive-response sen 97.9 2.1E-05 4.6E-10 90.2 7.9 71 887-957 146-224 (380)
84 KOG3559 Transcriptional regula 97.8 7.4E-05 1.6E-09 80.1 9.4 211 621-860 82-315 (598)
85 COG5000 NtrY Signal transducti 97.8 0.00021 4.6E-09 81.7 13.0 132 599-743 351-483 (712)
86 COG3290 CitA Signal transducti 97.7 0.00036 7.8E-09 79.6 12.5 120 611-747 208-330 (537)
87 cd00082 HisKA Histidine Kinase 97.7 0.00012 2.6E-09 59.7 6.5 61 891-951 3-65 (65)
88 COG3829 RocR Transcriptional r 97.6 0.00023 5E-09 81.1 10.1 126 613-752 112-237 (560)
89 COG2202 AtoS FOG: PAS/PAC doma 97.6 0.00087 1.9E-08 66.4 13.0 127 608-740 102-231 (232)
90 COG4191 Signal transduction hi 97.5 0.0062 1.3E-07 70.3 20.0 59 893-951 385-447 (603)
91 PRK10490 sensor protein KdpD; 97.4 0.00027 5.8E-09 89.7 8.7 70 889-958 661-733 (895)
92 KOG3560 Aryl-hydrocarbon recep 97.4 0.00054 1.2E-08 76.4 9.3 229 621-873 114-385 (712)
93 PRK15053 dpiB sensor histidine 97.4 0.0023 5E-08 77.3 15.8 122 610-749 214-337 (545)
94 PRK13837 two-component VirA-li 97.4 0.00041 8.9E-09 88.0 8.8 66 891-956 449-516 (828)
95 KOG0501 K+-channel KCNQ [Inorg 97.3 0.00064 1.4E-08 76.5 8.8 100 771-876 39-138 (971)
96 COG4251 Bacteriophytochrome (l 97.3 0.00072 1.6E-08 77.6 9.3 74 882-955 514-591 (750)
97 PRK10820 DNA-binding transcrip 97.3 0.001 2.2E-08 79.2 10.8 110 744-874 75-188 (520)
98 PF13188 PAS_8: PAS domain; PD 97.3 0.00032 7E-09 57.9 4.2 43 618-664 1-43 (64)
99 PRK11388 DNA-binding transcrip 97.1 0.02 4.4E-07 70.4 19.5 114 613-740 198-312 (638)
100 KOG0501 K+-channel KCNQ [Inorg 97.1 0.0012 2.6E-08 74.3 7.8 116 619-739 15-138 (971)
101 PRK09959 hybrid sensory histid 97.1 0.0058 1.3E-07 81.1 15.3 135 606-748 564-702 (1197)
102 PRK15429 formate hydrogenlyase 96.9 0.039 8.4E-07 68.4 19.9 203 216-450 11-224 (686)
103 KOG1229 3'5'-cyclic nucleotide 96.7 0.0015 3.3E-08 71.0 4.4 115 741-866 150-264 (775)
104 PRK10604 sensor protein RstB; 96.6 0.0032 6.9E-08 73.7 6.9 65 888-957 208-273 (433)
105 PRK10815 sensor protein PhoQ; 96.6 0.0046 1E-07 73.3 7.8 65 890-956 264-330 (485)
106 PF13188 PAS_8: PAS domain; PD 96.6 0.0027 6E-08 52.3 4.2 41 749-796 1-41 (64)
107 PRK10364 sensor protein ZraS; 96.6 0.0065 1.4E-07 71.6 8.9 64 891-954 236-301 (457)
108 COG2461 Uncharacterized conser 96.5 0.006 1.3E-07 66.6 7.2 115 618-743 290-404 (409)
109 smart00091 PAS PAS domain. PAS 96.4 0.0089 1.9E-07 46.0 5.9 63 619-682 2-64 (67)
110 PF08670 MEKHLA: MEKHLA domain 96.2 0.065 1.4E-06 51.9 11.7 110 618-734 32-145 (148)
111 TIGR02916 PEP_his_kin putative 96.1 0.21 4.4E-06 62.1 18.9 152 217-399 308-460 (679)
112 TIGR03785 marine_sort_HK prote 96.0 0.018 3.8E-07 71.5 9.0 68 888-955 481-549 (703)
113 KOG3558 Hypoxia-inducible fact 95.7 0.015 3.4E-07 67.5 5.8 84 632-720 278-361 (768)
114 PRK10337 sensor protein QseC; 95.5 0.038 8.3E-07 64.8 8.4 65 891-955 236-302 (449)
115 COG4192 Signal transduction hi 95.5 0.034 7.4E-07 61.8 7.2 64 893-956 452-519 (673)
116 TIGR02916 PEP_his_kin putative 95.4 0.13 2.8E-06 63.9 13.0 56 892-947 475-531 (679)
117 PRK10549 signal transduction h 95.2 0.033 7.2E-07 65.6 6.9 68 889-957 237-305 (466)
118 PRK09467 envZ osmolarity senso 95.2 0.037 8E-07 64.6 7.0 64 886-954 223-287 (435)
119 PRK09835 sensor kinase CusS; P 95.1 0.052 1.1E-06 64.2 8.3 69 889-957 259-329 (482)
120 PRK11100 sensory histidine kin 94.9 0.058 1.3E-06 63.6 7.9 66 891-956 255-321 (475)
121 TIGR01386 cztS_silS_copS heavy 94.9 0.054 1.2E-06 63.5 7.4 68 890-957 239-308 (457)
122 TIGR02373 photo_yellow photoac 94.8 0.16 3.5E-06 47.1 8.4 60 624-683 22-81 (124)
123 PRK10755 sensor protein BasS/P 94.7 0.071 1.5E-06 60.5 7.6 60 891-955 136-196 (356)
124 COG3852 NtrB Signal transducti 94.7 0.35 7.6E-06 51.7 11.7 112 621-743 10-122 (363)
125 PRK09470 cpxA two-component se 94.5 0.07 1.5E-06 62.7 7.1 64 888-954 239-303 (461)
126 smart00086 PAC Motif C-termina 94.3 0.24 5.1E-06 33.7 7.0 40 834-873 3-42 (43)
127 PF08670 MEKHLA: MEKHLA domain 94.3 0.86 1.9E-05 44.2 12.6 110 749-870 32-144 (148)
128 TIGR02851 spore_V_T stage V sp 94.2 1.7 3.8E-05 43.9 15.2 126 230-397 53-180 (180)
129 COG2461 Uncharacterized conser 94.1 0.094 2E-06 57.6 6.3 113 749-878 290-402 (409)
130 smart00091 PAS PAS domain. PAS 93.7 0.2 4.3E-06 38.0 6.1 45 751-798 3-47 (67)
131 PRK10841 hybrid sensory kinase 93.5 0.86 1.9E-05 58.5 14.6 114 608-749 324-438 (924)
132 TIGR02373 photo_yellow photoac 93.5 0.37 8E-06 44.8 8.1 46 755-803 22-67 (124)
133 PRK11644 sensory histidine kin 93.4 0.27 5.8E-06 58.5 9.1 59 891-949 301-361 (495)
134 KOG1229 3'5'-cyclic nucleotide 92.7 0.097 2.1E-06 57.5 3.6 104 620-728 159-263 (775)
135 COG3283 TyrR Transcriptional r 92.5 0.54 1.2E-05 51.4 8.6 54 618-672 80-133 (511)
136 KOG3753 Circadian clock protei 92.3 0.4 8.7E-06 57.4 8.1 201 630-854 194-418 (1114)
137 COG0642 BaeS Signal transducti 91.6 0.26 5.7E-06 54.1 5.7 64 891-955 114-178 (336)
138 KOG0519 Sensory transduction h 90.9 0.032 6.9E-07 69.6 -2.9 71 886-958 213-286 (786)
139 PRK13837 two-component VirA-li 90.8 12 0.00025 47.9 19.9 134 230-398 293-427 (828)
140 smart00086 PAC Motif C-termina 90.2 1.4 3E-05 29.5 6.6 36 701-736 7-42 (43)
141 COG1956 GAF domain-containing 89.4 16 0.00035 35.7 14.5 116 238-395 40-159 (163)
142 PRK10618 phosphotransfer inter 88.5 5 0.00011 51.2 13.9 46 608-653 333-379 (894)
143 KOG3560 Aryl-hydrocarbon recep 88.1 1.6 3.4E-05 49.9 7.8 94 637-736 292-385 (712)
144 KOG3559 Transcriptional regula 86.5 1.4 3E-05 48.3 6.1 87 629-720 226-312 (598)
145 PRK10490 sensor protein KdpD; 86.2 35 0.00076 43.9 19.7 49 346-398 595-644 (895)
146 COG3284 AcoR Transcriptional a 86.1 3.8 8.2E-05 48.6 9.9 182 603-796 59-267 (606)
147 KOG3561 Aryl-hydrocarbon recep 85.3 0.37 8E-06 58.8 1.2 97 768-872 378-476 (803)
148 KOG3561 Aryl-hydrocarbon recep 85.2 0.49 1.1E-05 57.7 2.2 60 74-149 90-150 (803)
149 COG3605 PtsP Signal transducti 85.0 6 0.00013 46.1 10.4 147 216-397 5-155 (756)
150 PF07310 PAS_5: PAS domain; I 83.3 8.1 0.00018 37.2 9.4 85 639-731 52-136 (137)
151 PF14689 SPOB_a: Sensor_kinase 82.9 7.2 0.00016 31.9 7.5 48 894-945 14-61 (62)
152 COG3283 TyrR Transcriptional r 80.5 5.6 0.00012 43.8 7.6 47 749-798 80-126 (511)
153 PF07310 PAS_5: PAS domain; I 79.0 14 0.0003 35.6 9.4 85 773-868 52-136 (137)
154 PF04340 DUF484: Protein of un 75.6 42 0.00092 35.3 12.7 136 218-397 82-221 (225)
155 PRK10600 nitrate/nitrite senso 73.4 1.3E+02 0.0029 36.4 18.1 124 217-399 223-347 (569)
156 PF08348 PAS_6: YheO-like PAS 73.0 14 0.0003 34.6 7.2 45 830-876 67-111 (118)
157 PF07568 HisKA_2: Histidine ki 72.2 12 0.00027 31.9 6.2 49 899-947 2-50 (76)
158 COG3887 Predicted signaling pr 69.8 40 0.00087 39.9 11.3 38 616-653 73-110 (655)
159 COG3920 Signal transduction hi 64.4 23 0.0005 37.2 7.6 61 870-937 3-63 (221)
160 PF08348 PAS_6: YheO-like PAS 61.8 30 0.00065 32.4 7.0 42 701-744 75-116 (118)
161 PRK14538 putative bifunctional 60.2 31 0.00067 43.5 8.9 44 618-664 102-146 (838)
162 PF08446 PAS_2: PAS fold; Int 55.0 11 0.00024 34.8 2.9 46 630-676 17-66 (110)
163 PRK13719 conjugal transfer tra 47.3 27 0.00059 36.2 4.5 39 618-656 19-57 (217)
164 COG3275 LytS Putative regulato 45.2 68 0.0015 37.1 7.6 119 234-398 226-349 (557)
165 PF14827 Cache_3: Sensory doma 36.6 70 0.0015 29.6 5.3 74 763-871 40-113 (116)
166 COG4564 Signal transduction hi 36.2 4.1E+02 0.0088 29.5 11.2 68 749-833 80-148 (459)
167 COG5385 Uncharacterized protei 35.8 64 0.0014 31.6 4.8 44 895-941 18-61 (214)
168 COG3284 AcoR Transcriptional a 35.6 1E+02 0.0023 36.9 7.5 110 744-868 69-179 (606)
169 PF03472 Autoind_bind: Autoind 34.9 3.9E+02 0.0085 25.1 11.3 109 238-373 8-123 (149)
170 PF09884 DUF2111: Uncharacteri 33.2 1.2E+02 0.0026 26.2 5.4 47 821-872 37-83 (84)
171 KOG0387 Transcription-coupled 33.2 23 0.0005 43.1 1.7 32 244-298 614-645 (923)
172 KOG3753 Circadian clock protei 33.1 69 0.0015 39.5 5.5 79 635-718 338-419 (1114)
173 PRK04158 transcriptional repre 32.7 4.3E+02 0.0093 28.3 10.7 49 346-399 110-158 (256)
174 PF02743 Cache_1: Cache domain 32.3 67 0.0015 27.3 4.1 56 708-777 12-68 (81)
175 PRK10935 nitrate/nitrite senso 31.7 4.5E+02 0.0098 31.5 12.8 56 891-946 359-420 (565)
176 PF09884 DUF2111: Uncharacteri 31.6 78 0.0017 27.3 4.1 33 702-735 51-83 (84)
177 COG3887 Predicted signaling pr 30.7 2.8E+02 0.0061 33.2 9.7 37 747-786 73-109 (655)
178 COG1098 VacB Predicted RNA bin 27.9 39 0.00084 31.6 1.8 26 92-117 15-40 (129)
179 PRK14538 putative bifunctional 25.8 5.2E+02 0.011 32.9 11.7 57 736-798 82-146 (838)
180 PF13192 Thioredoxin_3: Thiore 25.1 87 0.0019 26.4 3.5 24 447-470 52-75 (76)
181 PF02070 NMU: Neuromedin U; I 24.4 52 0.0011 21.3 1.4 16 86-101 6-21 (25)
182 COG4191 Signal transduction hi 24.1 5.8E+02 0.012 30.7 10.8 92 748-870 88-179 (603)
183 PF06785 UPF0242: Uncharacteri 22.0 2E+02 0.0043 31.6 6.0 91 750-854 284-378 (401)
184 PRK10963 hypothetical protein; 21.9 9.3E+02 0.02 25.2 13.5 50 344-398 168-218 (223)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=2.6e-125 Score=1036.44 Aligned_cols=510 Identities=33% Similarity=0.568 Sum_probs=450.5
Q ss_pred hHHHH-HhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCCCcccccccccccCCccccccCCchHHHHHHHHhc
Q 002152 79 QITAY-LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAAS 157 (959)
Q Consensus 79 ~~~~~-~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~~ 157 (959)
.+|.| .+|||+||+||||||||++|+.++.|+|+|+||..+||+.| ++++|+++.++|+..+...++.++..
T Consensus 11 ~l~nce~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~-------e~l~~~tl~~vl~~~qv~~l~~~l~~ 83 (750)
T COG4251 11 TLTNCEREPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREP-------EDLLGRTLGAVLTSEQVPPLQSALTV 83 (750)
T ss_pred cccccccCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCCh-------hhhhcCCHHHhcchhhccHHHHhccc
Confidence 44555 66699999999999999999999999999999999999998 68999999999999999999999998
Q ss_pred ccccccCcceeeccCCCCCcceEEEEEeeCCEEEEEeccCCCCCCcchhhhHHHHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 002152 158 REISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDT 237 (959)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~E~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~ 237 (959)
+.....||..+.. + .+..||+++||+++.+|+||||....+.. ..+.++.++..++.+|++ +.++.++|+.
T Consensus 84 ~~~~~~np~~~w~--~-~~~~fDv~~HR~~~llIlEfEp~~t~e~~----~~l~f~h~~k~a~~~lq~--a~~l~~l~~~ 154 (750)
T COG4251 84 GGLTTLNPTKMWT--R-KGGSFDVSAHRSKELLILEFEPAGTGETA----SFLGFYHLAKLAMNRLQS--AANLRDLLSR 154 (750)
T ss_pred cCcccCCchhhhh--h-cCCceeEEEEecCcEEEEEEecCcccccc----cccchHHHHHHHHHHHhc--CccHHHHHHH
Confidence 8888888855433 1 23389999999999999999997554421 233567888889999999 5599999999
Q ss_pred HHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCCccccc--c
Q 002152 238 VVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQ--S 315 (959)
Q Consensus 238 ~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~~~l~~--~ 315 (959)
++++||++|||||||+|||++||+|+||||++.++++||||+||||||||+|||+||.+|++|+|+|++|+|||++| +
T Consensus 155 ~tqeVr~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavN 234 (750)
T COG4251 155 TTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVN 234 (750)
T ss_pred HHHHHHHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998 7
Q ss_pred cccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHHHHHH
Q 002152 316 KELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQ 395 (959)
Q Consensus 316 ~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~s~~ 395 (959)
|.+++|+|||+|.||||||||+|||+||||.||||||||++| +|||||+|||.+||++||+.|.+||+++|++|.+
T Consensus 235 p~t~~p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~g----~LWGLIACHH~sPk~ip~~vR~acef~gq~~s~~ 310 (750)
T COG4251 235 PETNEPLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVDG----KLWGLIACHHQSPKVIPYEVRKACEFFGQVLSME 310 (750)
T ss_pred cccCCcccchHHHHhccChHHHHHHHhcCcceeeEEEEEECC----eeEEeeeeccCCCccCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHhhcccC-CcccccCCchhhhhccCCeEEEEECCeEEEecCCCCHHHHHHHHHHH
Q 002152 396 LYMELQVAMQLAEKNILRTQ-VLLCDMLLRDA-PFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWL 473 (959)
Q Consensus 396 l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~l~~l~~a~g~a~~~~~~~~~~G~~p~~~~~~~l~~wl 473 (959)
|+...+.+......+....+ +++..|...++ ..++....+++++|++|||+++|++|+|.++|.||+..++..|+.||
T Consensus 311 i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~Ll~wl 390 (750)
T COG4251 311 ISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQWL 390 (750)
T ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHHHHHH
Confidence 98654322222211222222 34444544444 47889999999999999999999999999999999999999999999
Q ss_pred HhccCCCceeecccccccCCCCccccccccceEEEEEecC--CCeEEEeecccceEEeecCCCCCCCc-CCCCCcccCCc
Q 002152 474 LNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITS--KDFLFWFRSHTAKEVKWGGAKHHPEH-KDNGGKMHPRS 550 (959)
Q Consensus 474 ~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~l~~~i~~--~~~l~~fR~e~~~~v~W~G~p~~~~~-~~~g~~l~PR~ 550 (959)
.+... ..+|+||+|+.. ||+++.|+.++|||||++|+. ++|++|||||++++|+|||+|+|++. .++|.||+||+
T Consensus 391 ~~~~~-~~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL~PRk 468 (750)
T COG4251 391 AEREE-GDVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRLTPRK 468 (750)
T ss_pred hcCCc-ccEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCcccCCcc
Confidence 88854 479999999985 999999999999999999997 89999999999999999999999976 55678999999
Q ss_pred hHHHHHHhhcccccCCccchHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccchHHHHHHH
Q 002152 551 SFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVA 617 (959)
Q Consensus 551 SF~~w~e~V~~~s~pW~~~el~aa~~L~~iL~~~l~~i~~~~~~~~~~~~~l~~~l~~~~~eL~~~~ 617 (959)
||+.|+|+|+++|.||+..|++++.+++..+ ..+.. +++.+..+++.++.++++||++..
T Consensus 469 SFe~WkE~vRl~s~PWs~~ei~~A~~LR~ai----v~ivl---~~aeela~l~r~lersn~el~~f~ 528 (750)
T COG4251 469 SFELWKETVRLQSQPWSEVEIEAALELRKAI----VGIVL---RHAEELAQLRRELERSNAELRAFA 528 (750)
T ss_pred cHHHHHHHHhccCCCCCHHHHHHHHHHHHHH----HHHHH---HHHHHHHHHHHHHhhhhHHHHHHH
Confidence 9999999999999999999999999995543 33333 455567888888888888887765
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=100.00 E-value=4.4e-33 Score=280.57 Aligned_cols=168 Identities=34% Similarity=0.663 Sum_probs=139.4
Q ss_pred HHHHHhhcc-cC-CcccccCCchhhhhccCCeEEEEECCeEEEecCCCCHHHHHHHHHHHHhccCCCceeecccccccCC
Q 002152 416 VLLCDMLLR-DA-PFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGY 493 (959)
Q Consensus 416 ~~~~~~~~~-~~-~~~~~~~~~~l~~l~~a~g~a~~~~~~~~~~G~~p~~~~~~~l~~wl~~~~~~~~~~~t~~l~~~~~ 493 (959)
..|..++.. .+ ...+..+.++|++|++|||+||+++|+++++|.+|+..++.+|++||.... ...+|+|++|++. |
T Consensus 6 ~~L~~~~~~~~~~~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~-~~~v~~T~~L~~~-~ 83 (182)
T PF00360_consen 6 QRLLEALSSSRDLLEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQA-DGEVFATDSLSED-Y 83 (182)
T ss_dssp HHHHHHHHCSSSHHHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTT-T-SEEEESBGGGT-S
T ss_pred HHHHHHHccCCChhHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhC-CCccchhhhHhHh-C
Confidence 334444433 33 477888999999999999999999999999999999999999999999774 4579999999985 9
Q ss_pred CCccccccccceEEEEEecC--CCeEEEeecccceEEeecCCCCCCCcCC-CCCcccCCchHHHHHHhhcccccCCccch
Q 002152 494 PGAALLGQAVCGMATARITS--KDFLFWFRSHTAKEVKWGGAKHHPEHKD-NGGKMHPRSSFKAFLEVVKNRSFPWEVSE 570 (959)
Q Consensus 494 p~~~~~~~~~~g~l~~~i~~--~~~l~~fR~e~~~~v~W~G~p~~~~~~~-~g~~l~PR~SF~~w~e~V~~~s~pW~~~e 570 (959)
|++.++.+.+||||+++|++ ++|++|||+|+.++|+|||+|+|++..+ ++.+++||+||+.|+|+|+|+|.||+..|
T Consensus 84 p~~~~~~~~aaGvLai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~~~d 163 (182)
T PF00360_consen 84 PDAAALAERAAGVLAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWSDAD 163 (182)
T ss_dssp GGGGGGCCCHSEEEEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---HHH
T ss_pred hhhhhhcccCCCcEEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCCHHH
Confidence 99999999999999999986 6899999999999999999999998744 57899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 002152 571 INAIHSLQIVMRDSF 585 (959)
Q Consensus 571 l~aa~~L~~iL~~~l 585 (959)
+.++..++..+...+
T Consensus 164 ~~~A~~lr~~l~~~~ 178 (182)
T PF00360_consen 164 LEAAERLRRALLEVI 178 (182)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999976665544
No 3
>PRK13560 hypothetical protein; Provisional
Probab=99.97 E-value=1.1e-29 Score=319.91 Aligned_cols=329 Identities=16% Similarity=0.172 Sum_probs=263.5
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc
Q 002152 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (959)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~ 685 (959)
+++++++|++++++|+.+++++|++++++|.+|+++++|+++++++||+.++++|+++. ++.++...+.........+.
T Consensus 192 rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~-~~~~~~~~~~~~~~~~~~~~ 270 (807)
T PRK13560 192 RKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIH-DFAPAQPADDYQEADAAKFD 270 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcch-hcCCcchhHHHHHHHHHHhc
Confidence 56678889999999999999999999999999999999999999999999999999998 88777666555444455555
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEE--EEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 002152 686 GEEDKNVELKLRKFELQKQHSVVYILV--NACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIP 763 (959)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v--~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~ 763 (959)
.+....++..+ .+++|..+|+.+ +..++.+.+|.+.|++++++|||++|++|++|++++++|+.++++++.
T Consensus 271 ~~~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~--- 343 (807)
T PRK13560 271 ADGSQIIEAEF----QNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPI--- 343 (807)
T ss_pred cCCceEEEEEE----EcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcc---
Confidence 55555556665 688999996655 456678999999999999999999999999999999999999999985
Q ss_pred CeeeeCCCCcEEee-cHHHHHHhCCCchhhcCCCcccccc---------------------------------------c
Q 002152 764 PIFASDENACCSEW-NAAMEKVTGWMRHEVIGKMLPREIF---------------------------------------G 803 (959)
Q Consensus 764 ~I~~~D~~g~i~~~-N~a~~~l~G~~~eeviGk~~~~~i~---------------------------------------~ 803 (959)
+++.+|.+|+++++ |+++++++||+.++++|+.+.+... .
T Consensus 344 ~i~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 423 (807)
T PRK13560 344 AAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDG 423 (807)
T ss_pred cEEEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccC
Confidence 49999999999987 5778889999999998875421000 0
Q ss_pred --------------------------------------------------------------------------------
Q 002152 804 -------------------------------------------------------------------------------- 803 (959)
Q Consensus 804 -------------------------------------------------------------------------------- 803 (959)
T Consensus 424 ~e~~~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~ 503 (807)
T PRK13560 424 QEVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKN 503 (807)
T ss_pred ceEEEEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecch
Confidence
Q ss_pred ----------------ccccccChhhHHHHHHHHHhhhc-CCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEE
Q 002152 804 ----------------NFCRMKGQDMLTKFMILLYQGIT-GQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFC 866 (959)
Q Consensus 804 ----------------~~~~l~~~e~~~~~~~~l~~~~~-~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~ 866 (959)
.+..+.||++...+...+..... +...+..++++.+++|..+|+.....|++|.+|.+.++++
T Consensus 504 ~~~~G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g 583 (807)
T PRK13560 504 ITQFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEG 583 (807)
T ss_pred hhhcCCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEE
Confidence 00011233333333333333333 2345667889999999999999999999999999999999
Q ss_pred EEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002152 867 FMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG 946 (959)
Q Consensus 867 i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d 946 (959)
+.+|||++|++|.++++ +.+.|.+|++.|||||||||++|.|+++|+.....+++.+.++..+......|..+++.
T Consensus 584 ~~~DITerK~aE~~L~~----a~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 659 (807)
T PRK13560 584 IVIDISERKHAEEKIKA----ALTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAMALAHEK 659 (807)
T ss_pred EEechHHHHHHHHHHHH----HHHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999877654 34567899999999999999999999999988667777888887776666666665554
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=99.93 E-value=5.1e-25 Score=260.99 Aligned_cols=310 Identities=12% Similarity=0.005 Sum_probs=223.5
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEE
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLR 697 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~ 697 (959)
+.|+.+++.++++++++|.+|+++++|+++++++|+++++++|+... .+.++.........+...+..+..+..++..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 81 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNES-VLSNHTTPPEVYQALWGSLAEQKPWAGKLLN- 81 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCch-hhcCCCCCHHHHHHHHHHHHhCCcccceeec-
Confidence 46889999999999999999999999999999999999999999865 5555444433333444444444444444444
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEee
Q 002152 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEW 777 (959)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~ 777 (959)
.+++|..+|+.....|+++.+|.+.+++++++|||++|++++++++++..++.++++++. +++++|.+|+++++
T Consensus 82 ---~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~---~i~~~d~~~~i~~~ 155 (494)
T TIGR02938 82 ---RRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPV---AFVLLDPTGRVILD 155 (494)
T ss_pred ---cCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccc---eEEEEcCCCCEEEe
Confidence 578999999999999999999999999999999999999999999999999999999875 49999999999999
Q ss_pred cHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCc-EEEEEEEEeeeeC
Q 002152 778 NAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQ-FVEVALTASRRTD 856 (959)
Q Consensus 778 N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~-~~~v~~~~~pi~d 856 (959)
|+++++++|+...+..+..+.+ ..+++....+...+. .+......+.++...+|. .+|+.....++.+
T Consensus 156 N~~~~~~~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (494)
T TIGR02938 156 NQEYKKLATDLRVKEPAHTVLD--------LLREAWREALAENWP---QQLAFSNREARFDRGGGRPARWLSCTGSVIGM 224 (494)
T ss_pred chhHHHhhchhhhhHHHHHHHH--------HhhHHhhhhhhhcch---hhhccccceeeeccCCCceeeEEEecCceEEe
Confidence 9999999998887766654322 122332222211111 111122234444555555 7899988888877
Q ss_pred CCCCE---------EEEEEEEeecccccHHHHHHHhHHH-------HHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcC
Q 002152 857 AEGKV---------IGCFCFMQILVPDLQPALEAQGLED-------MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESS 920 (959)
Q Consensus 857 ~~G~i---------~g~v~i~~DITerk~~Elelq~~ae-------~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~ 920 (959)
..|.. .+++++++|||++|++|.+++..+. +..+...++++.++|++||||+.|.++.+++...
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 66654 3455678999999998876644322 2223445667888999999999999999999864
Q ss_pred CCC---HHHHHHHHHHHHHHHHHHHhhcc
Q 002152 921 SIS---ENQRQYLETSDACERQIMTIIDG 946 (959)
Q Consensus 921 ~l~---e~~~~~l~~i~~~~~rl~~LI~d 946 (959)
..+ ++....+..+.....++...+.+
T Consensus 305 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 333 (494)
T TIGR02938 305 GDDAGNPASAAMLQQALSAGREHMEALRQ 333 (494)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222 33444444444444444444444
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=99.91 E-value=1.2e-24 Score=200.91 Aligned_cols=105 Identities=35% Similarity=0.508 Sum_probs=91.7
Q ss_pred HhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCC---CcccccccccccCCccccccCCchHHHHHHHHhcccc
Q 002152 84 LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLR---SRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREI 160 (959)
Q Consensus 84 ~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~---~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~~~~~ 160 (959)
+||||+||+|||||+|||+|+++++|++||+|++++||.+ + .+++|+++.++|++...+.+++++.....
T Consensus 3 ~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~-------~~llG~~l~~ll~~~~~~~l~~~~~~~~~ 75 (110)
T PF08446_consen 3 REPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPELP-------EELLGRPLSELLGAESAERLREALQSESL 75 (110)
T ss_dssp GS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS----H-------HHHTTCBHHHHSCCCCHHHHHHHCTCCCC
T ss_pred cccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccccc-------hhhcccCHHHHhCHHHHHHHHHhhhccCc
Confidence 6789999999999999999999999999999999999998 5 57999999999999999999999887776
Q ss_pred cccCcceeeccCCCCCcceEEEEEeeCCEEEEEeccC
Q 002152 161 SLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPS 197 (959)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~E~Ep~ 197 (959)
...+|+.++. ..+++.|++++||+++++||||||+
T Consensus 76 ~~~~~~~~~~--~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 76 SLSNPIALRL--RIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCEEEEE--EEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred cccCCeEEEe--ccCCeeEEEEEEEECCEEEEEEeeC
Confidence 6678888875 4478899999999999999999995
No 6
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.91 E-value=1.1e-22 Score=264.95 Aligned_cols=265 Identities=14% Similarity=0.082 Sum_probs=233.7
Q ss_pred ccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcC
Q 002152 607 MQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLG 686 (959)
Q Consensus 607 ~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~ 686 (959)
++.+++|++++++++.++++++++++.+|.+|+++++|+++++++||+.++++|+++. +++++++.+.....+.....+
T Consensus 272 r~~~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~-~~~~~~d~~~~~~~~~~~~~~ 350 (1092)
T PRK09776 272 RAERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQ-QLTWPEDLNKDLQQVEKLLSG 350 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCce-eccCcchhHhHHHHHHHHHcC
Confidence 3446778899999999999999999999999999999999999999999999999998 889998888777777777766
Q ss_pred CC-cceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCe
Q 002152 687 EE-DKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPI 765 (959)
Q Consensus 687 ~~-~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I 765 (959)
+. ....+.++ .++||..+|+..+..++++.+|.+.+++++++|||++|++|+++++++++++.+++..+. ++
T Consensus 351 ~~~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~---~i 423 (1092)
T PRK09776 351 EINSYSMEKRY----YRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGI---GI 423 (1092)
T ss_pred CccceeeeeEE----EcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCc---eE
Confidence 53 23445555 688999999999999999999999999999999999999999999999999999998875 49
Q ss_pred eeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEE
Q 002152 766 FASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFV 845 (959)
Q Consensus 766 ~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~ 845 (959)
|.+|.++++++||+++++++||+.++..+.. .+....+|++...+...+.+...++..+..++++.++|| .+
T Consensus 424 ~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~-------~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~ 495 (1092)
T PRK09776 424 WEWDLKPNIISWDKRMFELYEIPPHIKPTWQ-------VWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VR 495 (1092)
T ss_pred EEEecCCCeEeeCHHHHHHhCCCcccCCCHH-------HHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eE
Confidence 9999999999999999999999998843322 133467789988888888888888889999999999999 99
Q ss_pred EEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHH
Q 002152 846 EVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDM 887 (959)
Q Consensus 846 ~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~ 887 (959)
|+.....++.|.+|++.+++++.+|||++|+++.++++..++
T Consensus 496 w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~ 537 (1092)
T PRK09776 496 HIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKER 537 (1092)
T ss_pred EEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998877655443
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.89 E-value=2.2e-22 Score=252.20 Aligned_cols=212 Identities=17% Similarity=0.188 Sum_probs=190.4
Q ss_pred ecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccCh
Q 002152 732 QDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQ 811 (959)
Q Consensus 732 ~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~ 811 (959)
++|+++++++++++++++.++.++++++.+ ++++|.+|++++||+++++++||+.++++|+++.+ +.++
T Consensus 138 ~~i~~r~~~~~~l~~~~~~l~~il~~~~~~---i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~--------l~~~ 206 (779)
T PRK11091 138 NEIKEREETQIELEQQSSLLRSFLDASPDL---VYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKD--------VYSP 206 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcce---EEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHH--------hCCH
Confidence 599999999999999999999999999864 99999999999999999999999999999998653 3345
Q ss_pred hhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHH
Q 002152 812 DMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYA 891 (959)
Q Consensus 812 e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~a 891 (959)
+....+.........++....++..+..++|+.+|+.++..|+.+.+|.+.|++++++|||++|+++.+++ ++++.
T Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~----~a~~~ 282 (779)
T PRK11091 207 EAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALE----KASRD 282 (779)
T ss_pred HHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHH----HHHHH
Confidence 66666666667777777788889999999999999999999999999999999999999999998876543 44557
Q ss_pred HHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 892 KIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 892 k~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
|.+|+++|||||||||++|.|+.+++....++++++++++.+..+++++..+++| ||++|+++|++.
T Consensus 283 ~~~~~a~isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~ 350 (779)
T PRK11091 283 KTTFISTISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKLQ 350 (779)
T ss_pred HHHHHHHhhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCcE
Confidence 8899999999999999999999999998888999999999999999999999999 999999998764
No 8
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.89 E-value=7.5e-22 Score=257.02 Aligned_cols=265 Identities=17% Similarity=0.188 Sum_probs=222.6
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc
Q 002152 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (959)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~ 685 (959)
++++++++++.+++++.+++..++++|.+|.++++++||+++.+++|++.++..+...+...++|++.+.....+.....
T Consensus 398 rk~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~ 477 (1092)
T PRK09776 398 LKRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQ 477 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHh
Confidence 45567888899999999999999999999999999999999999999999885554333267889888888888888888
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCe
Q 002152 686 GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPI 765 (959)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I 765 (959)
++.....++++ .++|| .+|+.....+++|.+|++.+++++.+|||++|++++++++++++++.++++++.. +
T Consensus 478 ~~~~~~~e~r~----~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~---i 549 (1092)
T PRK09776 478 GRSPFKLEFRI----VVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEA---V 549 (1092)
T ss_pred cCCCeeEEEEE----EcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccE---E
Confidence 88887888877 78899 9999999999999999999999999999999999999999999999999999854 9
Q ss_pred eeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCc--ceeeEEEEccCCc
Q 002152 766 FASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT--ENFPFGFFNRQGQ 843 (959)
Q Consensus 766 ~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~--~~~e~~~~~~dG~ 843 (959)
+.+|.+|+++++|+++++++||+.++++|++... ++. ..++++...... +......... ...++.+.+++|+
T Consensus 550 ~~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~-~~~----~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~G~ 623 (1092)
T PRK09776 550 VCTDMAMKVTFMNPVAEKMTGWTQEEALGVPLLT-VLH----ITFGDNGPLMEN-IYSCLTSRSAAYLEQDVVLHCRSGG 623 (1092)
T ss_pred EEECCCCeEEEEcHHHHHHhCCCHHHHcCCCHHH-Hcc----cccCCcchhhHH-HHHHHhcCCCccccceEEEEeCCCc
Confidence 9999999999999999999999999999997643 222 122222222222 3333333322 4566778999999
Q ss_pred EEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhH
Q 002152 844 FVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGL 884 (959)
Q Consensus 844 ~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ 884 (959)
.+|+..+..|+.+.+|++.|++++.+|||++|+.+.+++..
