Query 001564
Match_columns 1052
No_of_seqs 737 out of 4865
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 03:56:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001564hhsearch_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 1E-133 3E-138 1114.8 59.5 640 71-1038 17-668 (750)
2 PRK13560 hypothetical protein; 100.0 1.2E-36 2.5E-41 388.8 48.3 412 605-1036 193-743 (807)
3 TIGR02938 nifL_nitrog nitrogen 100.0 1.1E-35 2.5E-40 357.1 37.1 396 616-1037 4-421 (494)
4 PF00360 PHY: Phytochrome regi 100.0 1E-33 2.3E-38 288.9 12.8 171 412-584 4-179 (182)
5 PRK11091 aerobic respiration c 100.0 1.3E-31 2.8E-36 339.9 34.3 288 729-1036 138-426 (779)
6 COG5002 VicK Signal transducti 99.9 8.8E-27 1.9E-31 244.4 20.9 282 729-1051 93-379 (459)
7 PRK11006 phoR phosphate regulo 99.9 2.4E-23 5.1E-28 246.1 27.5 268 727-1038 79-348 (430)
8 PRK13557 histidine kinase; Pro 99.9 1E-22 2.2E-27 248.0 31.5 274 739-1035 23-305 (540)
9 PRK09776 putative diguanylate 99.9 7.5E-23 1.6E-27 270.2 29.5 268 604-888 271-538 (1092)
10 TIGR02966 phoR_proteo phosphat 99.9 1.4E-22 3.1E-27 230.2 25.8 256 742-1038 2-260 (333)
11 PRK13559 hypothetical protein; 99.9 4.5E-22 9.7E-27 229.7 28.0 250 743-1034 40-297 (361)
12 PF08446 PAS_2: PAS fold; Int 99.9 5.7E-24 1.2E-28 199.1 8.4 106 70-185 2-110 (110)
13 PRK11360 sensory histidine kin 99.9 2E-21 4.3E-26 239.7 33.4 277 737-1038 253-531 (607)
14 PRK09776 putative diguanylate 99.9 8E-22 1.7E-26 260.4 31.5 261 605-882 399-662 (1092)
15 PRK10841 hybrid sensory kinase 99.9 2.9E-21 6.2E-26 246.0 32.6 261 739-1038 327-592 (924)
16 PRK11073 glnL nitrogen regulat 99.9 2.8E-21 6E-26 221.9 28.4 259 745-1035 6-266 (348)
17 PRK10618 phosphotransfer inter 99.9 6.1E-21 1.3E-25 239.3 30.8 256 737-1038 334-595 (894)
18 PRK09959 hybrid sensory histid 99.9 1.2E-20 2.6E-25 250.9 30.6 306 728-1051 558-869 (1197)
19 COG3852 NtrB Signal transducti 99.9 4.3E-20 9.3E-25 192.3 24.0 257 750-1034 11-272 (363)
20 TIGR02040 PpsR-CrtJ transcript 99.9 2.6E-20 5.6E-25 220.9 25.4 242 608-878 125-368 (442)
21 PRK13560 hypothetical protein; 99.9 7.1E-20 1.5E-24 234.2 29.0 262 605-887 56-333 (807)
22 COG5000 NtrY Signal transducti 99.8 1.7E-17 3.8E-22 187.0 26.0 247 739-1024 363-617 (712)
23 PRK11359 cyclic-di-GMP phospho 99.8 6.8E-18 1.5E-22 215.8 25.7 246 616-880 12-257 (799)
24 TIGR02040 PpsR-CrtJ transcript 99.8 4.3E-18 9.2E-23 202.0 20.8 234 621-880 1-249 (442)
25 PRK11086 sensory histidine kin 99.7 1.6E-15 3.5E-20 185.0 35.7 275 710-1038 147-466 (542)
26 COG2205 KdpD Osmosensitive K+ 99.7 4.2E-17 9E-22 190.5 18.2 154 887-1051 655-812 (890)
27 PRK09303 adaptive-response sen 99.7 3.5E-16 7.6E-21 181.5 21.5 147 887-1035 146-300 (380)
28 TIGR02956 TMAO_torS TMAO reduc 99.7 2.3E-16 5E-21 205.9 22.1 155 882-1038 454-609 (968)
29 PRK15347 two component system 99.7 1.1E-15 2.3E-20 198.7 21.5 155 882-1038 388-543 (921)
30 PRK11107 hybrid sensory histid 99.7 1.5E-15 3.2E-20 197.4 22.7 164 884-1051 285-449 (919)
31 COG4191 Signal transduction hi 99.7 1.5E-13 3.3E-18 156.6 33.3 146 894-1052 386-537 (603)
32 PRK11466 hybrid sensory histid 99.6 5.4E-15 1.2E-19 191.8 22.1 153 884-1038 436-591 (914)
33 PRK15053 dpiB sensor histidine 99.6 2.9E-13 6.4E-18 165.3 35.8 275 710-1038 148-467 (545)
34 COG3290 CitA Signal transducti 99.5 1.8E-12 3.9E-17 147.2 27.5 284 710-1051 141-467 (537)
35 PRK10490 sensor protein KdpD; 99.5 1.5E-13 3.4E-18 174.7 20.5 147 888-1038 660-809 (895)
36 PRK13837 two-component VirA-li 99.5 1.3E-12 2.9E-17 166.6 28.9 139 891-1036 449-589 (828)
37 PRK10364 sensor protein ZraS; 99.5 2E-12 4.4E-17 154.3 21.6 142 891-1038 236-379 (457)
38 PF08448 PAS_4: PAS fold; Int 99.4 8E-13 1.7E-17 123.9 11.9 110 622-736 1-110 (110)
39 PF13426 PAS_9: PAS domain; PD 99.4 1.9E-12 4.2E-17 119.9 12.6 104 626-733 1-104 (104)
40 PRK10815 sensor protein PhoQ; 99.4 8.8E-12 1.9E-16 149.1 20.0 141 891-1038 265-407 (485)
41 PF00989 PAS: PAS fold; Inter 99.4 3.9E-12 8.4E-17 119.9 13.5 112 616-731 1-113 (113)
42 TIGR03785 marine_sort_HK prote 99.4 1.8E-11 4E-16 152.3 22.5 145 890-1038 483-628 (703)
43 PF01590 GAF: GAF domain; Int 99.4 4.3E-12 9.4E-17 127.0 12.6 153 218-394 1-154 (154)
44 PRK10549 signal transduction h 99.4 2E-11 4.4E-16 146.1 19.6 146 889-1038 237-383 (466)
45 PRK10604 sensor protein RstB; 99.3 3.2E-11 6.9E-16 142.8 19.0 138 890-1038 210-348 (433)
46 PRK10755 sensor protein BasS/P 99.3 3.9E-11 8.5E-16 138.3 18.8 140 892-1038 137-278 (356)
47 PF13426 PAS_9: PAS domain; PD 99.3 4.6E-12 9.9E-17 117.4 8.4 103 760-873 2-104 (104)
48 PRK11091 aerobic respiration c 99.3 5.2E-11 1.1E-15 151.8 20.9 142 604-749 143-284 (779)
49 PF00989 PAS: PAS fold; Inter 99.3 9.9E-12 2.2E-16 117.1 10.3 112 746-871 1-113 (113)
50 PRK09835 sensor kinase CusS; P 99.3 1.1E-10 2.4E-15 140.3 21.7 145 890-1038 260-406 (482)
51 PRK10337 sensor protein QseC; 99.3 7.2E-11 1.6E-15 140.6 19.6 140 893-1034 238-379 (449)
52 TIGR01386 cztS_silS_copS heavy 99.3 9E-11 1.9E-15 139.9 19.9 143 891-1038 240-384 (457)
53 PRK11100 sensory histidine kin 99.3 2E-10 4.3E-15 137.7 20.9 143 892-1038 256-399 (475)
54 COG4192 Signal transduction hi 99.2 2.4E-10 5.2E-15 125.1 17.5 134 896-1035 455-593 (673)
55 PF08448 PAS_4: PAS fold; Int 99.2 2.1E-11 4.5E-16 114.3 7.2 110 752-876 1-110 (110)
56 TIGR02916 PEP_his_kin putative 99.2 9.2E-10 2E-14 137.7 20.9 133 893-1038 476-610 (679)
57 PRK10060 RNase II stability mo 99.1 1E-09 2.2E-14 136.6 18.9 168 700-886 70-238 (663)
58 PRK09470 cpxA two-component se 99.1 1.7E-09 3.7E-14 129.2 19.9 141 890-1038 241-382 (461)
59 PRK09467 envZ osmolarity senso 99.1 2.3E-09 5E-14 127.1 19.8 137 886-1038 223-360 (435)
60 PRK13559 hypothetical protein; 99.1 1.8E-09 3.8E-14 124.8 16.4 133 614-750 41-176 (361)
61 PRK11644 sensory histidine kin 99.0 5E-09 1.1E-13 125.5 19.1 139 890-1038 300-440 (495)
62 smart00065 GAF Domain present 99.0 6.5E-09 1.4E-13 101.1 15.6 140 218-397 1-142 (149)
63 PRK13558 bacterio-opsin activa 99.0 3.7E-09 8.1E-14 132.4 16.9 136 617-756 149-287 (665)
64 PF00512 HisKA: His Kinase A ( 99.0 1.1E-09 2.3E-14 93.6 7.8 65 891-955 1-68 (68)
65 COG0642 BaeS Signal transducti 99.0 1.6E-08 3.4E-13 114.0 19.7 143 891-1038 114-258 (336)
66 PRK13557 histidine kinase; Pro 99.0 4.3E-09 9.3E-14 128.3 16.1 131 611-745 25-158 (540)
67 COG3829 RocR Transcriptional r 99.0 1.4E-08 3.1E-13 116.0 17.6 226 619-882 4-230 (560)
68 PRK11359 cyclic-di-GMP phospho 99.0 1.8E-08 3.8E-13 129.3 20.3 123 615-741 135-258 (799)
69 PRK10060 RNase II stability mo 98.9 1.1E-08 2.4E-13 127.4 17.1 162 611-778 106-284 (663)
70 TIGR00229 sensory_box PAS doma 98.9 8.2E-09 1.8E-13 94.5 12.1 120 616-740 3-123 (124)
71 PF13596 PAS_10: PAS domain; P 98.9 7.5E-09 1.6E-13 97.0 9.7 106 618-732 1-106 (106)
72 PF08447 PAS_3: PAS fold; Int 98.8 1.5E-08 3.2E-13 91.7 10.0 90 771-868 1-91 (91)
73 PRK13558 bacterio-opsin activa 98.8 3.6E-08 7.7E-13 123.6 16.1 125 747-885 149-276 (665)
74 TIGR02938 nifL_nitrog nitrogen 98.8 1.3E-08 2.8E-13 122.3 11.4 128 745-886 3-130 (494)
75 TIGR00229 sensory_box PAS doma 98.8 5E-08 1.1E-12 89.2 11.3 119 746-879 3-122 (124)
76 COG2203 FhlA FOG: GAF domain [ 98.7 1E-07 2.2E-12 96.0 10.1 157 204-398 6-166 (175)
77 KOG3558 Hypoxia-inducible fact 98.6 3E-07 6.5E-12 106.2 13.8 226 621-873 124-378 (768)
78 PRK11360 sensory histidine kin 98.6 7.1E-07 1.5E-11 110.2 18.4 131 608-745 254-385 (607)
79 PF08447 PAS_3: PAS fold; Int 98.6 2.2E-07 4.8E-12 84.0 10.1 86 638-728 1-91 (91)
80 PF13492 GAF_3: GAF domain; PD 98.5 1.6E-06 3.4E-11 83.7 14.5 128 218-395 1-128 (129)
81 COG5002 VicK Signal transducti 98.5 8E-07 1.7E-11 95.3 12.9 129 604-743 99-227 (459)
82 cd00130 PAS PAS domain; PAS mo 98.5 2E-06 4.3E-11 74.5 12.9 103 625-731 1-103 (103)
83 PRK11388 DNA-binding transcrip 98.4 9.8E-06 2.1E-10 100.7 21.5 220 617-875 63-310 (638)
84 TIGR02966 phoR_proteo phosphat 98.4 1.5E-06 3.3E-11 98.5 13.2 113 612-741 2-114 (333)
85 PF12860 PAS_7: PAS fold 98.4 9.7E-07 2.1E-11 83.9 9.5 104 622-739 1-115 (115)
86 KOG0519 Sensory transduction h 98.3 1.3E-07 2.8E-12 118.3 1.5 149 886-1038 213-364 (786)
87 COG3920 Signal transduction hi 98.3 5.3E-05 1.1E-09 80.4 20.0 150 870-1038 3-156 (221)
88 PRK11073 glnL nitrogen regulat 98.3 4.6E-06 9.9E-11 95.8 12.9 117 616-744 7-124 (348)
89 cd00130 PAS PAS domain; PAS mo 98.3 4.8E-06 1E-10 72.0 10.2 101 760-871 3-103 (103)
90 PF13185 GAF_2: GAF domain; PD 98.3 1.1E-05 2.4E-10 79.8 13.2 136 218-394 3-147 (148)
91 COG2202 AtoS FOG: PAS/PAC doma 98.3 5.5E-05 1.2E-09 76.4 18.7 228 630-877 3-231 (232)
92 PRK11006 phoR phosphate regulo 98.2 1.3E-05 2.9E-10 94.9 14.8 119 605-742 87-205 (430)
93 TIGR01817 nifA Nif-specific re 98.2 4.5E-05 9.8E-10 92.7 19.3 153 202-396 5-158 (534)
94 PRK10935 nitrate/nitrite senso 98.1 0.00017 3.8E-09 88.6 22.6 133 892-1036 360-499 (565)
95 PRK10820 DNA-binding transcrip 98.1 3.5E-05 7.5E-10 92.9 15.6 112 611-736 75-190 (520)
96 PF13596 PAS_10: PAS domain; P 98.1 3.4E-06 7.3E-11 78.9 5.4 106 748-872 1-106 (106)
97 COG3604 FhlA Transcriptional r 98.0 0.00014 3.1E-09 82.7 16.7 205 217-460 47-257 (550)
98 PRK11086 sensory histidine kin 98.0 5.4E-05 1.2E-09 92.5 14.9 123 609-747 214-339 (542)
99 PRK05022 anaerobic nitric oxid 98.0 0.00026 5.7E-09 85.3 20.2 154 206-399 8-161 (509)
100 PRK10600 nitrate/nitrite senso 98.0 0.00016 3.5E-09 89.0 18.7 128 898-1038 368-499 (569)
101 smart00388 HisKA His Kinase A 98.0 1.9E-05 4E-10 66.0 6.4 63 892-954 2-65 (66)
102 PF14598 PAS_11: PAS domain; P 97.9 4.7E-05 1E-09 71.7 9.7 96 763-869 6-104 (111)
103 PRK15429 formate hydrogenlyase 97.9 0.0008 1.7E-08 84.3 23.0 150 216-401 197-348 (686)
104 PF14598 PAS_11: PAS domain; P 97.9 0.00014 3.1E-09 68.4 11.7 101 629-733 5-108 (111)
105 PF12860 PAS_7: PAS fold 97.9 2.3E-05 4.9E-10 74.5 6.2 113 752-878 1-114 (115)