T Consensus 624 ~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~L~~~ 664 (1092)
T PRK09776 624 SYDVHYSITPLSTLDGENIGSVLVIQDVTESRKMLRQLSYS 664 (1092)
T ss_pred EEEEEEEeeeeecCCCCEEEEEEEEEecchHHHHHHHHHhh
Confidence 99999999999999999999999999999999888776543
No 9
>PRK13560 hypothetical protein; Provisional
Probab=99.86 E-value=2.7e-20 Score=234.76 Aligned_cols=263 Identities=16% Similarity=0.123 Sum_probs=204.0
Q ss_pred cccchHHHHHHHHHH-HHHHHhcCccEEEEcCCCc----eehhcHHHHHHhCCCcccccCCC-ccccccCCCchHHHH--
Q 002152 606 KMQGVDELSSVACEM-VRLIETATAPIFGVDSSGT----INGWNAKVAELTGLPASEAMGKS-LIDEVVHEESQGAVE-- 677 (959)
Q Consensus 606 l~~~~~eL~~~~~~l-~~lie~~~~~I~~~D~dg~----iv~~N~~~~~l~G~~~eeliGk~-~~~~l~~~~~~~~~~-- 677 (959)
++.++.+|+++++++ +.+++++|.+++.++.+|. +.+++.+...++|+...++++.. +...++||++.+.+.
T Consensus 55 r~~~~~~l~~~~e~~~r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~ 134 (807)
T PRK13560 55 RAIAEAEAQDCREQCERNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFAN 134 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhC
Confidence 455678888888888 9999999999999877665 33377777888888888766532 222678888876553
Q ss_pred -----HHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHH
Q 002152 678 -----NLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYE 752 (959)
Q Consensus 678 -----~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~ 752 (959)
+.+..+...+....+++++ +++||+ |+.+...|.++.+|.+ ++.++++|||++|++|++|++++.+|+
T Consensus 135 ~~~~~~~~~~~~~~~~~~~~e~r~----~~~dg~--~~~~~~~~~~~~~g~~-~~~g~~~DIT~rk~ae~~l~~~~~~l~ 207 (807)
T PRK13560 135 PFRSAETIAMALQSDDWQEEEGHF----RCGDGR--FIDCCLRFERHAHADD-QVDGFAEDITERKRAEERIDEALHFLQ 207 (807)
T ss_pred hhhHHHHHHHHhccCcccceEEEE----EeCCcc--EEEEEeeeeecCCCce-EEEEEEEccchHHHHHHHHHHHHHHHH
Confidence 3344445555566677777 677885 6667778888888875 688999999999999999999999999
Q ss_pred HHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcce
Q 002152 753 AIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTEN 832 (959)
Q Consensus 753 ~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~ 832 (959)
.++++++.. ++..|.+|+++++|+++++++||+.++++|+++.+ + .+++....+.......+..+....
T Consensus 208 ~l~e~~~~~---i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~-~-------~~~~~~~~~~~~~~~~~~~~~~~~ 276 (807)
T PRK13560 208 QLLDNIADP---AFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHD-F-------APAQPADDYQEADAAKFDADGSQI 276 (807)
T ss_pred HHHhhCCCe---EEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchh-c-------CCcchhHHHHHHHHHHhccCCceE
Confidence 999999864 99999999999999999999999999999998653 2 223333333333344445555677
Q ss_pred eeEEEEccCCcEEEEEEEE--eeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHH
Q 002152 833 FPFGFFNRQGQFVEVALTA--SRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLED 886 (959)
Q Consensus 833 ~e~~~~~~dG~~~~v~~~~--~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae 886 (959)
++.++.+++|+.+|+.+.. .|+.+.+|.+.|++++++|||++|++|.++++..+
T Consensus 277 ~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~ 332 (807)
T PRK13560 277 IEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKED 332 (807)
T ss_pred EEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHH
Confidence 8889999999999766554 56789999999999999999999999987765443
No 10
>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=99.86 E-value=1.8e-20 Score=219.29 Aligned_cols=242 Identities=16% Similarity=0.124 Sum_probs=184.7
Q ss_pred hHHHHHHHHHHHHHHHhcCccEEEEcC-CCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCC
Q 002152 610 VDELSSVACEMVRLIETATAPIFGVDS-SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEE 688 (959)
Q Consensus 610 ~~eL~~~~~~l~~lie~~~~~I~~~D~-dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~ 688 (959)
.++|++++++|+.+++.+++++|++|. +|+|+++|+++++++||+.++++|+++. +++++++.+.+...+.....++.
T Consensus 125 ~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~-~~~~~~~~~~~~~~l~~~~~~g~ 203 (442)
T TIGR02040 125 YWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFP-QEFEGRRREELMLTLRNVRATGS 203 (442)
T ss_pred HHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHH-HhCCHHHHHHHHHHHHHHHhcCC
Confidence 347888889999999999999999998 8999999999999999999999999998 88888888878888877776655
Q ss_pred cceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeee
Q 002152 689 DKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFAS 768 (959)
Q Consensus 689 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~ 768 (959)
....++.. ++|+..| .+...++.. ++.. .+++.++|||+++++++++. .+|+.+++++++ +|+++
T Consensus 204 ~~~~~~~~------~~~~~~~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~~~---~~~~~l~e~~~d---~I~v~ 268 (442)
T TIGR02040 204 AAPVRILL------RRSQKRL-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDELS---ENLARLYHEAPD---AIVFS 268 (442)
T ss_pred CcceEEEE------cCCCeEE-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHHHH---HHHHHHHHhCCc---eEEEE
Confidence 44433332 2333334 345555553 3333 45678889999998876653 379999999985 49999
Q ss_pred CCCCcEEeecHHHHHHhCCC-chhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEE
Q 002152 769 DENACCSEWNAAMEKVTGWM-RHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEV 847 (959)
Q Consensus 769 D~~g~i~~~N~a~~~l~G~~-~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v 847 (959)
|.+|+|+++|++|++++||+ .++++|+++... +. ....+.. ..+.....++....++..+.+++|..+|+
T Consensus 269 D~~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~-~~-----~~~~~~~---~~~~~~~~~g~~~~~~~~~~~~~G~~~~v 339 (442)
T TIGR02040 269 DADGTIRGANEAFLELTDSSSLEAVRGRTLDRW-LG-----RGGVDLR---VLLSNVRRTGQVRLYATTLTGEFGAQTEV 339 (442)
T ss_pred cCCCcEEehhHHHHHHhCCCChHHHcCCCHHHH-hC-----CCcccHH---HHHHHHhhcCceEEEEEEEEcCCCCEEEE
Confidence 99999999999999999997 578999986531 11 1112222 22333334555556777889999999999
Q ss_pred EEEEeeeeCCCCCEEEEEEEEeecccccHHH
Q 002152 848 ALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (959)
Q Consensus 848 ~~~~~pi~d~~G~i~g~v~i~~DITerk~~E 878 (959)
.+++.|+.+.++. .++++++|||+||+.+
T Consensus 340 e~s~~~i~~~~~~--~~~~v~rDITeR~~~~ 368 (442)
T TIGR02040 340 EISAAWVDQGERP--LIVLVIRDISRRLTMR 368 (442)
T ss_pred EEEEEEeccCCce--EEEEEEecchhhccCC
Confidence 9999999876553 4678889999988874
No 11
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.80 E-value=4.8e-18 Score=214.13 Aligned_cols=242 Identities=14% Similarity=0.105 Sum_probs=190.1
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCc----ceEE
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED----KNVE 693 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~----~~~e 693 (959)
..+..+++.++++++++|.+|+|++||+++++++||+.++++|+++. .+++++........+.....++.. ...+
T Consensus 12 ~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 90 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNID-MLIPRDLRPAHPEYIRHNREGGKARVEGMSRE 90 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHH-HhcCccccccchHHHhhhhccCCcccccccee
Confidence 34577889999999999999999999999999999999999999988 888877665554555555444322 1224
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCc
Q 002152 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENAC 773 (959)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~ 773 (959)
+++ .++||..+|+.+...++. .+|.. +++++.+|||++++.+++. ..+..++++++. +++.+|.+|+
T Consensus 91 ~~~----~~~dG~~~~v~~~~~~~~-~~g~~-~~~~~~~DiT~~~~~~~~~----~~~~~~~~~~~~---~i~~~d~~g~ 157 (799)
T PRK11359 91 LQL----EKKDGSKIWTRFALSKVS-AEGKV-YYLALVRDASVEMAQKEQT----RQLIIAVDHLDR---PVIVLDPERR 157 (799)
T ss_pred eEE----ecCCcCEEEEEEEeeeec-cCCce-EEEEEEeeccchhhhHHHH----HHHHHHHhcCCC---cEEEEcCCCc
Confidence 444 688999999999988864 44554 5678889999988776553 445667888775 4999999999
Q ss_pred EEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEee
Q 002152 774 CSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASR 853 (959)
Q Consensus 774 i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~p 853 (959)
++++|+++++++||+.++++|+.....+. ++++.......+...+.++..+..+++..+++|..+|+..+..|
T Consensus 158 i~~~N~~~~~l~G~~~~e~~g~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~ 230 (799)
T PRK11359 158 IVQCNRAFTEMFGYCISEASGMQPDTLLN-------IPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISP 230 (799)
T ss_pred EEEEChhhHhhhCCCHHHHCCCChHHhcC-------CCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeee
Confidence 99999999999999999999997653221 12222333444555566666777888899999999999999999
Q ss_pred eeCCCCCEEEEEEEEeecccccHHHHH
Q 002152 854 RTDAEGKVIGCFCFMQILVPDLQPALE 880 (959)
Q Consensus 854 i~d~~G~i~g~v~i~~DITerk~~Ele 880 (959)
+.+.+|.+.+++++.+|||++|+.+..
T Consensus 231 v~d~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 231 VYDVLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred eecCCCceeEEEEEeehhhhHHHHHHH
Confidence 999999999999999999998876643
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=1.1e-17 Score=195.68 Aligned_cols=232 Identities=17% Similarity=0.153 Sum_probs=173.8
Q ss_pred HHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCC-cceEEEEEEeeeec
Q 002152 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEE-DKNVELKLRKFELQ 702 (959)
Q Consensus 624 ie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~-~~~~e~~~~~~~~~ 702 (959)
++.++++++++|.+|+|++||..+++++||+.++++|+++. +++++++.+.+...+.....++. .+.++... ..
T Consensus 2 ~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~----~~ 76 (442)
T TIGR02040 2 LATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWE-EIVTAESVEKFELRLSEALRTGRGAVRVELNH----ID 76 (442)
T ss_pred CcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHh-HhhCcchHHHHHHHHHHHhccCCCcceEeecc----CC
Confidence 57889999999999999999999999999999999999998 99999887777777766666543 22223222 45
Q ss_pred cCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHH-----------HH---HHHHHHHHHHHHHHhcCCCCCCeeee
Q 002152 703 KQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVL-----------MD---KFIRLQGDYEAIIQSVNPLIPPIFAS 768 (959)
Q Consensus 703 ~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~-----------E~---~L~~se~~l~~i~e~~~~~i~~I~~~ 768 (959)
++|...|+.++..++.+. .+++++.+|||+++.. |+ +|++++++|+.++++++. ++|++
T Consensus 77 ~~g~~~~~~~~~~~~~~~----~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l~~~e~r~~~l~e~~~~---~i~~~ 149 (442)
T TIGR02040 77 PSSFELPMRFILVRLGAD----RGVLALGRDLRAVAELQQQLVAAQQAMERDYWTLREMETRYRVVLEVSSD---AVLLV 149 (442)
T ss_pred CCCCccCeEEEEEEeCCC----CeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCc---eEEEE
Confidence 566677787777776542 2567889999875543 33 677788899999999875 49999
Q ss_pred CC-CCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEE
Q 002152 769 DE-NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEV 847 (959)
Q Consensus 769 D~-~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v 847 (959)
|. +|+++++|+++++++||+.++++|+.+.. +.++++...+...+.....++.....+ +..++|...|
T Consensus 150 d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~--------~~~~~~~~~~~~~l~~~~~~g~~~~~~--~~~~~~~~~~- 218 (442)
T TIGR02040 150 DMSTGRIVEANSAAAALLGGVGQSLVGRAFPQ--------EFEGRRREELMLTLRNVRATGSAAPVR--ILLRRSQKRL- 218 (442)
T ss_pred ECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHH--------hCCHHHHHHHHHHHHHHHhcCCCcceE--EEEcCCCeEE-
Confidence 97 89999999999999999999999998553 445777777777787777665544444 3345555444
Q ss_pred EEEEeeeeCCCCCEEEEEEEEeecccccHHHHH
Q 002152 848 ALTASRRTDAEGKVIGCFCFMQILVPDLQPALE 880 (959)
Q Consensus 848 ~~~~~pi~d~~G~i~g~v~i~~DITerk~~Ele 880 (959)
.+...++.. +|.. .+++.+.|||++++.+.+
T Consensus 219 ~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~ 249 (442)
T TIGR02040 219 LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDE 249 (442)
T ss_pred EEEEEEEEe-CCce-EEEEEEcccchhhhhhHH
Confidence 345555543 3333 467788999998766644
No 13
>PRK13559 hypothetical protein; Provisional
Probab=99.67 E-value=2.9e-15 Score=170.58 Aligned_cols=186 Identities=12% Similarity=0.089 Sum_probs=149.0
Q ss_pred HHHHHHHHHHHhcCCCCCCeeeeCC---CCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHH
Q 002152 746 RLQGDYEAIIQSVNPLIPPIFASDE---NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLY 822 (959)
Q Consensus 746 ~se~~l~~i~e~~~~~i~~I~~~D~---~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~ 822 (959)
.+...|+.++++.+. +++++|. +|++++||+++++++||+.++++|+.+.. +.++.+.......+.
T Consensus 40 ~~~~~~~~~~e~~~~---~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~--------l~~~~~~~~~~~~~~ 108 (361)
T PRK13559 40 ASGRLFEQAMEQTRM---AMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRF--------LQGAATDPIAVAKIR 108 (361)
T ss_pred hhhhHHHHHHHhCCC---cEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhh--------hcCCCCCHHHHHHHH
Confidence 346678889999875 4999996 56899999999999999999999997542 222233333444556
Q ss_pred hhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 002152 823 QGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQE 902 (959)
Q Consensus 823 ~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHE 902 (959)
..+.++..+..++...+++|..+|+..+..|+++.+|.+.+++++.+|||++|+.+.+. +.+.+|++.++|+
T Consensus 109 ~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~--------~~~~~l~~~l~H~ 180 (361)
T PRK13559 109 AAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE--------AHERRLAREVDHR 180 (361)
T ss_pred HHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH--------HHHHHHHHHHHHh
Confidence 66667777788888899999999999999999999999999999999999998765332 2334688899999
Q ss_pred hHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002152 903 VKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (959)
Q Consensus 903 lRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe 953 (959)
+||||+.|.++..++.. .++..++++.+...+.+|.+++++ |+.++.+
T Consensus 181 ~~n~L~~i~~~~~l~~~---~~~~~~~~~~i~~~~~~l~~~~~~ll~~~~~~ 229 (361)
T PRK13559 181 SKNVFAVVDSIVRLTGR---ADDPSLYAAAIQERVQALARAHETLLDERGWE 229 (361)
T ss_pred hhhHHHHHHHHHHhhcc---CCCHHHHHHHHHHHHHHHHHHHHHHhccCCcC
Confidence 99999999999998873 234566888888999999999988 7777654
No 14
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.66 E-value=1.5e-15 Score=158.55 Aligned_cols=197 Identities=12% Similarity=0.174 Sum_probs=153.2
Q ss_pred eecchhhHH-HHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCccccccccccccc
Q 002152 731 GQDITHEKV-LMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMK 809 (959)
Q Consensus 731 ~~DITerk~-~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~ 809 (959)
+.|.|++.+ ++..+.....++..++..+. ||++.+|..|+|+.+|..+.+++|.+.++++|+...+.+-
T Consensus 92 fn~Lt~~~~~aq~n~e~Er~kL~SvlayMt---DGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~------- 161 (459)
T COG5002 92 FNDLTKRVQEAQANTEQERRKLDSVLAYMT---DGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLK------- 161 (459)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHc---CceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhC-------
Confidence 446776654 44445555667888988886 4599999999999999999999999999999998664221
Q ss_pred ChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHH
Q 002152 810 GQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDI 889 (959)
Q Consensus 810 ~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~ 889 (959)
-.+... +...+........ ...+ .++..-..++.+.+.-+.|-+.|++.+++|+||+.+.|.+
T Consensus 162 i~d~y~-----~~dL~e~~~s~ll--d~~~-~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~E--------- 224 (459)
T COG5002 162 IEDTYT-----FEDLVEKNDSLLL--DSSD-EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERE--------- 224 (459)
T ss_pred Ccccee-----HHHHHhcCCcEEE--eecC-CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHH---------
Confidence 112211 2222222222222 2222 7788888899999999999999999999999986655533
Q ss_pred HHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHH--HHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN--QRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 890 ~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~--~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
+.+|.+++|||+||||+++.++++-|+.....++ ..+|+.......+||.+|++| |.+||++.++
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 5589999999999999999999999998666555 789999999999999999999 9999999875
No 15
>PRK13557 histidine kinase; Provisional
Probab=99.65 E-value=4.3e-15 Score=178.51 Aligned_cols=198 Identities=13% Similarity=0.079 Sum_probs=158.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCeeeeCC---CCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHH
Q 002152 743 KFIRLQGDYEAIIQSVNPLIPPIFASDE---NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMI 819 (959)
Q Consensus 743 ~L~~se~~l~~i~e~~~~~i~~I~~~D~---~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~ 819 (959)
.....+..|+.++++++. +++++|. +|+|+|+|+++++++||+.++++|+++.. +.++++......
T Consensus 24 ~~~~~~~~~~~~~~~~~~---~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~--------l~~~~~~~~~~~ 92 (540)
T PRK13557 24 VSDHRSDIFFAAVETTRM---PMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRF--------LQGPETDRATVA 92 (540)
T ss_pred hhhhhhHHHHHHHHhCcC---cEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHh--------hcCCCCCHHHHH
Confidence 344557789999999874 5999985 78999999999999999999999998553 233444444455
Q ss_pred HHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHH
Q 002152 820 LLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYI 899 (959)
Q Consensus 820 ~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~i 899 (959)
.+...+..+..+..+++..+++|..+|+..+..|+.+.+|.+++++++.+|||++++++.++++..+ ......+++.+
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~~--~~~l~~~~~~i 170 (540)
T PRK13557 93 EVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQK--MEALGQLTGGI 170 (540)
T ss_pred HHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHHH--HHHhhhhhhhh
Confidence 5556666666677788888999999999999999999999999999999999999888766543322 23455788999
Q ss_pred HHHhHhhhhHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002152 900 RQEVKNPLNGIRFVHKLLES-----SSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (959)
Q Consensus 900 SHElRnPL~~I~g~~~LL~~-----~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe 953 (959)
+||+||||+.|.++.+++.. ....+...++++.+...++++..++++ +++++..
T Consensus 171 ~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~~ 230 (540)
T PRK13557 171 AHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARKQ 230 (540)
T ss_pred hHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC
Confidence 99999999999999998864 123355678899999999999999999 7887654
No 16
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=99.58 E-value=2.8e-14 Score=166.54 Aligned_cols=192 Identities=13% Similarity=0.118 Sum_probs=144.2
Q ss_pred EEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCccccccccccc
Q 002152 728 CFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCR 807 (959)
Q Consensus 728 v~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~ 807 (959)
..+.+++++.++.++++++.+++|+.++++++. +++++|.+|+|+++|+++++++||+.++..|+++... +
T Consensus 77 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~-~----- 147 (430)
T PRK11006 77 YGLYQMQLRNRKRRRELGNLIKRFRSGAESLPD---AVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNL-L----- 147 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---eEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHH-h-----
Confidence 344578889999999999999999999999985 4999999999999999999999999999999975431 1
Q ss_pred ccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHH
Q 002152 808 MKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDM 887 (959)
Q Consensus 808 l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~ 887 (959)
.+.+. ...+... .......+...+|.. +.+...|..+ +. ++.+.+|||++++.+.
T Consensus 148 --~~~~~---~~~~~~~-----~~~~~~~~~~~~~~~--~~~~~~~~~~--~~---~~~~~~dit~~~~~e~-------- 202 (430)
T PRK11006 148 --RYPEF---TQYLKTR-----DFSRPLTLVLNNGRH--LEIRVMPYTE--GQ---LLMVARDVTQMHQLEG-------- 202 (430)
T ss_pred --cCHHH---HHHHHhc-----ccCCCeEEEcCCCCE--EEEEEEEcCC--Cc---EEEEEehhhHHHHHHH--------
Confidence 12221 1112111 111223334455654 4455555542 22 4567899998665442
Q ss_pred HHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSI-SENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 888 ~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l-~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
++.+|++.+||||||||++|.++++++..... ++...++++.+.+++++|..++++ ++++|++.+.
T Consensus 203 ---~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~~ 270 (430)
T PRK11006 203 ---ARRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAAP 270 (430)
T ss_pred ---HHHHHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34579999999999999999999999986443 455778999999999999999999 8999998874
No 17
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.57 E-value=1.4e-13 Score=167.32 Aligned_cols=200 Identities=21% Similarity=0.305 Sum_probs=160.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHH
Q 002152 740 LMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMI 819 (959)
Q Consensus 740 ~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~ 819 (959)
+.+.++.++..++.++++++. +++++|.+|+++++|+++++++|++.++++|+.+.. +++ ++. .+..
T Consensus 253 ~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~-~~~-------~~~--~~~~ 319 (607)
T PRK11360 253 LAQALRETRSLNELILESIAD---GVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSE-LFP-------PNT--PFAS 319 (607)
T ss_pred HHHHHHHHHHHHHHHHHhccC---eEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHH-HcC-------Cch--hHHH
Confidence 445677777888999999875 599999999999999999999999999999987553 222 111 1122
Q ss_pred HHHhhhc-CCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHH
Q 002152 820 LLYQGIT-GQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAY 898 (959)
Q Consensus 820 ~l~~~~~-~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~ 898 (959)
.+.+.+. +......++.+..++|... +.++..|+.+.+|++.|++++++|||++++++.++++..+.+ +..++++.
T Consensus 320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~~~--~l~~~~~~ 396 (607)
T PRK11360 320 PLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQERLA--ALGELVAG 396 (607)
T ss_pred HHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHHHH--HHHHHHHH
Confidence 2223333 4444556777888888877 899999999999999999999999999999988776544333 45688999
Q ss_pred HHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 899 IRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 899 iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
++||+||||+.|.++.+++.....+++..++++.+...+++|..++++ +++++.+..
T Consensus 397 ~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~~~ 454 (607)
T PRK11360 397 VAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPRES 454 (607)
T ss_pred HHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcC
Confidence 999999999999999999987666777889999999999999999999 888887654
No 18
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=99.54 E-value=1.4e-13 Score=155.84 Aligned_cols=185 Identities=17% Similarity=0.138 Sum_probs=137.3
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCC
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~ 828 (959)
..++.++++++. +++++|.+|+|+++|+++++++||+.++++|+++.+ ++... ..+... +...+..+
T Consensus 7 ~~~~~il~~~~~---gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~-~~~~~-----~~~~~~----~~~~~~~~ 73 (348)
T PRK11073 7 PDAGQILNSLIN---SILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPE-LLSYF-----SLNIEL----MRESLQAG 73 (348)
T ss_pred chHHHHHhcCcC---eEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHH-HcCcc-----hhhHHH----HHHHHHcC
Confidence 356789999985 499999999999999999999999999999998653 22210 111111 22233322
Q ss_pred CcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhh
Q 002152 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLN 908 (959)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~ 908 (959)
..+..+.....++|+.+|+.++..|+. . .+++..++|+|++++.+.++.+.++. ....+|++.++||+||||+
T Consensus 74 ~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~~~--~~~~~~~~~iaHelr~pL~ 146 (348)
T PRK11073 74 QGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHAQQ--VAARDLVRGLAHEIKNPLG 146 (348)
T ss_pred CcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHHHH--HHHHHHHHhhhHhhcChHH
Confidence 222222233456999999999999987 2 23566789999988776554433322 3456889999999999999
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002152 909 GIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (959)
Q Consensus 909 ~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe 953 (959)
+|.++.+++.....+++.+++++.+...+++|..++++ +++.+..
T Consensus 147 ~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~~~ 192 (348)
T PRK11073 147 GLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQRPG 192 (348)
T ss_pred HHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCC
Confidence 99999999987666677889999999999999999999 7776654
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=99.54 E-value=8.8e-14 Score=155.80 Aligned_cols=177 Identities=14% Similarity=0.146 Sum_probs=138.2
Q ss_pred HHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhh
Q 002152 745 IRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQG 824 (959)
Q Consensus 745 ~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~ 824 (959)
++..++++.++++++. +++++|.+|++++||+++++++||+.++++|+.+.+. .++++ +...+...
T Consensus 2 ~~~~~~l~~~~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~--------~~~~~---~~~~l~~~ 67 (333)
T TIGR02966 2 SALLSRFRAAAQALPD---AVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNL--------IRHPE---FVEYLAAG 67 (333)
T ss_pred hhHHHHHHHHHHhCcC---cEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHH--------ccCHH---HHHHHHhc
Confidence 3567789999999985 4999999999999999999999999999999876542 22222 22222222
Q ss_pred hcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhH
Q 002152 825 ITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVK 904 (959)
Q Consensus 825 ~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElR 904 (959)
.. .....+..++|..+|+.....|+.+.+ ++++.+|||++++.+. .+.+|++.++||+|
T Consensus 68 ~~-----~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~-----------~~~~~~~~l~h~l~ 126 (333)
T TIGR02966 68 RF-----SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQ-----------MRRDFVANVSHELR 126 (333)
T ss_pred cc-----CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHH-----------HHHHHHHhhhhhhc
Confidence 21 223555668889999999999987653 5677899997665442 24468999999999
Q ss_pred hhhhHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 905 NPLNGIRFVHKLLESS--SISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 905 nPL~~I~g~~~LL~~~--~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
|||+.|.++.+++... ..+++.+++++.+..++++|..++++ +++++++.+.
T Consensus 127 ~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~~~ 181 (333)
T TIGR02966 127 TPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRLESAA 181 (333)
T ss_pred ccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 9999999999988753 45566888999999999999999999 8999988754
No 20
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.44 E-value=2.1e-12 Score=169.83 Aligned_cols=217 Identities=15% Similarity=0.096 Sum_probs=146.1
Q ss_pred EeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCccccccccccccc
Q 002152 730 VGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMK 809 (959)
Q Consensus 730 v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~ 809 (959)
..++++.+++++.+++..+..++.++++++. +++++|.+|+|+++|+++++++|.+.....+..... ...++
T Consensus 557 l~~~i~~r~~~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~-~~~~~---- 628 (1197)
T PRK09959 557 LLRSVRRRKVIQGDLENQISFRKALSDSLPN---PTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLEN-SDSPF---- 628 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---cEEEEcCCCcEEEehHHHHHHhCccccccccccccc-ccCch----
Confidence 3578899999999999999999999999985 499999999999999999999997654333222110 00000
Q ss_pred ChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEE-EeeeeCCCCCEEEEEEEEeecccccHHHHHHHh---HH
Q 002152 810 GQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALT-ASRRTDAEGKVIGCFCFMQILVPDLQPALEAQG---LE 885 (959)
Q Consensus 810 ~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~-~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~---~a 885 (959)
.+.................. +...+...+|....+... ..+.....+...++++..+|||++++.+.+++. .+
T Consensus 629 -~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~~~ 705 (1197)
T PRK09959 629 -KDVFSNAHEVTAETKENRTI--YTQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERNKA 705 (1197)
T ss_pred -hhhHhHHHHHHHHHhhcccc--ceeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHHHH
Confidence 01000000001111111111 122223334433222221 222222344455678888999998877666543 34
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 886 DMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 886 e~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~-~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
+++..++.+|++.|||||||||++|.|+++++.....+++ ..++++.+..++++|..+|++ ++++|+++|..
T Consensus 706 ~~~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~ 779 (1197)
T PRK09959 706 INATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNY 779 (1197)
T ss_pred HHHHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 4555688999999999999999999999999986555544 557899999999999999999 99999999864
No 21
>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=99.42 E-value=1.4e-12 Score=119.20 Aligned_cols=104 Identities=29% Similarity=0.345 Sum_probs=90.8
Q ss_pred CccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcE
Q 002152 628 TAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSV 707 (959)
Q Consensus 628 ~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~ 707 (959)
|++++++|.+|+|+++|+++++++|++.++++|+++. ++++++........+.+.+.++.....++.+ .+++|+.
T Consensus 1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~----~~~~g~~ 75 (104)
T PF13426_consen 1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSIS-DFFPEEDRPEFEEQIERALEEGGSWSGEVRL----RRKDGET 75 (104)
T ss_dssp -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGG-GGCSTTSCHHHHHHHHHHHHHTSSEEEEEEE----EETTSEE
T ss_pred CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcc-cccCcccchhhHHHHHHHHhcCCceeEEEEE----EcCCCCE
Confidence 6899999999999999999999999999999999998 8888777777777777777766666667777 6889999
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEeecchh
Q 002152 708 VYILVNACTSRDYKNNVKGVCFVGQDITH 736 (959)
Q Consensus 708 ~~v~v~~~pi~d~~g~~~gvv~v~~DITe 736 (959)
+|+.+++.|+.+.+|++.+++++++||||
T Consensus 76 ~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 76 FWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 99999999999999999999999999997
No 22
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=99.41 E-value=1.4e-12 Score=120.62 Aligned_cols=110 Identities=27% Similarity=0.356 Sum_probs=99.6
Q ss_pred HHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeecc
Q 002152 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQK 703 (959)
Q Consensus 624 ie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~ 703 (959)
|+++|++++++|.+|+|+++|+++.+++|++.++++|+++. +++++...+.+...+.+++.++.....+... ..
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ 74 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLF-DLLPPEDREEFQAALRRALAGGEPVFFEEIL-----LR 74 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHH-HHSCCGCHHHHHHHHHHHHHHTSEEEEEEEE-----CT
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccch-hccccchhhhhHHHHHHhhccCceEEEEEEE-----ee
Confidence 68899999999999999999999999999999999999999 8999888999999999999988766555544 33
Q ss_pred CCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHH
Q 002152 704 QHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKV 739 (959)
Q Consensus 704 dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~ 739 (959)
+|+.+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 75 ~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 75 DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 899999999999999999999999999999999985
No 23
>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=99.40 E-value=2.3e-12 Score=127.28 Aligned_cols=153 Identities=18% Similarity=0.217 Sum_probs=115.2
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCC
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 309 (959)
|++++++.+++.+++++|+||++||.+++++..-...-.....-.+..+..++.. - ....+....+..-.|+|+...|
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~i~d~~~~~ 78 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMD-E-SICGQVLQSREPIVISDVAADP 78 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETT-S-SHHHHHHHHTSCEEESSSGGST
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccccccccccc-c-cHHHHHHhCCCeEeeccccccc
Confidence 6899999999999999999999999999999876444333222122222222221 1 1255667778888899987654
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCC-CCCChhHHHHHHHH
Q 002152 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSP-RYIPFPLRYACEFL 388 (959)
Q Consensus 310 ~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~p-r~~~~~~r~~~~~l 388 (959)
- ..+.......+++.++++.+|+..+|++|.|++||..+| ++||+|+++++.| |.|+.+++.+++.+
T Consensus 79 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g----~~~G~l~l~~~~~~~~~~~~d~~ll~~~ 146 (154)
T PF01590_consen 79 R--------FAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGG----RLIGVLSLYRTRPGRPFTEEDLALLESF 146 (154)
T ss_dssp T--------SSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETT----EEEEEEEEEEESSSSS--HHHHHHHHHH
T ss_pred c--------ccccccccccccccccccccccccccCceeeEeeeeccc----CcEEEEEEEECCCCCCcCHHHHHHHHHH
Confidence 3 122223344567889999999999999999999999988 9999999999997 99999999999999
Q ss_pred HHHHHHHH
Q 002152 389 VQAFSLQL 396 (959)
Q Consensus 389 ~~~~s~~l 396 (959)
++++++.|
T Consensus 147 a~~~a~ai 154 (154)
T PF01590_consen 147 AQQLAIAI 154 (154)
T ss_dssp HHHHHHHH
T ss_pred HHHHHhhC
Confidence 99998765
No 24
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=99.40 E-value=1.2e-11 Score=156.11 Aligned_cols=183 Identities=15% Similarity=0.187 Sum_probs=134.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCeeeeC-CCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHH
Q 002152 742 DKFIRLQGDYEAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMIL 820 (959)
Q Consensus 742 ~~L~~se~~l~~i~e~~~~~i~~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~ 820 (959)
.+++++++.++.++++++.+ +++++ .+|.++..|+.+..++|+...+. ...+...
T Consensus 327 ~~L~e~e~~~r~iv~~~p~g---i~i~~~~~g~~~~~N~~a~~~~~l~~~~~---------------------~~~~~~~ 382 (924)
T PRK10841 327 LRLEEHEQFNRKIVASAPVG---ICILRTSDGTNILSNELAHNYLNMLTHED---------------------RQRLTQI 382 (924)
T ss_pred HHHHHHHHHHHHHHHhCCcc---EEEEEcCCCcEEEehHHHHHHhccCChhH---------------------HHHHHHH
Confidence 46788888999999999865 77775 79999999999999887643221 1111111
Q ss_pred HHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHh---HHHHHHHHHHHHHH
Q 002152 821 LYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQG---LEDMDIYAKIKELA 897 (959)
Q Consensus 821 l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~---~ae~~~~ak~~fLa 897 (959)
+ ...... . ......++....+........ +.. ..++++.|||++++.+.++++ .+++++++|.+|++
T Consensus 383 ~----~~~~~~-~-~~~~~~~~~~~~i~~~~~~~~---~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~a~~~k~~fla 452 (924)
T PRK10841 383 I----CGQQVN-F-VDVLTSNNTNLQISFVHSRYR---NEN-VAICVLVDVSARVKMEESLQEMAQAAEQASQSKSMFLA 452 (924)
T ss_pred H----hccccc-e-eeEEcCCCcEEEEEEEeeeec---Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 111110 1 122334455444433332222 222 357888999999998877654 45566778999999
Q ss_pred HHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 898 YIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 898 ~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
.|||||||||++|.|++++|....++++++++++.+..++++|..+|+| ||++|+++|.+.