106 COG3829 RocR Transcriptional r 97.9 8.8E-05 1.9E-09 85.6 11.8 126 611-749 112-237 (560)
107 PRK11061 fused phosphoenolpyru 97.7 0.00069 1.5E-08 84.7 16.9 150 206-396 7-156 (748)
108 COG3290 CitA Signal transducti 97.7 0.00032 7E-09 81.0 12.5 122 609-746 208-332 (537)
109 COG2202 AtoS FOG: PAS/PAC doma 97.6 0.0012 2.6E-08 66.4 14.9 126 607-737 103-231 (232)
110 PRK15053 dpiB sensor histidine 97.6 0.0009 1.9E-08 81.9 15.5 122 609-747 215-338 (545)
111 PF13188 PAS_8: PAS domain; PD 97.5 0.00012 2.6E-09 61.4 4.9 46 616-665 1-46 (64)
112 COG5000 NtrY Signal transducti 97.5 0.00072 1.6E-08 78.4 12.3 125 604-740 358-483 (712)
113 PRK10820 DNA-binding transcrip 97.5 0.00055 1.2E-08 82.6 11.9 112 741-876 75-190 (520)
114 cd00082 HisKA Histidine Kinase 97.4 0.0005 1.1E-08 56.7 7.0 59 892-950 4-64 (65)
115 KOG3560 Aryl-hydrocarbon recep 97.3 0.001 2.3E-08 75.2 9.3 229 619-873 114-385 (712)
116 KOG3559 Transcriptional regula 97.2 0.00064 1.4E-08 74.0 7.0 208 620-858 83-313 (598)
117 PRK15429 formate hydrogenlyase 97.1 0.24 5.3E-06 62.3 29.6 204 204-449 11-225 (686)
118 PRK09959 hybrid sensory histid 97.1 0.0074 1.6E-07 81.3 16.8 137 605-746 565-703 (1197)
119 PRK11388 DNA-binding transcrip 97.1 0.0081 1.8E-07 74.9 15.6 112 612-736 199-311 (638)
120 COG2461 Uncharacterized conser 97.0 0.0017 3.6E-08 71.7 7.2 115 616-740 290-404 (409)
121 KOG0501 K+-channel KCNQ [Inorg 96.9 0.0027 5.9E-08 72.4 8.7 98 635-737 39-139 (971)
122 COG3851 UhpB Signal transducti 96.9 0.083 1.8E-06 57.9 18.7 141 891-1051 302-446 (497)
123 PF13188 PAS_8: PAS domain; PD 96.8 0.00098 2.1E-08 55.8 3.2 42 746-794 1-42 (64)
124 KOG0501 K+-channel KCNQ [Inorg 96.8 0.0015 3.3E-08 74.4 5.4 100 768-876 39-138 (971)
125 PF02518 HATPase_c: Histidine 96.8 0.0017 3.7E-08 61.0 4.7 42 1003-1051 1-42 (111)
126 COG3850 NarQ Signal transducti 96.7 0.051 1.1E-06 62.9 16.3 133 891-1037 368-510 (574)
127 smart00091 PAS PAS domain. PAS 96.7 0.0054 1.2E-07 48.0 6.5 63 617-679 2-64 (67)
128 PF08670 MEKHLA: MEKHLA domain 96.5 0.041 9E-07 54.0 12.3 109 616-730 32-144 (148)
129 COG4585 Signal transduction hi 96.0 0.19 4E-06 58.2 17.0 138 890-1051 169-315 (365)
130 KOG1229 3'5'-cyclic nucleotide 95.9 0.008 1.7E-07 66.4 4.3 116 738-867 150-265 (775)
131 KOG3558 Hypoxia-inducible fact 95.4 0.023 5E-07 66.9 5.9 82 632-717 280-361 (768)
132 TIGR02916 PEP_his_kin putative 95.4 0.52 1.1E-05 59.4 18.7 153 204-397 307-460 (679)
133 COG4564 Signal transduction hi 95.2 1.1 2.3E-05 48.9 17.3 135 894-1038 253-389 (459)
134 COG3852 NtrB Signal transducti 95.1 0.19 4.1E-06 54.4 11.1 112 619-740 10-122 (363)
135 PRK10547 chemotaxis protein Ch 95.1 0.19 4.1E-06 62.0 12.9 70 965-1038 344-428 (670)
136 TIGR02373 photo_yellow photoac 95.0 0.11 2.3E-06 48.9 7.9 46 752-800 22-67 (124)
137 TIGR02373 photo_yellow photoac 94.9 0.24 5.2E-06 46.6 10.1 72 622-693 22-95 (124)
138 KOG3753 Circadian clock protei 94.8 0.083 1.8E-06 63.6 8.2 201 628-854 194-418 (1114)
139 COG2972 Predicted signal trans 94.5 0.75 1.6E-05 54.9 15.9 116 896-1038 263-385 (456)
140 smart00091 PAS PAS domain. PAS 94.5 0.084 1.8E-06 40.8 5.5 45 747-794 2-46 (67)
141 COG3275 LytS Putative regulato 94.5 2.4 5.1E-05 48.9 18.3 118 900-1051 373-497 (557)
142 COG3283 TyrR Transcriptional r 94.3 0.16 3.4E-06 56.0 8.3 54 616-669 80-133 (511)
143 KOG1229 3'5'-cyclic nucleotide 94.3 0.042 9E-07 61.0 4.0 104 619-726 160-264 (775)
144 PRK10841 hybrid sensory kinase 94.0 0.91 2E-05 59.2 16.3 117 605-748 323-440 (924)
145 PF08670 MEKHLA: MEKHLA domain 93.5 0.86 1.9E-05 44.9 11.1 109 746-869 32-143 (148)
146 PF07568 HisKA_2: Histidine ki 93.0 0.69 1.5E-05 40.2 8.8 73 899-979 2-74 (76)
147 PRK14868 DNA topoisomerase VI 92.6 0.26 5.5E-06 60.3 7.2 57 982-1038 21-80 (795)
148 smart00387 HATPase_c Histidine 92.4 0.28 6.2E-06 44.7 6.1 36 1003-1038 1-36 (111)
149 COG2461 Uncharacterized conser 92.0 0.33 7.1E-06 54.2 6.5 113 746-878 290-402 (409)
150 COG5385 Uncharacterized protei 91.9 1.4 2.9E-05 43.2 9.7 126 896-1038 19-144 (214)
151 TIGR02851 spore_V_T stage V sp 91.2 8 0.00017 39.7 15.4 125 218-394 53-179 (180)
152 COG3284 AcoR Transcriptional a 91.2 3.5 7.6E-05 49.5 14.4 185 598-793 56-267 (606)
153 PRK10618 phosphotransfer inter 90.9 1.7 3.7E-05 56.1 12.5 45 607-651 334-379 (894)
154 smart00086 PAC Motif C-termina 90.9 0.44 9.6E-06 32.7 4.5 40 834-873 3-42 (43)
155 TIGR01925 spIIAB anti-sigma F 88.8 0.85 1.8E-05 44.4 5.9 36 1003-1038 35-73 (137)
156 smart00086 PAC Motif C-termina 87.0 1.8 3.9E-05 29.4 5.4 35 699-733 8-42 (43)
157 PF14501 HATPase_c_5: GHKL dom 85.2 1.7 3.6E-05 39.9 5.3 35 1004-1038 2-39 (100)
158 PF10090 DUF2328: Uncharacteri 84.9 9.2 0.0002 39.3 11.1 113 908-1038 2-116 (182)
159 PF07310 PAS_5: PAS domain; I 84.7 6.7 0.00014 38.3 9.6 92 630-728 43-136 (137)
160 PRK04184 DNA topoisomerase VI 84.3 1.7 3.7E-05 52.1 6.1 36 1001-1036 30-68 (535)
161 KOG3561 Aryl-hydrocarbon recep 84.2 0.66 1.4E-05 57.4 2.7 98 764-872 377-476 (803)
162 COG3283 TyrR Transcriptional r 84.1 2.4 5.3E-05 47.1 6.6 45 747-794 81-125 (511)
163 cd00075 HATPase_c Histidine ki 84.0 1.9 4.2E-05 38.3 5.2 31 1008-1038 1-32 (103)
164 PRK13837 two-component VirA-li 83.9 44 0.00095 43.3 19.4 134 218-396 293-427 (828)
165 KOG0519 Sensory transduction h 83.7 2.3 5E-05 54.2 7.4 152 884-1036 378-533 (786)
166 KOG3560 Aryl-hydrocarbon recep 83.3 3.5 7.6E-05 47.8 7.7 94 635-733 292-385 (712)
167 PF14689 SPOB_a: Sensor_kinase 83.2 7.4 0.00016 32.3 7.8 47 894-944 14-60 (62)
168 COG3605 PtsP Signal transducti 80.5 12 0.00026 44.4 10.7 146 204-394 5-154 (756)
169 PRK03660 anti-sigma F factor; 80.2 3.4 7.3E-05 40.7 5.7 35 1004-1038 36-73 (146)
170 COG0643 CheA Chemotaxis protei 80.0 6.8 0.00015 49.0 9.3 69 966-1038 392-475 (716)
171 COG3887 Predicted signaling pr 79.6 15 0.00033 43.7 11.3 101 614-744 73-173 (655)
172 KOG3559 Transcriptional regula 79.2 4.2 9E-05 45.3 6.3 87 627-717 226-312 (598)
173 PF04340 DUF484: Protein of un 78.8 41 0.00088 35.9 13.8 137 205-395 81-221 (225)
174 PRK04069 serine-protein kinase 77.5 4.7 0.0001 40.6 5.9 41 1004-1051 39-82 (161)
175 PRK10490 sensor protein KdpD; 76.5 1E+02 0.0022 40.3 19.1 49 334-396 595-644 (895)
176 PF13581 HATPase_c_2: Histidin 76.1 5.6 0.00012 37.9 5.8 41 1004-1051 28-71 (125)
177 COG5381 Uncharacterized protei 74.5 5.1 0.00011 38.5 4.7 30 1008-1038 64-93 (184)
178 TIGR01052 top6b DNA topoisomer 73.8 4.8 0.0001 47.7 5.4 35 1001-1035 22-59 (488)
179 TIGR01924 rsbW_low_gc serine-p 72.5 7.6 0.00016 39.0 5.8 34 1005-1038 40-76 (159)
180 PRK14538 putative bifunctional 71.3 31 0.00068 44.1 12.1 46 616-664 102-148 (838)
181 PF07310 PAS_5: PAS domain; I 71.1 17 0.00037 35.5 7.8 85 770-868 52-136 (137)
182 KOG3561 Aryl-hydrocarbon recep 69.4 2.5 5.5E-05 52.4 1.9 47 749-798 98-144 (803)
183 PF08446 PAS_2: PAS fold; Int 67.6 6.1 0.00013 37.0 3.7 47 628-674 17-67 (110)
184 COG2172 RsbW Anti-sigma regula 63.2 13 0.00029 36.7 5.2 36 1003-1038 36-75 (146)
185 PF08348 PAS_6: YheO-like PAS 60.4 27 0.00059 33.1 6.6 43 697-741 74-116 (118)
186 PRK10600 nitrate/nitrite senso 60.0 4E+02 0.0087 32.6 19.2 125 204-396 222-346 (569)
187 COG3887 Predicted signaling pr 56.6 2.8E+02 0.006 33.7 15.0 38 743-783 72-109 (655)
188 PF08348 PAS_6: YheO-like PAS 56.5 31 0.00067 32.8 6.2 47 830-878 67-113 (118)
189 PRK14867 DNA topoisomerase VI 54.1 21 0.00046 44.0 5.9 35 1002-1036 28-68 (659)
190 PF14827 Cache_3: Sensory doma 47.1 85 0.0018 29.5 7.7 76 625-731 38-113 (116)
191 KOG3753 Circadian clock protei 46.9 33 0.00071 42.5 5.8 80 634-717 339-421 (1114)
192 PF07536 HWE_HK: HWE histidine 43.9 1.2E+02 0.0025 26.9 7.5 68 899-979 2-71 (83)
193 COG1956 GAF domain-containing 42.2 3.7E+02 0.008 27.0 14.2 109 232-392 47-158 (163)
194 PRK13719 conjugal transfer tra 42.1 3.9E+02 0.0085 28.3 12.1 38 616-653 19-56 (217)
195 COG5388 Uncharacterized protei 41.6 1E+02 0.0023 31.5 7.4 98 625-729 57-157 (209)
196 COG3275 LytS Putative regulato 33.6 7.9E+02 0.017 29.3 13.7 121 220-396 224-349 (557)
197 PRK14538 putative bifunctional 32.5 1.2E+03 0.027 30.1 19.1 57 733-795 82-146 (838)
198 KOG0387 Transcription-coupled 32.4 25 0.00054 43.4 1.8 27 232-280 614-640 (923)
199 PF02743 Cache_1: Cache domain 32.4 37 0.00079 29.4 2.5 57 704-774 11-68 (81)
200 PRK10963 hypothetical protein; 29.3 5.2E+02 0.011 27.5 11.1 40 205-247 78-117 (223)
201 TIGR00585 mutl DNA mismatch re 29.2 64 0.0014 36.3 4.4 27 1007-1035 22-48 (312)
202 PF14827 Cache_3: Sensory doma 28.2 1.4E+02 0.003 28.0 5.9 52 216-275 19-70 (116)
203 COG1098 VacB Predicted RNA bin 27.4 40 0.00086 31.9 1.8 28 79-106 15-42 (129)
204 PRK13719 conjugal transfer tra 27.4 70 0.0015 33.7 3.9 38 745-785 18-55 (217)
205 PF09884 DUF2111: Uncharacteri 26.3 2.2E+02 0.0048 25.0 5.9 30 702-732 54-83 (84)
206 PRK04158 transcriptional repre 24.4 6.3E+02 0.014 27.5 10.3 49 335-398 111-159 (256)
207 PRK13870 transcriptional regul 22.8 7.7E+02 0.017 26.4 11.0 111 216-367 15-130 (234)
208 PF05651 Diacid_rec: Putative 22.4 7.3E+02 0.016 24.1 13.7 110 220-395 3-112 (135)
209 PF13192 Thioredoxin_3: Thiore 21.0 1.1E+02 0.0025 26.1 3.5 24 445-468 52-75 (76)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=1.3e-133 Score=1114.77 Aligned_cols=640 Identities=29% Similarity=0.486 Sum_probs=551.3
Q ss_pred hhcccCCCCCCCcceEEEEecCCceEEEEccChhhhhCCCCCCCCCCCCCCccCCCCchhhcCChhhHHHHHHHhcCCCC
Q 001564 71 LHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEV 150 (1052)
Q Consensus 71 ~~~i~~~g~iQ~~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~~~~~ 150 (1052)
-+|||+||+||||||||++|+.++.|+|+|+||..+||+.|+. ++|+++.++++..+...|+.++..+..
T Consensus 17 ~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~----------l~~~tl~~vl~~~qv~~l~~~l~~~~~ 86 (750)
T COG4251 17 REPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPED----------LLGRTLGAVLTSEQVPPLQSALTVGGL 86 (750)
T ss_pred cCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhh----------hhcCCHHHhcchhhccHHHHhccccCc
Confidence 3689999999999999999999999999999999999998865 789999999999999999999999888
Q ss_pred ccCCceeEeecCCCceeEEEEeecCCeEEEEEeecCCCCCCcchhhHhhHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHH
Q 001564 151 SLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEV 230 (1052)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~h~~~~~~~ie~E~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~v~~v 230 (1052)
...||..+..+. +..|++++||+++.+|+||||....+. . ..+.+|+++..++.+||+.+ |+.++|+.+++||
T Consensus 87 ~~~np~~~w~~~-~~~fDv~~HR~~~llIlEfEp~~t~e~-~---~~l~f~h~~k~a~~~lq~a~--~l~~l~~~~tqeV 159 (750)
T COG4251 87 TTLNPTKMWTRK-GGSFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDLLSRTTQEV 159 (750)
T ss_pred ccCCchhhhhhc-CCceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHHHHHHHHHH
Confidence 888884443333 337999999999999999999755442 2 23347788888999999955 9999999999999
Q ss_pred HhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCccceee--CCCCCC
Q 001564 231 FELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQ--DEKLPF 308 (1052)
Q Consensus 231 r~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~~~~~~--~~~~~~ 308 (1052)
|++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|+|||+.| +|.+++
T Consensus 160 r~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavNp~t~~ 239 (750)
T COG4251 160 RRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNE 239 (750)
T ss_pred HHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccCcccCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998 689999
Q ss_pred cccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCCCCchhHHHHHHHHH
Q 001564 309 DLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQ 388 (1052)
Q Consensus 309 ~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~ 388 (1052)
|+|||+|.|||+||||+|||+||||.||||||||+| |+|||||+|||.|||++||+.|.+|||++|
T Consensus 240 p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~--------------g~LWGLIACHH~sPk~ip~~vR~acef~gq 305 (750)
T COG4251 240 PLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD--------------GKLWGLIACHHQSPKVIPYEVRKACEFFGQ 305 (750)
T ss_pred cccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC--------------CeeEEeeeeccCCCccCCHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhccCC-CcccccCCcchhhhcCCCEEEEEECCeEEEecCCCCHHHHHH
Q 001564 389 VFAIHVNKELELEYQILEKNILRTQT-LLCDMLMRDA-PLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHD 466 (1052)
Q Consensus 389 ~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~l~~l~~~dg~~~~~~~~~~~~g~~p~~~~~~~ 466 (1052)
+++.+++...+.+...........+. ++..|...+. ..+++...++|++|++|||+++|++|++.++|.||+..++..
T Consensus 306 ~~s~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~ 385 (750)
T COG4251 306 VLSMEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQR 385 (750)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHH
Confidence 99999987654333222222222333 4444555555 477888899999999999999999999999999999999999
Q ss_pred HHHHHhhccCCCceEEeccCCccCCCCccccCcccceEEEEEeCC--CCEEEEeccCcceEEeccCCCCCCCC-CCCCCC
Q 001564 467 IVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISP--KDMIFWFRSQTASEVRWGGAKHEPDE-KDDGRK 543 (1052)
Q Consensus 467 l~~~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~G~~~~~i~~--~~~~~~fR~e~~~~v~W~G~p~~~~~-~~~~~~ 543 (1052)
|+.||.+... ..+|.||+|+.. ||.++.|+..||||||++|+. ++|++|||||.+++|+|||||+|+.. .++|.|
T Consensus 386 Ll~wl~~~~~-~~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~r 463 (750)
T COG4251 386 LLQWLAEREE-GDVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIR 463 (750)
T ss_pred HHHHHhcCCc-ccEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCcc
Confidence 9999988844 479999999985 999999999999999999997 89999999999999999999999976 455789
Q ss_pred ccccchhHhHHHhhhcccCCCChhHHHHHHHHHHHHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 001564 544 MHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIE 623 (1052)
Q Consensus 544 l~pR~SF~~w~e~v~g~s~pW~~~ei~aa~~L~~iL~~~~~~~~~~~e~l~~~~~~l~~~~~~~~~eL~~~~~~l~~lle 623 (1052)
|+||+||+.|+|+|++++.||+..|++++.+++..+.+...+-.
T Consensus 464 L~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~~a------------------------------------ 507 (750)
T COG4251 464 LTPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRHA------------------------------------ 507 (750)
T ss_pred cCCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------------------------
Confidence 99999999999999999999999999999888333221110000
Q ss_pred hCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCc
Q 001564 624 TATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDD 703 (1052)
Q Consensus 624 ~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~ 703 (1052)
+
T Consensus 508 ------------------------------e------------------------------------------------- 508 (750)
T COG4251 508 ------------------------------E------------------------------------------------- 508 (750)
T ss_pred ------------------------------H-------------------------------------------------
Confidence 0
Q ss_pred eEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhC
Q 001564 704 PITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTG 783 (1052)
Q Consensus 704 ~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G 783 (1052)
T Consensus 509 -------------------------------------------------------------------------------- 508 (750)
T COG4251 509 -------------------------------------------------------------------------------- 508 (750)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEE
Q 001564 784 WKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTG 863 (1052)
Q Consensus 784 ~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g 863 (1052)
|+-+
T Consensus 509 ----ela~------------------------------------------------------------------------ 512 (750)
T COG4251 509 ----ELAQ------------------------------------------------------------------------ 512 (750)
T ss_pred ----HHHH------------------------------------------------------------------------
Confidence 0000
Q ss_pred EeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHHHHHH
Q 001564 864 VFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEG---TELGAEQKRLLHTSAQCQRQL 940 (1052)
Q Consensus 864 ~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~---~~l~~e~~~~l~~i~~~~~rl 940 (1052)
+.+..|+.+....+|...+||++++||+.|.+++++|.+ ..++++.++++..+.+.+..|
T Consensus 513 -----------------l~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~ 575 (750)
T COG4251 513 -----------------LRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLM 575 (750)
T ss_pred -----------------HHHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHH
Confidence 000111112222356778899999999999999999986 578889999999999999999
Q ss_pred HHHHhh-ccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhH
Q 001564 941 HKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSIS 1019 (1052)
Q Consensus 941 ~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NA 1019 (1052)
..||+| +.++++..-. ....+.|+.+++++++..+...+.+.++.+.+. + +|. |.+|+.++.||+.||+.||
T Consensus 576 ~~lidd~l~~s~l~~~~--~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~--~-lp~--v~~d~~~l~qv~~NLi~Na 648 (750)
T COG4251 576 QQLIDDLLTYSKLGLTE--APLQPTDVQKVVDKVLLELSQRIADTGAEIRIA--P-LPV--VAADATQLGQVFQNLIANA 648 (750)
T ss_pred HHHHHHHhhhhhhcccc--CCCCCcchHHHHHHHHHhcccccccccceEEec--c-cce--eecCHHHHHHHHHHHHhhh
Confidence 999999 7999986544 444588999999999999999999999988876 3 665 9999999999999999999
Q ss_pred hhccCCC-CeEEEEEEEccC
Q 001564 1020 INFVPNG-GQLMVSSSLTKD 1038 (1052)
Q Consensus 1020 ik~~~~~-g~I~I~v~~~~~ 1038 (1052)
+||..++ .+|+|+.....+
T Consensus 649 ik~~~~e~~~i~I~~~r~ed 668 (750)
T COG4251 649 IKFGGPENPDIEISAERQED 668 (750)
T ss_pred eecCCCCCCceEEeeeccCC
Confidence 9998765 788888666555
No 2
>PRK13560 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-36 Score=388.75 Aligned_cols=412 Identities=13% Similarity=0.114 Sum_probs=318.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCC
Q 001564 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQ 684 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~ 684 (1052)
++++++|++++++|+.+++++|++++++|.+|+++++|+++++++||+.++++|+++.++.++...+.+.......+..+
T Consensus 193 k~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 (807)
T PRK13560 193 KRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDAD 272 (807)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccC
Confidence 34567788999999999999999999999999999999999999999999999999999887776665555545555444
Q ss_pred ccceEEEEEEEeccccCCceEEEE--EEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCc
Q 001564 685 EEQNIQFEIKTHGSKINDDPITLI--VNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPI 762 (1052)
Q Consensus 685 ~~~~~e~~~~~~~~~~dg~~~~v~--v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I 762 (1052)
....++..+ .+++|..+|+. ++..|+.+.+|.+.|++++++|||++|++|++|++++++|+.++++++ .++
T Consensus 273 ~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~---~~i 345 (807)
T PRK13560 273 GSQIIEAEF----QNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAP---IAA 345 (807)
T ss_pred CceEEEEEE----EcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCc---ccE
Confidence 433333333 36788888554 455677899999999999999999999999999999999999999999 788
Q ss_pred cccCCCCcceee-chHHHHHhCCChHHHhhhhhhhh---------------hhc-----------------C--------
Q 001564 763 FGSDEFGWCCEW-NPAMVKLTGWKREEVIDKLLLAE---------------VFG-----------------T-------- 801 (1052)
Q Consensus 763 ~~~D~~g~i~~v-N~a~~~i~G~~~eeliG~~l~~~---------------v~~-----------------~-------- 801 (1052)
+.+|.+|+++++ |+++++++||+.++++|+++.+. +++ .