T Consensus 453 ~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~~ 514 (924)
T PRK10841 453 TVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLK 514 (924)
T ss_pred HhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCce
Confidence 9999999999999999999998888999999999999999999999999 999999998754
No 25
>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=99.39 E-value=2e-12 Score=118.19 Aligned_cols=103 Identities=20% Similarity=0.282 Sum_probs=87.9
Q ss_pred CCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCC
Q 002152 763 PPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQG 842 (959)
Q Consensus 763 ~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG 842 (959)
++++++|.+|+|+++|+++++++||+.++++|+++.. + ..++....+...+.+++.++..+..+..+.+++|
T Consensus 2 ~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~-~-------~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g 73 (104)
T PF13426_consen 2 DGIFILDPDGRILYVNPAFERLFGYSREELIGKSISD-F-------FPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDG 73 (104)
T ss_dssp SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGG-G-------CSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTS
T ss_pred EEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCccc-c-------cCcccchhhHHHHHHHHhcCCceeEEEEEEcCCC
Confidence 4699999999999999999999999999999998653 2 2344445566777777776667899999999999
Q ss_pred cEEEEEEEEeeeeCCCCCEEEEEEEEeeccc
Q 002152 843 QFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (959)
Q Consensus 843 ~~~~v~~~~~pi~d~~G~i~g~v~i~~DITe 873 (959)
+.+|+.+++.|+.+++|++.+++++++||||
T Consensus 74 ~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 74 ETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred CEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 9999999999999999999999999999995
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=6.9e-12 Score=116.56 Aligned_cols=112 Identities=26% Similarity=0.407 Sum_probs=93.1
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc-CCCcceEEEEE
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL-GEEDKNVELKL 696 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~-~~~~~~~e~~~ 696 (959)
++|+.++++++++++++|.+|+|+++|++++++||++.++++|+++. +++++++.......+...+. +......+..+
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLF-DLIHPEDRRELRERLRQALSQGESGESFEVRF 79 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGG-GGCSGGGHHHHHHHHHHHHHHCCHECEEEEEE
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHH-HhcCchhhHHHHHHHHHHHHcCCCceeEEEEE
Confidence 47899999999999999999999999999999999999999999999 88888766555555555554 33344445554
Q ss_pred EeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecc
Q 002152 697 RKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDI 734 (959)
Q Consensus 697 ~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DI 734 (959)
..++|+.+|+.++..|+++.+|++.|++++++||
T Consensus 80 ----~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 80 ----RLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp ----EETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred ----EecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 2368999999999999999999999999999997
No 27
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.32 E-value=2.5e-11 Score=152.64 Aligned_cols=144 Identities=16% Similarity=0.149 Sum_probs=125.2
Q ss_pred cccccccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHH
Q 002152 602 QNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLIC 681 (959)
Q Consensus 602 l~~~l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~ 681 (959)
...++++++++|++.+++++.+++++|++++++|.+|+|++||+++++++|++.++++|+++. ++++++....+.....
T Consensus 139 ~i~~r~~~~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~-~l~~~~~~~~~~~~~~ 217 (779)
T PRK11091 139 EIKEREETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPK-DVYSPEAAEKVIETDE 217 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChH-HhCCHHHHHHHHHHHH
Confidence 334456678889999999999999999999999999999999999999999999999999998 8888876666666666
Q ss_pred HHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHH
Q 002152 682 RALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGD 750 (959)
Q Consensus 682 ~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~ 750 (959)
....++.....+..+ ..++|..+|+.++..|+++.+|.+.|++++++|||++|++++++++..+.
T Consensus 218 ~~~~~~~~~~~e~~~----~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~~~ 282 (779)
T PRK11091 218 KVFRHNVSLTYEQWL----DYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKASRD 282 (779)
T ss_pred HHHhcCCCeEEEEEE----EcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHHHH
Confidence 777766666666665 67899999999999999999999999999999999999999988776553
No 28
>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=99.31 E-value=2.4e-11 Score=112.83 Aligned_cols=112 Identities=29% Similarity=0.393 Sum_probs=89.3
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhc-C
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT-G 827 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~-~ 827 (959)
++|+.++++++. +++++|.+|+|+++|+++++++||+.++++|+++.+ +.++++.......+.+.+. +
T Consensus 1 e~~~~i~~~~~~---~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~--------~~~~~~~~~~~~~~~~~~~~~ 69 (113)
T PF00989_consen 1 ERYRAILENSPD---GIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFD--------LIHPEDRRELRERLRQALSQG 69 (113)
T ss_dssp HHHHHHHHCSSS---EEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGG--------GCSGGGHHHHHHHHHHHHHHC
T ss_pred CHHHHHHhcCCc---eEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHH--------hcCchhhHHHHHHHHHHHHcC
Confidence 478999999985 599999999999999999999999999999999775 3334543344445555554 3
Q ss_pred CCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeec
Q 002152 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQIL 871 (959)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DI 871 (959)
......+..+..++|+.+|+.+.++|+++.+|++.|++++++||
T Consensus 70 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 70 ESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp CHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred CCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 33445555566689999999999999999999999999999997
No 29
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.31 E-value=5e-11 Score=148.53 Aligned_cols=179 Identities=15% Similarity=0.115 Sum_probs=128.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCeeeeC-CCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHH
Q 002152 740 LMDKFIRLQGDYEAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFM 818 (959)
Q Consensus 740 ~E~~L~~se~~l~~i~e~~~~~i~~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~ 818 (959)
...+++..+..++.++++++.+ ++++| .+|+++.+|+++++++|...-.-+. . . .+.. .
T Consensus 334 l~~~L~~~~~l~~~Ii~~lp~G---ilv~D~~~~~Ii~~N~aA~~ll~~~~l~~i~--------~----~--~~~~---~ 393 (894)
T PRK10618 334 MSHELRILRALNEEIVSNLPLG---LLVYDFESNRTVISNKIADHLLPHLNLQKIT--------T----M--AEQH---Q 393 (894)
T ss_pred HHHHHHHHHHHHHHHHHhCCce---EEEEECCCCeEEEEhHHHHHHhCccchhhHH--------H----H--HHhc---c
Confidence 3346778888899999999854 89999 7899999999999999753211000 0 0 0000 0
Q ss_pred HHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHH---HhHHHHHHHHHHHH
Q 002152 819 ILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEA---QGLEDMDIYAKIKE 895 (959)
Q Consensus 819 ~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elel---q~~ae~~~~ak~~f 895 (959)
..+.. ..+++..++...... ....+.+.+++|+++++..+.++ ++..+++.++|.+|
T Consensus 394 ~~i~~---------------~i~~~~~eir~~~~~-----~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le~~~~~k~~f 453 (894)
T PRK10618 394 GVIQA---------------TINNELYEIRMFRSQ-----LAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQQARKAF 453 (894)
T ss_pred hhhhh---------------hccCceeEEEEeecc-----ccCceEEEEEeehHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00000 112222222222211 12234677889999877666555 34556667899999
Q ss_pred HHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 896 LAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 896 La~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
+++|||||||||++|.++.+++.....+++++++++.+..++++|..+|++ +|++|+++|++.
T Consensus 454 la~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~~ 517 (894)
T PRK10618 454 LQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDWK 517 (894)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc
Confidence 999999999999999999999988777888999999999999999999999 999999999764
No 30
>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=99.30 E-value=1.5e-11 Score=113.60 Aligned_cols=110 Identities=19% Similarity=0.230 Sum_probs=93.9
Q ss_pred HHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceee
Q 002152 755 IQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFP 834 (959)
Q Consensus 755 ~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e 834 (959)
+++++. +++++|.+|+++++|+++.+++|++.++++|+++.+ +.+++....+...+.+++.++.....+
T Consensus 1 l~~~p~---~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (110)
T PF08448_consen 1 LDSSPD---GIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFD--------LLPPEDREEFQAALRRALAGGEPVFFE 69 (110)
T ss_dssp HHHCSS---EEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHH--------HSCCGCHHHHHHHHHHHHHHTSEEEEE
T ss_pred CCCCCc---eeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchh--------ccccchhhhhHHHHHHhhccCceEEEE
Confidence 356664 599999999999999999999999999999998663 333567778888999999988777766
Q ss_pred EEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccH
Q 002152 835 FGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQ 876 (959)
Q Consensus 835 ~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~ 876 (959)
..... +|+.+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 70 ~~~~~-~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 70 EILLR-DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp EEECT-TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred EEEee-cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 65555 999999999999999999999999999999999875
No 31
>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=99.23 E-value=1.9e-11 Score=103.08 Aligned_cols=65 Identities=35% Similarity=0.543 Sum_probs=61.3
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhc-CCCCHHH-HHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQ-RQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~-~~l~e~~-~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
+|.+|++.++|||||||++|.++.+++.. ...++++ +++++.+..++++|..+|++ |+|+|+|+|
T Consensus 1 s~~~~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G 68 (68)
T PF00512_consen 1 SKGEFLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred CHHHHHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 47799999999999999999999999999 8888988 99999999999999999999 999999998
No 32
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=99.17 E-value=1.6e-09 Score=130.51 Aligned_cols=202 Identities=15% Similarity=0.161 Sum_probs=128.5
Q ss_pred EEEEEeecCCCCEEEEEEEeecchhhHHHHH--------------------------------------HHHHHHHHHHH
Q 002152 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLMD--------------------------------------KFIRLQGDYEA 753 (959)
Q Consensus 712 v~~~pi~d~~g~~~gvv~v~~DITerk~~E~--------------------------------------~L~~se~~l~~ 753 (959)
....|+++..|.++|++.+..++.+....-. ++....+.+++
T Consensus 146 ~~~~p~~~~~~~~iG~v~vg~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~l~~l~~~ei~~l~~~~~~ 225 (542)
T PRK11086 146 RVFTPVYDENGKQIGVVAVGISLSEVTEQINESRWSIYWSILFGALVGLIGTVILVRVLKRILFGLEPYEISTLFEQRQA 225 (542)
T ss_pred EEEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3557888889999999877665443322111 22334456678
Q ss_pred HHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCc---hhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCc
Q 002152 754 IIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMR---HEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT 830 (959)
Q Consensus 754 i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~---eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~ 830 (959)
++++++. +++.+|.+|+|+++|+++++++|++. .+.+|+.... ...... +...+..+..
T Consensus 226 il~~~~~---gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~--------~~~~~~-------~~~~~~~~~~ 287 (542)
T PRK11086 226 MLQSIKE---GVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVES--------WMPVSR-------LKEVLRTGTP 287 (542)
T ss_pred HHHHhcC---cEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHH--------hCCchh-------HHHHHhcCCC
Confidence 8999875 59999999999999999999998763 3455554321 111111 2223333322
Q ss_pred ce-eeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhhH
Q 002152 831 EN-FPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNG 909 (959)
Q Consensus 831 ~~-~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~~ 909 (959)
.. .+. ..+|. ++.....|+.+ +|.+.|++++++|+|+.++.+.++... ....++++.++||+||||++
T Consensus 288 ~~~~~~---~~~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~-----~~~~~~l~~~sHel~npL~~ 356 (542)
T PRK11086 288 RRDEEI---NINGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGM-----VNYADALRAQSHEFMNKLHV 356 (542)
T ss_pred ccceEE---EECCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHH-----HHHHHHHHhhchhhcCHHHH
Confidence 21 222 22453 45566789988 899999999999999977665444322 23346678899999999999
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHH-HHHHHHHHHHhhcc
Q 002152 910 IRFVHKLLESSSISENQRQYLET-SDACERQIMTIIDG 946 (959)
Q Consensus 910 I~g~~~LL~~~~l~e~~~~~l~~-i~~~~~rl~~LI~d 946 (959)
|.|++++... ++..+++.. +.....++..++++
T Consensus 357 I~g~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 390 (542)
T PRK11086 357 ILGLLHLKSY----DQLEDYILKTANNYQEEIGSLLGK 390 (542)
T ss_pred HHHHHHhCch----HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999887543 233334333 23333444444444
No 33
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=99.14 E-value=1.1e-09 Score=114.01 Aligned_cols=176 Identities=21% Similarity=0.232 Sum_probs=123.7
Q ss_pred HHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhc-CCCcc
Q 002152 753 AIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT-GQGTE 831 (959)
Q Consensus 753 ~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~-~~~~~ 831 (959)
.+++++. .+++..|.+|.|.|+|++++.+||.+...+.|..+.. +++. ... ....+.+... +....
T Consensus 11 ~~Ln~~~---~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~-l~~~-----gs~----ll~ll~q~~~~~~~~~ 77 (363)
T COG3852 11 AILNNLI---NPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSE-LLPF-----GSL----LLSLLDQVLERGQPVT 77 (363)
T ss_pred hHHhccC---CceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHH-HcCC-----CcH----HHHHHHHHHHhcCCcc
Confidence 4566664 4689999999999999999999999999999887653 3321 111 2334444444 33333
Q ss_pred eeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhhHHH
Q 002152 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIR 911 (959)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~~I~ 911 (959)
.++..+. .+|....+...+.|+-...|.+.- .++-+....+-..++. .....++-.....+++|||||||.+|.
T Consensus 78 ~~~v~l~-~~g~~~~v~~~v~~v~~~~G~vll---e~~~~~~~~ridre~~--q~a~~~a~~~L~r~LAHEIKNPL~GiR 151 (363)
T COG3852 78 EYEVTLV-ILGRSHIVDLTVAPVPEEPGSVLL---EFHPRDMQRRLDREQT--QHAQQRAVKGLVRGLAHEIKNPLGGIR 151 (363)
T ss_pred cceeeee-ecCccceEEEEEeeccCCCCeEEE---EechhHHHhHhhHHHH--HHHHHHHHHHHHHHHHHHhcCcccchh
Confidence 4455555 789999999999999877776542 2233332222221111 111223455678899999999999999
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q 002152 912 FVHKLLESSSISENQRQYLETSDACERQIMTIIDGM 947 (959)
Q Consensus 912 g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~dL 947 (959)
|..+||++.--++..++|.+.|...++|+..|+|.|
T Consensus 152 GAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRm 187 (363)
T COG3852 152 GAAQLLERALPDEALRELTQLIIEEADRLRNLVDRL 187 (363)
T ss_pred hHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999985555659999999999999999999985
No 34
>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=99.12 E-value=2e-09 Score=103.36 Aligned_cols=140 Identities=26% Similarity=0.403 Sum_probs=111.4
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCC
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 309 (959)
|++++++.+++.+.+++|+||+.||.++++..+............+..+..+|..+ ...+..+..+...++.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999878887777665544445667777766 5567778888888888876443
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhc-CceeEEEEEEEEcCCCCCceeEEEEeecC-CCCCCChhHHHHHHH
Q 002152 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNM-GSIASLVMAVIINSKDSMKLWGLVVCHHT-SPRYIPFPLRYACEF 387 (959)
Q Consensus 310 ~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nm-gv~asl~v~i~~~~~~~~~LWGLi~~hh~-~pr~~~~~~r~~~~~ 387 (959)
.+ . ..+...+ |+++.+++||..+| ++||+|.+.++ .++.|+.+.+..++.
T Consensus 79 ~~-----------------------~-~~~~~~~~~~~s~~~~Pl~~~~----~~~G~l~~~~~~~~~~~~~~~~~~l~~ 130 (149)
T smart00065 79 VF-----------------------A-LDLLGRYQGVRSFLAVPLVADG----ELVGVLALHNKDSPRPFTEEDEELLQA 130 (149)
T ss_pred cc-----------------------c-cccccceeceeeEEEeeeeecC----EEEEEEEEEecCCCCCCCHHHHHHHHH
Confidence 21 1 1122233 49999999999988 99999999999 699999999999999
Q ss_pred HHHHHHHHHHHH
Q 002152 388 LVQAFSLQLYME 399 (959)
Q Consensus 388 l~~~~s~~l~~~ 399 (959)
++++++..|+..
T Consensus 131 ~~~~i~~~l~~~ 142 (149)
T smart00065 131 LANQLAIALANA 142 (149)
T ss_pred HHHHHHHHHHHH
Confidence 999999888643
No 35
>PRK10060 RNase II stability modulator; Provisional
Probab=99.11 E-value=1.9e-09 Score=132.28 Aligned_cols=169 Identities=12% Similarity=0.042 Sum_probs=124.7
Q ss_pred ccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHH
Q 002152 702 QKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAM 781 (959)
Q Consensus 702 ~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~ 781 (959)
+.+|+..|+.+.+.++.+. ...|....+.|++. ....+......++.+++.++.+ |+++|.+|+|+++|+++
T Consensus 69 ~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~~~~~g---I~i~D~~g~I~~~N~a~ 140 (663)
T PRK10060 69 TLDGEPLSVHLVGRKINKR--EWAGTASAWHDTPS---VARDLSHGLSFAEQVVSEANSV---IVILDSRGNIQRFNRLC 140 (663)
T ss_pred EeCCcEEEEEEeeeccCcc--cccchhhHHHHHHH---HHHHHHHHHHHHHHHHhhCCce---EEEEeCCCCEEEEcHHH
Confidence 4489999999877775432 34444444555555 3445566667788899998754 99999999999999999
Q ss_pred HHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCE
Q 002152 782 EKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKV 861 (959)
Q Consensus 782 ~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i 861 (959)
++++||+.++++|+++...+ .++++...+...+...+..+..+..+.++.+++|+.+|+.....+..+.++..
T Consensus 141 ~~l~Gy~~~eliG~~~~~l~-------~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~~~~~~g~~~ 213 (663)
T PRK10060 141 EEYTGLKEHDVIGQSVFKLF-------MSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKFVHSGSGKNE 213 (663)
T ss_pred HHHHCcCHHHHcCCCHHHHh-------CChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeEEEcCCCCce
Confidence 99999999999999865422 23455555566667767777788899999999999998876554433333345
Q ss_pred EEEEEEEeecccccHHHHHHHhHH
Q 002152 862 IGCFCFMQILVPDLQPALEAQGLE 885 (959)
Q Consensus 862 ~g~v~i~~DITerk~~Elelq~~a 885 (959)
.+++++.+|||++|+++.++++.+
T Consensus 214 ~~~i~~~~DITe~k~~e~~l~~~a 237 (663)
T PRK10060 214 IFLICSGTDITEERRAQERLRILA 237 (663)
T ss_pred EEEEEEEEechHHHHHHHHHHHHh
Confidence 668889999999998887765543
No 36
>PRK13559 hypothetical protein; Provisional
Probab=99.08 E-value=1.5e-09 Score=123.54 Aligned_cols=132 Identities=14% Similarity=0.028 Sum_probs=106.2
Q ss_pred HHHHHHHHHHhcCccEEEEcC---CCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceE
Q 002152 616 VACEMVRLIETATAPIFGVDS---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNV 692 (959)
Q Consensus 616 ~~~~l~~lie~~~~~I~~~D~---dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~ 692 (959)
..+.++.+++.++++++++|. +|.++++|+++++++||+.++++|+++. .+.++.........+...+.++.....
T Consensus 41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (361)
T PRK13559 41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCR-FLQGAATDPIAVAKIRAAIAAEREIVV 119 (361)
T ss_pred hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChh-hhcCCCCCHHHHHHHHHHhccCCceEE
Confidence 356788899999999999997 5689999999999999999999999986 666555555455556666666655555
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHH
Q 002152 693 ELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYE 752 (959)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~ 752 (959)
+... .+++|..+|+.++..|+++.+|.+.+++++++|||++|++++..+..+..++
T Consensus 120 e~~~----~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~~~~~l~~ 175 (361)
T PRK13559 120 ELLN----YRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEAHERRLAR 175 (361)
T ss_pred EEEE----EcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHHHHHHHHH
Confidence 5544 6789999999999999999999999999999999999988766554444333
No 37
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.04 E-value=3.1e-09 Score=131.29 Aligned_cols=137 Identities=19% Similarity=0.179 Sum_probs=114.5
Q ss_pred HHHHHHHHhcCccEEEEc---CCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEE
Q 002152 618 CEMVRLIETATAPIFGVD---SSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVEL 694 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D---~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~ 694 (959)
+.+..+++.++.+++.+| .+|.+++||+++++++||+.++++|+++. .+.+++........+...+..+.....++
T Consensus 148 r~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 226 (665)
T PRK13558 148 RLKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCR-FLQGEDTNEERVAELREAIDEERPTSVEL 226 (665)
T ss_pred HHHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHH-HhcCCCccHHHHHHHHHHHhcCCCeEEEE
Confidence 345679999999999997 47899999999999999999999999987 77776655555555555666555556666
Q ss_pred EEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcC
Q 002152 695 KLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVN 759 (959)
Q Consensus 695 ~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~ 759 (959)
+. .+++|..+|+.++..|+++.+|.+.+++++++|||++|++|+++++.+..++.+++.++
T Consensus 227 ~~----~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~ 287 (665)
T PRK13558 227 RN----YRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVE 287 (665)
T ss_pred EE----ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 65 68999999999999999999999999999999999999999999988888877766543
No 38
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=99.02 E-value=6e-09 Score=117.53 Aligned_cols=187 Identities=16% Similarity=0.196 Sum_probs=127.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHH
Q 002152 743 KFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLY 822 (959)
Q Consensus 743 ~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~ 822 (959)
++++....++++++.++. +++..|.+|++..+|++++.|+|.+.++++|..+.. + .|+ +...+.
T Consensus 364 ~~e~rr~f~E~VLsgvta---GVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa-~--------ap~----~~~vf~ 427 (712)
T COG5000 364 ALEQRRRFLEAVLSGLTA---GVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSA-I--------APE----LEEVFA 427 (712)
T ss_pred HHHHHHHHHHHHHhcCce---eEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhh-h--------hhH----HHHHHH
Confidence 334444456667887764 599999999999999999999999999999998542 1 122 222222
Q ss_pred hhhc-CCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 002152 823 QGIT-GQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQ 901 (959)
Q Consensus 823 ~~~~-~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSH 901 (959)
..-. ++.....+..+ .+.|+.+.+.+.++-...++ --|++.++.|||+-..++. +.+=.+-..-++|
T Consensus 428 ~~~a~~~~~~~~ev~~-~r~g~~rtl~Vq~t~~~~d~--~~gyVvt~DDITdLV~AQR---------s~AW~dVArRIAH 495 (712)
T COG5000 428 EAGAAARTDKRVEVKL-AREGEERTLNVQATREPEDN--GNGYVVTFDDITDLVIAQR---------SAAWGDVARRIAH 495 (712)
T ss_pred HhhhhcCCCccceeec-ccCCCceeeeeeeeeccccc--CCceEEEecchHHHHHHHH---------HHHHHHHHHHHHH
Confidence 2222 22233444444 34556666666665543322 2357888899998554442 2233455678999
Q ss_pred HhHhhhhHHHHHHHHHhc---CCCCHH---HHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 902 EVKNPLNGIRFVHKLLES---SSISEN---QRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 902 ElRnPL~~I~g~~~LL~~---~~l~e~---~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
||||||+.|.-+.+-|++ +.++++ -.+..++|.+.+..+.+++|+ -+|+|+=+=++
T Consensus 496 EIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afARmP~p~~ 558 (712)
T COG5000 496 EIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFARMPAPKL 558 (712)
T ss_pred HhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 999999999977766664 445552 468889999999999999999 89988755443
No 39
>PRK13557 histidine kinase; Provisional
Probab=99.01 E-value=3.4e-09 Score=127.34 Aligned_cols=131 Identities=16% Similarity=0.114 Sum_probs=107.1
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcC---CCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCc
Q 002152 613 LSSVACEMVRLIETATAPIFGVDS---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED 689 (959)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~---dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~ 689 (959)
.......+..++++++++++++|. +|+|+++|+++++++||+.++++|+++. .+++++........+...+..+..
T Consensus 25 ~~~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~~ 103 (540)
T PRK13557 25 SDHRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCR-FLQGPETDRATVAEVRDAIAERRE 103 (540)
T ss_pred hhhhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChH-hhcCCCCCHHHHHHHHHHHHcCCC
Confidence 344567899999999999999995 7899999999999999999999999988 777776555444445555544444
Q ss_pred ceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHH
Q 002152 690 KNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQ 748 (959)
Q Consensus 690 ~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se 748 (959)
...++.. .+++|..+|+.+...|+++.+|.+++++++.+|||+++++++++...+
T Consensus 104 ~~~~~~~----~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~ 158 (540)
T PRK13557 104 IATEILN----YRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQ 158 (540)
T ss_pred ceEEEEE----EeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHH
Confidence 4445444 578999999999999999999999999999999999999988775443
No 40
>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=98.95 E-value=9.9e-09 Score=92.65 Aligned_cols=120 Identities=27% Similarity=0.344 Sum_probs=97.5
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCC-CcceEEEEE
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE-EDKNVELKL 696 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~-~~~~~e~~~ 696 (959)
+.+..+++.++.+++++|.+|+++++|+++.+++|++..+++|+.+. .++++.........+.....+. .....++.+
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVL-ELIPEEDREEVRERIERLLEGEREPVSEERRV 81 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchh-hhcChhhhHHHHHHHHHHHcCCCCCcceEeee
Confidence 45678899999999999999999999999999999999999999987 7777766666666666666533 222333333
Q ss_pred EeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHH
Q 002152 697 RKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (959)
Q Consensus 697 ~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~ 743 (959)
...+|...|+.....|+. .+|...++++++.|||++++++++
T Consensus 82 ----~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 82 ----RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred ----EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhc
Confidence 367889999999999988 788899999999999999987654
No 41
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.94 E-value=1.9e-08 Score=113.45 Aligned_cols=224 Identities=21% Similarity=0.219 Sum_probs=154.2
Q ss_pred HHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeee
Q 002152 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFE 700 (959)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~ 700 (959)
..+++..+++++++|....+..+|..+..+++-....++|+++. ++++....+.+. +++.. ......
T Consensus 4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~~~~-~i~~~~~~~~v~-------~~~~~-~~~~~~---- 70 (560)
T COG3829 4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGRPLR-EILETLGMERVE-------QSRDK-ELTERL---- 70 (560)
T ss_pred hhhhhhcccceEEEEcCCceeeechHHHHhhhcceEEEecccce-eeccccCcceee-------ccCcc-ceeeee----
Confidence 45889999999999999999999999999999999999999887 666654433222 22211 111121
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHH-HHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecH
Q 002152 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF-IRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNA 779 (959)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L-~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~ 779 (959)
..+ . ....+...++.++.++++|++.++.|+++....-++. +...+.|+.+++.+.. +++++|.+|+++++|+
T Consensus 71 ~~~--~-~~~~~~~~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~---~l~vvD~~G~~i~~N~ 144 (560)
T COG3829 71 KLK--V-KRIVVVGKTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDD---GLLVVDEDGIIIYYNK 144 (560)
T ss_pred ecc--c-eeEEEcCCceeecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhccC---ceEEEcCCCcEEEEcH
Confidence 111 2 3344445556678899999999999999987766655 6667889999999875 5999999999999999
Q ss_pred HHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCC
Q 002152 780 AMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEG 859 (959)
Q Consensus 780 a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G 859 (959)
++.+++|++.++++|+++.+.+ .. ..+. ...+++..+.+.... .....|... ..+..|++ .+|
T Consensus 145 ~~~~~~gl~~e~~~gk~~~~v~-~~-----~~~s------~~l~vl~~~kp~~~~--~~~~~~~~~--i~~~~pv~-~~g 207 (560)
T COG3829 145 AYAKLLGLSPEEVLGKHLLDVV-SA-----GEDS------TLLEVLRTGKPIRDV--VQTYNGNKI--IVNVAPVY-ADG 207 (560)
T ss_pred HHHHHhCCCHHHHcCCcHHHHH-hc-----cCCc------eehhhhhcCCcceee--eeeecCCce--eEeeccEe-cCC
Confidence 9999999999999999765422 10 0000 122233333332222 222333332 33444554 667
Q ss_pred CEEEEEEEEeecccccHHHHH
Q 002152 860 KVIGCFCFMQILVPDLQPALE 880 (959)
Q Consensus 860 ~i~g~v~i~~DITerk~~Ele 880 (959)
.++|.+++.+|+++-+....+
T Consensus 208 ~l~G~v~~~~~~~~l~~l~~~ 228 (560)
T COG3829 208 QLIGVVGISKDVSELERLTRE 228 (560)
T ss_pred cEEEEEEeecchHHHHHHHHH
Confidence 999999999999975544433
No 42
>PRK10060 RNase II stability modulator; Provisional
Probab=98.94 E-value=1.2e-08 Score=125.31 Aligned_cols=129 Identities=21% Similarity=0.249 Sum_probs=101.0
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCcccccc-CCCchHHHHHHHHHHHcCCCcce
Q 002152 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVV-HEESQGAVENLICRALLGEEDKN 691 (959)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~-~~~~~~~~~~~l~~~l~~~~~~~ 691 (959)
++.....++.+++.++++|+++|.+|+|+++|+++++++||+.++++|+++. +++ ++++.......+...+..+..+.
T Consensus 106 ~~~~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (663)
T PRK10060 106 LSHGLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVF-KLFMSRREAAASRRNIRGFFRSGNAYE 184 (663)
T ss_pred HHHHHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHH-HHhCChhhHHHHHHHHHHHHhcCCceE
Confidence 4455566788999999999999999999999999999999999999999987 554 55555555666666676666666
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCC-CEEEEEEEeecchhhHHHHHHHHHH
Q 002152 692 VELKLRKFELQKQHSVVYILVNACTSRDYKN-NVKGVCFVGQDITHEKVLMDKFIRL 747 (959)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g-~~~gvv~v~~DITerk~~E~~L~~s 747 (959)
.+..+ .+++|..+|+.....+ .+..| ...+++++.+|||++|++++++++.
T Consensus 185 ~e~~~----~~~~G~~~~~~~~~~~-~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~ 236 (663)
T PRK10060 185 VERWI----KTRKGQRLFLFRNKFV-HSGSGKNEIFLICSGTDITEERRAQERLRIL 236 (663)
T ss_pred EEEEE----EeCCCCEEEEEeeeEE-EcCCCCceEEEEEEEEechHHHHHHHHHHHH
Confidence 66666 6788988887655444 44444 4567788999999999999988763
No 43
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=98.93 E-value=5.1e-09 Score=93.52 Aligned_cols=90 Identities=13% Similarity=0.200 Sum_probs=74.7
Q ss_pred EEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHh-hhcCCCcceeeEEEEccCCcEEEEEEEEe
Q 002152 774 CSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQ-GITGQGTENFPFGFFNRQGQFVEVALTAS 852 (959)
Q Consensus 774 i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~-~~~~~~~~~~e~~~~~~dG~~~~v~~~~~ 852 (959)
|++||+.+++++||+++++ +..... .|....||+|...+...+.+ ...++..+..++++++++|+++|+..++.
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~----~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~ 75 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFE----EWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGR 75 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHH----HHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHH----HHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEE
Confidence 5899999999999999999 655332 24568999999999999999 77788899999999999999999999999
Q ss_pred eeeCCCCCEEEEEEEE
Q 002152 853 RRTDAEGKVIGCFCFM 868 (959)
Q Consensus 853 pi~d~~G~i~g~v~i~ 868 (959)
+++|.+|+++.++|+.
T Consensus 76 ~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 76 PIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEETTTS-EEEEEEEE
T ss_pred EEECCCCCEEEEEEEC
Confidence 9999999999999874
No 44
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.92 E-value=2.6e-08 Score=125.87 Aligned_cols=125 Identities=17% Similarity=0.187 Sum_probs=101.7
Q ss_pred HHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccC-CCchHHHHHHHHHHHcCCCcceEE
Q 002152 615 SVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVH-EESQGAVENLICRALLGEEDKNVE 693 (959)
Q Consensus 615 ~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~-~~~~~~~~~~l~~~l~~~~~~~~e 693 (959)
+.++++..+++.++++++++|.+|+++++|+++++++|++.++++|+.+. ++++ +.........+.....+......+
T Consensus 133 ~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 211 (799)
T PRK11359 133 EQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPD-TLLNIPEFPADNRIRLQQLLWKTARDQDE 211 (799)
T ss_pred HHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChH-HhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence 34455677899999999999999999999999999999999999999887 5554 444444444555555555555556
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHH
Q 002152 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF 744 (959)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L 744 (959)
+++ .+++|..+|+.++..|+.+.+|.+.+++++.+|||++|++++..
T Consensus 212 ~~~----~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~ 258 (799)
T PRK11359 212 FLL----LTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLE 258 (799)
T ss_pred eEE----eCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHH
Confidence 555 67899999999999999999999999999999999999887544
No 45
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.86 E-value=3.8e-08 Score=121.61 Aligned_cols=123 Identities=18% Similarity=0.210 Sum_probs=99.3
Q ss_pred HHHHHHhcCCCCCCeeeeC---CCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcC
Q 002152 751 YEAIIQSVNPLIPPIFASD---ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (959)
Q Consensus 751 l~~i~e~~~~~i~~I~~~D---~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~ 827 (959)
++.+++..+. +++..| .+|++++||+++++++||+.++++|+.+.. +.++++.......+...+.+
T Consensus 150 ~~~~~~~~~~---gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~--------l~~~~~~~~~~~~~~~~~~~ 218 (665)
T PRK13558 150 KERALDEAPV---GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRF--------LQGEDTNEERVAELREAIDE 218 (665)
T ss_pred HHHHHhcCCc---cEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHH--------hcCCCccHHHHHHHHHHHhc
Confidence 4567888764 488887 479999999999999999999999997542 22233333344445556666
Q ss_pred CCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhH
Q 002152 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGL 884 (959)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ 884 (959)
+.....++++.+++|..+|+..+..|+.+.+|.+.+++++.+|||++|++|.++++.
T Consensus 219 ~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~ 275 (665)
T PRK13558 219 ERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRE 275 (665)
T ss_pred CCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHH
Confidence 667889999999999999999999999999999999999999999999998776643
No 46
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=98.81 E-value=5e-07 Score=108.98 Aligned_cols=199 Identities=16% Similarity=0.182 Sum_probs=124.1
Q ss_pred EEEEEeecCCCCEEEEEEEeecchhhHHHH--------------------------------------HHHHHHHHHHHH
Q 002152 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLM--------------------------------------DKFIRLQGDYEA 753 (959)
Q Consensus 712 v~~~pi~d~~g~~~gvv~v~~DITerk~~E--------------------------------------~~L~~se~~l~~ 753 (959)
..+.|+++.+|.++|++.+...+.+..... .++......++.
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 378999999999999987766443332210 111222344567
Q ss_pred HHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCc--hhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcc
Q 002152 754 IIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMR--HEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE 831 (959)
Q Consensus 754 i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~--eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~ 831 (959)
+++++++ +++.+|.+|+|+++|+++++++|++. ++++|+...+ ++. +... +. .... ....
T Consensus 227 il~~~~e---gii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~-~~~-------~~~~--~~----~~~~-~~~~ 288 (545)
T PRK15053 227 LFSSVYE---GLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAE-VVR-------PADF--FT----EQID-EKRQ 288 (545)
T ss_pred HHHHhCc---eEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHH-hCC-------Cchh--hh----hhcC-Cccc
Confidence 8888764 59999999999999999999999975 4688987543 221 1110 00 1111 1111
Q ss_pred eeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhhHHH
Q 002152 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIR 911 (959)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~~I~ 911 (959)
..+ ...+| ..+..+..|+.. +|.+.|++.+++|+|+.++.+.++.... ...+.+..++||++|||++|.
T Consensus 289 ~~~---~~~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~-----~~~e~l~~~~he~~n~L~~i~ 357 (545)
T PRK15053 289 DVV---ANFNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIK-----QYVESLRTLRHEHLNWMSTLN 357 (545)
T ss_pred ceE---EEECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhhhHHHHH
Confidence 111 22244 334566677764 5678899999999998665544432221 223557789999999999999
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002152 912 FVHKLLESSSISENQRQYLETSDACERQIMTIIDG 946 (959)
Q Consensus 912 g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d 946 (959)
|+.++-+ ..+.++.+...+.++..++++
T Consensus 358 g~l~~~~-------~~~~~~~i~~~s~~~~~l~~~ 385 (545)
T PRK15053 358 GLLQMKE-------YDRVLEMVQGESQAQQQLIDS 385 (545)
T ss_pred HHHhhch-------hhHHHHHHHHHHHHHHHHHHH
Confidence 9877532 223444455555555555544
No 47
>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=98.80 E-value=1.5e-08 Score=120.13 Aligned_cols=125 Identities=14% Similarity=0.131 Sum_probs=98.8
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCC
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~ 828 (959)
..|+.++++++. ++++.|.+|+++++|+++++++||++++++|+.... + .++.........+.+.+..+
T Consensus 4 ~~~~~i~~~~~~---~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~-~-------~~~~~~~~~~~~~~~~~~~~ 72 (494)
T TIGR02938 4 EAYRQTVDQAPL---AISITDLKANILYANDAFTRITGYTKEEIIGKNESV-L-------SNHTTPPEVYQALWGSLAEQ 72 (494)
T ss_pred HHHHHHHHhCCc---eEEEECCCCcEEEEchhheeecCCCHHHHhCCCchh-h-------cCCCCCHHHHHHHHHHHHhC
Confidence 468899999875 499999999999999999999999999999986432 1 11221222233344444455
Q ss_pred CcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhH
Q 002152 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGL 884 (959)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ 884 (959)
..+..++...+++|+.+|+.....|+.+.+|.+.+++++.+|||++|+++.++++.
T Consensus 73 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~ 128 (494)
T TIGR02938 73 KPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQ 128 (494)
T ss_pred CcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHH
Confidence 56777777889999999999999999999999999999999999999888776543
No 48
>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=98.80 E-value=5.2e-08 Score=87.86 Aligned_cols=119 Identities=17% Similarity=0.180 Sum_probs=91.4
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCC
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~ 828 (959)
..++.++++++. +++++|.+|+++++|+++.+++|++..+++|+.+.. +.++++...+...+.....+.
T Consensus 3 ~~~~~~~~~~~~---~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~ 71 (124)
T TIGR00229 3 ERYRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLE--------LIPEEDREEVRERIERLLEGE 71 (124)
T ss_pred hHHHHHHhhCCc---eEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhh--------hcChhhhHHHHHHHHHHHcCC
Confidence 456778888875 499999999999999999999999999999987553 223444444444455555533
Q ss_pred -CcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHH
Q 002152 829 -GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPAL 879 (959)
Q Consensus 829 -~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~El 879 (959)
.....++.+..++|..+|+.....|+. .+|...+++++..|||++++.+.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 72 REPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred CCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 334455566688999999999999998 88899999999999998776653
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=98.76 E-value=3.8e-08 Score=87.79 Aligned_cols=86 Identities=23% Similarity=0.276 Sum_probs=73.0
Q ss_pred eehhcHHHHHHhCCCcccccCCC----ccccccCCCchHHHHHHHHH-HHcCCCcceEEEEEEeeeeccCCcEEEEEEEE
Q 002152 640 INGWNAKVAELTGLPASEAMGKS----LIDEVVHEESQGAVENLICR-ALLGEEDKNVELKLRKFELQKQHSVVYILVNA 714 (959)
Q Consensus 640 iv~~N~~~~~l~G~~~eeliGk~----~~~~l~~~~~~~~~~~~l~~-~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~ 714 (959)
|++||+.+++++||+++++ +.. +. .++||++.+.+...+.. ....+.....++++ ++++|+.+|+.+++
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~-~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~----~~~~G~~~wi~~~~ 74 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWL-ERIHPDDRERVRQAIQQAALQNGEPFEIEYRI----RRKDGEYRWIEVRG 74 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHH-HHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEE----EGTTSTEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHH-hhcCHHHHHHHHHHHHHHhhccCcceEEEEEE----ECCCCCEEEEEEEE
Confidence 5899999999999999999 766 66 89999999999999999 77777788888888 78999999999999
Q ss_pred EEeecCCCCEEEEEEEe
Q 002152 715 CTSRDYKNNVKGVCFVG 731 (959)
Q Consensus 715 ~pi~d~~g~~~gvv~v~ 731 (959)
.+++|.+|++++++|+.
T Consensus 75 ~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 75 RPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEETTTS-EEEEEEEE
T ss_pred EEEECCCCCEEEEEEEC
Confidence 99999999999998874
No 50
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=98.74 E-value=2.1e-06 Score=97.37 Aligned_cols=199 Identities=18% Similarity=0.185 Sum_probs=128.0
Q ss_pred CcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHH--------------------------------------HHHH
Q 002152 705 HSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMD--------------------------------------KFIR 746 (959)
Q Consensus 705 G~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~--------------------------------------~L~~ 746 (959)
|..-+..=-..|++|++|+++|++.+.--+++--..-. ++..
T Consensus 133 Gslg~s~R~~~PI~d~~g~~IGvVsVG~~l~~i~~~i~~~~~~l~~~~vl~lligl~ga~~la~~ikr~~~glEP~EIa~ 212 (537)
T COG3290 133 GSLGKSLRAKVPIFDEDGKQIGVVSVGYLLSEIDDVILEFLRPLALIVVLGLLIGLLGAWILARHIKRQMLGLEPEEIAT 212 (537)
T ss_pred ccchhhheeecceECCCCCEEEEEEEeeEhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence 44334444468999999999999988765554322111 2223
Q ss_pred HHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCch--hhcCCCcccccccccccccChhhHHHHHHHHHhh
Q 002152 747 LQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRH--EVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQG 824 (959)
Q Consensus 747 se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~e--eviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~ 824 (959)
.-+.-.++++++.. |++.+|..|.+..+|.++++++|+... +.+|++..+. +. |+. .+...++
T Consensus 213 l~~er~A~l~si~E---GviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v-~~-------p~~--~l~~vl~-- 277 (537)
T COG3290 213 LLEERQAMLQSIKE---GVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEV-LP-------PDS--DLPEVLE-- 277 (537)
T ss_pred HHHHHHHHHHHhhc---eEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEe-ec-------ccc--CcHHHHh--
Confidence 33344577788765 499999999999999999999999765 6888876642 22 211 1111111
Q ss_pred hcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhH
Q 002152 825 ITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVK 904 (959)
Q Consensus 825 ~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElR 904 (959)
.++.....+ .+-+|. ++..+..|+. .+|+++|++.+++|-||-++...++... ++-.+-|...+||+.
T Consensus 278 -~~~~~~~~e---~~~ng~--~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~v-----r~ya~aLRaq~HEfm 345 (537)
T COG3290 278 -TGKPQHDEE---IRINGR--LLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGV-----RQYAEALRAQSHEFM 345 (537)
T ss_pred -cCCcccchh---hhcCCe--EEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHH-----HHHHHHHHHhhHHHH
Confidence 122222222 223443 5667777876 6789999999999988755554443221 122345777899999
Q ss_pred hhhhHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 002152 905 NPLNGIRFVHKLLESSSISENQRQYLETSD 934 (959)
Q Consensus 905 nPL~~I~g~~~LL~~~~l~e~~~~~l~~i~ 934 (959)
|-|+.|.|++++=+- ++..+|+..+.
T Consensus 346 NkLhtI~GLlql~~y----d~a~~~I~~~~ 371 (537)
T COG3290 346 NKLHTILGLLQLGEY----DDALDYIQQES 371 (537)
T ss_pred HHHHHHHHHHhhccH----HHHHHHHHHHH
Confidence 999999999987542 34555665554
No 51
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.73 E-value=3.8e-08 Score=90.84 Aligned_cols=106 Identities=24% Similarity=0.314 Sum_probs=80.4
Q ss_pred HHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEee
Q 002152 620 MVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKF 699 (959)
Q Consensus 620 l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~ 699 (959)
+..++++++.++.++|.+++|.++|+++.++|++.+.+ +|+++. ++.++...+.+...+..+..++.. ..+...
T Consensus 1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~~-iGr~l~-~~~~~~~~~~l~~~i~~~~~~~~~-~~~~~~--- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPSD-IGRPLF-DIHPPLSYPNLKKIIEQVRSGKEE-EFEIVI--- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GGG-TTSBCC-CSS-HHHHHHHHHHHHHHHTTSBS-EEEEEE---
T ss_pred ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChHH-CCCCHH-HcCCccchHHHHHHHHHHHcCCCc-eEEEEe---
Confidence 46889999999999999999999999999999988755 699998 888877778888888888877653 223232
Q ss_pred eeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecch
Q 002152 700 ELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT 735 (959)
Q Consensus 700 ~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DIT 735 (959)
..+ .+|+.++..|+++.+|+..|++.++.|||
T Consensus 75 --~~~--~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 --PNG--GRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp --EET--TEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred --cCC--CEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 123 36788999999999999999999999998
No 52
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.72 E-value=1.5e-07 Score=107.25 Aligned_cols=226 Identities=10% Similarity=0.128 Sum_probs=156.5
Q ss_pred HHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCC---------Ccce
Q 002152 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE---------EDKN 691 (959)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~---------~~~~ 691 (959)
..++++....+++++.||.++|+++.....+|++.-|+.|..++ +++||-+.+.+.+.+....... ....
T Consensus 122 ~~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvF-DfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRs 200 (768)
T KOG3558|consen 122 DHILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVF-DFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERS 200 (768)
T ss_pred hhHHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhh-hccCccCHHHHHHHhccccCCCcccccccCcccee
Confidence 35677777888999999999999999999999999999999999 9999999988877765444311 1245
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEE---------eecCCCC----------EEEEEEEeecchhhHHHHHHHHHHHHHHH
Q 002152 692 VELKLRKFELQKQHSVVYILVNACT---------SRDYKNN----------VKGVCFVGQDITHEKVLMDKFIRLQGDYE 752 (959)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~p---------i~d~~g~----------~~gvv~v~~DITerk~~E~~L~~se~~l~ 752 (959)
+-+++++. ..+-|+...+...... +++..+. ..+.+.+..-|---+-.|--|
T Consensus 201 FflRMKsT-LT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL-------- 271 (768)
T KOG3558|consen 201 FFLRMKST-LTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPL-------- 271 (768)
T ss_pred EEEEeeee-eccCCceeeeeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCccccccc--------
Confidence 56666655 3444543332221111 1111111 222222222221111111000
Q ss_pred HHHHhcCCCCCCee--eeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCc
Q 002152 753 AIIQSVNPLIPPIF--ASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT 830 (959)
Q Consensus 753 ~i~e~~~~~i~~I~--~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~ 830 (959)
. -..| ....|-+|+|+.+.+.+++||.+++++|+..+ +++|+.|.+.+.......+..+..
T Consensus 272 -------~--~~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Y--------e~~Ha~Ds~~v~KSh~dL~~KGQv 334 (768)
T KOG3558|consen 272 -------D--CHMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCY--------EFVHALDSDRVRKSHHDLLTKGQV 334 (768)
T ss_pred -------C--CceeEEeeecceeEEEEchhHHHHhcCCHHHhhchhHH--------HhhhHhhhhHHHHHHHHHHhcCcc
Confidence 0 0122 34568899999999999999999999999854 588899999999999999998889
Q ss_pred ceeeEEEEccCCcEEEEEEEEeeeeCCC-CCEEEEEEEEeeccc
Q 002152 831 ENFPFGFFNRQGQFVEVALTASRRTDAE-GKVIGCFCFMQILVP 873 (959)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~~~pi~d~~-G~i~g~v~i~~DITe 873 (959)
...-||+..|+|.++|+...++.+.+.. ++...++|+---|+.
T Consensus 335 ~TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~ 378 (768)
T KOG3558|consen 335 VTGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSN 378 (768)
T ss_pred chhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeecc
Confidence 9999999999999999999999887643 344556666555554
No 53
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.70 E-value=6.8e-08 Score=95.90 Aligned_cols=153 Identities=17% Similarity=0.227 Sum_probs=109.7
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCC--eEEEEEecCCC----CCCccCCccCCCCchHH
Q 002152 216 AVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDH--GEVVSEIRRSD----LEPYLGIHFPANDIPQA 289 (959)
Q Consensus 216 ~~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~--G~viaE~~~~~----~~s~lg~~~pa~dip~~ 289 (959)
+..+...+.. +.+++++++.+++.+.+.+|+||..||++++++. +.++++..... ..+-.+.. ..... .
T Consensus 6 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~ 80 (175)
T COG2203 6 LNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLV--ILPAC-L 80 (175)
T ss_pred HHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhccc--Ccchh-h
Confidence 3455566666 6699999999999999999999999999999995 66666554442 11111111 00011 1
Q ss_pred HHHHHHhCCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEe
Q 002152 290 ARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVC 369 (959)
Q Consensus 290 ar~ly~~~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~ 369 (959)
...........++.|+...|.. ..+|..++... ++|.+++||+.++ ++||.+++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~-i~~~l~vPl~~~~----~~~G~l~~ 134 (175)
T COG2203 81 IGIALREGRPVVVEDILQDPRF---------------------RDNPLVLLEPP-IRSYLGVPLIAQG----ELLGLLCV 134 (175)
T ss_pred hhhhhcCCceEEeeccccCccc---------------------ccCHHHHHHHH-HHHheeeeeeECC----EeeEEeee
Confidence 1222345566677776655431 12566666655 9999999999998 99999999
Q ss_pred ecCCCC-CCChhHHHHHHHHHHHHHHHHHHH
Q 002152 370 HHTSPR-YIPFPLRYACEFLVQAFSLQLYME 399 (959)
Q Consensus 370 hh~~pr-~~~~~~r~~~~~l~~~~s~~l~~~ 399 (959)
||+.++ .|+.++..+.+.++++++..|...
T Consensus 135 ~~~~~~~~~~~~e~~ll~~la~~~a~ai~~~ 165 (175)
T COG2203 135 HDSEPRRQWSEEELELLEELAEQVAIAIERA 165 (175)
T ss_pred eccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 999966 699999999999999999988644
No 54
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.64 E-value=7.3e-07 Score=84.81 Aligned_cols=128 Identities=19% Similarity=0.230 Sum_probs=91.3
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCC
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 309 (959)
|++++++.+++.+++++|+|++.||.++++..--.++... .+ .+-+...+| .+-|- ....+..+++..+++....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~~-~~~~~~~l~-~~~~~-~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW-GG-DPRLSESLP-EDDPL-IGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE-SS--GCGHHCEE-TTSHH-HHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe-CC-CccccccCC-CCccH-HHHHHhhCCeEEeccccccc
Confidence 6899999999999999999999999999885433333333 11 111222555 33333 33667777776665533211
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHH
Q 002152 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLV 389 (959)
Q Consensus 310 ~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~ 389 (959)
..+.++.|.+||..++ +++|+|.++...++.|+......++.++
T Consensus 77 --------------------------------~~~~~s~~~vPl~~~~----~~~Gvl~~~~~~~~~~~~~d~~~l~~~a 120 (129)
T PF13492_consen 77 --------------------------------FLGIRSLLVVPLRSRD----RVIGVLCLDSREPEEFSDEDLQLLESLA 120 (129)
T ss_dssp --------------------------------TTTTCEEEEEEEEETT----EEEEEEEEEECTTCG-SHHHHHHHHHHH
T ss_pred --------------------------------CCCCCEEEEEEEeECC----EEEEEEEEEECCCCCCCHHHHHHHHHHH
Confidence 0566889999999988 9999999988888899999999999999
Q ss_pred HHHHHHHH
Q 002152 390 QAFSLQLY 397 (959)
Q Consensus 390 ~~~s~~l~ 397 (959)
.++|..|+
T Consensus 121 ~~~a~ale 128 (129)
T PF13492_consen 121 NQLAIALE 128 (129)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 99998875
No 55
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.59 E-value=4.6e-07 Score=110.25 Aligned_cols=132 Identities=18% Similarity=0.276 Sum_probs=103.3
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcc
Q 002152 611 DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDK 690 (959)
Q Consensus 611 ~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~ 690 (959)
+.++..+..+..++++++++++++|.+|+++++|+++++++|++.++++|+++. ++++++.. ...........+....
T Consensus 255 ~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~-~~~~~~~~-~~~~~~~~~~~~~~~~ 332 (607)
T PRK11360 255 QALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYS-ELFPPNTP-FASPLLDTLEHGTEHV 332 (607)
T ss_pred HHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHH-HHcCCchh-HHHHHHHHHhcCCCcc
Confidence 456666677889999999999999999999999999999999999999999987 77665432 2222223333333444
Q ss_pred eEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHH
Q 002152 691 NVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (959)
Q Consensus 691 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~ 749 (959)
..++.+ ..++|... +.++..|+.+.+|++.|++++++|||++|++|+++++.+.
T Consensus 333 ~~~~~~----~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~ 386 (607)
T PRK11360 333 DLEISF----PGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQER 386 (607)
T ss_pred ceEEEE----EcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHH
Confidence 445555 45667665 8899999999999999999999999999999998876543
No 56
>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=98.54 E-value=1.6e-06 Score=84.60 Aligned_cols=137 Identities=15% Similarity=0.162 Sum_probs=90.9
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCcc--CCC--CchHHHH-----HHHHhCCEE
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHF--PAN--DIPQAAR-----FLFKQNRVR 300 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~--pa~--dip~~ar-----~ly~~~~~r 300 (959)
+++++++.+++.+.+++|+|...||-+++++.-..++-+..+ ...++..+ |.. ..|...+ .++..++..
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 789999999999999999999999999888732333333332 22222221 111 1111110 115567776
Q ss_pred EEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChh
Q 002152 301 MICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFP 380 (959)
Q Consensus 301 ~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~ 380 (959)
++. .+... .+. .......|+++.+++||+.+| ++||+|...+..++.++..
T Consensus 81 ~~~-~~~~~-----------------------~~~-~~~~~~~~~~s~l~vPl~~~~----~~~Gvl~l~~~~~~~f~~~ 131 (148)
T PF13185_consen 81 IIN-DDDSS-----------------------FPP-WELARHPGIRSILCVPLRSGG----EVIGVLSLYSKEPNAFSEE 131 (148)
T ss_dssp EES-CCCGG-----------------------GST-THHHCCTT-SEEEEEEEEETT----EEEEEEEEEESSTT---HH
T ss_pred EEe-Ccccc-----------------------ccc-hhhhccccCCEEEEEEEeECC----EEEEEEEEeeCCCCCcCHH
Confidence 776 11000 011 366899999999999999998 9999999999889999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q 002152 381 LRYACEFLVQAFSLQLY 397 (959)
Q Consensus 381 ~r~~~~~l~~~~s~~l~ 397 (959)
.+..++.+++++|..|+
T Consensus 132 ~~~~l~~la~~~a~aie 148 (148)
T PF13185_consen 132 DLELLEALADQIAIAIE 148 (148)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999988763
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=98.53 E-value=1.3e-06 Score=74.58 Aligned_cols=103 Identities=29% Similarity=0.409 Sum_probs=85.2
Q ss_pred cCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCc
Q 002152 627 ATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHS 706 (959)
Q Consensus 627 ~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~ 706 (959)
++++++++|.+|.++++|+.+.+++|++..+++|+.+. .+++++....+...+.....+......++.+ ...+|.
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ 75 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLL-DLIHPEDREELRERLENLLSGGEPVTLEVRL----RRKDGS 75 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHH-HhcCCccchHHHHHHHHHHhcCcCeEEEEEE----EccCCC
Confidence 36789999999999999999999999999999999988 7888877766666666666554444555555 456788
Q ss_pred EEEEEEEEEEeecCCCCEEEEEEEeecc
Q 002152 707 VVYILVNACTSRDYKNNVKGVCFVGQDI 734 (959)
Q Consensus 707 ~~~v~v~~~pi~d~~g~~~gvv~v~~DI 734 (959)
..|+.+...++.+..|...+++++.+||
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 76 VIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999999998888999999998886
No 58
>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=98.46 E-value=1.1e-06 Score=98.13 Aligned_cols=114 Identities=15% Similarity=0.198 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEE
Q 002152 614 SSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE 693 (959)
Q Consensus 614 ~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e 693 (959)
+...++++.++++++++++++|.+|++++||+++++++|++.++.+|+++. ++.++++ +...+. .+... ..
T Consensus 2 ~~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~~~~~---~~~~l~---~~~~~--~~ 72 (333)
T TIGR02966 2 SALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRIT-NLIRHPE---FVEYLA---AGRFS--EP 72 (333)
T ss_pred hhHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHH-HHccCHH---HHHHHH---hcccC--CC
Confidence 345677899999999999999999999999999999999999999999987 6665432 222222 11111 12
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHH
Q 002152 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFI 745 (959)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~ 745 (959)
+.+ ..++|..+|+.+...|+.+.. ++++++|||++++.++...
T Consensus 73 ~~~----~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~~ 115 (333)
T TIGR02966 73 LEL----PSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMRR 115 (333)
T ss_pred eEe----ecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHHH
Confidence 333 346788899999999987643 5788899999998876544
No 59
>PF12860 PAS_7: PAS fold
Probab=98.43 E-value=6.5e-07 Score=83.95 Aligned_cols=104 Identities=21% Similarity=0.318 Sum_probs=71.5
Q ss_pred HHhcCccEEEEcCCCceehhcHHHHHHhCCCcccc-cCCCcccccc---------CCCch-HHHHHHHHHHHcCCCcceE
Q 002152 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEA-MGKSLIDEVV---------HEESQ-GAVENLICRALLGEEDKNV 692 (959)
Q Consensus 624 ie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eel-iGk~~~~~l~---------~~~~~-~~~~~~l~~~l~~~~~~~~ 692 (959)
+++++.||+++|.+|++++||+++.+++|++.+.+ .|.++. +++ .+.+. ..+.+.+..... .....+
T Consensus 1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~-~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~~~~ 78 (115)
T PF12860_consen 1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFR-DLLRRLAERGEFPPGDPEAWVRQRLARLRR-RQPRSF 78 (115)
T ss_pred CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHH-HHHHHHHHcCCCCCCCHHHHHHHHHHHHhc-CCCcee
Confidence 47899999999999999999999999999999987 788765 433 11222 223333322222 233233
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHH
Q 002152 693 ELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMD 742 (959)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~ 742 (959)
++. ..+| +|+.+...|..+ | |++.++.|||++|++|+
T Consensus 79 ~~~------~~dg--r~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 79 ELR------LPDG--RWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred EEE------CCCC--EEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 332 3455 567788888754 4 56789999999998874
No 60
>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=98.43 E-value=2.2e-05 Score=94.13 Aligned_cols=153 Identities=10% Similarity=0.067 Sum_probs=110.1
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHH
Q 002152 214 KLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFL 293 (959)
Q Consensus 214 ~~~~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~l 293 (959)
+.+.++...+.+ +.+++++++.+++.+.+++|+||..||-+++++...+++ +....-+..-...|+... --+...
T Consensus 5 ~~L~~is~~l~~--~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~a-a~g~~~~~~~~~~~~~~~--gi~g~v 79 (534)
T TIGR01817 5 AALYEISKILSA--PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLVA-AIGWSEEGFAPIRYRVGE--GAIGQI 79 (534)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEEE-EeCCChhhcccccccCCc--cHHHHH
Confidence 444555666666 679999999999999999999999999999887654443 322111111113343321 234566
Q ss_pred HHhCCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002152 294 FKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (959)
Q Consensus 294 y~~~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~ 373 (959)
+..+..-+|.|+...|-.. .+ .-+...+++|.|+|||+.+| +++|.|..++..
T Consensus 80 ~~~~~pvii~Dv~~d~~~~---------------------~~--~~~~~~~~~S~l~VPL~~~g----~viGvL~v~s~~ 132 (534)
T TIGR01817 80 VATGNSLVVPDVAAEPLFL---------------------DR--LSLYDPGPVPFIGVPIKADS----ETIGVLAADRDF 132 (534)
T ss_pred HhcCCeEEecccccCchhh---------------------hc--cccccCCcceEEEEEEcCCC----EEEEEEEEEecc
Confidence 7789999999987654311 00 01335678999999999888 999999999886
Q ss_pred -CCCCChhHHHHHHHHHHHHHHHHHH
Q 002152 374 -PRYIPFPLRYACEFLVQAFSLQLYM 398 (959)
Q Consensus 374 -pr~~~~~~r~~~~~l~~~~s~~l~~ 398 (959)
++.+..+...+++.+|.+++..|..
T Consensus 133 ~~~~ft~~d~~lL~~lA~~ia~aI~~ 158 (534)
T TIGR01817 133 RSRERLEEEVRFLEMVANLIGQTVRL 158 (534)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHH
Confidence 6777999999999999999988863
No 61
>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=98.41 E-value=3.7e-06 Score=71.76 Aligned_cols=100 Identities=19% Similarity=0.232 Sum_probs=81.4
Q ss_pred CeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCc
Q 002152 764 PIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQ 843 (959)
Q Consensus 764 ~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~ 843 (959)
+++.+|.+|.++++|+++++++|++..+++|+.+.. +.++++...+...+.....+......++.+...+|.
T Consensus 4 ~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (103)
T cd00130 4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLD--------LIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGS 75 (103)
T ss_pred eEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHH--------hcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCC
Confidence 589999999999999999999999999999987553 233444445555566665555566778888889999
Q ss_pred EEEEEEEEeeeeCCCCCEEEEEEEEeec
Q 002152 844 FVEVALTASRRTDAEGKVIGCFCFMQIL 871 (959)
Q Consensus 844 ~~~v~~~~~pi~d~~G~i~g~v~i~~DI 871 (959)
.+|+.....++.+..|...+++++.+||
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 76 VIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999999999999999999988886
No 62
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.38 E-value=3.8e-05 Score=76.39 Aligned_cols=226 Identities=23% Similarity=0.279 Sum_probs=141.2
Q ss_pred EEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEE
Q 002152 632 FGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYIL 711 (959)
Q Consensus 632 ~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~ 711 (959)
+..+..+.+...|......+++......+ .. ............................... ...++...++.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 75 (232)
T COG2202 3 LVLDRDGRIIYANEAAEELLGYSAEELLG--LL-LALHPEDRDRLRELLRRLLAGEELLSEELRL----VRKDGEERWVE 75 (232)
T ss_pred EEEcccccEEEecccchhhcCCChHHhhh--hh-hccCccchhhhHHHHHHHhccCCcchhhHHh----hhcCCcEEEEE
Confidence 44566777788888888888877666555 11 1111111111111222222211111111111 23344555554
Q ss_pred EEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchh
Q 002152 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHE 791 (959)
Q Consensus 712 v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~ee 791 (959)
..........+........ .|+++.+..+..+...+.+++.++++.+.. ++..|.+|.+.++|+++.+++|++..+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~d~~~~~~~~n~~~~~~~g~~~~~ 151 (232)
T COG2202 76 LSAAPLRDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASPDG---IWVLDEDGRILYANPAAEELLGYSPEE 151 (232)
T ss_pred ecceEEEcCCCCEEEEEee-eecchHHHHHHHHHHHHHHHHHHHhhCCce---EEEEeCCCCEEEeCHHHHHHhCCChHH
Confidence 4444434445555555556 899999999999999999999999998854 999999999999999999999999888
Q ss_pred hcCCCcccccccccccccChhhHHHHHHHHHhh-hcCCCcceeeEEEEccCCcE-EEEEEEEeeeeCCCCCEEEEEEEEe
Q 002152 792 VIGKMLPREIFGNFCRMKGQDMLTKFMILLYQG-ITGQGTENFPFGFFNRQGQF-VEVALTASRRTDAEGKVIGCFCFMQ 869 (959)
Q Consensus 792 viGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~-~~~~~~~~~e~~~~~~dG~~-~~v~~~~~pi~d~~G~i~g~v~i~~ 869 (959)
..+......... ...+.. ........ .........++....++|.. .+......+... .|.+.++.+...
T Consensus 152 ~~~~~~~~~~~~-----~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 223 (232)
T COG2202 152 ELGRGLSDLIHP-----EDEERR--ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIAR 223 (232)
T ss_pred hcCCChhheEec-----CCCchh--hHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEe
Confidence 886654332111 111110 11112222 22334567888889999996 888777777655 788999999999
Q ss_pred ecccccH
Q 002152 870 ILVPDLQ 876 (959)
Q Consensus 870 DITerk~ 876 (959)
|+|++++
T Consensus 224 d~~~~~~ 230 (232)
T COG2202 224 DITERKQ 230 (232)
T ss_pred chHHHhh
Confidence 9998665
No 63
>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=98.36 E-value=6.6e-07 Score=115.72 Aligned_cols=77 Identities=27% Similarity=0.420 Sum_probs=71.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 882 q~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
+..+++++++|.+|++.|||||||||++|.|+.++|....++++++++++.|..++++|..+|++ |+++|+|+|++.
T Consensus 454 ~~~~~~~~~~~~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~~~~ 531 (968)
T TIGR02956 454 RAEAEEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGHLS 531 (968)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCe
Confidence 45677788899999999999999999999999999998889999999999999999999999999 999999999754
No 64
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.36 E-value=2.1e-06 Score=91.01 Aligned_cols=130 Identities=16% Similarity=0.210 Sum_probs=103.4
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc
Q 002152 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (959)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~ 685 (959)
++.+++-++...+++.+++-.+.+|++..|..|+|+.+|..+.+++|.+.++++|+++. +++.-++.-.+.+. ..
T Consensus 99 ~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~-elL~i~d~y~~~dL----~e 173 (459)
T COG5002 99 VQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSIL-ELLKIEDTYTFEDL----VE 173 (459)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHH-HHhCCccceeHHHH----Hh
Confidence 34445566777788999999999999999999999999999999999999999999988 77766554433333 22
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHH
Q 002152 686 GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRL 747 (959)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~s 747 (959)
... ++-+. .+..++...+.++.+.++-+.|-+.|++++..|+||+.+.|++.++.
T Consensus 174 ~~~----s~lld---~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRef 228 (459)
T COG5002 174 KND----SLLLD---SSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERREF 228 (459)
T ss_pred cCC----cEEEe---ecCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHHHH
Confidence 222 22222 23367888889999999999999999999999999999999876653
No 65
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.32 E-value=3.3e-06 Score=77.86 Aligned_cols=106 Identities=18% Similarity=0.173 Sum_probs=74.1
Q ss_pred HHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCc
Q 002152 751 YEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT 830 (959)
Q Consensus 751 l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~ 830 (959)
++.++++++. ++..+|.+++|.++|+++.++++... ..+|+++.+ +..+...+.+...+..+..++.
T Consensus 1 L~~il~s~~~---~i~~vD~~~~I~~~n~~a~~~f~~~~-~~iGr~l~~--------~~~~~~~~~l~~~i~~~~~~~~- 67 (106)
T PF13596_consen 1 LNNILDSMPI---GIIFVDRNLRIRYFNPAAARLFNLSP-SDIGRPLFD--------IHPPLSYPNLKKIIEQVRSGKE- 67 (106)
T ss_dssp HHHHHHHSSS---EEEEEETTSBEEEE-SCGC-SS---G-GGTTSBCCC--------SS-HHHHHHHHHHHHHHHTTSB-
T ss_pred ChHHHhcCCC---CEEEEcCCCeEEEeChhHhhhcCCCh-HHCCCCHHH--------cCCccchHHHHHHHHHHHcCCC-
Confidence 3578888875 49999999999999999999999775 457998664 3345666677777877777664
Q ss_pred ceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecc
Q 002152 831 ENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILV 872 (959)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DIT 872 (959)
...+... ..+| +|+.++..|+++.+|+..|++.++.|||
T Consensus 68 ~~~~~~~-~~~~--~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 68 EEFEIVI-PNGG--RWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp SEEEEEE-EETT--EEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred ceEEEEe-cCCC--EEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 2233332 2344 5778899999999999999999999998
No 66
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.32 E-value=3.7e-06 Score=95.20 Aligned_cols=116 Identities=13% Similarity=0.125 Sum_probs=86.0
Q ss_pred HHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCc-ceEEEEEE
Q 002152 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED-KNVELKLR 697 (959)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~-~~~e~~~~ 697 (959)
.+..++++++++++++|.+|+|+++|+++++++|++.++++|+++. ++++..... ...+...+..+.. ...++.
T Consensus 8 ~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-- 82 (348)
T PRK11073 8 DAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLP-ELLSYFSLN--IELMRESLQAGQGFTDNEVT-- 82 (348)
T ss_pred hHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHH-HHcCcchhh--HHHHHHHHHcCCcccccceE--
Confidence 4688999999999999999999999999999999999999999987 776543221 1222333333222 222222
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHH
Q 002152 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRL 747 (959)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~s 747 (959)
...+|+.+|+.++..|+. . .+++..++|||++++.++++.+.
T Consensus 83 ---~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~ 124 (348)
T PRK11073 83 ---LVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQH 124 (348)
T ss_pred ---EEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHH
Confidence 245899999999999987 1 34567789999999987766443
No 67
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=98.32 E-value=8.3e-07 Score=114.15 Aligned_cols=77 Identities=25% Similarity=0.453 Sum_probs=71.1
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 882 q~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
++.+++++..|.+|++.+||||||||++|.|++++|....++++++++++.+..++.+|..+|++ |+++|+|+|++.
T Consensus 388 ~~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~~ 465 (921)
T PRK15347 388 KQRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMT 465 (921)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcc
Confidence 45666777789999999999999999999999999999889999999999999999999999999 999999999764
No 68
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.25 E-value=1.4e-05 Score=97.96 Aligned_cols=220 Identities=15% Similarity=0.181 Sum_probs=124.4
Q ss_pred HHHHHHHhcCccEEEEcCCCceehhcHHHHHH-----hCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEE
Q 002152 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAEL-----TGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE 693 (959)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l-----~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e 693 (959)
.+..++...+..+++.|.+|.|+.++....-+ .|+. .|..|..+.+.. ..+..++..+.+..+.
T Consensus 63 ~l~~~l~~~~~~~~l~D~~G~vL~~~g~~~~~~~~~~~~~~----~G~~w~E~~~GT-------naig~al~~~~pv~v~ 131 (638)
T PRK11388 63 DAWEYMADRECALLILDETGCILSRNGDPQTLQQLSALGFN----DGTYCAEGIIGT-------NALSLAAISGQPVKTM 131 (638)
T ss_pred HHHHHhcCCCcEEEEEcCCceEEEEeCCHHHHHHHHHcCCc----cCCccchhccCc-------CHHHHHHhcCCceEEe
Confidence 34556677788999999999999865322211 1221 233333111111 1222333222221110
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecch------------------hhHHHHHHH---HHHHHHHH
Q 002152 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT------------------HEKVLMDKF---IRLQGDYE 752 (959)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DIT------------------erk~~E~~L---~~se~~l~ 752 (959)
.-+ |--.....+...+.|++|.+|+++|++.+..+.. .+....... ......+.