T Consensus 346 ~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 425 (807)
T PRK13560 346 IGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQE 425 (807)
T ss_pred EEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCce
Confidence 999999999987 67888899999999988764210 000 0
Q ss_pred --------------------------------------------------------------------------------
Q 001564 802 -------------------------------------------------------------------------------- 801 (1052)
Q Consensus 802 -------------------------------------------------------------------------------- 801 (1052)
T Consensus 426 ~~~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~~~ 505 (807)
T PRK13560 426 VLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKNIT 505 (807)
T ss_pred EEEEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecchhh
Confidence
Q ss_pred ------------chhhhhccchhhHHhhHHHHHhhhcC-CCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeeh
Q 001564 802 ------------NMACCRLKNQEAFVNLGIVLNKAMSG-QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFL 868 (1052)
Q Consensus 802 ------------~~~~~~l~~~d~~~~~~~~l~~~l~g-~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~ 868 (1052)
...+..+.||++...+...+.....+ ...+..++++.+++|..+|+.....|++|.+|.+.++++++
T Consensus 506 ~~G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~~ 585 (807)
T PRK13560 506 QFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGIV 585 (807)
T ss_pred hcCCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEEE
Confidence 00011123344444444444433333 34457889999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhcc
Q 001564 869 QLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSD 948 (1052)
Q Consensus 869 ~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd 948 (1052)
+|||++|++|+++++. ...|..|++.|||||||||++|.++++++.....+++...++..+......+..+++.+.
T Consensus 586 ~DITerK~aE~~L~~a----~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 661 (807)
T PRK13560 586 IDISERKHAEEKIKAA----LTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAMALAHEKLY 661 (807)
T ss_pred echHHHHHHHHHHHHH----HHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999998776543 445778999999999999999999999998776777777777777666666666665542
Q ss_pred ccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCC---
Q 001564 949 LDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN--- 1025 (1052)
Q Consensus 949 ~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~--- 1025 (1052)
.. ....++++.++++.++..+...+......+.+.++.+.+. ....+...+.|||.||++||+||+++
T Consensus 662 ~~--------~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~il~NLl~NAik~~~~~~~ 732 (807)
T PRK13560 662 QS--------EDLADIDFLDYIESLTAHLKNSFAIDFGRIDCKIDADDGC-LDIDKAIPCGLIISELLSNALKHAFPDGA 732 (807)
T ss_pred cc--------ccchhccHHHHHHHHHHHHHHHhccccCceEEEEecCccc-cccccccchHHHHHHHHHHHHHhhccCCC
Confidence 11 1346789999999999999887766665555555544332 23345667899999999999999854
Q ss_pred CCeEEEEEEEc
Q 001564 1026 GGQLMVSSSLT 1036 (1052)
Q Consensus 1026 ~g~I~I~v~~~ 1036 (1052)
.|.|.|++...
T Consensus 733 ~~~i~i~~~~~ 743 (807)
T PRK13560 733 AGNIKVEIREQ 743 (807)
T ss_pred CceEEEEEEEc
Confidence 35777776654
No 3
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=100.00 E-value=1.1e-35 Score=357.06 Aligned_cols=396 Identities=13% Similarity=0.059 Sum_probs=290.9
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1052)
+.|+.+++.++++++++|.+|+++++|+++++++||+.++++|++...+.++.........+...+..+.....++
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---- 79 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKL---- 79 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCccccee----
Confidence 4688999999999999999999999999999999999999999987766655544444444444444443322222
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeec
Q 001564 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWN 775 (1052)
Q Consensus 696 ~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN 775 (1052)
...+++|..+|+.....|+++.+|.+.+++++++|||++|++++++++++..++.++++++ .+++++|.+|+++++|
T Consensus 80 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~---~~i~~~d~~~~i~~~N 156 (494)
T TIGR02938 80 LNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAP---VAFVLLDPTGRVILDN 156 (494)
T ss_pred eccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhccc---ceEEEEcCCCCEEEec
Confidence 2346789999999999999999999999999999999999999999999999999999999 7889999999999999
Q ss_pred hHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCc-EEEEEEEeeEe
Q 001564 776 PAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGK-YAECLLCVNKK 854 (1052)
Q Consensus 776 ~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~-~~~v~~~~~pi 854 (1052)
+++++++|+...+..+..+.. ..+++....+...+. .+......+.++...+|. .+|+.....++
T Consensus 157 ~~~~~~~g~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (494)
T TIGR02938 157 QEYKKLATDLRVKEPAHTVLD-----------LLREAWREALAENWP---QQLAFSNREARFDRGGGRPARWLSCTGSVI 222 (494)
T ss_pred hhHHHhhchhhhhHHHHHHHH-----------HhhHHhhhhhhhcch---hhhccccceeeeccCCCceeeEEEecCceE
Confidence 999999999988877766432 122222222211111 111112334455555555 78998888887
Q ss_pred eCCCCCE---------EEEeeehHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhhhHHHHHHHHHHHHc
Q 001564 855 LDREGAV---------TGVFCFLQLASHELQQALHVQRLSEQT-------ALKRLKALAYTKRQIRNPLSGIIFSRKMME 918 (1052)
Q Consensus 855 ~d~~G~i---------~g~i~v~~DITerk~~e~elq~~ae~~-------~~~k~~~la~isHEirnPL~~I~g~~~lL~ 918 (1052)
.+.+|.. .+++++++|||++|+++++++..+.+. .....++++.++|++||||+.|.++++++.
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~~~al~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~i~~~~~~l~ 302 (494)
T TIGR02938 223 GMESDCADSFFCAAEQPYLLLTIADISNLREEQERARLSALQALMAEEERLEAIRETLSAAIHRLQGPMNLISAAISVLQ 302 (494)
T ss_pred EeecchhhheeccCCCchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHH
Confidence 7666543 345668999999999887665433222 222345577888999999999999999998
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCc
Q 001564 919 GTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIM 997 (1052)
Q Consensus 919 ~~~l~~e~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp 997 (1052)
+...+.........+.....++..++..+ ++.. ........++|+..++++++..+...+..+++.+.++.+..+|
T Consensus 303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~~~~dl~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ 379 (494)
T TIGR02938 303 RRGDDAGNPASAAMLQQALSAGREHMEALRQVIP---QSPQEIVVPVNLNQILRDVITLSTPRLLAAGIVVDWQPAATLP 379 (494)
T ss_pred hccccccCHHHHHHHHHHHHHHHHHHHHHHHhhc---cCcccccccccHHHHHHHHHHHhHHHHHhCCCEEEEecCCCCC
Confidence 64322222233333333344444444442 2221 1233456799999999999999999999999999999888877
Q ss_pred ceeEEEcHHHHHHHHHHHHHhHhhccCCCC----eEEEEEEEcc
Q 001564 998 SETLYGDSIRLQQVLADFLSISINFVPNGG----QLMVSSSLTK 1037 (1052)
Q Consensus 998 ~~~v~~D~~~L~QVL~NLL~NAik~~~~~g----~I~I~v~~~~ 1037 (1052)
. +.+|+.+|+|||.||+.||+||+++++ .|.|.+...+
T Consensus 380 ~--v~~d~~~l~~vl~Nl~~NAik~~~~~~~~~~~i~i~~~~~~ 421 (494)
T TIGR02938 380 A--ILGRELQLRSLFKALVDNAIEAMNIKGWKRRELSITTALNG 421 (494)
T ss_pred e--eecCHHHHHHHHHHHHHHHHHHhhccCCCcceEEEEEEecC
Confidence 5 899999999999999999999997663 3555544433
No 4
>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=1e-33 Score=288.91 Aligned_cols=171 Identities=33% Similarity=0.648 Sum_probs=142.2
Q ss_pred HHHHHHHHhcc-CC-CcccccCCcchhhhcCCCEEEEEECCeEEEecCCCCHHHHHHHHHHHhhccCCCceEEeccCCcc
Q 001564 412 TQTLLCDMLMR-DA-PLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDA 489 (1052)
Q Consensus 412 ~~~~~~~~~~~-~~-~~~~~~~~~~l~~l~~~dg~~~~~~~~~~~~g~~p~~~~~~~l~~~l~~~~~~~~~~~t~~l~~~ 489 (1052)
+++.|..++.. .. ..++..+.++|++|++|||+|++++|+++++|.+|+..++.+|++||.... +..+|+|++|.+.
T Consensus 4 ~~~~L~~~~~~~~~~~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~-~~~v~~T~~L~~~ 82 (182)
T PF00360_consen 4 LQQRLLEALSSSRDLLEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQA-DGEVFATDSLSED 82 (182)
T ss_dssp HHHHHHHHHHCSSSHHHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTT-T-SEEEESBGGGT
T ss_pred HHHHHHHHHccCCChhHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhC-CCccchhhhHhHh
Confidence 34455555554 33 467888999999999999999999999999999999999999999999774 4579999999985
Q ss_pred CCCCccccCcccceEEEEEeCC--CCEEEEeccCcceEEeccCCCCCCCCCC-CCCCccccchhHhHHHhhhcccCCCCh
Q 001564 490 GYLGALALGDVVCGMAAVRISP--KDMIFWFRSQTASEVRWGGAKHEPDEKD-DGRKMHPRSSFKAFLEVVKTRSLPWKD 566 (1052)
Q Consensus 490 ~~p~~~~~~~~~~G~~~~~i~~--~~~~~~fR~e~~~~v~W~G~p~~~~~~~-~~~~l~pR~SF~~w~e~v~g~s~pW~~ 566 (1052)
||++.++.+.+||||+++|+. ++||+|||+|+.++|+|||||+|+...+ ++.+|+||+||+.|+|+|+|+|.||+.
T Consensus 83 -~p~~~~~~~~aaGvLai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~~ 161 (182)
T PF00360_consen 83 -YPDAAALAERAAGVLAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWSD 161 (182)
T ss_dssp -SGGGGGGCCCHSEEEEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---H
T ss_pred -ChhhhhhcccCCCcEEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCCH
Confidence 999999999999999999986 6899999999999999999999997644 478999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHhh
Q 001564 567 YEMDAIHSLQLILRNAFK 584 (1052)
Q Consensus 567 ~ei~aa~~L~~iL~~~~~ 584 (1052)
.|++++..|+..|.+.+.
T Consensus 162 ~d~~~A~~lr~~l~~~~~ 179 (182)
T PF00360_consen 162 ADLEAAERLRRALLEVIL 179 (182)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999877666543
No 5
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=100.00 E-value=1.3e-31 Score=339.94 Aligned_cols=288 Identities=19% Similarity=0.213 Sum_probs=261.2
Q ss_pred EccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhc
Q 001564 729 QDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRL 808 (1052)
Q Consensus 729 ~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l 808 (1052)
++|++++++++++++++++++.++++++ ++|++.|.+|++++||+++++++||+.++++|+++. .+
T Consensus 138 ~~i~~r~~~~~~l~~~~~~l~~il~~~~---~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~-----------~l 203 (779)
T PRK11091 138 NEIKEREETQIELEQQSSLLRSFLDASP---DLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPK-----------DV 203 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCc---ceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChH-----------Hh
Confidence 5899999999999999999999999999 888999999999999999999999999999999853 33
Q ss_pred cchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHH
Q 001564 809 KNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQT 888 (1052)
Q Consensus 809 ~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~ 888 (1052)
.+++....+.......+.++.....+..+.+++|+.+|+.++..|+.+.+|.+.|++++++|||++++.+.++++ .
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~----a 279 (779)
T PRK11091 204 YSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEK----A 279 (779)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHH----H
Confidence 445555556666666777777888899999999999999999999999999999999999999999988866543 3
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHH
Q 001564 889 ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1052)
Q Consensus 889 ~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~ 967 (1052)
.+.|.+|++.|||||||||++|.|+++++....++++++++++.+..+++++..++++ +++++++.++..+++.++++.
T Consensus 280 ~~~~~~~~a~isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~~~~~l~ 359 (779)
T PRK11091 280 SRDKTTFISTISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKLQLDNQPIDFT 359 (779)
T ss_pred HHHHHHHHHHhhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCcEEEeeccCHH
Confidence 4567899999999999999999999999998888999999999999999999999999 799999999999999999999
Q ss_pred HHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEc
Q 001564 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLT 1036 (1052)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~ 1036 (1052)
+++++++..+...+..+++.+.++.++++|. .+.+|+.+|.|||.|||.||+||++ +|.|.|++...