T Consensus 132 -g~E----H~~~~~~~~~c~aaPI~d~~G~liGvl~l~~~~~~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~~~~~~~ 206 (638)
T PRK11388 132 -GDQ----HFKQALHNWAFCATPVFDSKGRLTGTIALACPVEQTSAADLPLTLSIAREVGNLLLTDSLLAESNRHLNQLN 206 (638)
T ss_pred -cHH----HHHHhccCceEEeeEEEcCCCCEEEEEEEEecccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 000 0001223356788999999999999997765432 222111111 22223344
Q ss_pred HHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcc-
Q 002152 753 AIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE- 831 (959)
Q Consensus 753 ~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~- 831 (959)
.++++++ ++++++|.+|+|+++|+++++++|++.++++|+.+.+ ++. .+.. +.+++..+...
T Consensus 207 ~il~~~~---~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~-l~~------~~~~-------l~~vl~~~~~~~ 269 (638)
T PRK11388 207 ALLESMD---DGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITE-LLT------LPAV-------LQQAIKQAHPLK 269 (638)
T ss_pred HHHhccC---CcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHH-Hhc------cchH-------HHHHHhcCCcee
Confidence 5777765 4699999999999999999999999999999997553 222 0111 12223323222
Q ss_pred eeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccc
Q 002152 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPD 874 (959)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITer 874 (959)
..+.. ...+|..+++.++..|+.+..|. +++.+.+|++..
T Consensus 270 ~~~~~-l~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~ 309 (638)
T PRK11388 270 HVEVT-FESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQM 309 (638)
T ss_pred eEEEE-EecCCceEEEEEEEEeecccCce--EEEEEehhhHHH
Confidence 22222 23457777888999999755453 355556777753
No 69
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=98.25 E-value=1.4e-06 Score=102.30 Aligned_cols=69 Identities=16% Similarity=0.273 Sum_probs=61.6
Q ss_pred HHHHHHHHHHHHHhHhhhhHHHHHHHHHhc--CCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLES--SSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 890 ~ak~~fLa~iSHElRnPL~~I~g~~~LL~~--~~l~e~-~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
+.++.+|+.|||||||||++|+|..+.|.. ..++++ +.+.+..|...+++|.+++++ ||++||++|-+.
T Consensus 658 ~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~ 730 (890)
T COG2205 658 RLRSALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVN 730 (890)
T ss_pred HHHHHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCcc
Confidence 467889999999999999999999998875 556666 788999999999999999999 999999999653
No 70
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=98.24 E-value=1.8e-06 Score=71.18 Aligned_cols=64 Identities=39% Similarity=0.592 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 892 KIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 892 k~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
+.++++.++||+||||++|.++.+++.....+++..++++.+..+++++..++++ +++++++++
T Consensus 2 ~~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~ 66 (66)
T smart00388 2 KREFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIEAG 66 (66)
T ss_pred HHHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3578899999999999999999998887666777789999999999999999999 899998764
No 71
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.21 E-value=2.2e-06 Score=110.21 Aligned_cols=77 Identities=25% Similarity=0.417 Sum_probs=69.9
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 882 q~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
++.++++++.|.+|++.|||||||||++|.|+.+++....+++++++|++.|..++++|..+|++ |+++|+++|++.
T Consensus 283 ~~~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~ 360 (919)
T PRK11107 283 KKRAQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKLV 360 (919)
T ss_pred HHHHHHHHHHHHHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcE
Confidence 34556667788999999999999999999999999888788999999999999999999999999 999999999763
No 72
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=98.19 E-value=0.00018 Score=85.44 Aligned_cols=214 Identities=12% Similarity=0.056 Sum_probs=129.3
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHh
Q 002152 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (959)
Q Consensus 217 ~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~ 296 (959)
.++...|-+ +.+++++++.+++.+.+++++|.+-|+.++++ .....+..+.-....+..|+..+=|--... ...
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---QLVPLAIDGLSPDVLGRRFALEEHPRLEAI-LRA 80 (509)
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC---cEEEEEEcCCChHhhCCccCCCcchHHHHH-Hhc
Confidence 445556666 78999999999999999999999999999753 222223322223345567776665533222 243
Q ss_pred CCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCC
Q 002152 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRY 376 (959)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~ 376 (959)
+++..|+|...-|.++- |-.. ....++|++|.|+|||.++| +.+|.|.++...|..
T Consensus 81 g~~v~v~~~~~~p~~~~----------------~~~~----~~~~~~gi~S~l~vPL~~~~----~~~GvL~l~~~~~~~ 136 (509)
T PRK05022 81 GDPVRFPADSELPDPYD----------------GLIP----GVQESLPVHDCMGLPLFVDG----RLIGALTLDALDPGQ 136 (509)
T ss_pred CCeEEEecCCCCCcccc----------------cccc----cccccCCcceEEEEEEEECC----EEEEEEEEeeCCCCc
Confidence 66666665543332210 0000 01345799999999999998 999999999988888
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc-CCcccccCCchhhhhccCCeEEEEECCeEE
Q 002152 377 IPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRD-APFSIVTQSPSIMDLVKCDGAALYYGGRCW 455 (959)
Q Consensus 377 ~~~~~r~~~~~l~~~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~l~~a~g~a~~~~~~~~ 455 (959)
+.......++.++.+++..|...........+...+ ......+..+. .+..++.+++.+..+..--..+--.+..+.
T Consensus 137 f~~~~~~~l~~~a~~~a~Al~~a~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~iig~s~~~~~~~~~i~~~a~~~~pVl 214 (509)
T PRK05022 137 FDAFSDEELRALAALAAATLRNALLIEQLESQAELP--QDVAEFLRQEALKEGEMIGQSPAMQQLKKEIEVVAASDLNVL 214 (509)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhhhccCCceeecCHHHHHHHHHHHHHhCCCCcEE
Confidence 888888999999999999887543322221111111 11111111111 345677777666554432222222344555
Q ss_pred EecCCCC
Q 002152 456 LVGVTPT 462 (959)
Q Consensus 456 ~~G~~p~ 462 (959)
+.|.+=+
T Consensus 215 I~Ge~Gt 221 (509)
T PRK05022 215 ILGETGV 221 (509)
T ss_pred EECCCCc
Confidence 6666544
No 73
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=98.19 E-value=0.00019 Score=88.75 Aligned_cols=147 Identities=6% Similarity=0.007 Sum_probs=103.7
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEec--CCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecC
Q 002152 228 GGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIR--RSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDC 305 (959)
Q Consensus 228 ~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~--~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~ 305 (959)
..+++++++.+++.+++++|+|++.|+-++++...-++.-+. ..+.....+...|... --+...+..+...++.|.
T Consensus 197 ~~dl~ell~~I~~~i~~~~~a~~~~I~L~d~~~~~L~~~aa~g~~~~~~~~~~~~~~~~~--~l~g~V~~~~~p~lv~~~ 274 (686)
T PRK15429 197 RLDMDELVSEVAKEIHYYFDIDAISIVLRSHRKNKLNIYSTHYLDKQHPAHEQSEVDEAG--TLTERVFKSKEMLLINLH 274 (686)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCcEEEEEecccChhhcccccccCCccc--chHHHHHhcCceEEEECc
Confidence 579999999999999999999999999998887654443222 2222233333333321 123456777888888776
Q ss_pred CCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHH
Q 002152 306 HAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYAC 385 (959)
Q Consensus 306 ~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~ 385 (959)
...+.... .....+ +..-++++.|+|||+.+| +.=|.|...++.++.++......+
T Consensus 275 ~~d~~~~~-------------------~~~~~~-~~~~~~~s~l~vPL~~~~----~v~GvL~l~~~~~~~F~~~dl~lL 330 (686)
T PRK15429 275 ERDDLAPY-------------------ERMLFD-TWGNQIQTLCLLPLMSGD----TMLGVLKLAQCEEKVFTTTNLKLL 330 (686)
T ss_pred cCcccchh-------------------hhhhhh-cccccceEEEEEeEEECC----EEEEEEEEeeCCCCcCCHHHHHHH
Confidence 54432100 000111 223468999999999988 999999998888888999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 002152 386 EFLVQAFSLQLYMEL 400 (959)
Q Consensus 386 ~~l~~~~s~~l~~~~ 400 (959)
..+|+++++.|+.+.
T Consensus 331 ~~iA~~~A~Aie~a~ 345 (686)
T PRK15429 331 RQIAERVAIAVDNAL 345 (686)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987543
No 74
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.16 E-value=1.2e-05 Score=93.95 Aligned_cols=118 Identities=14% Similarity=0.153 Sum_probs=82.9
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCC
Q 002152 608 QGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (959)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (959)
+..++|++.+++++.+++++|++++++|.+|+|+++|+++++++|++.++..|+++. +++...+. ...+.. ..
T Consensus 88 ~~~~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~-~~~~~~~~---~~~~~~---~~ 160 (430)
T PRK11006 88 KRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNIL-NLLRYPEF---TQYLKT---RD 160 (430)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHH-HHhcCHHH---HHHHHh---cc
Confidence 446778888899999999999999999999999999999999999999999999987 66543221 111111 11
Q ss_pred CcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHH
Q 002152 688 EDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFI 745 (959)
Q Consensus 688 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~ 745 (959)
.... ..+ ...++. ++.+...|..+ + +.+.+.+|||++++.+++.+
T Consensus 161 ~~~~--~~~----~~~~~~--~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~~~ 205 (430)
T PRK11006 161 FSRP--LTL----VLNNGR--HLEIRVMPYTE--G---QLLMVARDVTQMHQLEGARR 205 (430)
T ss_pred cCCC--eEE----EcCCCC--EEEEEEEEcCC--C---cEEEEEehhhHHHHHHHHHH
Confidence 1111 122 123343 55566666543 2 24677899999998887654
No 75
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.14 E-value=2.6e-05 Score=72.39 Aligned_cols=102 Identities=13% Similarity=0.138 Sum_probs=83.1
Q ss_pred eeeeCCCCcEEeecHH-HHHHhCCCchhhcCCCcccccccccccccChhhHHH-HHHHHHhhhcCCCcceeeEEEEccCC
Q 002152 765 IFASDENACCSEWNAA-MEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTK-FMILLYQGITGQGTENFPFGFFNRQG 842 (959)
Q Consensus 765 I~~~D~~g~i~~~N~a-~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~-~~~~l~~~~~~~~~~~~e~~~~~~dG 842 (959)
....+.+|+|+++-+. ...++||.++|++|+.+.+ +.||+|... +......++..+.....-+|++.++|
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~--------~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g 76 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYD--------FVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNG 76 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGG--------GBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTS
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHH--------hCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCC
Confidence 3456889999999999 6999999999999998654 788999997 77788888877767777899999999
Q ss_pred cEEEEEEEEeeeeC-CCCCEEEEEEEEeecccc
Q 002152 843 QFVEVALTASRRTD-AEGKVIGCFCFMQILVPD 874 (959)
Q Consensus 843 ~~~~v~~~~~pi~d-~~G~i~g~v~i~~DITer 874 (959)
.++|+...+....+ ..+++..++++-.-|+++
T Consensus 77 ~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vlse~ 109 (111)
T PF14598_consen 77 GYVWVQTKATLFYNPWTSKPEFIVCTNTVLSEE 109 (111)
T ss_dssp SEEEEEEEEEEEEETTTTCEEEEEEEEEEESCE
T ss_pred cEEEEEEEEEEEECCCCCCccEEEEEEEEeccC
Confidence 99999999999886 445667777777777653
No 76
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=98.10 E-value=0.00013 Score=81.99 Aligned_cols=205 Identities=18% Similarity=0.114 Sum_probs=122.4
Q ss_pred CCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHH-HHHHhCC-EEEE-ecC
Q 002152 229 GDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAAR-FLFKQNR-VRMI-CDC 305 (959)
Q Consensus 229 ~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar-~ly~~~~-~r~i-~d~ 305 (959)
.+++.++..+++.+..+.|||+++++++|.+. .+..+...-..+.+|.+-+....|.+.- +....+. ++++ .|.
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 58999999999999999999999999999988 4444444334455565322333333322 2333444 5552 221
Q ss_pred CCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHH
Q 002152 306 HAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYAC 385 (959)
Q Consensus 306 ~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~ 385 (959)
..|++..+ -+--.+++++-|.|.+||.+++ ++||.+..-|+.|-...+..-...
T Consensus 124 ------~~~~~~~~----------------l~~~~~~~~~~a~i~~PL~~~~----~~~G~Ltld~~~~~~f~~~~~~~l 177 (550)
T COG3604 124 ------LFPDPYDG----------------LLPDTEGNKKHACIGVPLKSGD----KLIGALTLDHTEPDQFDEDLDEEL 177 (550)
T ss_pred ------ccCCcccc----------------cccCccCCcceeEEeeeeeeCC----eeeeeEEeeeecccccchhHHHHH
Confidence 12222111 0111567788999999999999 999999999999888888888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhcc--cCCcccccCCchhhhhccCCeEEEEECCeEEEecCCCC
Q 002152 386 EFLVQAFSLQLYMELQVAMQLAEKNILRT-QVLLCDMLLR--DAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPT 462 (959)
Q Consensus 386 ~~l~~~~s~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~l~~l~~a~g~a~~~~~~~~~~G~~p~ 462 (959)
++|+...+..+....-.+.....++.+.. +..+..-+.. ....+|+.+++.+..+++.--++--.+-.+.+.|.|-+
T Consensus 178 r~La~~a~la~~~~~l~~~l~~~~~~l~~e~~~~~~~~~~~~~~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGt 257 (550)
T COG3604 178 RFLAALAALAVANALLHRELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGT 257 (550)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccchhcccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCc
Confidence 88888887776543211111111111111 1111111111 12356777777777666544444444555556666544
No 77
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=98.08 E-value=8.6e-05 Score=91.37 Aligned_cols=151 Identities=11% Similarity=0.059 Sum_probs=109.8
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHh
Q 002152 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (959)
Q Consensus 217 ~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~ 296 (959)
.++...+.+ +.+++++++.+++.+++++|+|++.||-+++|+..-+++-+...+-+..-..+||... --+...+..
T Consensus 6 ~eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~ge--Gi~G~Va~t 81 (748)
T PRK11061 6 REIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDE--GIVGLVGRL 81 (748)
T ss_pred HHHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCc--chHHHHhcc
Confidence 344455555 6699999999999999999999999999999987666665543222222223444322 123455667
Q ss_pred CCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCC
Q 002152 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRY 376 (959)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~ 376 (959)
+..-.|+|+...|--. +...+...+++|.|++||+.+| ++=|.|.+++..|+.
T Consensus 82 g~pV~V~Dv~~dprf~-----------------------~~~~~~~~~~~S~L~VPL~~~g----eVIGVL~v~~~~~~~ 134 (748)
T PRK11061 82 AEPINLADAQKHPSFK-----------------------YIPSVKEERFRAFLGVPIIYRR----QLLGVLVVQQRELRQ 134 (748)
T ss_pred CceEEECCcccCcccc-----------------------cCccccCccceEEEEEEEeeCC----EEEEEEEEeeCCCCC
Confidence 7888889987654310 0001224689999999999887 999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHH
Q 002152 377 IPFPLRYACEFLVQAFSLQLYM 398 (959)
Q Consensus 377 ~~~~~r~~~~~l~~~~s~~l~~ 398 (959)
++......+..|+.+++..|+.
T Consensus 135 Fs~~d~~lL~~LA~~aAiAL~n 156 (748)
T PRK11061 135 FDESEESFLVTLATQLAAILSQ 156 (748)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999888887754
No 78
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.06 E-value=7.2e-05 Score=88.91 Aligned_cols=112 Identities=13% Similarity=0.130 Sum_probs=81.1
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceE
Q 002152 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNV 692 (959)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~ 692 (959)
++....++..+++++++||+++|.+|+|+++|++++++||++.++++|+++. ++++.... ..++........
T Consensus 75 ~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~-eli~~~~l-------~~~le~~~~~~~ 146 (520)
T PRK10820 75 SEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAA-QLINGFNF-------LRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHH-HHcCcchH-------HHHHHcCCCccc
Confidence 4555677899999999999999999999999999999999999999999998 77765332 223332322111
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEee--cCCCCE--EEEEEEeecchhhHH
Q 002152 693 ELKLRKFELQKQHSVVYILVNACTSR--DYKNNV--KGVCFVGQDITHEKV 739 (959)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~--d~~g~~--~gvv~v~~DITerk~ 739 (959)
...+ ..+|..+ .+...|+. +.+|.. .|++.+++|+++..+
T Consensus 147 ~~~v-----~~~g~~~--~v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 NEHV-----VINGQDF--LMEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred eEEE-----EECCEEE--EEEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 1122 2245543 46667776 666654 899999999998643
No 79
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.04 E-value=9.6e-06 Score=104.26 Aligned_cols=73 Identities=27% Similarity=0.366 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 884 LEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 884 ~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
..++..++|..|++.|||||||||++|.|+.++|.....+++++++++.+..++++|..+|++ |++++++.|.
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 445566788999999999999999999999999998888899999999999999999999999 9999999884
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=97.98 E-value=5.6e-05 Score=70.21 Aligned_cols=101 Identities=14% Similarity=0.168 Sum_probs=81.2
Q ss_pred EEEEcCCCceehhcHH-HHHHhCCCcccccCCCccccccCCCchHH-HHHHHHHHHcCCCcceEEEEEEeeeeccCCcEE
Q 002152 631 IFGVDSSGTINGWNAK-VAELTGLPASEAMGKSLIDEVVHEESQGA-VENLICRALLGEEDKNVELKLRKFELQKQHSVV 708 (959)
Q Consensus 631 I~~~D~dg~iv~~N~~-~~~l~G~~~eeliGk~~~~~l~~~~~~~~-~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~ 708 (959)
+...+.+|+|+++..+ ...++||.++|++|+++. +++||++... +......++..+.....-+++ +.++|..+
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y-~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~----~~k~g~~v 79 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIY-DFVHPDDLQRVLKQHHREVLQKGQSVSPYYRF----RTKNGGYV 79 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGG-GGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEE----E-TTSSEE
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchH-HhCCHhhhhhHHHHHHHHHhhCCCcCcceEEE----EecCCcEE
Confidence 4556899999999999 699999999999999999 9999999996 888888888766665556777 78899999
Q ss_pred EEEEEEEEeecC-CCCEEEEEEEeecchh
Q 002152 709 YILVNACTSRDY-KNNVKGVCFVGQDITH 736 (959)
Q Consensus 709 ~v~v~~~pi~d~-~g~~~gvv~v~~DITe 736 (959)
|+...+.+..++ .+++..++++-+=|++
T Consensus 80 wvqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 80 WVQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 999999999875 4566666666554444
No 81
>PF12860 PAS_7: PAS fold
Probab=97.97 E-value=2.4e-05 Score=73.25 Aligned_cols=110 Identities=10% Similarity=0.116 Sum_probs=67.6
Q ss_pred HhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhh-cCCCcccccccccc--cccChhhHHHHHHHHHhhhcCCCcce
Q 002152 756 QSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEV-IGKMLPREIFGNFC--RMKGQDMLTKFMILLYQGITGQGTEN 832 (959)
Q Consensus 756 e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eev-iGk~~~~~i~~~~~--~l~~~e~~~~~~~~l~~~~~~~~~~~ 832 (959)
++++. ||.++|.+|++++||+++.+++|++.+.+ .|.++.. ++..+. ....+.+..................
T Consensus 2 d~l~~---Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~-l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~- 76 (115)
T PF12860_consen 2 DSLPQ---GVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRD-LLRRLAERGEFPPGDPEAWVRQRLARLRRRQPR- 76 (115)
T ss_pred CCcCc---eEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHH-HHHHHHHcCCCCCCCHHHHHHHHHHHHhcCCCc-
Confidence 44553 59999999999999999999999999998 6776443 332211 1111233222222222222222233
Q ss_pred eeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHH
Q 002152 833 FPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (959)
Q Consensus 833 ~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~E 878 (959)
.+.+...||. |+.++..|.- +| |++.+..|||+++++|
T Consensus 77 -~~~~~~~dgr--~l~~~~~~~~--~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 77 -SFELRLPDGR--WLEVRAQPLP--DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred -eeEEECCCCE--EEEEEeEECC--CC---CEEEEEEeCCHHHHhc
Confidence 3345667776 4556666663 44 4677789999988876
No 82
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=97.97 E-value=7.4e-05 Score=89.96 Aligned_cols=121 Identities=14% Similarity=0.205 Sum_probs=87.5
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCC---cccccCCCccccccCCCchHHHHHHHHHHHcCC
Q 002152 611 DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLP---ASEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (959)
Q Consensus 611 ~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~---~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (959)
.++....++++.++++++++++++|.+|+|+++|+++++++|++ ..+.+|+.+. .+.+.. .+..++..+
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~-~~~~~~-------~~~~~~~~~ 285 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVE-SWMPVS-------RLKEVLRTG 285 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHH-HhCCch-------hHHHHHhcC
Confidence 46666677789999999999999999999999999999999865 3456666655 444322 223333333
Q ss_pred Cc-ceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHH
Q 002152 688 ED-KNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (959)
Q Consensus 688 ~~-~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~ 749 (959)
.. ...+... +| .++.++..|+.+ +|.+.|++.+++|+|+.++.++++.....
T Consensus 286 ~~~~~~~~~~-------~g--~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~~ 338 (542)
T PRK11086 286 TPRRDEEINI-------NG--RLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMVN 338 (542)
T ss_pred CCccceEEEE-------CC--EEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHHH
Confidence 32 2222222 34 345667789988 89999999999999999998888765544
No 83
>PRK09303 adaptive-response sensory kinase; Validated
Probab=97.91 E-value=2.1e-05 Score=90.18 Aligned_cols=71 Identities=15% Similarity=0.185 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCC-------HHHHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 887 MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSIS-------ENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 887 ~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~-------e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
+..+.+.+|++++||||||||++|.++++++.....+ +..+++++.+..+.++|..+|++ +++++.+.+.+
T Consensus 146 e~~~~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~ 224 (380)
T PRK09303 146 EQLKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEAL 224 (380)
T ss_pred HHHHHHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 3445688999999999999999999999999853322 33788999999999999999999 99999998765
No 84
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.82 E-value=7.4e-05 Score=80.08 Aligned_cols=211 Identities=18% Similarity=0.193 Sum_probs=131.8
Q ss_pred HHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHH---cCCCcceEEEEEE
Q 002152 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRAL---LGEEDKNVELKLR 697 (959)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l---~~~~~~~~e~~~~ 697 (959)
..+++.....|++++++|+|+|+++.+.-.+|++.-|+.|..+. +.+|+.+.+.+...+...- +-+....+.++.+
T Consensus 82 shlLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~-eYIH~~D~demna~L~~h~H~qeyeIErsfflrmk 160 (598)
T KOG3559|consen 82 SHLLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIY-EYIHPQDHDEMNAVLTAHQHLQEYEIERSFFLRMK 160 (598)
T ss_pred HhHHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhh-hhhcccchHHHHHHHhhhhhhhhhhhhhhhhhhhh
Confidence 45677778889999999999999999999999999999999999 9999988876665543221 1111112222222
Q ss_pred eeeecc------CCc-EE----EEEEEEEEeec-CCC---CEEEEEEEeec-----chhhHHHHHHHHHHHHHHHHHHHh
Q 002152 698 KFELQK------QHS-VV----YILVNACTSRD-YKN---NVKGVCFVGQD-----ITHEKVLMDKFIRLQGDYEAIIQS 757 (959)
Q Consensus 698 ~~~~~~------dG~-~~----~v~v~~~pi~d-~~g---~~~gvv~v~~D-----ITerk~~E~~L~~se~~l~~i~e~ 757 (959)
+....+ .|. .+ ++.+...++.- ..+ ..+|++.+..- ||+.| +-.
T Consensus 161 Cvlakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteik---------------l~s- 224 (598)
T KOG3559|consen 161 CVLAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIK---------------LHS- 224 (598)
T ss_pred hhheeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEE---------------ecc-
Confidence 211111 111 11 11222222221 111 44566666432 44433 112
Q ss_pred cCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEE
Q 002152 758 VNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGF 837 (959)
Q Consensus 758 ~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~ 837 (959)
+.. +|....|-++++......+++||.+.+++++++.. ++|..|...+...-.-.+..+....--+|+
T Consensus 225 -NmF---mfraslDlkliF~D~rv~qltgYepqdliektLY~--------~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~ 292 (598)
T KOG3559|consen 225 -NMF---MFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYH--------HIHGCDSFHLRCAHHLLLVKGQVTTKYYRF 292 (598)
T ss_pred -ceE---EEEeecceEEEeehhhHHHhhCCCchhhhhHHHHH--------HhhhhhHHHHHHHHHHHHhccccccHHHHH
Confidence 222 67778899999999999999999999999998764 344444443333333333333333334678
Q ss_pred EccCCcEEEEEEEEeeeeCCCCC
Q 002152 838 FNRQGQFVEVALTASRRTDAEGK 860 (959)
Q Consensus 838 ~~~dG~~~~v~~~~~pi~d~~G~ 860 (959)
..+.|.+.|+......+.+....
T Consensus 293 l~k~ggwvwvqsyat~vHnSrSS 315 (598)
T KOG3559|consen 293 LLKQGGWVWVQSYATFVHNSRSS 315 (598)
T ss_pred HHcCCceEEEEEeeEEEeccccC
Confidence 88999999999888777665433
No 85
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.79 E-value=0.00021 Score=81.66 Aligned_cols=132 Identities=23% Similarity=0.284 Sum_probs=97.5
Q ss_pred ccccccccccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHH
Q 002152 599 NTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVEN 678 (959)
Q Consensus 599 ~~~l~~~l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~ 678 (959)
++.+.++++++..++++.++.++.+++..+.|++.+|.+|+|..+|+++++++|.+.++++|.++. .+.+. +..
T Consensus 351 L~~qq~~l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~ls-a~ap~-----~~~ 424 (712)
T COG5000 351 LSSQQEALERAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLS-AIAPE-----LEE 424 (712)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhh-hhhhH-----HHH
Confidence 444455677778888999999999999999999999999999999999999999999999999976 44332 222
Q ss_pred HHHHHHc-CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHH
Q 002152 679 LICRALL-GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (959)
Q Consensus 679 ~l~~~l~-~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~ 743 (959)
.+...-. +...+..++.+ ...|+.+.+.+..+....+ +--|++.++.|||+...+|..
T Consensus 425 vf~~~~a~~~~~~~~ev~~-----~r~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~AQRs 483 (712)
T COG5000 425 VFAEAGAAARTDKRVEVKL-----AREGEERTLNVQATREPED--NGNGYVVTFDDITDLVIAQRS 483 (712)
T ss_pred HHHHhhhhcCCCccceeec-----ccCCCceeeeeeeeecccc--cCCceEEEecchHHHHHHHHH
Confidence 2322222 23444555555 3457777777777665433 233678999999999988764
No 86
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.67 E-value=0.00036 Score=79.62 Aligned_cols=120 Identities=21% Similarity=0.376 Sum_probs=90.7
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcc--cccCCCccccccCCCchHHHHHHHHHHH-cCC
Q 002152 611 DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPAS--EAMGKSLIDEVVHEESQGAVENLICRAL-LGE 687 (959)
Q Consensus 611 ~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~e--eliGk~~~~~l~~~~~~~~~~~~l~~~l-~~~ 687 (959)
.|+...-++..++++++..|++.+|..|.|..+|.++++++|+... +.+|+++. ++++|+.. +..++ .+.
T Consensus 208 ~EIa~l~~er~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~-~v~~p~~~------l~~vl~~~~ 280 (537)
T COG3290 208 EEIATLLEERQAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIV-EVLPPDSD------LPEVLETGK 280 (537)
T ss_pred HHHHHHHHHHHHHHHHhhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccce-EeeccccC------cHHHHhcCC
Confidence 4566666777899999999999999999999999999999998765 68899998 77776221 12222 233
Q ss_pred CcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHH
Q 002152 688 EDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRL 747 (959)
Q Consensus 688 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~s 747 (959)
...+.++++ +| .++.++..|++ .+|+++|.+.++||-||-+++-++|...
T Consensus 281 ~~~~~e~~~-------ng--~~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~v 330 (537)
T COG3290 281 PQHDEEIRI-------NG--RLLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGV 330 (537)
T ss_pred cccchhhhc-------CC--eEEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHH
Confidence 333444444 23 46778888887 5789999999999999999887766443
No 87
>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=97.66 E-value=0.00012 Score=59.70 Aligned_cols=61 Identities=34% Similarity=0.479 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHHHHHhhcc-cCccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESS-SISENQRQYLETSDACERQIMTIIDG-MDLRC 951 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~-~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~sr 951 (959)
.+.++.+.++||+||||++|.++.+.+... ...++...+++.+..++.++..++++ ++++|
T Consensus 3 ~~~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ 65 (65)
T cd00082 3 AKGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLSR 65 (65)
T ss_pred HHHHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 356788999999999999999998888763 23577889999999999999999999 77764
No 88
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.62 E-value=0.00023 Score=81.15 Aligned_cols=126 Identities=21% Similarity=0.313 Sum_probs=89.2
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceE
Q 002152 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNV 692 (959)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~ 692 (959)
|......+..+++.+.++++++|.+|+++++|.++..++|++.++++|+++. +++..... ...+.....+......
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~-~v~~~~~~---s~~l~vl~~~kp~~~~ 187 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLL-DVVSAGED---STLLEVLRTGKPIRDV 187 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHH-HHHhccCC---ceehhhhhcCCcceee
Confidence 4566678999999999999999999999999999999999999999999887 66511000 0122222223332222
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHH
Q 002152 693 ELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYE 752 (959)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~ 752 (959)
...+ .|... ..+..|++ .+|.+.|++++++|+++-+.+..++.+++...+
T Consensus 188 ~~~~-------~~~~~--i~~~~pv~-~~g~l~G~v~~~~~~~~l~~l~~~~~~~~~~~~ 237 (560)
T COG3829 188 VQTY-------NGNKI--IVNVAPVY-ADGQLIGVVGISKDVSELERLTRELEESEGLLR 237 (560)
T ss_pred eeee-------cCCce--eEeeccEe-cCCcEEEEEEeecchHHHHHHHHHHHHHhhhhc
Confidence 2111 12222 45555655 567999999999999999999888877766443
No 89
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.59 E-value=0.00087 Score=66.42 Aligned_cols=127 Identities=23% Similarity=0.311 Sum_probs=89.1
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHH-HHHHHHHHH-c
Q 002152 608 QGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGA-VENLICRAL-L 685 (959)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~-~~~~l~~~l-~ 685 (959)
..+.++.....++..+++..+.+++.+|.+|.++++|+.+.+++|++..+..+.... .+........ ......... .
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 180 (232)
T COG2202 102 RAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLS-DLIHPEDEERRELELARALAEG 180 (232)
T ss_pred HHHHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChh-heEecCCCchhhHHHHHHhhcc
Confidence 335556666677999999999999999999999999999999999998887777655 4433322221 122222222 2
Q ss_pred CCCcceEEEEEEeeeeccCCcE-EEEEEEEEEeecCCCCEEEEEEEeecchhhHHH
Q 002152 686 GEEDKNVELKLRKFELQKQHSV-VYILVNACTSRDYKNNVKGVCFVGQDITHEKVL 740 (959)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~-~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~ 740 (959)
.......++.. ..++|.. .+......+... .|.+.++.....|+|++++.
T Consensus 181 ~~~~~~~~~~~----~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 181 RGGPLEIEYRV----RRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred CCCCcceEEEE----EecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 22334445555 5678885 777777666554 78888889999999998764
No 90
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=97.54 E-value=0.0062 Score=70.29 Aligned_cols=59 Identities=25% Similarity=0.279 Sum_probs=47.3
Q ss_pred HHHHHHHHHHhHhhhhHHHHHHH---HHhcCCCCHHHHHHHHHHHHHHHHHHHhhccc-Cccc
Q 002152 893 IKELAYIRQEVKNPLNGIRFVHK---LLESSSISENQRQYLETSDACERQIMTIIDGM-DLRC 951 (959)
Q Consensus 893 ~~fLa~iSHElRnPL~~I~g~~~---LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~dL-d~sr 951 (959)
.++.+.|+||||+||++|..+.+ +|.+....++..+.++.|..-++||.+|...| .|+|
T Consensus 385 GQmSA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FAr 447 (603)
T COG4191 385 GQMSAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFAR 447 (603)
T ss_pred HHHHHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44567889999999999995543 33345778889999999999999999999985 5554
No 91
>PRK10490 sensor protein KdpD; Provisional
Probab=97.45 E-value=0.00027 Score=89.72 Aligned_cols=70 Identities=11% Similarity=0.113 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 889 IYAKIKELAYIRQEVKNPLNGIRFVHKLLESSS--ISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 889 ~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~--l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
.+.+..|++.+||||||||++|.|+.+++.... ..+...+.++.+.+...++..+|++ |+++|+++|.+.
T Consensus 661 e~lr~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~~~ 733 (895)
T PRK10490 661 EQLRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFN 733 (895)
T ss_pred HHHHHHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc
Confidence 345678999999999999999999999887422 2234456788899999999999999 999999998653
No 92
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=97.42 E-value=0.00054 Score=76.44 Aligned_cols=229 Identities=14% Similarity=0.077 Sum_probs=142.5
Q ss_pred HHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCc-ceEEEEEEe-
Q 002152 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED-KNVELKLRK- 698 (959)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~-~~~e~~~~~- 698 (959)
+.++++....++++..+|.|-|++...+..+|+...+++.++++ +++|.++++.+.+.+.-++.-... .......++
T Consensus 114 e~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVY-dlIHseDR~dfqrQLhwa~~ppq~~~s~q~~~e~~ 192 (712)
T KOG3560|consen 114 ELLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVY-DLIHSEDRQDFQRQLHWAMDPPQVVFSQQPPLETG 192 (712)
T ss_pred HHHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHH-HHhhhhhHHHHHHHHhhccCCchhhccCCCccccc
Confidence 45788888899999999999999999999999999999999999 999999999887766543321100 000000000
Q ss_pred ------eeeccCCc--------EEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHH--------------------
Q 002152 699 ------FELQKQHS--------VVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF-------------------- 744 (959)
Q Consensus 699 ------~~~~~dG~--------~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L-------------------- 744 (959)
.....|+- .+.+.++..-+.|... |++. .|+-.+.+.---.
T Consensus 193 ~~~~~~~~~~~d~~ppens~yleRcficR~RCLLDnTs---GFLa--mdfqGklk~LhGqkkk~~~g~~lpP~LaLf~ia 267 (712)
T KOG3560|consen 193 DDAILRAQEWGDGTPPENSAYLERCFICRFRCLLDNTS---GFLA--MDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIA 267 (712)
T ss_pred cccceeeeccCccCCcccchHHhhhheeeEEEeecCCc---ceee--eecccceeeecCCcccCCCCccCCCceeEEEEe
Confidence 00011111 2344445555554333 2222 2443321110000
Q ss_pred ------HHHHHH-HHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHH
Q 002152 745 ------IRLQGD-YEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKF 817 (959)
Q Consensus 745 ------~~se~~-l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~ 817 (959)
..+|-+ -..|+.+-.. .|+..+.+......++||...|+.|.... .++|-+|..-.
T Consensus 268 tP~~pPS~lEi~~k~~i~rtKhk---------lDfa~vs~Dak~k~~lgy~eaEL~~m~gY--------~lvH~~D~~y~ 330 (712)
T KOG3560|consen 268 TPFLPPSALEIKMKSAILRTKHK---------LDFALVSMDAKVKATLGYCEAELHGMPGY--------NLVHVEDKVYM 330 (712)
T ss_pred cCCCCchhhhhhhhhhhhhcccc---------cccceeccchhhhhhhccchhhccCCCcc--------ceeehhhhhhh
Confidence 000000 0111221111 14445556677788999999999986533 47778888777
Q ss_pred HHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeeccc
Q 002152 818 MILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (959)
Q Consensus 818 ~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITe 873 (959)
.....+.++.+++--+.+|..+++|++.||..++.-++ .+|++-.+++.-+-.++
T Consensus 331 Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 331 AEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred hHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee-ecCCCCEEEecCCCccc
Confidence 77788888888888889999999999999998886554 67777766654444443
No 93
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.41 E-value=0.0023 Score=77.26 Aligned_cols=122 Identities=16% Similarity=0.254 Sum_probs=85.4
Q ss_pred hHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCc--ccccCCCccccccCCCchHHHHHHHHHHHcCC
Q 002152 610 VDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPA--SEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (959)
Q Consensus 610 ~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~--eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (959)
..++.....++..+++++++|++++|.+|+|+.+|+++++++|++. ++++|+++. +++++... +..... .
T Consensus 214 ~~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~-~~~~~~~~------~~~~~~-~ 285 (545)
T PRK15053 214 PKQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIA-EVVRPADF------FTEQID-E 285 (545)
T ss_pred HHHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHH-HhCCCchh------hhhhcC-C
Confidence 3445555567889999999999999999999999999999999875 468899887 66654311 111111 1
Q ss_pred CcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHH
Q 002152 688 EDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (959)
Q Consensus 688 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~ 749 (959)
........ .+| ..+.++..|+.. +|.+.|++.+++|+|+.++.+.++...+.
T Consensus 286 ~~~~~~~~-------~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~ 337 (545)
T PRK15053 286 KRQDVVAN-------FNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQ 337 (545)
T ss_pred cccceEEE-------ECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHH
Confidence 11111222 123 345567778764 56778999999999999988887765544
No 94
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=97.36 E-value=0.00041 Score=87.96 Aligned_cols=66 Identities=15% Similarity=0.071 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~-~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
+..+|++.+||||||||++|.++.+++.. ...+++.+++++.|..+++++..+|++ ++++|...+.
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 55689999999999999999999998765 334567889999999999999999999 9999977664
No 95
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.34 E-value=0.00064 Score=76.45 Aligned_cols=100 Identities=16% Similarity=0.221 Sum_probs=78.5
Q ss_pred CCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEE
Q 002152 771 NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALT 850 (959)
Q Consensus 771 ~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~ 850 (959)
|.-|+|+|..||++.||.+.|++.|...-.+. ..++.+.+..+++ ++.+...+...+|.-+..|+...+|+.+.
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FM--yGEltdk~ti~k~----~~t~eN~~~~qfEillyKKN~TPvW~~vq 112 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFM--YGELTDKGTIEKV----RQTLENYETNQFEILLYKKNRTPVWLLVQ 112 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeee--eccccchhhHHHH----HHHHHhhhhcceeeEeeecCCCceEEEEE
Confidence 56789999999999999999999986431111 1234444555544 44445555677999999999999999999
Q ss_pred EeeeeCCCCCEEEEEEEEeecccccH
Q 002152 851 ASRRTDAEGKVIGCFCFMQILVPDLQ 876 (959)
Q Consensus 851 ~~pi~d~~G~i~g~v~i~~DITerk~ 876 (959)
..|++++...++-++|.+.|||.-|+
T Consensus 113 iAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 113 IAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred eecccCCCceEEEEEeecccchhhcC
Confidence 99999999999999999999997654
No 96
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=97.34 E-value=0.00072 Score=77.64 Aligned_cols=74 Identities=11% Similarity=0.136 Sum_probs=62.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhc---CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLES---SSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 882 q~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~---~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
++..|+.+....+|...+||++|+||+.|.++.+||.+ ..++++.++++..+.+.+..|.+||+| +.+|++..-
T Consensus 514 ~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~~~ 591 (750)
T COG4251 514 RRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLGLT 591 (750)
T ss_pred HHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccc
Confidence 33446666555677777799999999999999999986 468899999999999999999999999 999988654
No 97
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.31 E-value=0.001 Score=79.24 Aligned_cols=110 Identities=10% Similarity=0.105 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHh
Q 002152 744 FIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQ 823 (959)
Q Consensus 744 L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~ 823 (959)
+++.+..+++++++++. ||+.+|.+|+|+++|+++++++|++.++++|++... +++ .... ..
T Consensus 75 ~e~e~~~L~aIL~sm~e---GVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~e-li~-------~~~l---~~---- 136 (520)
T PRK10820 75 SEREHRALSALLEALPE---PVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQ-LIN-------GFNF---LR---- 136 (520)
T ss_pred HHHHHHHHHHHHHhCCC---cEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHH-HcC-------cchH---HH----
Confidence 34456678899999985 599999999999999999999999999999998653 222 1111 11
Q ss_pred hhcCCCcceeeEEEEccCCcEEEEEEEEeeee--CCCCCE--EEEEEEEeecccc
Q 002152 824 GITGQGTENFPFGFFNRQGQFVEVALTASRRT--DAEGKV--IGCFCFMQILVPD 874 (959)
Q Consensus 824 ~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~--d~~G~i--~g~v~i~~DITer 874 (959)
.+..+...... .....+|..++ +...|+. +++|.. +|++.+++|+++.
T Consensus 137 ~le~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l 188 (520)
T PRK10820 137 WLESEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARM 188 (520)
T ss_pred HHHcCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHH
Confidence 22222221111 12334566544 5567776 666664 8999999999864
No 98
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.26 E-value=0.00032 Score=57.91 Aligned_cols=43 Identities=23% Similarity=0.256 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCcc
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLI 664 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~ 664 (959)
++|+.+++++|.||+++| +++|+++|+++++++||+ ..|+.+.
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~ 43 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIG 43 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHH
Confidence 468999999999999999 889999999999999998 4565543
No 99
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.11 E-value=0.02 Score=70.38 Aligned_cols=114 Identities=16% Similarity=0.230 Sum_probs=78.5
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCC-cce
Q 002152 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEE-DKN 691 (959)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~-~~~ 691 (959)
+......+..++++.++|++++|.+|+|+++|+++++++|++.++++|+++. +++... . .+..++..+. ...
T Consensus 198 ~~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~-~l~~~~--~----~l~~vl~~~~~~~~ 270 (638)
T PRK11388 198 SNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAIT-ELLTLP--A----VLQQAIKQAHPLKH 270 (638)
T ss_pred HHHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHH-HHhccc--h----HHHHHHhcCCceee
Confidence 3344455677899999999999999999999999999999999999999987 666421 1 1222333222 222
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHH
Q 002152 692 VELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVL 740 (959)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~ 740 (959)
.+..+ ..+|..+++.+...|+.+..|. +++.+.+|++..++.
T Consensus 271 ~~~~l-----~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~~~ 312 (638)
T PRK11388 271 VEVTF-----ESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMRQL 312 (638)
T ss_pred EEEEE-----ecCCceEEEEEEEEeecccCce--EEEEEehhhHHHHHH
Confidence 23222 2346667888899998754443 356667888876543
No 100
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.10 E-value=0.0012 Score=74.31 Aligned_cols=116 Identities=23% Similarity=0.236 Sum_probs=82.1
Q ss_pred HHHHHHHhcC--ccEEEE-cC---CCceehhcHHHHHHhCCCcccccCCCccccccCCCc--hHHHHHHHHHHHcCCCcc
Q 002152 619 EMVRLIETAT--APIFGV-DS---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEES--QGAVENLICRALLGEEDK 690 (959)
Q Consensus 619 ~l~~lie~~~--~~I~~~-D~---dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~--~~~~~~~l~~~l~~~~~~ 690 (959)
.++.++..+. +.-+++ +. |.-|+|+|+.|+++.||.+.|++.++..-.+.+.+. .+. .+.++..+...+..
T Consensus 15 FLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~t-i~k~~~t~eN~~~~ 93 (971)
T KOG0501|consen 15 FLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGT-IEKVRQTLENYETN 93 (971)
T ss_pred HHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhh-HHHHHHHHHhhhhc
Confidence 3445554443 444443 22 557999999999999999999999875423444432 222 22334444444444
Q ss_pred eEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHH
Q 002152 691 NVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKV 739 (959)
Q Consensus 691 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~ 739 (959)
.+|+-+ .+++..++|+.+...|++++...++-+++++.|||.-|+
T Consensus 94 qfEill----yKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 94 QFEILL----YKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred ceeeEe----eecCCCceEEEEEeecccCCCceEEEEEeecccchhhcC
Confidence 566666 678899999999999999999999999999999999886
No 101
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.06 E-value=0.0058 Score=81.10 Aligned_cols=135 Identities=10% Similarity=-0.078 Sum_probs=77.7
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHH---
Q 002152 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICR--- 682 (959)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~--- 682 (959)
++.++++|+..++.++.++++++.+++++|.+|+|+++|++++++||+......+.... . ..+...+.+......
T Consensus 564 r~~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~ 641 (1197)
T PRK09959 564 RKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLE-N-SDSPFKDVFSNAHEVTAE 641 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccccccc-c-ccCchhhhHhHHHHHHHH
Confidence 35567788888889999999999999999999999999999999999775443332221 1 111111111111111
Q ss_pred HHcCCCcceEEEEEEeeeeccCCcEEEE-EEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHH
Q 002152 683 ALLGEEDKNVELKLRKFELQKQHSVVYI-LVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQ 748 (959)
Q Consensus 683 ~l~~~~~~~~e~~~~~~~~~~dG~~~~v-~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se 748 (959)
...........+. ..+|...++ .....+.....+...++++.++|||++++.+++++...
T Consensus 642 ~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~ 702 (1197)
T PRK09959 642 TKENRTIYTQVFE------IDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVER 702 (1197)
T ss_pred HhhccccceeeEe------eecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHH
Confidence 1111111111111 122322222 22222222233445567888899999998887776543
No 102
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=96.93 E-value=0.039 Score=68.40 Aligned_cols=203 Identities=11% Similarity=0.039 Sum_probs=116.3
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHH
Q 002152 216 AVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFK 295 (959)
Q Consensus 216 ~~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~ 295 (959)
+..+...+-+ ..|++++++.+-..++++.-+|||-|.-+|+.. +.+.-=....+-++. .| + ......
T Consensus 11 l~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~---~~----~---~~~~~~ 77 (686)
T PRK15429 11 LFDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV---KY----E---DETVLA 77 (686)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch---hc----c---chhhhc
Confidence 3344444445 559999999999999999999999999999976 555421111111110 00 0 011222
Q ss_pred hCCEEEEecCCCCCcccccccccCCccccccccccCCChhhH--HHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002152 296 QNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHL--QYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (959)
Q Consensus 296 ~~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~--~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~ 373 (959)
.+++.++-- +++|+-+++...+-.-|--. .+...| ++.+.|||.+.| +..|-|..-.+.
T Consensus 78 ~g~~g~vl~-------------~~~~l~~~~~~~~~~~~~l~~~~~~~~~--~~~lgvPl~~~~----~v~G~l~l~~~~ 138 (686)
T PRK15429 78 HGPVRRILS-------------RPDTLHCSYEEFCETWPQLAAGGLYPKF--GHYCLMPLAAEG----HIFGGCEFIRYD 138 (686)
T ss_pred cCcceEEee-------------cCceEEEchHHhhhccHHHhhcccccCc--cceEEeceeeCC----eeEEEEEEEEcC
Confidence 333332221 23344333333222111111 112233 558899999998 999999998888
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH---HHHHHHHHhh---c-ccCCcc-cccCCchhhhhccCC
Q 002152 374 PRYIPFPLRYACEFLVQAFSLQLYMELQVA-MQLAEKNIL---RTQVLLCDML---L-RDAPFS-IVTQSPSIMDLVKCD 444 (959)
Q Consensus 374 pr~~~~~~r~~~~~l~~~~s~~l~~~~~~~-~~~~~~~~~---~~~~~~~~~~---~-~~~~~~-~~~~~~~l~~l~~a~ 444 (959)
+..++.+....+..|+++++..++.....+ .+.++.... ..+..+.++. . ...+.. +..-...+..+++++
T Consensus 139 ~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~eIs~~l~s~~dl~ell~~I~~~i~~~~~a~ 218 (686)
T PRK15429 139 DRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVAITNAVLSRLDMDELVSEVAKEIHYYFDID 218 (686)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhCCC
Confidence 999999999999999999999997543211 111111110 1122232221 1 112222 222245677889999
Q ss_pred eEEEEE
Q 002152 445 GAALYY 450 (959)
Q Consensus 445 g~a~~~ 450 (959)
.+.|+.
T Consensus 219 ~~~I~L 224 (686)
T PRK15429 219 AISIVL 224 (686)
T ss_pred EEEEEE
Confidence 987765
No 103
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.70 E-value=0.0015 Score=71.04 Aligned_cols=115 Identities=15% Similarity=0.094 Sum_probs=89.2
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHH
Q 002152 741 MDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMIL 820 (959)
Q Consensus 741 E~~L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~ 820 (959)
.-+++.....|..+-+ ... +|-++|.+..|.|+|++|++|+||-..|++|+...+. .+....+..+...
T Consensus 150 afkiRAcnalFaaLD~-c~e---AiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adl-------pkkdknradlldt 218 (775)
T KOG1229|consen 150 AFKIRACNALFAALDE-CDE---AIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADL-------PKKDKNRADLLDT 218 (775)
T ss_pred HHHHhhhHHHHHHHhh-hhh---hheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhc-------cccccchhhhhhh
Confidence 3445544454444433 333 4888999999999999999999999999999986541 1223445567788
Q ss_pred HHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEE
Q 002152 821 LYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFC 866 (959)
Q Consensus 821 l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~ 866 (959)
++.+++.+..+..++..+++.|......+..+|+.+..|++..++.
T Consensus 219 intcikkgke~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfvs 264 (775)
T KOG1229|consen 219 INTCIKKGKEAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFVS 264 (775)
T ss_pred hhHhhhcCccccchHHHhhccCCcccceEEEeeecCCCCceeeehh
Confidence 8999998888999988899999999889999999999999887764
No 104
>PRK10604 sensor protein RstB; Provisional
Probab=96.64 E-value=0.0032 Score=73.69 Aligned_cols=65 Identities=17% Similarity=0.268 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 888 ~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
..+.+.++++.+||||||||+.|.+..++++. .+++..+ .+.+..++|..++++ +.++|++.+..
T Consensus 208 ~~~~~~~l~~~vsHeLrtPL~~i~~~l~~l~~--~~~~~~~---~i~~~~~~l~~li~~ll~~~rl~~~~~ 273 (433)
T PRK10604 208 LIASKKQLIDGIAHELRTPLVRLRYRLEMSDN--LSAAESQ---ALNRDIGQLEALIEELLTYARLDRPQN 273 (433)
T ss_pred HHHHHHHHHHHhhHhhcChHHHHHHHHHHhcC--CCcHHHH---HHHHHHHHHHHHHHHHHHHHhccCCCc
Confidence 33466789999999999999999999998874 2333332 266778999999999 89999998754
No 105
>PRK10815 sensor protein PhoQ; Provisional
Probab=96.58 E-value=0.0046 Score=73.34 Aligned_cols=65 Identities=15% Similarity=0.077 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLESSS-ISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 890 ~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
+...+|++.+||||||||+.|.+.++.+.... .+. .+....+.+...++.+++++ |+.++++++.
T Consensus 264 ~~~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~--~~~~~~~~~~i~ri~~~i~~ll~~~~~~~~~ 330 (485)
T PRK10815 264 TKYRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSV--EQAEPIMLEQISRISQQIGYYLHRASMRSEH 330 (485)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 34457899999999999999999999887633 332 23344566777888899988 8888877754
No 106
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=96.57 E-value=0.0027 Score=52.28 Aligned_cols=41 Identities=20% Similarity=0.277 Sum_probs=33.4
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCC
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKM 796 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~ 796 (959)
++|+.++++++. +|+++| +++|+++|+++++++||+ ..|+.
T Consensus 1 e~~~~l~~~~~~---~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~ 41 (64)
T PF13188_consen 1 ERYRSLFDNSPD---GILIID-GGRIIYVNPAFEELFGYS---LEGED 41 (64)
T ss_dssp HHHHHHHCCSSS---EEEEEE-TSBEEEE-HHHHHHHCS----HTCCC
T ss_pred CHHHHHHHcCcc---ceEEEE-CCChHHhhHHHHHHhCCC---CCCCC
Confidence 478999999985 499999 889999999999999998 45554
No 107
>PRK10364 sensor protein ZraS; Provisional
Probab=96.55 E-value=0.0065 Score=71.61 Aligned_cols=64 Identities=16% Similarity=0.200 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~-~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~ 954 (959)
...++.+.++||+||||++|.++.+++.. ...+++.+++++.+.+..+++..++++ +++++...
T Consensus 236 ~~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~~~ 301 (457)
T PRK10364 236 ALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKPTH 301 (457)
T ss_pred HHHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCC
Confidence 45578899999999999999999999875 334466778899999999999999999 88887543
No 108
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.49 E-value=0.006 Score=66.62 Aligned_cols=115 Identities=20% Similarity=0.180 Sum_probs=90.3
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEE
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLR 697 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~ 697 (959)
+++.+++++.|.-|-.+|.++++.++|.. .++|-.++.. +|+++. ...+|.+...+...+.....|... ..++-+
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-IGRRVQ-LCHPPKSVHIVEKILKDFKSGEKD-FAEFWI- 364 (409)
T ss_pred HHHHHHHhhCCCceEEecccceEEecCCc-ceecccChHh-hCCccc-CCCCCchHHHHHHHHHHhhcCCcc-hHHHhc-
Confidence 56789999999999999999999999988 8899888865 599987 666677777777777777766544 223322
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHH
Q 002152 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (959)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~ 743 (959)
+..+ ..+.++..+++|.+|+..|++-+.+|||..|..+-+
T Consensus 365 ----~~~~--~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ge 404 (409)
T COG2461 365 ----NMGD--KFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELEGE 404 (409)
T ss_pred ----cCCC--ceEEEEEEEEEcCCCceeeeehhhhhhHHHHhccch
Confidence 2222 456778899999999999999999999999876543
No 109
>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=96.36 E-value=0.0089 Score=46.00 Aligned_cols=63 Identities=32% Similarity=0.481 Sum_probs=52.4
Q ss_pred HHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHH
Q 002152 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICR 682 (959)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~ 682 (959)
+++.+++.++++++.+|.++.+.++|..+.+++|++..++.|+.+. .++++.+...+...+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 64 (67)
T smart00091 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLL-ELIHPEDREEVQEALQR 64 (67)
T ss_pred hHHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHH-HhcCcccHHHHHHHHHH
Confidence 3567889999999999999999999999999999999999998877 77777766655554443
No 110
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=96.20 E-value=0.065 Score=51.90 Aligned_cols=110 Identities=13% Similarity=0.016 Sum_probs=83.1
Q ss_pred HHHHHHHHhcCccEEEEcC--CCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEE-E
Q 002152 618 CEMVRLIETATAPIFGVDS--SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE-L 694 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~--dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e-~ 694 (959)
...+.+++ .|.+|+..+. +-.++|.|.++.++|+++-+++.+.+.. ....+..++.....+.++.+.+-...+. +
T Consensus 32 ~~~~~L~~-ap~ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr-~sae~~~r~er~~lL~~v~~qG~~~~y~Gi 109 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSR-LSAEEPERKERQSLLAQVMQQGYIDNYSGI 109 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHh-hccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence 33455566 8999988865 4599999999999999999999999986 5556667777777888888766543332 2
Q ss_pred EEEeeeeccCCcEEEEE-EEEEEeecCCCCEEEEEEEeecc
Q 002152 695 KLRKFELQKQHSVVYIL-VNACTSRDYKNNVKGVCFVGQDI 734 (959)
Q Consensus 695 ~~~~~~~~~dG~~~~v~-v~~~pi~d~~g~~~gvv~v~~DI 734 (959)
+ +.+.|+.++++ ..+-.+.|++|...|...++.+-
T Consensus 110 R-----iss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~W 145 (148)
T PF08670_consen 110 R-----ISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSNW 145 (148)
T ss_pred E-----EcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEeee
Confidence 3 46778887765 34556789999999988887653
No 111
>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=96.10 E-value=0.21 Score=62.14 Aligned_cols=152 Identities=16% Similarity=0.101 Sum_probs=90.7
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHh
Q 002152 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (959)
Q Consensus 217 ~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~ 296 (959)
.+..++|.+ +.+.+++++.+++.+.+++++++..+|-.++|+ +........ +++. .+...| .+.|-. ..+-..
T Consensus 308 l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~~-~~~~~~~~~-~~~~-~~~~~~-~~~~~~-~~~~~~ 380 (679)
T TIGR02916 308 LRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGND-GLYRPAARW-NQPL-AQAFEP-SDSAFC-QFLQES 380 (679)
T ss_pred HHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCCC-CEEeeehhc-CCCC-cccCCC-CCCHHH-HHHHhC
Confidence 456677776 568999999999999999999999999665544 433333211 1111 111222 222211 112222
Q ss_pred CCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC-CC
Q 002152 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS-PR 375 (959)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~-pr 375 (959)
+++--+.+....|. . . ++.+..+..+...++.+.+||..+| ++.|.+.+.+.. ++
T Consensus 381 ~~v~~~~~~~~~~~--~-----~-------------~~~~~~~~~~~~~~~~l~vPL~~~~----~~~G~l~l~~~~~~~ 436 (679)
T TIGR02916 381 GWIINLEEARSEPD--H-----Y-------------SGLVLPEWLREIPNAWLIVPLISGE----ELVGFVVLARPRTAG 436 (679)
T ss_pred CCcccchhhcCCcc--c-----c-------------cccccchhhhcCCCceEEEEeccCC----EEEEEEEEecCCCCC
Confidence 33322122111111 0 0 0001111222234578999999888 999999887764 77
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHH
Q 002152 376 YIPFPLRYACEFLVQAFSLQLYME 399 (959)
Q Consensus 376 ~~~~~~r~~~~~l~~~~s~~l~~~ 399 (959)
.++.+++...+.++++++..++..
T Consensus 437 ~~~~e~~~lL~~l~~q~a~~l~~~ 460 (679)
T TIGR02916 437 EFNWEVRDLLKTAGRQAASYLAQM 460 (679)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 889999999999999999888654
No 112
>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=96.03 E-value=0.018 Score=71.52 Aligned_cols=68 Identities=15% Similarity=0.252 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 888 ~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
......++.+.++||+||||+.|.+.++.+.....+++..++++.+..++++|..++++ ++++|++.+
T Consensus 481 ~~~~l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~~ 549 (703)
T TIGR03785 481 YTHYLENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQA 549 (703)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 33455678899999999999999999999988777888889999999999999999999 889988765
No 113
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=95.68 E-value=0.015 Score=67.50 Aligned_cols=84 Identities=18% Similarity=0.151 Sum_probs=74.2
Q ss_pred EEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEE
Q 002152 632 FGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYIL 711 (959)
Q Consensus 632 ~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~ 711 (959)
.-.+.|-+|.||.+++.+++||.+++++|+.++ +++|..+.+.+..-...++..+....-.+++ ..+.|+..|+.
T Consensus 278 tRhs~DmkityCedRisdlm~y~PeeLvGrS~Y-e~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~----lak~GGyvWlQ 352 (768)
T KOG3558|consen 278 TRHSLDMKITYCEDRISDLMDYEPEELVGRSCY-EFVHALDSDRVRKSHHDLLTKGQVVTGYYRL----LAKNGGYVWLQ 352 (768)
T ss_pred EeeecceeEEEEchhHHHHhcCCHHHhhchhHH-HhhhHhhhhHHHHHHHHHHhcCccchhHHHH----HHhcCCeEEEE
Confidence 345778899999999999999999999999999 9999999999998888888877776666777 78899999999
Q ss_pred EEEEEeecC
Q 002152 712 VNACTSRDY 720 (959)
Q Consensus 712 v~~~pi~d~ 720 (959)
..++.+.+.
T Consensus 353 TqATVi~~t 361 (768)
T KOG3558|consen 353 TQATVIYNT 361 (768)
T ss_pred eeeEEEecC
Confidence 999888764
No 114
>PRK10337 sensor protein QseC; Provisional
Probab=95.46 E-value=0.038 Score=64.80 Aligned_cols=65 Identities=12% Similarity=0.181 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~-~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
...+|++.++||+||||+.|.+..+.+.....+++ ...+++.+...++++..++++ ++++|++.+
T Consensus 236 ~~~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~~ 302 (449)
T PRK10337 236 RERRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDSL 302 (449)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 34468999999999999999988887765444443 567899999999999999999 899998865
No 115
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=95.45 E-value=0.034 Score=61.79 Aligned_cols=64 Identities=13% Similarity=0.209 Sum_probs=51.5
Q ss_pred HHHHHHHHHHhHhhhhHHHHH---HHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 893 IKELAYIRQEVKNPLNGIRFV---HKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 893 ~~fLa~iSHElRnPL~~I~g~---~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
++-+..++|||+.|||++..+ ..+.-+..-++....++++|+.-.+||.+|++. -.|+|=.+|+
T Consensus 452 GqTmTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~ 519 (673)
T COG4192 452 GQTMTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSD 519 (673)
T ss_pred HHHHHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 445678899999999999844 333334456677899999999999999999999 5899877775
No 116
>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=95.35 E-value=0.13 Score=63.88 Aligned_cols=56 Identities=14% Similarity=0.211 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCH-HHHHHHHHHHHHHHHHHHhhccc
Q 002152 892 KIKELAYIRQEVKNPLNGIRFVHKLLESSSISE-NQRQYLETSDACERQIMTIIDGM 947 (959)
Q Consensus 892 k~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e-~~~~~l~~i~~~~~rl~~LI~dL 947 (959)
..++.+.++||+|||++.+..+.+..+....++ ...++++.+.++.++|.+++++|
T Consensus 475 ~~~~~a~i~HdLrn~l~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l 531 (679)
T TIGR02916 475 FNRMSAFVVHDLKNLVAQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQL 531 (679)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356678899999999999998877776544444 46778899999999999999873
No 117
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=95.21 E-value=0.033 Score=65.61 Aligned_cols=68 Identities=16% Similarity=0.208 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 889 IYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 889 ~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
...+.++++.++||++|||+.|.+.++.+.. ...+...+.+..+...+.++..++++ +++++.+.|.+
T Consensus 237 ~~~~~~~~~~~shel~~pL~~i~~~~~~l~~-~~~~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~~ 305 (466)
T PRK10549 237 EQMRRDFMADISHELRTPLAVLRGELEAIQD-GVRKFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGAL 305 (466)
T ss_pred HHHHHHHHHHHhHHhCChHHHHHHHHHHHHh-ccccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc
Confidence 3456689999999999999999999998876 33333456778888889999999999 78888888754
No 118
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=95.17 E-value=0.037 Score=64.63 Aligned_cols=64 Identities=14% Similarity=0.196 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002152 886 DMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (959)
Q Consensus 886 e~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~ 954 (959)
++..+.+..|++.+||||||||+.|.+..+++... .....+.+....++|..++++ +++.|.+.
T Consensus 223 ~~~~~~~~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~~ 287 (435)
T PRK09467 223 KQLEDDRTLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTGQ 287 (435)
T ss_pred HHHHHHHHHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 34445677899999999999999999888776431 233455677888899999999 88877654
No 119
>PRK09835 sensor kinase CusS; Provisional
Probab=95.15 E-value=0.052 Score=64.24 Aligned_cols=69 Identities=12% Similarity=0.119 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 889 IYAKIKELAYIRQEVKNPLNGIRFVHKLLESSS-ISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 889 ~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
...+.+|++.++|||||||+.|.+..+.+.... ...+..+.+..+.....++..++++ +++++++.+..
T Consensus 259 ~~~~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~~~~ 329 (482)
T PRK09835 259 FTRQSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADNNQL 329 (482)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 345668899999999999999998888765433 3344667777777888999999999 89999887754
No 120
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=94.94 E-value=0.058 Score=63.57 Aligned_cols=66 Identities=20% Similarity=0.317 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccce
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGR 956 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~ 956 (959)
...++++.++||+|||++.|.+..+++......++..++++.+...++++..++++ +++++++.+.
T Consensus 255 ~~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~ 321 (475)
T PRK11100 255 YVEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQRQ 321 (475)
T ss_pred HHHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 34568899999999999999999999887545666889999999999999999999 8998887754
No 121
>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=94.91 E-value=0.054 Score=63.53 Aligned_cols=68 Identities=16% Similarity=0.175 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccccee
Q 002152 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLESSS-ISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRC 957 (959)
Q Consensus 890 ~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~-l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l 957 (959)
....++.+.++||+||||+.+.+..+++.... ..++..++++.+.....++.+++++ |++++++.+..
T Consensus 239 ~~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~~ 308 (457)
T TIGR01386 239 QRLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQL 308 (457)
T ss_pred HHHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 34456789999999999999998888775433 3345667888888889999999999 89999988643
No 122
>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=94.77 E-value=0.16 Score=47.15 Aligned_cols=60 Identities=18% Similarity=0.272 Sum_probs=49.9
Q ss_pred HHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHH
Q 002152 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRA 683 (959)
Q Consensus 624 ie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~ 683 (959)
++..|-|++-+|.+|.|+..|.+-.++.|++++.++|++++.++.+--....+...+...
T Consensus 22 lD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g 81 (124)
T TIGR02373 22 FDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEG 81 (124)
T ss_pred hhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhh
Confidence 789999999999999999999999999999999999999885665555555455555443
No 123
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=94.75 E-value=0.071 Score=60.47 Aligned_cols=60 Identities=23% Similarity=0.258 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
.+.+|++.++||+||||++|.+..+++... ..++.. .+....+++..++++ ++++|++..
T Consensus 136 ~~~~~~~~~sHelrtPL~~i~~~~e~l~~~-~~~~~~----~~~~~~~~l~~~i~~ll~~~r~~~~ 196 (356)
T PRK10755 136 QERLFTADVAHELRTPLAGIRLHLELLEKQ-HHIDVA----PLIARLDQMMHTVEQLLQLARAGQS 196 (356)
T ss_pred HHHHHHHHhhHhhcChHHHHHHHHHHHHhc-cchhHH----HHHHHHHHHHHHHHHHHHHHHcccc
Confidence 445689999999999999999999988752 222222 233445677777888 777776543
No 124
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=94.67 E-value=0.35 Score=51.72 Aligned_cols=112 Identities=16% Similarity=0.129 Sum_probs=80.2
Q ss_pred HHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc-CCCcceEEEEEEee
Q 002152 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL-GEEDKNVELKLRKF 699 (959)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~-~~~~~~~e~~~~~~ 699 (959)
..++++.+.+++++|.+|.|.|+|++++.+||.+...+.|..+. .+++.... ....+.+... +.....++..+
T Consensus 10 ~~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~-~l~~~gs~--ll~ll~q~~~~~~~~~~~~v~l--- 83 (363)
T COG3852 10 GAILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLS-ELLPFGSL--LLSLLDQVLERGQPVTEYEVTL--- 83 (363)
T ss_pred HhHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChH-HHcCCCcH--HHHHHHHHHHhcCCcccceeee---
Confidence 36789999999999999999999999999999999999999887 77665432 2233444433 33444445554
Q ss_pred eeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHH
Q 002152 700 ELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (959)
Q Consensus 700 ~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~ 743 (959)
..+|....++....|+....|.++ ..++-+....+..++
T Consensus 84 --~~~g~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~ridre 122 (363)
T COG3852 84 --VILGRSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRRLDRE 122 (363)
T ss_pred --eecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhHH
Confidence 257888999999999987666553 455555555544443
No 125
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=94.52 E-value=0.07 Score=62.70 Aligned_cols=64 Identities=17% Similarity=0.287 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002152 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (959)
Q Consensus 888 ~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~ 954 (959)
....+.+|++.+|||+||||+.|.+...++....... ..+..+...+++|.+++++ ++++|.+.
T Consensus 239 ~~~~~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~---~~~~~i~~~~~~l~~~i~~l~~~~~~~~ 303 (461)
T PRK09470 239 MMTSQQRLLSDISHELRTPLTRLQLATALLRRRQGES---KELERIETEAQRLDSMINDLLVLSRNQQ 303 (461)
T ss_pred HHHHHHHHHHhhhHhhCCHHHHHHHHHHHHhhccCCh---HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3345567899999999999999999988887643332 2456677889999999999 88888654
No 126
>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=94.31 E-value=0.24 Score=33.68 Aligned_cols=40 Identities=20% Similarity=0.390 Sum_probs=35.0
Q ss_pred eEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeeccc
Q 002152 834 PFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (959)
Q Consensus 834 e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITe 873 (959)
++.+...+|..+|+.....++.+.+|.+.+++++..|||+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 4556778999999999999999988999999999999986
No 127
>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=94.30 E-value=0.86 Score=44.23 Aligned_cols=110 Identities=14% Similarity=0.027 Sum_probs=78.1
Q ss_pred HHHHHHHHhcCCCCCCeeeeC--CCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhc
Q 002152 749 GDYEAIIQSVNPLIPPIFASD--ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT 826 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D--~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~ 826 (959)
..++.+.+. +. +|+..+ .+-.++|.|.++.++++++-+++.+.+..- -..+..+......+.++..
T Consensus 32 ~~~~~L~~a-p~---ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr~--------sae~~~r~er~~lL~~v~~ 99 (148)
T PF08670_consen 32 ELAKALWHA-PF---AILSHGTKADPIFIYANQAALDLFETTWDELVGLPSRL--------SAEEPERKERQSLLAQVMQ 99 (148)
T ss_pred HHHHHHHcC-CC---EEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHhh--------ccChhhHHHHHHHHHHHHH
Confidence 445666764 32 466654 456899999999999999999999987431 2224445555666777777
Q ss_pred CCCcceeeEEEEccCCcEEEEE-EEEeeeeCCCCCEEEEEEEEee
Q 002152 827 GQGTENFPFGFFNRQGQFVEVA-LTASRRTDAEGKVIGCFCFMQI 870 (959)
Q Consensus 827 ~~~~~~~e~~~~~~dG~~~~v~-~~~~pi~d~~G~i~g~v~i~~D 870 (959)
.+-...+.-.-..+.|+.+++. ..+-.+.|++|...|...++.+
T Consensus 100 qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 100 QGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSN 144 (148)
T ss_pred hCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEee
Confidence 6655555555578899988776 4566889999999987766554
No 128
>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=94.20 E-value=1.7 Score=43.86 Aligned_cols=126 Identities=12% Similarity=0.162 Sum_probs=91.5
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCC
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 309 (959)
++...++.+++-+.+.||+ -|+|-- .-.|+|=+- .+-.. |-|.+ +.+..++.+..+.+.+..+.+...