T Consensus 360 ~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~~-~v~~d~~~l~qvl~NLl~NAik~~~-~g~v~i~~~~~ 426 (779)
T PRK11091 360 DFLADLENLSGLQAEQKGLRFDLEPLLPLPH-KVITDGTRLRQILWNLISNAVKFTQ-QGGVTVRVRYE 426 (779)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEEEeCCCCCc-eEEeCHHHHHHHHHHHHHHHHHhCC-CCcEEEEEEEc
Confidence 9999999999999999999999998888764 6899999999999999999999997 67888887775
No 6
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.95 E-value=8.8e-27 Score=244.41 Aligned_cols=282 Identities=15% Similarity=0.228 Sum_probs=227.9
Q ss_pred EccchhhH-hHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhh
Q 001564 729 QDITPQKT-VMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCR 807 (1052)
Q Consensus 729 ~DITerk~-aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~ 807 (1052)
.|.|++-+ ++..+...+.++..++..+. +|++..|..|+|+.+|..+.+++|.+.++++|+.+. +++..
T Consensus 93 n~Lt~~~~~aq~n~e~Er~kL~SvlayMt---DGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~-elL~i------ 162 (459)
T COG5002 93 NDLTKRVQEAQANTEQERRKLDSVLAYMT---DGVIATDRRGKIILINKPALKMLGVSKEDALGRSIL-ELLKI------ 162 (459)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHc---CceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHH-HHhCC------
Confidence 46666544 34445556678999999999 888999999999999999999999999999999874 33322
Q ss_pred ccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHH
Q 001564 808 LKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQ 887 (1052)
Q Consensus 808 l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~ 887 (1052)
.+.. .+...+ ......-. ...+ .++..-..++.+.+..+.|-+.|++++++|+|++.+.+.
T Consensus 163 ---~d~y-~~~dL~----e~~~s~ll--d~~~-~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~-------- 223 (459)
T COG5002 163 ---EDTY-TFEDLV----EKNDSLLL--DSSD-EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVER-------- 223 (459)
T ss_pred ---ccce-eHHHHH----hcCCcEEE--eecC-CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHH--------
Confidence 1111 122222 22222222 2223 777888888888899999999999999999998765553
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEe
Q 001564 888 TALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE--QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1052)
Q Consensus 888 ~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e--~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~ 964 (1052)
.+.+|.+++|||+||||+++.++++.|++....+. ..+++.......+||.++++| |.+||+..+...++.+-+
T Consensus 224 ---ErRefvanvSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~~qln~e~i 300 (459)
T COG5002 224 ---ERREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNARYQLNKEWI 300 (459)
T ss_pred ---HHHHHHHhcchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchhhhhhHHHH
Confidence 35689999999999999999999999998666555 778999999999999999999 799999999999999999
Q ss_pred eHHHHHHHHHHHHHhhccccCcE-EEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCCCc
Q 001564 965 TLNEVLVASISQVMMKSNAKGIR-IVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQS 1043 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~-l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~~~ 1043 (1052)
|+...+..++..+...+.+..+. +..++|.. +.+|..|+..+.||+-|+|+||+||+|+||+|++++....+
T Consensus 301 nft~fl~~ii~R~e~~~~~e~~~~~vR~~p~~--~~~veiD~DK~tQVldNii~NA~KYsP~Gg~Itv~~~~~~~----- 373 (459)
T COG5002 301 NFTAFLNEIINRFEMILKKETIARFVRDIPKQ--DIWVEIDPDKMTQVLDNIISNALKYSPDGGRITVSVKQRET----- 373 (459)
T ss_pred HhHHHHHHHHHHHHHHHhhHHHHHHHhcCCCC--ceEEEeChhHHHHHHHHHHHHHhhcCCCCCeEEEEEeeeCc-----
Confidence 99999999999998886655554 66667765 47899999999999999999999999999999999988776
Q ss_pred eEEEEEEE
Q 001564 1044 VHLAYLEL 1051 (1052)
Q Consensus 1044 ~~~v~lev 1051 (1052)
++.+.|
T Consensus 374 --~v~iSI 379 (459)
T COG5002 374 --WVEISI 379 (459)
T ss_pred --EEEEEE
Confidence 565554
No 7
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=99.92 E-value=2.4e-23 Score=246.08 Aligned_cols=268 Identities=15% Similarity=0.157 Sum_probs=207.9
Q ss_pred EEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhh
Q 001564 727 VAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACC 806 (1052)
Q Consensus 727 i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~ 806 (1052)
+.+++++.++.++++++.+++|+.++++++ ++++++|.+|+|+++|+++++++||+.+++.|+++. .++..
T Consensus 79 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~---~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~-~~~~~----- 149 (430)
T PRK11006 79 LYQMQLRNRKRRRELGNLIKRFRSGAESLP---DAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNIL-NLLRY----- 149 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCC---CeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHH-HHhcC-----
Confidence 346888899999999999999999999999 888999999999999999999999999999999863 22221
Q ss_pred hccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHH
Q 001564 807 RLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSE 886 (1052)
Q Consensus 807 ~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae 886 (1052)
+ +. ...+... .......+...+|..+ .+...|.. ++. ++.+.+|||++++.+.
T Consensus 150 ----~-~~---~~~~~~~-----~~~~~~~~~~~~~~~~--~~~~~~~~--~~~---~~~~~~dit~~~~~e~------- 202 (430)
T PRK11006 150 ----P-EF---TQYLKTR-----DFSRPLTLVLNNGRHL--EIRVMPYT--EGQ---LLMVARDVTQMHQLEG------- 202 (430)
T ss_pred ----H-HH---HHHHHhc-----ccCCCeEEEcCCCCEE--EEEEEEcC--CCc---EEEEEehhhHHHHHHH-------
Confidence 1 11 1111111 1112233345566544 44555543 232 5678899998765542
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEe
Q 001564 887 QTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1052)
Q Consensus 887 ~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~-l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~ 964 (1052)
.+.+|++.++|||||||++|.++++++.... .++...++++.+.+.+++|..++++ +++++++.+........+
T Consensus 203 ----~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~~~~~~~~~~ 278 (430)
T PRK11006 203 ----ARRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAAPTIDLNEKV 278 (430)
T ss_pred ----HHHHHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCCcc
Confidence 2447999999999999999999999998644 3455778999999999999999999 699999988776677889
Q ss_pred eHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++..+++.+........ .+++.+.+++++.+ .+.+|+.+|.|||.||+.||+||+++++.|.|++....+
T Consensus 279 ~~~~~~~~l~~~~~~~~-~~~~~i~~~~~~~~---~i~~d~~~l~~vl~NLl~NAik~~~~~~~I~i~~~~~~~ 348 (430)
T PRK11006 279 DVPMMLRVLEREAQTLS-QGKHTITFEVDNSL---KVFGNEDQLRSAISNLVYNAVNHTPEGTHITVRWQRVPQ 348 (430)
T ss_pred CHHHHHHHHHHHHHHHh-cCCcEEEEecCCCc---eEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEcCC
Confidence 99999988777666554 56688888887664 489999999999999999999999988889888766544
No 8
>PRK13557 histidine kinase; Provisional
Probab=99.91 E-value=1e-22 Score=247.99 Aligned_cols=274 Identities=13% Similarity=0.075 Sum_probs=219.5
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCccccCC---CCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHH
Q 001564 739 DKFTRIEGDYKAIVQNPNPLIPPIFGSDE---FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFV 815 (1052)
Q Consensus 739 ~~L~~se~~lr~ile~~~~li~~I~~~D~---~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~ 815 (1052)
+.....+..|+.++++++ .+++++|. +|+|+|+|+++++++||+.++++|+++. .+.++++..
T Consensus 23 ~~~~~~~~~~~~~~~~~~---~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~-----------~l~~~~~~~ 88 (540)
T PRK13557 23 DVSDHRSDIFFAAVETTR---MPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCR-----------FLQGPETDR 88 (540)
T ss_pred hhhhhhhHHHHHHHHhCc---CcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChH-----------hhcCCCCCH
Confidence 334456788999999999 78899985 7899999999999999999999999853 223333333
Q ss_pred hhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001564 816 NLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKA 895 (1052)
Q Consensus 816 ~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~ 895 (1052)
.....+...+..+..+..++...+++|+.+|+.....|+.+.+|.+++++++.+|||++++.+.++++..+ ......+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~~--~~~l~~~ 166 (540)
T PRK13557 89 ATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQK--MEALGQL 166 (540)
T ss_pred HHHHHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHHH--HHHhhhh
Confidence 34445555566666677788888999999999999999999999999999999999999888766554322 2234467
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHH
Q 001564 896 LAYTKRQIRNPLSGIIFSRKMMEG-----TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1052)
Q Consensus 896 la~isHEirnPL~~I~g~~~lL~~-----~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~l 969 (1052)
++.++|++||||+.|.++++++.. ....+...+.++.+...++++..++++ +++++.. ......+++..+
T Consensus 167 ~~~i~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~~----~~~~~~~~l~~~ 242 (540)
T PRK13557 167 TGGIAHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARKQ----RLEGRVLNLNGL 242 (540)
T ss_pred hhhhhHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC----CCCCcccCHHHH
Confidence 889999999999999999998854 223455678899999999999999999 5887732 345678999999
Q ss_pred HHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEE
Q 001564 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSL 1035 (1052)
Q Consensus 970 i~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~ 1035 (1052)
++.+...+.... .+++.+.+..++.++. +.+|+.+|.|||.||+.||+||++.++.|.|++..
T Consensus 243 i~~~~~~~~~~~-~~~~~i~~~~~~~~~~--~~~d~~~l~~vl~nll~NA~~~~~~~~~i~i~~~~ 305 (540)
T PRK13557 243 VSGMGELAERTL-GDAVTIETDLAPDLWN--CRIDPTQAEVALLNVLINARDAMPEGGRVTIRTRN 305 (540)
T ss_pred HHHHHHHHHHhc-CCCeEEEEecCCCCCc--eeeCHHHHHHHHHHHHHHHHHhcccCCeEEEEEee
Confidence 998887766443 4668888887777665 89999999999999999999999988888877654
No 9
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.91 E-value=7.5e-23 Score=270.17 Aligned_cols=268 Identities=14% Similarity=0.117 Sum_probs=235.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcC
Q 001564 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1052)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g 683 (1052)
.++..++|++++++++.++++++++++.+|.+|+++++|+++++++||+.++++|+++.+++++++.+.....+.....+
T Consensus 271 ~r~~~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~ 350 (1092)
T PRK09776 271 FRAERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSG 350 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcC
Confidence 34455778899999999999999999999999999999999999999999999999999999999888877777777766
Q ss_pred CccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCcc
Q 001564 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIF 763 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~ 763 (1052)
+.. ....+. ...+++|..+|+..+..++++.+|++.+++++++|||++|++|+++++++++++.+++..+ .++|
T Consensus 351 ~~~-~~~~e~--~~~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~---~~i~ 424 (1092)
T PRK09776 351 EIN-SYSMEK--RYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGG---IGIW 424 (1092)
T ss_pred Ccc-ceeeee--EEEcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcC---ceEE
Confidence 533 222233 3347899999999999999999999999999999999999999999999999999999999 7889
Q ss_pred ccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCc
Q 001564 764 GSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGK 843 (1052)
Q Consensus 764 ~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~ 843 (1052)
.+|.+|++++||+++.+++||+.++..+... +....+|++...+...+...+.++..+..++++.++||
T Consensus 425 ~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~----------~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG- 493 (1092)
T PRK09776 425 EWDLKPNIISWDKRMFELYEIPPHIKPTWQV----------WYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG- 493 (1092)
T ss_pred EEecCCCeEeeCHHHHHHhCCCcccCCCHHH----------HHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-
Confidence 9999999999999999999999888444322 22456788888888888889999889999999999999
Q ss_pred EEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHH
Q 001564 844 YAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQT 888 (1052)
Q Consensus 844 ~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~ 888 (1052)
.+|+.....++.|.+|++.+++++.+|||++|+.++++++..++.
T Consensus 494 ~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l 538 (1092)
T PRK09776 494 VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERL 538 (1092)
T ss_pred eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998877655543
No 10
>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=99.90 E-value=1.4e-22 Score=230.21 Aligned_cols=256 Identities=16% Similarity=0.149 Sum_probs=209.2
Q ss_pred HHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHH
Q 001564 742 TRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVL 821 (1052)
Q Consensus 742 ~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l 821 (1052)
.+..++|+.++++.+ +|++++|.+|++++||+++++++|+++++++|+++.+ +.++++ +...+
T Consensus 2 ~~~~~~l~~~~~~~~---~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~-----------~~~~~~---~~~~l 64 (333)
T TIGR02966 2 SALLSRFRAAAQALP---DAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITN-----------LIRHPE---FVEYL 64 (333)
T ss_pred hhHHHHHHHHHHhCc---CcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHH-----------HccCHH---HHHHH
Confidence 456678999999999 8889999999999999999999999999999988642 222222 22222
Q ss_pred HhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001564 822 NKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKR 901 (1052)
Q Consensus 822 ~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isH 901 (1052)
..... ...+.+..++|..+|+.+...|..+.+ ++++++|||++++.+. .+.++++.++|
T Consensus 65 ~~~~~-----~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~-----------~~~~~~~~l~h 123 (333)
T TIGR02966 65 AAGRF-----SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQ-----------MRRDFVANVSH 123 (333)
T ss_pred Hhccc-----CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHH-----------HHHHHHHhhhh
Confidence 22111 223556668899999999999987543 6778899998765542 23468899999
Q ss_pred HhhhHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHHHHHHH
Q 001564 902 QIRNPLSGIIFSRKMMEGT--ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1052)
Q Consensus 902 EirnPL~~I~g~~~lL~~~--~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~~~~~ 978 (1052)
++||||+.|.++++++... ..+++..++++.+....+++..++++ +++++++.+.....+.++++.+++..++..+.