T Consensus 53 ~~~~~A~~~aeII~~~t~~-aVaITD-----r~~ILA~~G-~g~d~----~~~~~-is~~t~~~i~~gk~~~~~~~~~~~ 120 (180)
T TIGR02851 53 ELGDFAKEYAESLYQSLGH-IVLITD-----RDTVIAVAG-VSKKE----YLNKP-ISDELEDTMEERKTVILSDTKDGP 120 (180)
T ss_pred chHHHHHHHHHHHHHHhCC-EEEEEC-----CCcEEEEEC-CChhh----cCCCc-cCHHHHHHHHcCCEEEecCCccce
Confidence 6677788888889999999 888862 345666542 22222 33444 999999999999999988754221
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCC--CCChhHHHHHHH
Q 002152 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPR--YIPFPLRYACEF 387 (959)
Q Consensus 310 ~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr--~~~~~~r~~~~~ 387 (959)
++... -.+....+.+++||+.+| +.=|.|.-. ...+ .++.-++.+++-
T Consensus 121 i~c~~-------------------------~~~~~l~s~ii~Pl~~~g----~viGtLkly-~k~~~~~~~~~e~~la~g 170 (180)
T TIGR02851 121 IEIID-------------------------GQEFEYTSQVIAPIIAEG----DPIGAVIIF-SKEPGEKLGEVEQKAAET 170 (180)
T ss_pred ecccc-------------------------CCCCCcceEEEEEEEECC----eEEEEEEEE-ECCccCCCCHHHHHHHHH
Confidence 32110 011124789999999998 999977777 6566 789999999999
Q ss_pred HHHHHHHHHH
Q 002152 388 LVQAFSLQLY 397 (959)
Q Consensus 388 l~~~~s~~l~ 397 (959)
||+.||.||+
T Consensus 171 lA~lLS~QLE 180 (180)
T TIGR02851 171 AAAFLGKQME 180 (180)
T ss_pred HHHHHHHhhC
Confidence 9999999973
No 129
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=94.12 E-value=0.094 Score=57.62 Aligned_cols=113 Identities=14% Similarity=0.118 Sum_probs=77.2
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCC
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~ 828 (959)
..+.++++..|.- |-..|.++++.++|+. .++|-+++ .++|+.... |. +|.....+.. +.+.+..|
T Consensus 290 ~e~naif~~lP~D---itfvdk~diV~ffs~~-~rif~rt~-sviGr~v~~-----ch---pPksv~iv~k-i~~~fksG 355 (409)
T COG2461 290 EELNAIFKHLPVD---ITFVDKNDIVRFFSGG-ERIFPRTP-SVIGRRVQL-----CH---PPKSVHIVEK-ILKDFKSG 355 (409)
T ss_pred HHHHHHHhhCCCc---eEEecccceEEecCCc-ceecccCh-HhhCCcccC-----CC---CCchHHHHHH-HHHHhhcC
Confidence 4567889888733 6778999999999998 88887765 457886542 11 2333333333 33444455
Q ss_pred CcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccHHH
Q 002152 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (959)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~~E 878 (959)
.....++. .+..+ ..+.++..+++|++|+..|++-+.+|||.-++.+
T Consensus 356 ~kd~~efw-~~~~~--~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 356 EKDFAEFW-INMGD--KFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred CcchHHHh-ccCCC--ceEEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 56666666 23333 3567788899999999999999999999755433
No 130
>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=93.71 E-value=0.2 Score=38.00 Aligned_cols=45 Identities=33% Similarity=0.397 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcc
Q 002152 751 YEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (959)
Q Consensus 751 l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (959)
++.+++.++. +++.+|.++.+.++|+.+.+++|++..++.++.+.
T Consensus 3 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (67)
T smart00091 3 LRAILESLPD---GIFVLDLDGRILYANPAAEELLGYSPEELIGKSLL 47 (67)
T ss_pred HHHHHhhCCc---eEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHH
Confidence 4566777664 48999999999999999999999999888887543
No 131
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=93.53 E-value=0.86 Score=58.55 Aligned_cols=114 Identities=14% Similarity=0.106 Sum_probs=69.3
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEc-CCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcC
Q 002152 608 QGVDELSSVACEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLG 686 (959)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D-~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~ 686 (959)
+..++|++.++.++.+++++|.++++++ .+|.++.+|+.+..++|+...+. ..... .....
T Consensus 324 ~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~--------------~~~~~----~~~~~ 385 (924)
T PRK10841 324 SNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHED--------------RQRLT----QIICG 385 (924)
T ss_pred HHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChhH--------------HHHHH----HHHhc
Confidence 3455688888899999999999999997 69999999999999988643221 11111 11111
Q ss_pred CCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHH
Q 002152 687 EEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (959)
Q Consensus 687 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~ 749 (959)
......+ . ...++... .+.....+.. +.. ..++++.|||+++++++++++..+
T Consensus 386 ~~~~~~~--~----~~~~~~~~--~i~~~~~~~~-~~~-~~i~~~~Dit~r~~~e~~L~~~~~ 438 (924)
T PRK10841 386 QQVNFVD--V----LTSNNTNL--QISFVHSRYR-NEN-VAICVLVDVSARVKMEESLQEMAQ 438 (924)
T ss_pred cccceee--E----EcCCCcEE--EEEEEeeeec-Cce-EEEEEEEEhhHHHHHHHHHHHHHH
Confidence 1111111 1 12233333 3333333222 222 346788899999999988866544
No 132
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=93.51 E-value=0.37 Score=44.81 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=40.5
Q ss_pred HHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCccccccc
Q 002152 755 IQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFG 803 (959)
Q Consensus 755 ~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~ 803 (959)
++.++ .|++.+|.+|+|+..|.+-.++.|++++.++|+++..++.+
T Consensus 22 lD~lp---FGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAP 67 (124)
T TIGR02373 22 FDALP---FGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAP 67 (124)
T ss_pred hhcCC---cceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhccc
Confidence 45555 46999999999999999999999999999999998877665
No 133
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=93.39 E-value=0.27 Score=58.55 Aligned_cols=59 Identities=7% Similarity=0.120 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHHHHhhcc-cCc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSI-SENQRQYLETSDACERQIMTIIDG-MDL 949 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l-~e~~~~~l~~i~~~~~rl~~LI~d-Ld~ 949 (959)
.+.++.+.++||++|||++|.+..+++++... +++.++..+.+++.+.++.+++++ ++.
T Consensus 301 ~r~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~ 361 (495)
T PRK11644 301 VRRDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGR 361 (495)
T ss_pred HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45567788899999999999999999876433 344667888888888888888887 543
No 134
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=92.74 E-value=0.097 Score=57.52 Aligned_cols=104 Identities=11% Similarity=0.096 Sum_probs=72.6
Q ss_pred HHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCc-hHHHHHHHHHHHcCCCcceEEEEEEe
Q 002152 620 MVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEES-QGAVENLICRALLGEEDKNVELKLRK 698 (959)
Q Consensus 620 l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~-~~~~~~~l~~~l~~~~~~~~e~~~~~ 698 (959)
+-..++....+|-+.|.+..|.|+|+++++++|+...|++|++.. ++-..+. +..+.+.+...+..+..+..+...
T Consensus 159 lFaaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~a-dlpkkdknradlldtintcikkgke~qG~~~a-- 235 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEA-DLPKKDKNRADLLDTINTCIKKGKEAQGEEEA-- 235 (775)
T ss_pred HHHHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchh-hccccccchhhhhhhhhHhhhcCccccchHHH--
Confidence 345677888899999999999999999999999999999999987 5543322 233334444444444333333222
Q ss_pred eeeccCCcEEEEEEEEEEeecCCCCEEEEE
Q 002152 699 FELQKQHSVVYILVNACTSRDYKNNVKGVC 728 (959)
Q Consensus 699 ~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv 728 (959)
+++.|......+...|+....|++-.++
T Consensus 236 --RRksgdS~dqh~~itP~~gqggkirhfv 263 (775)
T KOG1229|consen 236 --RRKSGDSCDQHFIITPFAGQGGKIRHFV 263 (775)
T ss_pred --hhccCCcccceEEEeeecCCCCceeeeh
Confidence 5667777777777888887777776543
No 135
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=92.46 E-value=0.54 Score=51.38 Aligned_cols=54 Identities=19% Similarity=0.339 Sum_probs=48.7
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCc
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEES 672 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~ 672 (959)
..+.+++++.|++++.+|..|.+..+|++++++||.+.+++.|.... .++....
T Consensus 80 l~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~-~l~~~~n 133 (511)
T COG3283 80 LALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA-QLINGFN 133 (511)
T ss_pred HHHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHH-HhcCcCC
Confidence 45788999999999999999999999999999999999999999987 7766543
No 136
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=92.29 E-value=0.4 Score=57.39 Aligned_cols=201 Identities=14% Similarity=0.209 Sum_probs=112.5
Q ss_pred cEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHc-------CC--------CcceEEE
Q 002152 630 PIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL-------GE--------EDKNVEL 694 (959)
Q Consensus 630 ~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~-------~~--------~~~~~e~ 694 (959)
..++-+.+|+|+|+...+..++|+.++-+.+..+. +++++.+...+...+....- +. ....+..
T Consensus 194 ~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~Fv-dflapqD~~vF~sfta~~~lp~ws~~s~~ds~~~~c~~~ks~fc 272 (1114)
T KOG3753|consen 194 VVAVSFLDGRILYISEQAALILGCKRDVLSSAKFV-DFLAPQDVGVFYSFTARYKLPLWSMGSSADSFTQECAEEKSFFC 272 (1114)
T ss_pred EEEEeccCCcEEEeechhhhhccCchhhhccchhh-hhcchhhhhhhhhccccccCccccccccccchhhhhhhhcceee
Confidence 34455789999999999999999999999999999 99999887766544332211 00 0011111
Q ss_pred EEEeeeeccCCcEEE----EEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeeC-
Q 002152 695 KLRKFELQKQHSVVY----ILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASD- 769 (959)
Q Consensus 695 ~~~~~~~~~dG~~~~----v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~~I~~~D- 769 (959)
++.. +.......++ +.-..+-+++..|-.-+.+++. + + .+...-|++= .-.+.- -||.+-
T Consensus 273 Risg-r~~~~~~~~y~PFRl~pyl~ev~~~~~~~s~~ccLl--l-----a----erihSgYeAP-rIps~K--riFtT~H 337 (1114)
T KOG3753|consen 273 RISG-RKDRENEIRYHPFRLTPYLVEVRDQQGAESQPCCLL--L-----A----ERIHSGYEAP-RIPSNK--RIFTTTH 337 (1114)
T ss_pred eeec-ccCCcCccccCcccccceeEEeccccccCcCcceee--h-----h----hhhhcccccC-cCCccc--ceeEecc
Confidence 1110 0000000111 1111111222111111111111 0 0 0111112111 111111 155543
Q ss_pred -CCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhc-CCCc--ceeeEEEEccCCcEE
Q 002152 770 -ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT-GQGT--ENFPFGFFNRQGQFV 845 (959)
Q Consensus 770 -~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~-~~~~--~~~e~~~~~~dG~~~ 845 (959)
..+.+..+..++.-++||-+.++||+.+.. +.|++|+..+.+...++++ ++.+ ..-.+|+...||.++
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil~--------f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv 409 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSILA--------FVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYV 409 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchhh--------hhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEE
Confidence 455677889999999999999999998764 6678888877777777766 3333 344678899999998
Q ss_pred EEEEEEeee
Q 002152 846 EVALTASRR 854 (959)
Q Consensus 846 ~v~~~~~pi 854 (959)
.+....+..
T Consensus 410 ~ldTeWSsF 418 (1114)
T KOG3753|consen 410 RLDTEWSSF 418 (1114)
T ss_pred EEechhhhc
Confidence 776554433
No 137
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=91.64 E-value=0.26 Score=54.13 Aligned_cols=64 Identities=31% Similarity=0.502 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G 955 (959)
.+..+++.++||+|||++.+.+..+++... ..+..++++..+....+++..++++ +++++++.+
T Consensus 114 ~~~~~~~~~~hel~~pl~~i~~~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~ 178 (336)
T COG0642 114 AKREFLANISHELRTPLTAIRGLLELLLEG-LLDPQRELLEIIEEEAERLLRLVNDLLDLSRLEAG 178 (336)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHhccC-CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 367899999999999999999988866654 2222788899998899999999999 899999875
No 138
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=90.91 E-value=0.032 Score=69.62 Aligned_cols=71 Identities=23% Similarity=0.463 Sum_probs=61.4
Q ss_pred HHHHHHHHH--HHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccceee
Q 002152 886 DMDIYAKIK--ELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEGRCV 958 (959)
Q Consensus 886 e~~~~ak~~--fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~d-Ld~srIe~G~l~ 958 (959)
+++...+.+ +++.++||||+||++ |+...+..+..+.+++.+++....++.....++++ +|.+++++|+++
T Consensus 213 e~~~~~~sq~~~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g~~~ 286 (786)
T KOG0519|consen 213 EAAVWSPSQKGFLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESGKGE 286 (786)
T ss_pred hhcccCccchhhcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccccce
Confidence 334445555 999999999999999 66666677889999999999999999999999999 999999999875
No 139
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=90.77 E-value=12 Score=47.87 Aligned_cols=134 Identities=13% Similarity=0.038 Sum_probs=82.1
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCC
Q 002152 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (959)
Q Consensus 230 ~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 309 (959)
.++..++.+.+.+..++|.+++.++-|+.++...+... . |. .|..+.+...+.+-..- ...+
T Consensus 293 ~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---~------~~-~~~~~~~~~~~~~~~~~--------~~~~ 354 (828)
T PRK13837 293 ELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---P------GL-TPDPVWPDRLRALASTV--------KAAE 354 (828)
T ss_pred hhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---C------cc-CCCCCchHHHHHHHHHH--------hccC
Confidence 45689999999999999999999999988775444221 1 11 12333443333321110 0000
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCC-CCCChhHHHHHHHH
Q 002152 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSP-RYIPFPLRYACEFL 388 (959)
Q Consensus 310 ~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~p-r~~~~~~r~~~~~l 388 (959)
-.++.. .+..++....++...+..+.+++|+..++ ++.|++.+....+ ..+...+...++.+
T Consensus 355 ~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~g~l~~~~~~~~~~~~~~~~~~l~~~ 417 (828)
T PRK13837 355 RDVVFV-------------DRNGPVRKRSCLTRRGPALWACLAFKSGD----RIVALLGLGRQRYGLRPPAGELQLLELA 417 (828)
T ss_pred CceEEe-------------ecccchhhhcccccCCcceEEEEEeccCC----ceEEEEEecccccCCCCChhHHHHHHHH
Confidence 000000 01112333344556788999999998887 9999999987753 33446777788888
Q ss_pred HHHHHHHHHH
Q 002152 389 VQAFSLQLYM 398 (959)
Q Consensus 389 ~~~~s~~l~~ 398 (959)
+..++..+..
T Consensus 418 ~~~~~~~~~~ 427 (828)
T PRK13837 418 LDCLAHAIER 427 (828)
T ss_pred HHHHHHHHHH
Confidence 8887777654
No 140
>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=90.18 E-value=1.4 Score=29.49 Aligned_cols=36 Identities=36% Similarity=0.481 Sum_probs=31.3
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchh
Q 002152 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITH 736 (959)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITe 736 (959)
...+|...|+.....++.+..+.+.+++++..|||+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 7 RRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 456788889998889998888999999999999986
No 141
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=89.35 E-value=16 Score=35.67 Aligned_cols=116 Identities=18% Similarity=0.220 Sum_probs=82.4
Q ss_pred HHHHHHHHh-CCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHH---HHHHHHhCCEEEEecCCCCCcccc
Q 002152 238 VVEDVQKLT-GYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQA---ARFLFKQNRVRMICDCHAIPVMVI 313 (959)
Q Consensus 238 ~v~~vr~~~-g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~---ar~ly~~~~~r~i~d~~~~~~~l~ 313 (959)
+..-+.+.+ .+|=|=.|.++ +++-|- .||-|. -+-.+||-- ...--..|++-.|.||++-|=
T Consensus 40 ~sall~~~l~~~nW~GFYl~~---~~~LvL-------gPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~g--- 105 (163)
T COG1956 40 ASALLKERLPDVNWVGFYLLE---GDELVL-------GPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHAFPG--- 105 (163)
T ss_pred HHHHHHhhccCCceEEEEEec---CCeEEE-------ecccCC-cceEEeccCcchhHHHHhcCCeEEecccccCCC---
Confidence 333444444 48888888888 556654 478886 444566632 234456799999999997654
Q ss_pred cccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHHHH
Q 002152 314 QSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFS 393 (959)
Q Consensus 314 ~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~s 393 (959)
|+.- .--++|-+++||+++| ++-|.|=.-..+|-+++.+.+..++.++..+.
T Consensus 106 ----------------------hiaC--D~as~SEIVvPi~~~g----~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~~l~ 157 (163)
T COG1956 106 ----------------------HIAC--DAASNSEIVVPIFKDG----KLIGVLDIDSPTPGRFDEEDEAGLEKLAALLE 157 (163)
T ss_pred ----------------------cccc--ccccCceEEEEEEECC----EEEEEEecCCCCcccCCHHHHHHHHHHHHHHH
Confidence 3211 2245889999999999 99999999988888889988888888777665
Q ss_pred HH
Q 002152 394 LQ 395 (959)
Q Consensus 394 ~~ 395 (959)
..
T Consensus 158 ~~ 159 (163)
T COG1956 158 KS 159 (163)
T ss_pred HH
Confidence 43
No 142
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=88.54 E-value=5 Score=51.23 Aligned_cols=46 Identities=13% Similarity=-0.016 Sum_probs=41.0
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEc-CCCceehhcHHHHHHhCC
Q 002152 608 QGVDELSSVACEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGL 653 (959)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D-~dg~iv~~N~~~~~l~G~ 653 (959)
+..++|+..+..++.+++++|+|++++| .+|+|+.+|+++.+++|.
T Consensus 333 ~l~~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 333 SMSHELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHHHHhCc
Confidence 3456788888999999999999999999 678999999999999975
No 143
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=88.14 E-value=1.6 Score=49.89 Aligned_cols=94 Identities=14% Similarity=0.046 Sum_probs=76.9
Q ss_pred CCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEE
Q 002152 637 SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACT 716 (959)
Q Consensus 637 dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~p 716 (959)
|+..+.+..+...++||...|+.|.+.+ +++|.++.-.+...-.+.+..++..-.-+++ ..++|++.|+..++..
T Consensus 292 Dfa~vs~Dak~k~~lgy~eaEL~~m~gY-~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~----qtk~grw~wvqssarl 366 (712)
T KOG3560|consen 292 DFALVSMDAKVKATLGYCEAELHGMPGY-NLVHVEDKVYMAEAHSEGIKTGESGMLVYRE----QTKAGRWAWVQSSARL 366 (712)
T ss_pred ccceeccchhhhhhhccchhhccCCCcc-ceeehhhhhhhhHHHHHHhhcCCcceEEEEE----eecCCcEEEeecccee
Confidence 5566777788889999999999998888 9999998877777777888877777777776 6889999999988877
Q ss_pred eecCCCCEEEEEEEeecchh
Q 002152 717 SRDYKNNVKGVCFVGQDITH 736 (959)
Q Consensus 717 i~d~~g~~~gvv~v~~DITe 736 (959)
++ .+|++..++.+-+-.++
T Consensus 367 ly-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 367 LY-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred ee-ecCCCCEEEecCCCccc
Confidence 66 57787777777776666
No 144
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=86.48 E-value=1.4 Score=48.30 Aligned_cols=87 Identities=16% Similarity=0.127 Sum_probs=66.9
Q ss_pred ccEEEEcCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEE
Q 002152 629 APIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVV 708 (959)
Q Consensus 629 ~~I~~~D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~ 708 (959)
..++....|-++++...+..+++||++.+++++.+. ..++..+...+..+-..++..+....--+++ ..+.|++.
T Consensus 226 mFmfraslDlkliF~D~rv~qltgYepqdliektLY-~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~----l~k~ggwv 300 (598)
T KOG3559|consen 226 MFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLY-HHIHGCDSFHLRCAHHLLLVKGQVTTKYYRF----LLKQGGWV 300 (598)
T ss_pred eEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHH-HHhhhhhHHHHHHHHHHHHhccccccHHHHH----HHcCCceE
Confidence 455666778899999999999999999999999998 8888888777776666666555444434444 56779999
Q ss_pred EEEEEEEEeecC
Q 002152 709 YILVNACTSRDY 720 (959)
Q Consensus 709 ~v~v~~~pi~d~ 720 (959)
|+.-.+..+.+.
T Consensus 301 wvqsyat~vHnS 312 (598)
T KOG3559|consen 301 WVQSYATFVHNS 312 (598)
T ss_pred EEEEeeEEEecc
Confidence 998777666543
No 145
>PRK10490 sensor protein KdpD; Provisional
Probab=86.20 E-value=35 Score=43.89 Aligned_cols=49 Identities=10% Similarity=0.076 Sum_probs=39.4
Q ss_pred eeEEEEEEEEcCCCCCceeEEEEeecCCC-CCCChhHHHHHHHHHHHHHHHHHH
Q 002152 346 IASLVMAVIINSKDSMKLWGLVVCHHTSP-RYIPFPLRYACEFLVQAFSLQLYM 398 (959)
Q Consensus 346 ~asl~v~i~~~~~~~~~LWGLi~~hh~~p-r~~~~~~r~~~~~l~~~~s~~l~~ 398 (959)
.+.+.+||...+ +++|++.+..+.+ +.++++.+...+.++.+++..++.
T Consensus 595 ~~~~~lPl~~~~----~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler 644 (895)
T PRK10490 595 VPYQILPLKSAQ----KTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALER 644 (895)
T ss_pred CceEEEEEEECC----EEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 346689999888 9999999977764 567888888888888888887764
No 146
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=86.14 E-value=3.8 Score=48.59 Aligned_cols=182 Identities=15% Similarity=0.141 Sum_probs=89.2
Q ss_pred ccccccchHHHHHHHHHHHHHHHh---cCccEEEEcCCCceehhcHHHHHHhCCCccc-ccCCCccccccCCCchHHHHH
Q 002152 603 NGSKMQGVDELSSVACEMVRLIET---ATAPIFGVDSSGTINGWNAKVAELTGLPASE-AMGKSLIDEVVHEESQGAVEN 678 (959)
Q Consensus 603 ~~~l~~~~~eL~~~~~~l~~lie~---~~~~I~~~D~dg~iv~~N~~~~~l~G~~~ee-liGk~~~~~l~~~~~~~~~~~ 678 (959)
++.+++...-|......|..++.. .+..+++.|.+|.++..+-.-......+.-- ..|..|. +-... ..
T Consensus 59 ~~~rE~~~~LL~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WS-E~~~G------TN 131 (606)
T COG3284 59 REARERAEALLTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWS-EPREG------TN 131 (606)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecChhhhhhhhhhccccccccc-ccccc------cc
Confidence 333444444455555556666554 4567888899999987654322211111100 1233332 11100 01
Q ss_pred HHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEe---ecchhhHHH------HHHHHHHHH
Q 002152 679 LICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVG---QDITHEKVL------MDKFIRLQG 749 (959)
Q Consensus 679 ~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~---~DITerk~~------E~~L~~se~ 749 (959)
.+-.++..++. +.+.-. .|=......+..++.|++|.+|+++|++.+. .|+++.-.. ...-+..|.
T Consensus 132 gIGTcLve~~a--VtI~~~---qHF~~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~~~~~~s~~~~~~iV~~~ar~IE~ 206 (606)
T COG3284 132 GIGTCLVEGEA--VTIHGD---QHFIQAHHGLSCSAAPIFDEQGELVGVLDISSCRSDLSEASQPLTLAIVTDAARRIEA 206 (606)
T ss_pred chhhhhccCcc--eEEehh---hhHhhcccCceeeeeccccCCCcEEEEEEeccCCcchhhhhhHHHHHHHHHHHHHHHH
Confidence 11122211111 111100 0111233457788999999999999987665 233333210 011111111
Q ss_pred H---------HHHHHHhcC----CCCCCeeeeCCCCcEEeecHHHHHHhCCC-chhhcCCC
Q 002152 750 D---------YEAIIQSVN----PLIPPIFASDENACCSEWNAAMEKVTGWM-RHEVIGKM 796 (959)
Q Consensus 750 ~---------l~~i~e~~~----~~i~~I~~~D~~g~i~~~N~a~~~l~G~~-~eeviGk~ 796 (959)
. +...+...+ ..-.+.+.+|.+|+++-.|+++..+++.+ ..-++|.+
T Consensus 207 ~~~~~~~~~~~~lr~~~~p~~~d~~~~~~lavd~~grvl~at~aA~~~La~~~~~~l~g~p 267 (606)
T COG3284 207 ELFLAAFEGHWLLRIALAPDYLDSQSEALLAVDQDGRVLGATRAARQLLALTDRQRLIGQP 267 (606)
T ss_pred HHHHHhcCcchHHHHhcCccccCcccceeeeecCcchhhhccHHHHHhhccchhhHhhcCC
Confidence 1 111111111 11235788999999999999999999887 34444444
No 147
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=85.28 E-value=0.37 Score=58.76 Aligned_cols=97 Identities=11% Similarity=0.084 Sum_probs=66.9
Q ss_pred eCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcC-CCcceeeEEEEccCCcEEE
Q 002152 768 SDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG-QGTENFPFGFFNRQGQFVE 846 (959)
Q Consensus 768 ~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~-~~~~~~e~~~~~~dG~~~~ 846 (959)
...+|.++++-.....+.||...++.|+.... ..|+++.......+..+... ......-++++.++|.+.|
T Consensus 378 ~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~--------s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~ 449 (803)
T KOG3561|consen 378 SSSDGSFTFVDQRASAILGYQPQELLGRSSYE--------SSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIP 449 (803)
T ss_pred cCcCCceeccccccccccccCchhhcCccccc--------ccCccccchhhchHHHHHHhcccccccccccccCCCCccc
Confidence 45678888888889999999999999997542 44566666555555554442 2244566788999999998
Q ss_pred EEEEEeeeeCCC-CCEEEEEEEEeecc
Q 002152 847 VALTASRRTDAE-GKVIGCFCFMQILV 872 (959)
Q Consensus 847 v~~~~~pi~d~~-G~i~g~v~i~~DIT 872 (959)
.........|.. ..+.++++...-+.
T Consensus 450 ~~~~~~~~~n~~s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 450 NKSSAYLFSNPGSDEVEYIVCTNSNVP 476 (803)
T ss_pred cccccccccCCCccccceeeecccccc
Confidence 887776655433 34556666655554
No 148
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=85.16 E-value=0.49 Score=57.69 Aligned_cols=60 Identities=20% Similarity=0.315 Sum_probs=47.9
Q ss_pred CCChhhHHHH-HhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCCCcccccccccccCCccccccCCchHH
Q 002152 74 GVPEEQITAY-LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGA 149 (959)
Q Consensus 74 ~~~~~~~~~~-~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 149 (959)
-++.+.+|.- |+-.- |||+||.-+ |+|++||+|+..+||..+ ++++|+.|-+++.+....
T Consensus 90 flS~~eL~~LmLeAlD--------GF~fvV~cd-G~IvyVSeSVT~~L~y~Q-------sDL~~qSly~ilhp~d~~ 150 (803)
T KOG3561|consen 90 FLSNDELTHLILEALD--------GFLFVVNCD-GRIVYVSESVTSVLGYLQ-------SDLMGQSLYDILHPLDND 150 (803)
T ss_pred ccchHHHHHHHHHHhc--------CeEEEEecC-ceEEEEecchHHhhCcCH-------HHHhcchHHHhcCccccC
Confidence 3446666665 55443 999999987 999999999999999988 689999999988655443
No 149
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=84.96 E-value=6 Score=46.15 Aligned_cols=147 Identities=15% Similarity=0.165 Sum_probs=101.3
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCC-eEEEEEecCCCCCCccCCccCCCCchHHHHHHH
Q 002152 216 AVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDH-GEVVSEIRRSDLEPYLGIHFPANDIPQAARFLF 294 (959)
Q Consensus 216 ~~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~-G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly 294 (959)
++++.+.+.+ ..++.+-++..|++|..-...+=+-||-.+.|++ =+..| .+|+.+.-|
T Consensus 5 Lr~i~E~va~--~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~A---TeGLnk~av---------------- 63 (756)
T COG3605 5 LRRIVEKVAS--ALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELMA---TEGLNKPAV---------------- 63 (756)
T ss_pred HHHHHHHHhc--ccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEe---ccccCcccc----------------
Confidence 3455666666 6699999999999999999999999999999984 33333 223322222
Q ss_pred HhCCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcC---ceeEEEEEEEEcCCCCCceeEEEEeec
Q 002152 295 KQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMG---SIASLVMAVIINSKDSMKLWGLVVCHH 371 (959)
Q Consensus 295 ~~~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmg---v~asl~v~i~~~~~~~~~LWGLi~~hh 371 (959)
..+++-+| ..=|.++ ....+||+|+.+. -||- -.|+..-| -.|-|.+||+..| ++-|.++.++
T Consensus 64 --~~~~l~~~--eGLVG~v--~~~aePlNLsdAq---sHPs-F~Y~petgEE~Y~sFLGvPIi~~~----r~lGVLVVQq 129 (756)
T COG3605 64 --HLVQLAFG--EGLVGLV--GRSAEPLNLADAQ---SHPS-FKYLPETGEERYHSFLGVPIIRRG----RLLGVLVVQQ 129 (756)
T ss_pred --ceEEecCC--Cchhhhh--hhccCCCChhhhh---hCCc-cccccccchHHHHHhhccceeecC----ceeEEEEEec
Confidence 12222222 1112222 3346788888764 1332 34666555 3577899999888 9999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHH
Q 002152 372 TSPRYIPFPLRYACEFLVQAFSLQLY 397 (959)
Q Consensus 372 ~~pr~~~~~~r~~~~~l~~~~s~~l~ 397 (959)
.++|.+...+-.+++.++.+++.-++
T Consensus 130 k~~R~y~E~Eve~L~T~A~~lA~iva 155 (756)
T COG3605 130 RELRQYDEDEVEFLVTLAMQLAEIVA 155 (756)
T ss_pred ccccccchHHHHHHHHHHHHHHHHHH
Confidence 99999999998888877766665543
No 150
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=83.27 E-value=8.1 Score=37.18 Aligned_cols=85 Identities=12% Similarity=-0.011 Sum_probs=68.7
Q ss_pred ceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEee
Q 002152 639 TINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSR 718 (959)
Q Consensus 639 ~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~ 718 (959)
++..+-...++++|.. +.|+.+. +++.++....+...+..+.....+.-..... ...+|....++.-..|+.
T Consensus 52 r~RLaGt~i~~~~G~d---~tG~~~~-el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~----~~~~g~~~~~e~l~LPL~ 123 (137)
T PF07310_consen 52 RYRLAGTRIVELFGRD---LTGRRLS-ELFPPEDRERVRRAYRAVVERPAPVRARGRA----EDADGRYLEYERLLLPLR 123 (137)
T ss_pred EEEEecHHHHHHhCCC---CCCCCHH-HhcChHhHHHHHHHHHHHHcCCceEEEEEEE----ecCCCCeeEEEEEEcccC
Confidence 5666788999999984 5699998 8999988888999999998877665555554 456788888999999999
Q ss_pred cCCCCEEEEEEEe
Q 002152 719 DYKNNVKGVCFVG 731 (959)
Q Consensus 719 d~~g~~~gvv~v~ 731 (959)
+.+|.+..++|+.
T Consensus 124 ~~~~~v~rilG~~ 136 (137)
T PF07310_consen 124 SDGGTVDRILGAL 136 (137)
T ss_pred CCCCCccEEEEec
Confidence 9999888877764
No 151
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=82.95 E-value=7.2 Score=31.88 Aligned_cols=48 Identities=19% Similarity=0.163 Sum_probs=38.1
Q ss_pred HHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhc
Q 002152 894 KELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIID 945 (959)
Q Consensus 894 ~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~ 945 (959)
+.+....||+.|-|+.|.|++++= -.++..+|++.+....+....+++
T Consensus 14 ~~lR~~RHD~~NhLqvI~gllqlg----~~~~a~eYi~~~~~~~~~~s~l~~ 61 (62)
T PF14689_consen 14 DSLRAQRHDFLNHLQVIYGLLQLG----KYEEAKEYIKELSKDLQQESELLK 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHhHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHHHHHHc
Confidence 446667999999999999998863 347788999999888888776653
No 152
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=80.46 E-value=5.6 Score=43.81 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=41.8
Q ss_pred HHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcc
Q 002152 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (959)
-.+.+++++++ ++++.+|..|.+..+|+++++++|.+.+++.|++..
T Consensus 80 l~L~aLL~al~---~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~ 126 (511)
T COG3283 80 LALSALLEALP---EPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA 126 (511)
T ss_pred HHHHHHHHhCC---CceEEecccCceeecCHHHHHHhCCChhhhcCccHH
Confidence 34678888887 469999999999999999999999999999999855
No 153
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=79.02 E-value=14 Score=35.59 Aligned_cols=85 Identities=8% Similarity=0.004 Sum_probs=69.4
Q ss_pred cEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEEe
Q 002152 773 CCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTAS 852 (959)
Q Consensus 773 ~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~ 852 (959)
++..+-...++++|+ |+.|+.+.+ +..++....+...+..+.....+.....+....+|....++...-
T Consensus 52 r~RLaGt~i~~~~G~---d~tG~~~~e--------l~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~L 120 (137)
T PF07310_consen 52 RYRLAGTRIVELFGR---DLTGRRLSE--------LFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLL 120 (137)
T ss_pred EEEEecHHHHHHhCC---CCCCCCHHH--------hcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEc
Confidence 566678888999986 456777553 444677778888899999988888888888899999999999999
Q ss_pred eeeCCCCCEEEEEEEE
Q 002152 853 RRTDAEGKVIGCFCFM 868 (959)
Q Consensus 853 pi~d~~G~i~g~v~i~ 868 (959)
|+.+.+|.+..++|.+
T Consensus 121 PL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 121 PLRSDGGTVDRILGAL 136 (137)
T ss_pred ccCCCCCCccEEEEec
Confidence 9999999998888864
No 154
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=75.59 E-value=42 Score=35.27 Aligned_cols=136 Identities=15% Similarity=0.014 Sum_probs=72.9
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhC
Q 002152 218 SAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQN 297 (959)
Q Consensus 218 ~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~ 297 (959)
.+.-+|-. +.++.+++++..+.+++..+.|-|-+--|++++.- +++.. .++..++ .........