T Consensus 124 ~l~~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~ 203 (333)
T TIGR02966 124 ELRTPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRLESAASPLEDEPVDMPALLDHLRDEAE 203 (333)
T ss_pred hhcccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccccccCHHHHHHHHHHHHH
Confidence 9999999999999988653 45566788899999999999999999 69999998888889999999999999999999
Q ss_pred hhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 979 MKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 979 ~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
.....+++.+.+..++. ..+.+|+..|.+||.||+.||++|+++++.|.|++....+
T Consensus 204 ~~~~~~~i~i~~~~~~~---~~~~~d~~~l~~vl~nll~Nai~~~~~~~~i~i~~~~~~~ 260 (333)
T TIGR02966 204 ALSQGKNHQITFEIDGG---VDVLGDEDELRSAFSNLVSNAIKYTPEGGTITVRWRRDGG 260 (333)
T ss_pred HHHHHcCcEEEEcCCCC---ceEEECHHHHHHHHHHHHHHhheeCCCCCeEEEEEEEcCC
Confidence 99999999999987432 3599999999999999999999999888889988776554
No 11
>PRK13559 hypothetical protein; Provisional
Probab=99.90 E-value=4.5e-22 Score=229.74 Aligned_cols=250 Identities=12% Similarity=0.061 Sum_probs=194.1
Q ss_pred HHHHHHHHHHhCCCCCCCCccccCC---CCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHH
Q 001564 743 RIEGDYKAIVQNPNPLIPPIFGSDE---FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGI 819 (1052)
Q Consensus 743 ~se~~lr~ile~~~~li~~I~~~D~---~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~ 819 (1052)
.+...|+.++++.+ ++++++|. +|++++||+++++++||+.++++|+.+. . +.+++.......
T Consensus 40 ~~~~~~~~~~e~~~---~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~----------l~~~~~~~~~~~ 105 (361)
T PRK13559 40 ASGRLFEQAMEQTR---MAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCR-F----------LQGAATDPIAVA 105 (361)
T ss_pred hhhhHHHHHHHhCC---CcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChh-h----------hcCCCCCHHHHH
Confidence 45667889999999 78899997 5689999999999999999999999852 1 122222223344
Q ss_pred HHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001564 820 VLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYT 899 (1052)
Q Consensus 820 ~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~i 899 (1052)
.+...+.++..+..++...+++|..+|+..+..|+.+.+|.+.+++++.+|||++++.+.+. +.+.++++.+
T Consensus 106 ~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~--------~~~~~l~~~l 177 (361)
T PRK13559 106 KIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE--------AHERRLAREV 177 (361)
T ss_pred HHHHHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH--------HHHHHHHHHH
Confidence 45566667777788888899999999999999999999999999999999999998765321 2234678899
Q ss_pred HHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHHHHHHH
Q 001564 900 KRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1052)
Q Consensus 900 sHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~~~~~ 978 (1052)
+|++||||+.|.++.+++.. .++..++++.+.....+|.+++++ ++.++ ..+++|.++++.++..+.
T Consensus 178 ~H~~~n~L~~i~~~~~l~~~---~~~~~~~~~~i~~~~~~l~~~~~~ll~~~~---------~~~v~l~~~~~~~~~~~~ 245 (361)
T PRK13559 178 DHRSKNVFAVVDSIVRLTGR---ADDPSLYAAAIQERVQALARAHETLLDERG---------WETVEVEELIRAQVAPYA 245 (361)
T ss_pred HHhhhhHHHHHHHHHHhhcc---CCCHHHHHHHHHHHHHHHHHHHHHHhccCC---------cCcccHHHHHHHHHHhhc
Confidence 99999999999999998873 223456788888888999999988 56544 467899999999988775
Q ss_pred hhccccCcEEEeeecCCCcceeEEEc-HHHHHHHHHHHHHhHhhc---cCCCCeEEEEEE
Q 001564 979 MKSNAKGIRIVNETAEQIMSETLYGD-SIRLQQVLADFLSISINF---VPNGGQLMVSSS 1034 (1052)
Q Consensus 979 ~~~~~~~i~l~~~~~~~lp~~~v~~D-~~~L~QVL~NLL~NAik~---~~~~g~I~I~v~ 1034 (1052)
.. +..+.++.+ .+ .+..+ ...|.|||.||+.||+|| ++++|.|.|++.
T Consensus 246 ~~----~~~i~~~~~-~~---~~~~~~~~~l~~vl~nLi~NA~k~~~~~~~~g~i~v~~~ 297 (361)
T PRK13559 246 PR----ATRVAFEGP-GI---RLGAASVQPLGLVLHELAVNAIKHGALSADQGRISISWK 297 (361)
T ss_pred CC----CceEEEECC-Ce---eeCHHHHHHHHHHHHHHHHhHHHhccccCCCcEEEEEEE
Confidence 43 345555532 21 23333 356999999999999999 566899999874
No 12
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=99.90 E-value=5.7e-24 Score=199.07 Aligned_cols=106 Identities=38% Similarity=0.559 Sum_probs=92.9
Q ss_pred hhhcccCCCCCCCcceEEEEecCCceEEEEccChhhhhCCC---CCCCCCCCCCCccCCCCchhhcCChhhHHHHHHHhc
Q 001564 70 YLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMV---NHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALG 146 (1052)
Q Consensus 70 ~~~~i~~~g~iQ~~G~ll~~~~~~~~i~~~S~N~~~~lg~~---~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~ 146 (1052)
+.+|||+||+|||||+|||+|+++++|+++|+|++++||.+ +++ ++|+++.++|++..++.+++++.
T Consensus 2 ~~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~----------llG~~l~~ll~~~~~~~l~~~~~ 71 (110)
T PF08446_consen 2 DREPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPELPEE----------LLGRPLSELLGAESAERLREALQ 71 (110)
T ss_dssp GGS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS----HHH----------HTTCBHHHHSCCCCHHHHHHHCT
T ss_pred CcccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccccchh----------hcccCHHHHhCHHHHHHHHHhhh
Confidence 45899999999999999999999999999999999999998 443 69999999999999999999998
Q ss_pred CCCCccCCceeEeecCCCceeEEEEeecCCeEEEEEeec
Q 001564 147 FGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPV 185 (1052)
Q Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~ie~E~~ 185 (1052)
.......+|+.+++..+++.|++++||+++++||||||+
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 72 SESLSLSNPIALRLRIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCCCCCEEEEEEEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred ccCccccCCeEEEeccCCeeEEEEEEEECCEEEEEEeeC
Confidence 887777889988777778899999999999999999995
No 13
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.90 E-value=2e-21 Score=239.66 Aligned_cols=277 Identities=16% Similarity=0.226 Sum_probs=229.0
Q ss_pred hHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHh
Q 001564 737 VMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVN 816 (1052)
Q Consensus 737 aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~ 816 (1052)
+.+.++.++..++.++++.+ ++++++|.+|+++++|+++++++|+++++++|+++ ..+++.. +.
T Consensus 253 ~~~~l~~~~~~~~~i~~~~~---~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~-~~~~~~~--------~~---- 316 (607)
T PRK11360 253 LAQALRETRSLNELILESIA---DGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPY-SELFPPN--------TP---- 316 (607)
T ss_pred HHHHHHHHHHHHHHHHHhcc---CeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcH-HHHcCCc--------hh----
Confidence 44567778888999999999 88899999999999999999999999999999985 3344321 11
Q ss_pred hHHHHHhhhc-CCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001564 817 LGIVLNKAMS-GQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKA 895 (1052)
Q Consensus 817 ~~~~l~~~l~-g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~ 895 (1052)
+...+...+. +......++.+.+++|... +.++..|+.+.+|++.|++++++|||++++.+.++++..+.. ...++
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~~~--~l~~~ 393 (607)
T PRK11360 317 FASPLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQERLA--ALGEL 393 (607)
T ss_pred HHHHHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHHHH--HHHHH
Confidence 1222223333 3334466778888888887 899999999999999999999999999999988776654433 35578
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHHH
Q 001564 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASI 974 (1052)
Q Consensus 896 la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~ 974 (1052)
++.++||+||||+.|.++++++.....+++..++++.+.+..+++..++++ +++++.... ...++++..+++.+.
T Consensus 394 ~~~~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~~~~~~ 469 (607)
T PRK11360 394 VAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPRES----QWQPVSLNALVEEVL 469 (607)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcC----ccceecHHHHHHHHH
Confidence 999999999999999999999887666777889999999999999999999 688886542 457899999999999
Q ss_pred HHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 975 SQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 975 ~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
..+......+++.+.++++++++. +.+|+..|.+|+.||+.||+||++.+|.|.|++....+
T Consensus 470 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~nli~na~~~~~~~~~i~v~~~~~~~ 531 (607)
T PRK11360 470 QLFQTAGVQARVDFETELDNELPP--IWADPELLKQVLLNILINAVQAISARGKIRIRTWQYSD 531 (607)
T ss_pred HHHHHhhhccCcEEEEEcCCCCCe--EEECHHHHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCC
Confidence 999988778889999988887765 89999999999999999999998878899988776544
No 14
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.90 E-value=8e-22 Score=260.43 Aligned_cols=261 Identities=13% Similarity=0.138 Sum_probs=216.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcc-cccccCCchHHHHHHHHHHHcC
Q 001564 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHF-LTLVEDSSIDTVKRMLYLALQG 683 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~-~~l~~~~~~~~~~~~l~~~l~g 683 (1052)
++.++++++.+++++.+++.+++++|.+|.+|++++||+++++++|++.++..+... .+.++|++.+.+...+.....+
T Consensus 399 k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~ 478 (1092)
T PRK09776 399 KRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQG 478 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhc
Confidence 345677888889999999999999999999999999999999999999988544333 3678899888888888888887
Q ss_pred CccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCcc
Q 001564 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIF 763 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~ 763 (1052)
+.....++++. +++| .+|+.....+++|.+|++.+++++.+|||++|++++++++++++++.++++++ ++++
T Consensus 479 ~~~~~~e~r~~----~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~---~~i~ 550 (1092)
T PRK09776 479 RSPFKLEFRIV----VKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIG---EAVV 550 (1092)
T ss_pred CCCeeEEEEEE----cCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccc---cEEE
Confidence 76655555443 7788 99999999999999999999999999999999999999999999999999999 7889
Q ss_pred ccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCc--ceeeEEEEccC
Q 001564 764 GSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP--EKVPFGFFARN 841 (1052)
Q Consensus 764 ~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~--~~~e~~~~~~d 841 (1052)
..|.+|+++++|+++++++||+.++++|+++. .++.. .++++...... +......... ...++.+.+++
T Consensus 551 ~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~~~~~-------~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 621 (1092)
T PRK09776 551 CTDMAMKVTFMNPVAEKMTGWTQEEALGVPLL-TVLHI-------TFGDNGPLMEN-IYSCLTSRSAAYLEQDVVLHCRS 621 (1092)
T ss_pred EECCCCeEEEEcHHHHHHhCCCHHHHcCCCHH-HHccc-------ccCCcchhhHH-HHHHHhcCCCccccceEEEEeCC
Confidence 99999999999999999999999999999863 33321 11222221222 3333333333 45677889999
Q ss_pred CcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHH
Q 001564 842 GKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQ 882 (1052)
Q Consensus 842 G~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq 882 (1052)
|+.+|+..+..|+.+.+|++.|++++++|||++|+.+++++
T Consensus 622 G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~L~ 662 (1092)
T PRK09776 622 GGSYDVHYSITPLSTLDGENIGSVLVIQDVTESRKMLRQLS 662 (1092)
T ss_pred CcEEEEEEEeeeeecCCCCEEEEEEEEEecchHHHHHHHHH
Confidence 99999999999999999999999999999999988775543
No 15
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=99.89 E-value=2.9e-21 Score=245.95 Aligned_cols=261 Identities=21% Similarity=0.236 Sum_probs=206.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCccccC-CCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhh
Q 001564 739 DKFTRIEGDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNL 817 (1052)
Q Consensus 739 ~~L~~se~~lr~ile~~~~li~~I~~~D-~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~ 817 (1052)
.++.++++.++.+++++| .++++++ .+|.++..|+.+..++|+...+...+.
T Consensus 327 ~~L~e~e~~~r~iv~~~p---~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~~~~~------------------------ 379 (924)
T PRK10841 327 LRLEEHEQFNRKIVASAP---VGICILRTSDGTNILSNELAHNYLNMLTHEDRQRL------------------------ 379 (924)
T ss_pred HHHHHHHHHHHHHHHhCC---ccEEEEEcCCCcEEEehHHHHHHhccCChhHHHHH------------------------
Confidence 467888899999999999 7778776 789999999999999987543321111
Q ss_pred HHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHH---HHHHHHHHHH
Q 001564 818 GIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRL---SEQTALKRLK 894 (1052)
Q Consensus 818 ~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~---ae~~~~~k~~ 894 (1052)
...+ ...... .......++....+.+..... .+.. ..++++.|||++++.+.++++. .++..+.|..
T Consensus 380 ~~~~----~~~~~~--~~~~~~~~~~~~~i~~~~~~~---~~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~a~~~k~~ 449 (924)
T PRK10841 380 TQII----CGQQVN--FVDVLTSNNTNLQISFVHSRY---RNEN-VAICVLVDVSARVKMEESLQEMAQAAEQASQSKSM 449 (924)
T ss_pred HHHH----hccccc--eeeEEcCCCcEEEEEEEeeee---cCce-EEEEEEEEhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0000 010000 112233445444333332222 2233 3688999999999988877654 4445567888
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHH
Q 001564 895 ALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVAS 973 (1052)
Q Consensus 895 ~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v 973 (1052)
|++.|||||||||++|.|++++|....++++++++++.+..++++|.++|++ +++++++++...+++++|++.++++++
T Consensus 450 fla~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~~l~~~~~~l~~li~~v 529 (924)
T PRK10841 450 FLATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLKIEPREFSPREVINHI 529 (924)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeeeEEecHHHHHHHH
Confidence 9999999999999999999999998888899999999999999999999999 799999999999999999999999999
Q ss_pred HHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 974 ISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 974 ~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+..+...+..+++.+.+++++++| ..+.+|+.+|+|||.|||+||+||++ +|.|.|++...++
T Consensus 530 ~~~~~~~~~~k~i~l~~~i~~~~~-~~v~~D~~~L~qvl~NLl~NAik~t~-~G~I~I~v~~~~~ 592 (924)
T PRK10841 530 TANYLPLVVKKRLGLYCFIEPDVP-VALNGDPMRLQQVISNLLSNAIKFTD-TGCIVLHVRVDGD 592 (924)
T ss_pred HHHHHHHHHHcCcEEEEEeCCCCC-cEEEECHHHHHHHHHHHHHHHHhhCC-CCcEEEEEEEeCC
Confidence 999999999999999999888776 36999999999999999999999998 6778888776444
No 16
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=99.89 E-value=2.8e-21 Score=221.90 Aligned_cols=259 Identities=12% Similarity=0.118 Sum_probs=198.5
Q ss_pred HHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhh
Q 001564 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1052)
Q Consensus 745 e~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1052)
...++.++++++ +|++++|.+|+|+++|+++++++||+.++++|+++. ++++.. ..+.. .+...
T Consensus 6 ~~~~~~il~~~~---~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~-~~~~~~--------~~~~~----~~~~~ 69 (348)
T PRK11073 6 LPDAGQILNSLI---NSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLP-ELLSYF--------SLNIE----LMRES 69 (348)
T ss_pred cchHHHHHhcCc---CeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHH-HHcCcc--------hhhHH----HHHHH
Confidence 346788999999 888999999999999999999999999999999863 343320 11111 12223
Q ss_pred hcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 001564 825 MSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIR 904 (1052)
Q Consensus 825 l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEir 904 (1052)
+..+.....+.....++|+.+|+.++..|+. + .+++..++|+|++++.+.++.+..+ .....+|++.++||+|
T Consensus 70 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~~--~~~~~~~~~~iaHelr 142 (348)
T PRK11073 70 LQAGQGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHAQ--QVAARDLVRGLAHEIK 142 (348)
T ss_pred HHcCCcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHHH--HHHHHHHHHhhhHhhc
Confidence 3333322222233456999999999999986 2 2466779999998877665443322 2344678999999999
Q ss_pred hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccc
Q 001564 905 NPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNA 983 (1052)
Q Consensus 905 nPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~ 983 (1052)
|||++|.++++++.+...+++.++++..+.+.++++..++++ +.+.+.. ....+++..+++.+...+.....
T Consensus 143 ~pL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~~~------~~~~~~l~~~~~~~~~~~~~~~~- 215 (348)
T PRK11073 143 NPLGGLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQRPG------THVTESIHKVAERVVQLVSLELP- 215 (348)
T ss_pred ChHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCC------CCccccHHHHHHHHHHHHhhhcc-
Confidence 999999999999987666677889999999999999999999 5765532 23567999999999888876654
Q ss_pred cCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhcc-CCCCeEEEEEEE
Q 001564 984 KGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV-PNGGQLMVSSSL 1035 (1052)
Q Consensus 984 ~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~-~~~g~I~I~v~~ 1035 (1052)
+++.+.++.+++.|. +.+|+.+|.|||.||+.||++|+ ++++.|.|++..
T Consensus 216 ~~i~i~~~~~~~~~~--i~~d~~~l~~vl~nLl~NA~~~~~~~~~~i~i~~~~ 266 (348)
T PRK11073 216 DNVRLIRDYDPSLPE--LAHDPDQIEQVLLNIVRNALQALGPEGGTITLRTRT 266 (348)
T ss_pred CCcEEEEecCCCCCc--eeeCHHHHHHHHHHHHHHHHHHhccCCCeEEEEEcc
Confidence 568888888777765 89999999999999999999998 668888887644
No 17
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.88 E-value=6.1e-21 Score=239.33 Aligned_cols=256 Identities=16% Similarity=0.142 Sum_probs=199.0
Q ss_pred hHHHHHHHHHHHHHHHhCCCCCCCCccccC-CCCcceeechHHHHHhCCChHH-HhhhhhhhhhhcCchhhhhccchhhH
Q 001564 737 VMDKFTRIEGDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREE-VIDKLLLAEVFGTNMACCRLKNQEAF 814 (1052)
Q Consensus 737 aE~~L~~se~~lr~ile~~~~li~~I~~~D-~~g~i~~vN~a~~~i~G~~~ee-liG~~l~~~v~~~~~~~~~l~~~d~~ 814 (1052)
..+++++.+..++.+++++| .|++++| .+|+++.+|+++++++|...-. +.... ..+.
T Consensus 334 l~~~L~~~~~l~~~Ii~~lp---~Gilv~D~~~~~Ii~~N~aA~~ll~~~~l~~i~~~~--------------~~~~--- 393 (894)
T PRK10618 334 MSHELRILRALNEEIVSNLP---LGLLVYDFESNRTVISNKIADHLLPHLNLQKITTMA--------------EQHQ--- 393 (894)
T ss_pred HHHHHHHHHHHHHHHHHhCC---ceEEEEECCCCeEEEEhHHHHHHhCccchhhHHHHH--------------Hhcc---
Confidence 33467888889999999999 8889999 6799999999999999864211 11000 0000
Q ss_pred HhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHH---HHHHHHHH
Q 001564 815 VNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQR---LSEQTALK 891 (1052)
Q Consensus 815 ~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~---~ae~~~~~ 891 (1052)
..+... .+++..++..... .....+.+.+++|++++...+.++++ ..++...+
T Consensus 394 ----~~i~~~---------------i~~~~~eir~~~~-----~~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le~~~~~ 449 (894)
T PRK10618 394 ----GVIQAT---------------INNELYEIRMFRS-----QLAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQQA 449 (894)
T ss_pred ----hhhhhh---------------ccCceeEEEEeec-----cccCceEEEEEeehHHHHHHHHHHHHHHHHHHHHHHH
Confidence 000000 1122222222111 11223467788999988766655543 44555678
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHH
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVL 970 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li 970 (1052)
|.+|++.|||||||||++|.++++++.....++++.++++.+..+++++.++|++ ++++++++|+..++.++|++.+++
T Consensus 450 k~~fla~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~~l~~~~~~L~~ll 529 (894)
T PRK10618 450 RKAFLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDWKPEQELFSLQDLI 529 (894)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccceeECHHHHH
Confidence 8999999999999999999999999988777888999999999999999999999 799999999999999999999999
Q ss_pred HHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 971 ~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++..+...+..+++.+.++++...+ ..+.+|+.+|+|||.|||+||+||++ +|.|.|++....+
T Consensus 530 ~~vl~~~~~~a~~k~i~l~~~~~~~~~-~~v~~D~~~L~QVL~NLL~NAik~t~-~G~I~I~v~~~~~ 595 (894)
T PRK10618 530 DEVLPEVLPAIKRKGLQLLIHNHLKAE-QLRIGDRDALRKILLLLLNYAITTTA-YGKITLEVDQDES 595 (894)
T ss_pred HHHHHHHHHHHHHCCCEEEEEeCCCCC-cEEEecHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEccC
Confidence 999999999999999999988765544 36899999999999999999999998 6888888876543
No 18
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.87 E-value=1.2e-20 Score=250.86 Aligned_cols=306 Identities=15% Similarity=0.124 Sum_probs=214.5
Q ss_pred EEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhh
Q 001564 728 AQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCR 807 (1052)
Q Consensus 728 ~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~ 807 (1052)
.++++.+++++.+++..+..++.++++++ .||+++|.+|+|+++|+++++++|.+.....+.... .. .
T Consensus 558 ~~~i~~r~~~~~~l~~~~~~~~~i~~~~~---~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~----~~-----~ 625 (1197)
T PRK09959 558 LRSVRRRKVIQGDLENQISFRKALSDSLP---NPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLE----NS-----D 625 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCC---CcEEEEcCCCcEEEehHHHHHHhCcccccccccccc----cc-----c
Confidence 46889999999999999999999999999 888999999999999999999999764332222110 00 0
Q ss_pred ccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEE-EeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHH-
Q 001564 808 LKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLL-CVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLS- 885 (1052)
Q Consensus 808 l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~-~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~a- 885 (1052)
....+................. .....+...+|...++.. ...+.....+...++++..+|||+.++.+.+++...
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~ 703 (1197)
T PRK09959 626 SPFKDVFSNAHEVTAETKENRT--IYTQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERN 703 (1197)
T ss_pred CchhhhHhHHHHHHHHHhhccc--cceeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHH
Confidence 0000000000000011111111 112222333443222222 122222233445568888999999887776655433
Q ss_pred --HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEe
Q 001564 886 --EQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE-QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEM 961 (1052)
Q Consensus 886 --e~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e-~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~ 961 (1052)
.+...++.+|++.|+|||||||++|.++++++.....+++ ..++++.+..+++++..+|++ +++++++++...+.+
T Consensus 704 ~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~~~~~ 783 (1197)
T PRK09959 704 KAINATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQP 783 (1197)
T ss_pred HHHHHHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCceeee
Confidence 3345568889999999999999999999999986555544 457889999999999999999 799999999999999
Q ss_pred EEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCC
Q 001564 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLG 1041 (1052)
Q Consensus 962 ~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~ 1041 (1052)
+++++.+++++++..+...+..+++.+.+...... ...+.+|+.+|.|||.|||.||+||++ +|.+.|.+..... .
T Consensus 784 ~~~~l~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~v~~d~~~l~qvl~NLl~NAik~~~-~g~i~i~~~~~~~--~ 859 (1197)
T PRK09959 784 QWVDIPTLVQNTCHSFGAIAASKSIALSCSSTFPD-HYLVKIDPQAFKQVLSNLLSNALKFTT-EGAVKITTSLGHI--D 859 (1197)
T ss_pred eeeCHHHHHHHHHHHHHHHHHhcCcEEEEecCCCC-ceEEEECHHHHHHHHHHHHHHHHHhCC-CCCEEEEEEEeee--c
Confidence 99999999999999999999999998887653221 135899999999999999999999998 5666666544322 2
Q ss_pred CceEEEEEEE
Q 001564 1042 QSVHLAYLEL 1051 (1052)
Q Consensus 1042 ~~~~~v~lev 1051 (1052)
++...+.++|
T Consensus 860 ~~~~~~~i~V 869 (1197)
T PRK09959 860 DNHAVIKMTI 869 (1197)
T ss_pred CCceEEEEEE
Confidence 3333444554
No 19
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=99.86 E-value=4.3e-20 Score=192.27 Aligned_cols=257 Identities=16% Similarity=0.172 Sum_probs=194.6
Q ss_pred HHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCC
Q 001564 750 AIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD 829 (1052)
Q Consensus 750 ~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~ 829 (1052)
.++++.+ .++++.|.+|.|.|+|++++.+||.+...+.|..+ .++++.. .. +...+.+....+.