T Consensus 82 ~l~l~LL~--a~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~~---~~~~~--------~~~~~~~---~~~~~~~~~ 145 (225)
T PF04340_consen 82 RLVLALLA--ARSLQELLQALDDGLREDFDVDAVRLRLFDDDAAP---GPSLT--------DHVWLSR---DAFAQVFID 145 (225)
T ss_dssp HHHHHHHC----SHHHHHHHHHHHHHHTS--SEEEEEEE-SS------SEE--------------E-H---HHHHHHHCC
T ss_pred HHHHHHhc--CCCHHHHHHHHHHHHHHhcCCCeEEEEeecccccc---ccchh--------hcccccH---HHHHHHHHH
Confidence 34444545 56999999999999999999999999999987662 11110 1111111 111101101
Q ss_pred CEEEEecCCCCCcccccccccCCccccccccccCCChh-hHHHHh--hcCceeEEEEEEEEcCCCCCceeEEEEeecCCC
Q 002152 298 RVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGC-HLQYMT--NMGSIASLVMAVIINSKDSMKLWGLVVCHHTSP 374 (959)
Q Consensus 298 ~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~-h~~yl~--nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~p 374 (959)
.. . ... |.. --++.. +...+- .-+|+|...+|+. .+ +.+|+|+-=...|
T Consensus 146 ~l---~--~~~--p~~----------------G~~~~~~~~~lF~~~~~~v~S~AlipL~-~~----~~~G~LalGS~D~ 197 (225)
T PF04340_consen 146 LL---G--LQQ--PYC----------------GRLSEEEAALLFGDEAAQVGSVALIPLG-SG----RPIGLLALGSRDP 197 (225)
T ss_dssp CH---T--T-----CC----------------CS--HHHHHHHHHHCHCC-SEEEEEEEE-SS----SEEEEEEEEESST
T ss_pred Hh---C--CCC--cee----------------CCCCcchhHHhcCCCCccccchheeecc-CC----CceEEEEecCCCh
Confidence 00 0 000 111 001111 222222 3568999999998 66 9999999877765
Q ss_pred -CCCChhHHHHHHHHHHHHHHHHH
Q 002152 375 -RYIPFPLRYACEFLVQAFSLQLY 397 (959)
Q Consensus 375 -r~~~~~~r~~~~~l~~~~s~~l~ 397 (959)
|+-|----.++++|+.+++..|.
T Consensus 198 ~rF~p~mgT~fL~~La~vv~~~L~ 221 (225)
T PF04340_consen 198 DRFQPDMGTDFLEQLAEVVSAALE 221 (225)
T ss_dssp TCCCSTTTTHHHHHHHHHHHHHGG
T ss_pred hhCCCCccHHHHHHHHHHHHHHHh
Confidence 55454557888889988887664
No 155
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=73.37 E-value=1.3e+02 Score=36.36 Aligned_cols=124 Identities=17% Similarity=0.165 Sum_probs=76.9
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEE-EecCCCCCCccCCccCCCCchHHHHHHHH
Q 002152 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVS-EIRRSDLEPYLGIHFPANDIPQAARFLFK 295 (959)
Q Consensus 217 ~~~~~~l~~~~~~~l~~~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~via-E~~~~~~~s~lg~~~pa~dip~~ar~ly~ 295 (959)
..+..++.. +..+...|+.+.+++.+++|.+.+.+.-.++++...... .+.. + . +.|+
T Consensus 223 y~~~~~l~~--~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-~--~----~~~~------------ 281 (569)
T PRK10600 223 WQANRRLHS--RAPLCERLSPVLNGLQNLTLLRDIELRVYETDDEENHQEFTCQS-D--M----TCDD------------ 281 (569)
T ss_pred HHHHHHHhc--CcchHHHHHHHHHHHHHhcCCCceEEEEeccccccceeeccCCC-c--c----Cccc------------
Confidence 334456655 557888999999999999999999998877665442211 1111 0 0 0000
Q ss_pred hCCEEEEecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCC
Q 002152 296 QNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPR 375 (959)
Q Consensus 296 ~~~~r~i~d~~~~~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr 375 (959)
..|..-+... .|.. .+ ...+.+||..++ +.-|.+...-..++
T Consensus 282 -------~~~~~~~~~~--------------------~~~~------~~-~~~~~~~l~~~~----~~~G~~~~~~~~~~ 323 (569)
T PRK10600 282 -------KGCQLCPRGV--------------------LPVG------DR-GTTLKWRLSDKH----GQYGILLATLPQGR 323 (569)
T ss_pred -------cccccccccC--------------------CCcC------CC-CceEEEEeecCC----cceEEEEEEcCCCC
Confidence 0011000000 0000 00 266789998776 88998876644467
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHH
Q 002152 376 YIPFPLRYACEFLVQAFSLQLYME 399 (959)
Q Consensus 376 ~~~~~~r~~~~~l~~~~s~~l~~~ 399 (959)
.++++.+..++.++.+++..++.+
T Consensus 324 ~l~~~~~~ll~~l~~~l~~~l~~~ 347 (569)
T PRK10600 324 HLSHDQQQLVDTLVEQLTATLALE 347 (569)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999999999988777543
No 156
>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=73.01 E-value=14 Score=34.65 Aligned_cols=45 Identities=18% Similarity=0.205 Sum_probs=35.5
Q ss_pred cceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecccccH
Q 002152 830 TENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQ 876 (959)
Q Consensus 830 ~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DITerk~ 876 (959)
.....|....++|+ .+..+...++|++|+++|++|+-.|+|.-.+
T Consensus 67 ~~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~ 111 (118)
T PF08348_consen 67 DYIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQ 111 (118)
T ss_pred CccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHH
Confidence 44455666788885 4577778899999999999999999996443
No 157
>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=72.22 E-value=12 Score=31.91 Aligned_cols=49 Identities=22% Similarity=0.259 Sum_probs=39.7
Q ss_pred HHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q 002152 899 IRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDGM 947 (959)
Q Consensus 899 iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~~LI~dL 947 (959)
+.|.+||-|+.|.+++.+-.+..-+++.++.+..+..-..-|..+=+.|
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 6899999999999999999887778888888888777676666555543
No 158
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=69.78 E-value=40 Score=39.86 Aligned_cols=38 Identities=5% Similarity=0.024 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCC
Q 002152 616 VACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGL 653 (959)
Q Consensus 616 ~~~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~ 653 (959)
.+.-++.++.++|.||+.+|.++.+.++|+-+..+|+-
T Consensus 73 ~~~~~~~al~nmPiGii~~~e~~~veW~Npf~~~if~~ 110 (655)
T COG3887 73 AEKSLEEALTNMPIGIILFNETNKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHhCCceEEEEcCCCceEEecHHHHHhcCh
Confidence 34557888999999999999999999999999999873
No 159
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=64.35 E-value=23 Score=37.19 Aligned_cols=61 Identities=20% Similarity=0.053 Sum_probs=40.3
Q ss_pred ecccccHHHHHHHhHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Q 002152 870 ILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACE 937 (959)
Q Consensus 870 DITerk~~Elelq~~ae~~~~ak~~fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~ 937 (959)
|+|++++.+..+... .+..++..+.|.++|-|+.|.+++.+-.+..-++ .++++.....-.
T Consensus 3 ~~~~~~~~e~~~~~~------~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~~~Ri 63 (221)
T COG3920 3 LTTARKETEERLAES------EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRESQNRI 63 (221)
T ss_pred hHHHHHHHHHHHHHH------HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHHHHHH
Confidence 556555555443221 4556789999999999999999999888755554 444444443333
No 160
>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=61.80 E-value=30 Score=32.39 Aligned_cols=42 Identities=14% Similarity=0.121 Sum_probs=35.2
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHH
Q 002152 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF 744 (959)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L 744 (959)
..++|+ .+..+...++|++|+++|++++-.|+|.-..++.-|
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 566774 477788899999999999999999999988776655
No 161
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=60.25 E-value=31 Score=43.53 Aligned_cols=44 Identities=16% Similarity=0.059 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCccEEEEc-CCCceehhcHHHHHHhCCCcccccCCCcc
Q 002152 618 CEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGLPASEAMGKSLI 664 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D-~dg~iv~~N~~~~~l~G~~~eeliGk~~~ 664 (959)
+-...++...|.|++++| .+|.|++.|+.+.+++| .+ ++|+++.
T Consensus 102 ~~~~~~l~~~p~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 102 QIGEEVLNELPIGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHHHHhCCceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 345678899999999999 69999999999999988 22 7899887
No 162
>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=54.97 E-value=11 Score=34.79 Aligned_cols=46 Identities=28% Similarity=0.476 Sum_probs=36.9
Q ss_pred cEEEEcC-CCceehhcHHHHHHhCCC---cccccCCCccccccCCCchHHH
Q 002152 630 PIFGVDS-SGTINGWNAKVAELTGLP---ASEAMGKSLIDEVVHEESQGAV 676 (959)
Q Consensus 630 ~I~~~D~-dg~iv~~N~~~~~l~G~~---~eeliGk~~~~~l~~~~~~~~~ 676 (959)
.++++|. +++|+.++..+.+++|.+ .++++|+++. +++.++....+
T Consensus 17 ~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~-~ll~~~~~~~l 66 (110)
T PF08446_consen 17 ALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLS-ELLGAESAERL 66 (110)
T ss_dssp EEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHH-HHSCCCCHHHH
T ss_pred EEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHH-HHhCHHHHHHH
Confidence 3456675 689999999999999999 9999999998 88877665533
No 163
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=47.33 E-value=27 Score=36.20 Aligned_cols=39 Identities=13% Similarity=0.007 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCccEEEEcCCCceehhcHHHHHHhCCCcc
Q 002152 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPAS 656 (959)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~iv~~N~~~~~l~G~~~e 656 (959)
+.+..+++..+.|+++-+.+|.++++|..|.++|.-+..
T Consensus 19 ~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~~ 57 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQ 57 (217)
T ss_pred HHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcCC
Confidence 467889999999999999999999999999999985543
No 164
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=45.21 E-value=68 Score=37.06 Aligned_cols=119 Identities=21% Similarity=0.217 Sum_probs=80.1
Q ss_pred HHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccC----CccCCCCchHH-HHHHHHhCCEEEEecCCCC
Q 002152 234 LCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLG----IHFPANDIPQA-ARFLFKQNRVRMICDCHAI 308 (959)
Q Consensus 234 ~~~~~v~~vr~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg----~~~pa~dip~~-ar~ly~~~~~r~i~d~~~~ 308 (959)
=+..+++-|.+.+|.+=|. +.-+..+-.|.| .|.|-.+|-.. .|.--..|.+- ..|-.+.
T Consensus 226 s~~~va~Ii~~~~~~~AVa--------------iTd~e~ilA~vg~g~dhhi~g~~i~s~~t~~ai~~g~vv-~~~~~e~ 290 (557)
T COG3275 226 SLMKVAEIIYEELGAGAVA--------------ITDREKLLAFVGIGDDHHIPGKPIISSLTRKAIKTGEVV-YADGNEV 290 (557)
T ss_pred hHHHHHHHHHHHhCCCeEE--------------ecCHHHHHHhhcccccccCCCCeeccHHHHHHHhhCCEE-EEccchh
Confidence 3556677788888887654 344444545544 46777775443 34444455553 3332222
Q ss_pred CcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHH
Q 002152 309 PVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFL 388 (959)
Q Consensus 309 ~~~l~~~~~~~~~ldls~s~lRsvsp~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l 388 (959)
+. |. -.-| .+.|.+++|+--+| +.=|-|--.-+.|+.++.-+|.+.+-+
T Consensus 291 ----~~------------cs---h~~c--------~l~s~lViPL~~~g----~ViGTiK~y~~~~~lis~~~r~la~Gi 339 (557)
T COG3275 291 ----YE------------CS---HPTC--------KLGSALVIPLRGKG----RVIGTIKLYEAKARLISSINRELAEGI 339 (557)
T ss_pred ----hc------------cC---CCCC--------CcCCceEeecccCC----ceeeeEEEEeccHhHhhHHHHHHHHHH
Confidence 10 00 0123 34889999997666 999999999999999999999999999
Q ss_pred HHHHHHHHHH
Q 002152 389 VQAFSLQLYM 398 (959)
Q Consensus 389 ~~~~s~~l~~ 398 (959)
++.+|.|++.
T Consensus 340 a~l~SaQie~ 349 (557)
T COG3275 340 AQLLSAQIEA 349 (557)
T ss_pred HHHHHHHHHH
Confidence 9999999963
No 165
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=36.64 E-value=70 Score=29.58 Aligned_cols=74 Identities=19% Similarity=0.197 Sum_probs=41.6
Q ss_pred CCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcCCCcceeeEEEEccCC
Q 002152 763 PPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQG 842 (959)
Q Consensus 763 ~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG 842 (959)
+-+++.|.+|++++-+. .+.+|+.+.+ .+ ..+++.|+ .+... ...++
T Consensus 40 ~~i~v~D~~g~~l~~s~----------~~~iG~~~~~------------~~-------~~~aL~G~-~~~~~---~~~~~ 86 (116)
T PF14827_consen 40 DYIVVTDRDGIVLAHSD----------PERIGDRYSD------------ED-------VRKALQGK-SYTSV---SQGTG 86 (116)
T ss_dssp SEEEEECTTSBECE-SS----------CCCTTSB-SS------------CC-------HCHHCCT---EEEE---EECTT
T ss_pred eEEEEEcCCCCEEEcCC----------hHHcCCcccC------------CC-------hhhhhcCC-ceEEe---eecCC
Confidence 45889999999876542 3457776442 11 23445443 32221 12222
Q ss_pred cEEEEEEEEeeeeCCCCCEEEEEEEEeec
Q 002152 843 QFVEVALTASRRTDAEGKVIGCFCFMQIL 871 (959)
Q Consensus 843 ~~~~v~~~~~pi~d~~G~i~g~v~i~~DI 871 (959)
-+......|++|.+|+++|++.+...+
T Consensus 87 --~~~~~~~~PV~d~~g~viG~V~VG~~~ 113 (116)
T PF14827_consen 87 --GPSLRAFAPVYDSDGKVIGVVSVGVSL 113 (116)
T ss_dssp --CEEEEEEEEEE-TTS-EEEEEEEEEEH
T ss_pred --ceEEEEEEeeECCCCcEEEEEEEEEEc
Confidence 345566789999999999999876543
No 166
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=36.16 E-value=4.1e+02 Score=29.46 Aligned_cols=68 Identities=15% Similarity=0.152 Sum_probs=41.1
Q ss_pred HHHHHHHHhcCCCCCC-eeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcC
Q 002152 749 GDYEAIIQSVNPLIPP-IFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (959)
Q Consensus 749 ~~l~~i~e~~~~~i~~-I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~ 827 (959)
+..++++-++..+.|| +|++|-+|+-+ .-=..-+..|++++ ++.+|+...-+...+.++-.|
T Consensus 80 ~evk~iLt~ldyG~DGYFF~YD~~G~Nl---------vHPrQpelvG~nlw--------~L~D~rGd~~Iq~Li~kAq~G 142 (459)
T COG4564 80 QEVKAILTNLDYGSDGYFFVYDYQGTNL---------VHPRQPELVGQNLW--------QLTDPRGDRVIQALIAKAQEG 142 (459)
T ss_pred HHHHHHHhhcccCCCceEEEEecCCccc---------cCCCCccccccchh--------hccCCCcChHHHHHHHHHHhC
Confidence 3455666666555455 45678777533 11123456777755 466677666677778888877
Q ss_pred CCccee
Q 002152 828 QGTENF 833 (959)
Q Consensus 828 ~~~~~~ 833 (959)
+....+
T Consensus 143 GG~~qY 148 (459)
T COG4564 143 GGLHQY 148 (459)
T ss_pred CCeEEE
Confidence 755444
No 167
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.77 E-value=64 Score=31.62 Aligned_cols=44 Identities=11% Similarity=0.245 Sum_probs=33.1
Q ss_pred HHHHHHHHhHhhhhHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Q 002152 895 ELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIM 941 (959)
Q Consensus 895 fLa~iSHElRnPL~~I~g~~~LL~~~~l~e~~~~~l~~i~~~~~rl~ 941 (959)
+.+.++|||-.|..+|..-++||++..-+++....+. .++..+.
T Consensus 18 LcsRvCHDiISPvgAInnGLeLLdeg~addDAm~LIr---sSArnas 61 (214)
T COG5385 18 LCSRVCHDIISPVGAINNGLELLDEGGADDDAMDLIR---SSARNAS 61 (214)
T ss_pred HHHHHHhhccCcHHHhhchhhhhccCCccHHHHHHHH---HHhhhHH
Confidence 3577899999999999999999998777766555544 4444444
No 168
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=35.56 E-value=1e+02 Score=36.93 Aligned_cols=110 Identities=11% Similarity=0.077 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchh-hcCCCcccccccccccccChhhHHHHHHHHH
Q 002152 744 FIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHE-VIGKMLPREIFGNFCRMKGQDMLTKFMILLY 822 (959)
Q Consensus 744 L~~se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~ee-viGk~~~~~i~~~~~~l~~~e~~~~~~~~l~ 822 (959)
|+..+..+..++..+...--.++.+|.+|.++..+-.-..-...+.-- ..|-.|.+...+. ..+-
T Consensus 69 L~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WSE~~~GT--------------NgIG 134 (606)
T COG3284 69 LTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWSEPREGT--------------NGIG 134 (606)
T ss_pred HHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecChhhhhhhhhhccccccccccccccc--------------cchh
Confidence 444555666666666554456888999999998754422221111111 1122222211110 0111
Q ss_pred hhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEE
Q 002152 823 QGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFM 868 (959)
Q Consensus 823 ~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~ 868 (959)
.++..+++...- .-.+-.-....+..++.|++|++|+++|++-+.
T Consensus 135 TcLve~~aVtI~-~~qHF~~~~~~lsCsAaPI~D~qG~L~gVLDIS 179 (606)
T COG3284 135 TCLVEGEAVTIH-GDQHFIQAHHGLSCSAAPIFDEQGELVGVLDIS 179 (606)
T ss_pred hhhccCcceEEe-hhhhHhhcccCceeeeeccccCCCcEEEEEEec
Confidence 122222221110 001111123456788899999999999886543
No 169
>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=34.89 E-value=3.9e+02 Score=25.10 Aligned_cols=109 Identities=10% Similarity=0.106 Sum_probs=57.8
Q ss_pred HHHHHHHHhCCCeEEEEeecCCCC--eEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCCEEEEecCCCCCcccccc
Q 002152 238 VVEDVQKLTGYDRVMLYNFHDDDH--GEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQS 315 (959)
Q Consensus 238 ~v~~vr~~~g~DRv~iY~F~~d~~--G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~~~l~~~ 315 (959)
++..+.+.+|||++++.....+.. ..+.. -+..|....+.|.++.... .. |++..
T Consensus 8 ~l~~~~~~~Gf~~~~~~~~~~~~~~~~~~~~----------------~~~~p~~w~~~Y~~~~~~~-----~D--Pv~~~ 64 (149)
T PF03472_consen 8 LLERLAARLGFDRFAYGAPSPDPRGDSDFLL----------------ISNYPDEWLEHYEERGYFR-----ID--PVVRH 64 (149)
T ss_dssp HHHHHHHCTTTSEEEEEEEETTSCECEEEEE----------------EESS-HHHHHHHHHTTGGG-----T---HHHHH
T ss_pred HHHHHHHHcCCCEEEEEeccCCCCCCccEEE----------------EecCCHHHHHHHHHcCCcC-----CC--HHHHH
Confidence 455678889999999992222221 11111 1244566777777665311 11 22210
Q ss_pred -cccCCccccccccccC-CCh---hhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002152 316 -KELKQPLCLVNSTLRS-PHG---CHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (959)
Q Consensus 316 -~~~~~~ldls~s~lRs-vsp---~h~~yl~nmgv~asl~v~i~~~~~~~~~LWGLi~~hh~~ 373 (959)
.....|+.-+....+. .+| .-.+..+.+|+++-+++|+--.+ +.. |+|+.....
T Consensus 65 ~~~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~~~p~~~~~---g~~-~~~s~~~~~ 123 (149)
T PF03472_consen 65 ARRSSGPFFWSDLFERDALSPEQRRFFDEARDFGLRSGVSVPLHGPD---GRF-GALSFAGDE 123 (149)
T ss_dssp HCHTSSEEEEECHCTSSSSSHHHHHHHHHHHHTTTSEEEEEEEEECC---GCE-EEEEEEESS
T ss_pred HHhCCCCEEEccchhhhhhhHHHHHHHHHHHHcCCCceEEEEeEcCC---CCE-EEEEEECCC
Confidence 1112233222222221 144 34456789999999999997554 455 888774433
No 170
>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=33.23 E-value=1.2e+02 Score=26.21 Aligned_cols=47 Identities=17% Similarity=0.206 Sum_probs=33.9
Q ss_pred HHhhhcCCCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEeecc
Q 002152 821 LYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILV 872 (959)
Q Consensus 821 l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~DIT 872 (959)
+++++..+.. .+-.-..|.+.=+-+...|+.+.+|++++.+|+ -|+|
T Consensus 37 Le~vl~~g~v----~r~~P~~G~Y~G~PViV~PI~~~~g~viaAiGv-VD~t 83 (84)
T PF09884_consen 37 LEEVLETGKV----IRVTPIEGPYKGVPVIVAPIKDEDGEVIAAIGV-VDLT 83 (84)
T ss_pred HHHHHHcCCE----EEeccCCcccCCeeEEEEEEEcCCCCEEEEEEE-EEcc
Confidence 4555554432 233556788877888899999999999999998 4554
No 171
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=33.22 E-value=23 Score=43.14 Aligned_cols=32 Identities=31% Similarity=0.558 Sum_probs=23.9
Q ss_pred HHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCccCCCCchHHHHHHHHhCC
Q 002152 244 KLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNR 298 (959)
Q Consensus 244 ~~~g~DRv~iY~F~~d~~G~viaE~~~~~~~s~lg~~~pa~dip~~ar~ly~~~~ 298 (959)
.|||++||+| |||||| |.+|-.+.-|+ |+-|.
T Consensus 614 NLTgAnRVII--fDPdWN--------------------PStD~QAreRa-wRiGQ 645 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN--------------------PSTDNQARERA-WRIGQ 645 (923)
T ss_pred ccccCceEEE--ECCCCC--------------------CccchHHHHHH-HhhcC
Confidence 6899999999 589997 67787666655 44443
No 172
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=33.12 E-value=69 Score=39.46 Aligned_cols=79 Identities=13% Similarity=0.169 Sum_probs=57.6
Q ss_pred cCCCceehhcHHHHHHhCCCcccccCCCccccccCCCchHHHHHHHHHHHcCC-Cc-c-eEEEEEEeeeeccCCcEEEEE
Q 002152 635 DSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE-ED-K-NVELKLRKFELQKQHSVVYIL 711 (959)
Q Consensus 635 D~dg~iv~~N~~~~~l~G~~~eeliGk~~~~~l~~~~~~~~~~~~l~~~l~~~-~~-~-~~e~~~~~~~~~~dG~~~~v~ 711 (959)
.+.+.+..+..++..++||-+.+++|+++. .++|++++..+.+....+++.+ .. + ...+++ ...+|.++.+.
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil-~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf----~aqNG~yv~ld 412 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSIL-AFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRF----CAQNGSYVRLD 412 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchh-hhhcCCchHHHHHHHHHHHHhCCCCcccccceee----eecCCcEEEEe
Confidence 456678889999999999999999999999 9999999988888877777533 22 1 223444 45677776665
Q ss_pred EEEEEee
Q 002152 712 VNACTSR 718 (959)
Q Consensus 712 v~~~pi~ 718 (959)
.....+.
T Consensus 413 TeWSsFV 419 (1114)
T KOG3753|consen 413 TEWSSFV 419 (1114)
T ss_pred chhhhcc
Confidence 5443333
No 173
>PRK04158 transcriptional repressor CodY; Validated
Probab=32.70 E-value=4.3e+02 Score=28.27 Aligned_cols=49 Identities=8% Similarity=0.089 Sum_probs=38.9
Q ss_pred eeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHHHHHHHHHH
Q 002152 346 IASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399 (959)
Q Consensus 346 ~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~s~~l~~~ 399 (959)
+=.+.+||..+| ..-|-|++-.+.. .+..+...++|..|.+++++|-..
T Consensus 110 ~~~tIvPI~ggG----eRLGTLvl~r~~~-~f~~dDliL~EyaATVVgLEIlR~ 158 (256)
T PRK04158 110 KLTTIVPIIGGG----ERLGTLILARFDK-EFTDDDLILAEYAATVVGMEILRE 158 (256)
T ss_pred ceEEEEEEecCC----eEEEEEEEEecCC-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 346789999888 8888888887662 356677889999999999998654
No 174
>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=32.30 E-value=67 Score=27.30 Aligned_cols=56 Identities=14% Similarity=0.121 Sum_probs=35.0
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEeecchhhHHHHHHHHHHHHHHHHHHHhcCCCCC-CeeeeCCCCcEEee
Q 002152 708 VYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIP-PIFASDENACCSEW 777 (959)
Q Consensus 708 ~~v~v~~~pi~d~~g~~~gvv~v~~DITerk~~E~~L~~se~~l~~i~e~~~~~i~-~I~~~D~~g~i~~~ 777 (959)
.++..-..|+++.+|+++|++++-.++.. +..++......-. -++++|.+|.++.-
T Consensus 12 ~~vi~~s~pi~~~~g~~~Gvv~~di~l~~--------------l~~~i~~~~~~~~g~~~ivd~~G~ii~h 68 (81)
T PF02743_consen 12 QPVITISVPIYDDDGKIIGVVGIDISLDQ--------------LSEIISNIKFGNNGYAFIVDKNGTIIAH 68 (81)
T ss_dssp EEEEEEEEEEEETTTEEEEEEEEEEEHHH--------------HHHHHTTSBBTTTBEEEEEETTSBBCE-
T ss_pred cEEEEEEEEEECCCCCEEEEEEEEeccce--------------eeeEEEeeEECCCEEEEEEECCCCEEEe
Confidence 45777789999999999999887544433 1223333221111 26778888887753
No 175
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=31.66 E-value=4.5e+02 Score=31.46 Aligned_cols=56 Identities=14% Similarity=0.153 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhHhhhhHHHHHHHH----Hhc--CCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002152 891 AKIKELAYIRQEVKNPLNGIRFVHKL----LES--SSISENQRQYLETSDACERQIMTIIDG 946 (959)
Q Consensus 891 ak~~fLa~iSHElRnPL~~I~g~~~L----L~~--~~l~e~~~~~l~~i~~~~~rl~~LI~d 946 (959)
+..+....++||+++|++.++.+..+ +.. ....++..+.+..+.....++...+.+
T Consensus 359 ~~~~~~~~la~el~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~ 420 (565)
T PRK10935 359 LLMEERATIARELHDSLAQVLSYLKIQLTLLKRSLDEDNAKAQSIIAEFDQALSDAYRQLRE 420 (565)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455677999999999988866543 332 222344556666666666666666655
No 176
>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=31.59 E-value=78 Score=27.32 Aligned_cols=33 Identities=18% Similarity=0.044 Sum_probs=27.5
Q ss_pred ccCCcEEEEEEEEEEeecCCCCEEEEEEEeecch
Q 002152 702 QKQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT 735 (959)
Q Consensus 702 ~~dG~~~~v~v~~~pi~d~~g~~~gvv~v~~DIT 735 (959)
...|.+.-+-+...|+++.+|++++.+++. |+|
T Consensus 51 P~~G~Y~G~PViV~PI~~~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 51 PIEGPYKGVPVIVAPIKDEDGEVIAAIGVV-DLT 83 (84)
T ss_pred cCCcccCCeeEEEEEEEcCCCCEEEEEEEE-Ecc
Confidence 345666667788899999999999999998 776
No 177
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=30.67 E-value=2.8e+02 Score=33.21 Aligned_cols=37 Identities=14% Similarity=0.058 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhC
Q 002152 747 LQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTG 786 (959)
Q Consensus 747 se~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G 786 (959)
.+.-++.++.++|. ||+..|.++.+.|+||-+..+|+
T Consensus 73 ~~~~~~~al~nmPi---Gii~~~e~~~veW~Npf~~~if~ 109 (655)
T COG3887 73 AEKSLEEALTNMPI---GIILFNETNKVEWVNPFASKIFN 109 (655)
T ss_pred HHHHHHHHHHhCCc---eEEEEcCCCceEEecHHHHHhcC
Confidence 34456778888875 59999999999999999999985
No 178
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=27.90 E-value=39 Score=31.55 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=20.5
Q ss_pred CCCccceEEEEeCCCceEEEEecChh
Q 002152 92 LIQPFGCMLAVEEPTFRIIGYSENCL 117 (959)
Q Consensus 92 ~iQp~G~ll~~~~~~~~i~~~S~N~~ 117 (959)
-|||||+.+.++..+-=.+|+|+=+.
T Consensus 15 gI~~yGAFV~l~~g~tGLVHISEIa~ 40 (129)
T COG1098 15 GITPYGAFVELEGGKTGLVHISEIAD 40 (129)
T ss_pred eeEecceEEEecCCCcceEEehHhhh
Confidence 48999999999986544789997333
No 179
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=25.78 E-value=5.2e+02 Score=32.93 Aligned_cols=57 Identities=16% Similarity=0.029 Sum_probs=38.7
Q ss_pred hhHHHHHHHHHHHH-------HHHHHHHhcCCCCCCeeeeC-CCCcEEeecHHHHHHhCCCchhhcCCCcc
Q 002152 736 HEKVLMDKFIRLQG-------DYEAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (959)
Q Consensus 736 erk~~E~~L~~se~-------~l~~i~e~~~~~i~~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (959)
+-|+.+.+|..... .-+..+..+|. |++++| .+|.|.+.|+.|.+++| .+ ++|+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~p~---gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 82 QIKRLQNKLSLWSKLSFHVSQIGEEVLNELPI---GIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHhCCc---eEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 34566666544332 23345555553 588999 79999999999999987 33 7888754
No 180
>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=25.05 E-value=87 Score=26.44 Aligned_cols=24 Identities=33% Similarity=0.631 Sum_probs=17.9
Q ss_pred EEEECCeEEEecCCCCHHHHHHHH
Q 002152 447 ALYYGGRCWLVGVTPTESQLKDIA 470 (959)
Q Consensus 447 a~~~~~~~~~~G~~p~~~~~~~l~ 470 (959)
+++.||+....|..|+.+++..++
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 457899999999999988777654
No 181
>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=24.42 E-value=52 Score=21.28 Aligned_cols=16 Identities=38% Similarity=0.372 Sum_probs=13.5
Q ss_pred hccCCCCCCccceEEE
Q 002152 86 KIQRGGLIQPFGCMLA 101 (959)
Q Consensus 86 ~i~~~g~iQp~G~ll~ 101 (959)
..|-||.||+-|+.|.
T Consensus 6 e~QgP~~~qsrgyFlf 21 (25)
T PF02070_consen 6 EFQGPGGIQSRGYFLF 21 (25)
T ss_pred hccCCcccccccEEEe
Confidence 4688999999999874
No 182
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=24.12 E-value=5.8e+02 Score=30.74 Aligned_cols=92 Identities=14% Similarity=0.198 Sum_probs=54.3
Q ss_pred HHHHHHHHHhcCCCCCCeeeeCCCCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhcC
Q 002152 748 QGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (959)
Q Consensus 748 e~~l~~i~e~~~~~i~~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~~ 827 (959)
...++.+-..+.. ..++++|.+|..+..++.- -+..++|.++. |..++..++.|
T Consensus 88 n~~L~~in~~a~s--s~iYlid~~G~~iaASNw~------~p~SFVG~nya------------------fRpYf~~Am~g 141 (603)
T COG4191 88 NRYLEQINEAAGS--SAIYLIDPTGLTLAASNWN------LPTSFVGRNYA------------------FRPYFQDAMAG 141 (603)
T ss_pred HHHHHHHHhhccC--CeEEEECCCCcEEeeccCC------CCCcccccCcc------------------cHHHHHHHHhc
Confidence 3444555555442 3699999999988776421 23445666532 56778888888
Q ss_pred CCcceeeEEEEccCCcEEEEEEEEeeeeCCCCCEEEEEEEEee
Q 002152 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQI 870 (959)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~v~i~~D 870 (959)
+....+-... -.|+. -...+.|+++..| ++|++++--|
T Consensus 142 g~~r~yalGt--ts~~p--Gyy~a~pV~~~~~-ilGvivvKvd 179 (603)
T COG4191 142 GSGRFYALGT--TSGRP--GYYLAAPVDDGGG-ILGVIVVKVD 179 (603)
T ss_pred CCceeEeecc--ccCCC--ceeEeeeeccCCc-eeEEEEEEEe
Confidence 7554443322 22222 2233567765555 9998887444
No 183
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=22.01 E-value=2e+02 Score=31.58 Aligned_cols=91 Identities=9% Similarity=0.098 Sum_probs=0.0
Q ss_pred HHHHHHHhc-CCCCCCeeeeCC-CCcEEeecHHHHHHhCCCchhhcCCCcccccccccccccChhhHHHHHHHHHhhhc-
Q 002152 750 DYEAIIQSV-NPLIPPIFASDE-NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT- 826 (959)
Q Consensus 750 ~l~~i~e~~-~~~i~~I~~~D~-~g~i~~~N~a~~~l~G~~~eeviGk~~~~~i~~~~~~l~~~e~~~~~~~~l~~~~~- 826 (959)
..|.++|++ +.-..+++++.. +.+.+++|.-+..++||+.++++... ++-...=...+...+.
T Consensus 284 dcRrLfDsLreEnlgmlfVYs~k~qRllFAN~~fk~wtGy~~edFl~~~--------------~dIV~eGl~qW~~dL~~ 349 (401)
T PF06785_consen 284 DCRRLFDSLREENLGMLFVYSPKSQRLLFANSQFKTWTGYSSEDFLKDF--------------SDIVQEGLAQWETDLQL 349 (401)
T ss_pred HHHHHHhhhcccccceEEEecchhhHHHHhHHHHHHHhccCHHHHHhcc--------------hHHHHhhHHHHHHHHHh
Q ss_pred -CCCcceeeEEEEccCCcEEEEEEEEeee
Q 002152 827 -GQGTENFPFGFFNRQGQFVEVALTASRR 854 (959)
Q Consensus 827 -~~~~~~~e~~~~~~dG~~~~v~~~~~pi 854 (959)
.....+....+++|+|..+.+......+
T Consensus 350 ~s~~E~~grlviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 350 LSRQERSGRLVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred hhhhhhhceEEEEecCCCceeeEEEEeec
No 184
>PRK10963 hypothetical protein; Provisional
Probab=21.86 E-value=9.3e+02 Score=25.17 Aligned_cols=50 Identities=6% Similarity=-0.107 Sum_probs=36.2
Q ss_pred CceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhH-HHHHHHHHHHHHHHHHH
Q 002152 344 GSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPL-RYACEFLVQAFSLQLYM 398 (959)
Q Consensus 344 gv~asl~v~i~~~~~~~~~LWGLi~~hh~~pr~~~~~~-r~~~~~l~~~~s~~l~~ 398 (959)
+|+|.-.+|+.- + +..|+|+.=...|.++.+.. -.++++|+++++..|..
T Consensus 168 ~v~S~AllpL~~-~----~~~GlLalGS~D~~rF~~~mgT~fL~~la~vvs~~L~~ 218 (223)
T PRK10963 168 AVGSVAMSLLGS-D----GDLGVLLFSSRDAQHYQQGQGTQLLQHLALMLPELLER 218 (223)
T ss_pred cCceeEEEeccC-C----CceEEEEEeCCChhhcCCCccHHHHHHHHHHHHHHHHH
Confidence 577778888843 2 45999999888776655544 67788888888876643
Done!