T Consensus 11 ~~Ln~~~---~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l-~~l~~~g--------s~----ll~ll~q~~~~~~ 74 (363)
T COG3852 11 AILNNLI---NPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRL-SELLPFG--------SL----LLSLLDQVLERGQ 74 (363)
T ss_pred hHHhccC---CceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCCh-HHHcCCC--------cH----HHHHHHHHHHhcC
Confidence 5777777 78899999999999999999999999999998886 4444431 11 3344444444433
Q ss_pred c-ceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 001564 830 P-EKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLS 908 (1052)
Q Consensus 830 ~-~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~ 908 (1052)
+ .++++.+. .+|....+...+.|+....|.+. ..++-+....+-..++. .....++-....++++|||||||+
T Consensus 75 ~~~~~~v~l~-~~g~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~ridre~~--q~a~~~a~~~L~r~LAHEIKNPL~ 148 (363)
T COG3852 75 PVTEYEVTLV-ILGRSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRRLDREQT--QHAQQRAVKGLVRGLAHEIKNPLG 148 (363)
T ss_pred Ccccceeeee-ecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhHHHH--HHHHHHHHHHHHHHHHHHhcCccc
Confidence 3 36666665 78999999999999987777653 33333332222221111 111222344668899999999999
Q ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEE
Q 001564 909 GIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRI 988 (1052)
Q Consensus 909 ~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l 988 (1052)
+|.|.++||++.-.++.-++|.+.|.+.++|+..+++.|.+..- ....+..+++++.+++.+...+...+.. ++.+
T Consensus 149 GiRGAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRme~~~~---~rp~~r~~~NIH~VLerV~~lv~~e~~~-~i~l 224 (363)
T COG3852 149 GIRGAAQLLERALPDEALRELTQLIIEEADRLRNLVDRLEVLGP---QRPGDRVPVNIHEVLERVRALVEAEFAD-NVRL 224 (363)
T ss_pred chhhHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCCcccccchHHHHHHHHHHHHhcccCC-ceEE
Confidence 99999999998666666889999999999999999999744432 3345667999999999999999888665 5999
Q ss_pred EeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCC----CCeEEEEEE
Q 001564 989 VNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN----GGQLMVSSS 1034 (1052)
Q Consensus 989 ~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~----~g~I~I~v~ 1034 (1052)
.-++++.+|+ |++|+.+|.|||.||+.||.++... +|.|.++.+
T Consensus 225 ~rdYDPSLP~--v~~d~DqliQv~LNlVrNAaqA~~~~~~~~g~I~LrTR 272 (363)
T COG3852 225 IRDYDPSLPE--VLGDRDQLIQVFLNLVRNAAQALGGRADEGGEIILRTR 272 (363)
T ss_pred eecCCCCCcc--ccCCHHHHHHHHHHHHHHHHHHhcCCCCCCceEEEEec
Confidence 9999999998 9999999999999999999999752 478887753
No 20
>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=2.6e-20 Score=220.93 Aligned_cols=242 Identities=15% Similarity=0.092 Sum_probs=184.7
Q ss_pred HHHHHHHHHHHHHHHHhCCceEEEEcC-CCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCcc
Q 001564 608 MKELEAVTSEMVRLIETATVPILAVDV-DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE 686 (1052)
Q Consensus 608 ~~eL~~~~~~l~~lle~~~~~I~~~D~-dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~ 686 (1052)
..+|++.+++|+.++++++++++++|. +|+|+++|+++++++||+.++++|+++.+++++++.+.+...+.....++..
T Consensus 125 ~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~ 204 (442)
T TIGR02040 125 YWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSA 204 (442)
T ss_pred HHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCC
Confidence 347888899999999999999999998 8999999999999999999999999999999998888888888887766553
Q ss_pred ceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccC
Q 001564 687 QNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSD 766 (1052)
Q Consensus 687 ~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D 766 (1052)
.. +++. .++++..| .+...++.. +|.. .+++.++|||+++++++++. ++|+.++++++ ++|+++|
T Consensus 205 ~~--~~~~----~~~~~~~~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~~~---~~~~~l~e~~~---d~I~v~D 269 (442)
T TIGR02040 205 AP--VRIL----LRRSQKRL-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDELS---ENLARLYHEAP---DAIVFSD 269 (442)
T ss_pred cc--eEEE----EcCCCeEE-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHHHH---HHHHHHHHhCC---ceEEEEc
Confidence 33 2332 12333333 334445543 3433 56677899999998887653 37999999999 8889999
Q ss_pred CCCcceeechHHHHHhCCC-hHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEE
Q 001564 767 EFGWCCEWNPAMVKLTGWK-REEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYA 845 (1052)
Q Consensus 767 ~~g~i~~vN~a~~~i~G~~-~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~ 845 (1052)
.+|+|+++|+++++++||+ .++++|+++.. ++.. ...+. ...+.....++....++..+.+++|..+
T Consensus 270 ~~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~-~~~~--------~~~~~---~~~~~~~~~~g~~~~~~~~~~~~~G~~~ 337 (442)
T TIGR02040 270 ADGTIRGANEAFLELTDSSSLEAVRGRTLDR-WLGR--------GGVDL---RVLLSNVRRTGQVRLYATTLTGEFGAQT 337 (442)
T ss_pred CCCcEEehhHHHHHHhCCCChHHHcCCCHHH-HhCC--------CcccH---HHHHHHHhhcCceEEEEEEEEcCCCCEE
Confidence 9999999999999999997 57899998632 2221 11122 2222333344444567778899999999
Q ss_pred EEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHH
Q 001564 846 ECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1052)
Q Consensus 846 ~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e 878 (1052)
|+.+++.|+.+.++. .++++++|||++++.+
T Consensus 338 ~ve~s~~~i~~~~~~--~~~~v~rDITeR~~~~ 368 (442)
T TIGR02040 338 EVEISAAWVDQGERP--LIVLVIRDISRRLTMR 368 (442)
T ss_pred EEEEEEEEeccCCce--EEEEEEecchhhccCC
Confidence 999999999876553 4788999999987764
No 21
>PRK13560 hypothetical protein; Provisional
Probab=99.85 E-value=7.1e-20 Score=234.24 Aligned_cols=262 Identities=15% Similarity=0.109 Sum_probs=198.8
Q ss_pred HHHHHHHHHHHHHH-HHHHHhCCceEEEEcCCCc----EeeccHHHHHHhCCCcchhcCCc--ccccccCCchHHHH---
Q 001564 605 IEGMKELEAVTSEM-VRLIETATVPILAVDVDGL----VNGWNTKIAELTGLSVDKAIGKH--FLTLVEDSSIDTVK--- 674 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l-~~lle~~~~~I~~~D~dg~----I~~~N~a~~~l~G~~~eeliG~~--~~~l~~~~~~~~~~--- 674 (1052)
..++.+|+++++++ +.+++++|.++|.++.+|. +.+++++..+++|+...++++.. +..++||++.+.+.
T Consensus 56 ~~~~~~l~~~~e~~~r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~ 135 (807)
T PRK13560 56 AIAEAEAQDCREQCERNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANP 135 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhCh
Confidence 34567777777778 9999999999999887666 33377777788888877766533 44678888877654
Q ss_pred ----HHHHHHHcCCccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHH
Q 001564 675 ----RMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKA 750 (1052)
Q Consensus 675 ----~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ 750 (1052)
+.+..+++++....+++++. +++|. |+.+...|.++.+|.+ ++.++++|||++|++|++|++++++|+.
T Consensus 136 ~~~~~~~~~~~~~~~~~~~e~r~~----~~dg~--~~~~~~~~~~~~~g~~-~~~g~~~DIT~rk~ae~~l~~~~~~l~~ 208 (807)
T PRK13560 136 FRSAETIAMALQSDDWQEEEGHFR----CGDGR--FIDCCLRFERHAHADD-QVDGFAEDITERKRAEERIDEALHFLQQ 208 (807)
T ss_pred hhHHHHHHHHhccCcccceEEEEE----eCCcc--EEEEEeeeeecCCCce-EEEEEEEccchHHHHHHHHHHHHHHHHH
Confidence 23333444444344444443 56664 5666777888888876 6889999999999999999999999999
Q ss_pred HHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCc
Q 001564 751 IVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP 830 (1052)
Q Consensus 751 ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~ 830 (1052)
++++++ +++|..|.+|+++++|+++++++||++++++|+++. ++++ ++....+.......+..+..
T Consensus 209 l~e~~~---~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~-~~~~----------~~~~~~~~~~~~~~~~~~~~ 274 (807)
T PRK13560 209 LLDNIA---DPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIH-DFAP----------AQPADDYQEADAAKFDADGS 274 (807)
T ss_pred HHhhCC---CeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcch-hcCC----------cchhHHHHHHHHHHhccCCc
Confidence 999999 788999999999999999999999999999999864 2222 22222232333444555566
Q ss_pred ceeeEEEEccCCcEEEEEEE--eeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHH
Q 001564 831 EKVPFGFFARNGKYAECLLC--VNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQ 887 (1052)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~--~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~ 887 (1052)
..++.++.++||..+|+.+. ..+..+.+|.+.|++++++|||++|+++.++++..++
T Consensus 275 ~~~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~ 333 (807)
T PRK13560 275 QIIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDM 333 (807)
T ss_pred eEEEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHH
Confidence 67888999999999966554 4567899999999999999999999999877665443
No 22
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=99.79 E-value=1.7e-17 Score=187.02 Aligned_cols=247 Identities=15% Similarity=0.177 Sum_probs=184.5
Q ss_pred HHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhH
Q 001564 739 DKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLG 818 (1052)
Q Consensus 739 ~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~ 818 (1052)
+++.+.+..++.+++..+ .|++.+|.+|++.-+|+++++++|.+.++++|.++. .+- |+ +.
T Consensus 363 ~~~e~rr~f~E~VLsgvt---aGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~ls-a~a-----------p~----~~ 423 (712)
T COG5000 363 DALEQRRRFLEAVLSGLT---AGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLS-AIA-----------PE----LE 423 (712)
T ss_pred HHHHHHHHHHHHHHhcCc---eeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhh-hhh-----------hH----HH
Confidence 345556667788999999 889999999999999999999999999999999852 111 11 22
Q ss_pred HHHHhhhc-CCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001564 819 IVLNKAMS-GQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALA 897 (1052)
Q Consensus 819 ~~l~~~l~-g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la 897 (1052)
..+...-. ++.....++.+.+. |+.+...+.++....++| -|++.++.|||+-..++ .+.+-.+-..
T Consensus 424 ~vf~~~~a~~~~~~~~ev~~~r~-g~~rtl~Vq~t~~~~d~~--~gyVvt~DDITdLV~AQ---------Rs~AW~dVAr 491 (712)
T COG5000 424 EVFAEAGAAARTDKRVEVKLARE-GEERTLNVQATREPEDNG--NGYVVTFDDITDLVIAQ---------RSAAWGDVAR 491 (712)
T ss_pred HHHHHhhhhcCCCccceeecccC-CCceeeeeeeeecccccC--CceEEEecchHHHHHHH---------HHHHHHHHHH
Confidence 23322222 22333455554444 445555555544332222 35889999999876554 2334455677
Q ss_pred HHHHHhhhHHHHHHHHHHHHcC---CCCCHH---HHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHH
Q 001564 898 YTKRQIRNPLSGIIFSRKMMEG---TELGAE---QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVL 970 (1052)
Q Consensus 898 ~isHEirnPL~~I~g~~~lL~~---~~l~~e---~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li 970 (1052)
.++|||||||+.|...++-|++ ..++++ ..++.++|.+.+..|.+++++ -+|+| ...+++++.||.+++
T Consensus 492 RIAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afAR----mP~p~~e~~dL~~ll 567 (712)
T COG5000 492 RIAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFAR----MPAPKLEKSDLRALL 567 (712)
T ss_pred HHHHHhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCCCCCcchHHHHH
Confidence 8999999999999999998875 444443 578899999999999999999 69999 456788999999999
Q ss_pred HHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccC
Q 001564 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP 1024 (1052)
Q Consensus 971 ~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~ 1024 (1052)
.+++...+..- ..|.+..+.+.+ ++...+|+.+|.|+|.|||.||.++..
T Consensus 568 ~e~~~L~e~~~--~~i~f~~e~g~e--pl~~~~D~~~l~Qvf~NliKNA~EAi~ 617 (712)
T COG5000 568 KEVSFLYEIGN--DHIVFAAEFGGE--PLIGMADATLLGQVFGNLLKNAAEAIE 617 (712)
T ss_pred HHHHHHHhccC--CCeEEEeecCCC--ceeeecCHHHHHHHHHHHHHhHHHHhh
Confidence 99998877653 458888888887 467888999999999999999999853
No 23
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.79 E-value=6.8e-18 Score=215.79 Aligned_cols=246 Identities=12% Similarity=0.066 Sum_probs=191.4
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1052)
..+...++.++++++++|.+|+|++||+++++++||+.++++|+++.++++++........+.....++......+....
T Consensus 12 ~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ 91 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSREL 91 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccceee
Confidence 34567889999999999999999999999999999999999999999998887766555555555544432211121122
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeec
Q 001564 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWN 775 (1052)
Q Consensus 696 ~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN 775 (1052)
...+++|..+|+.+...|+ +.+|.+ +++++.+|||++++.+++. ..++.++++++ .+++.+|.+|+++++|
T Consensus 92 ~~~~~dG~~~~v~~~~~~~-~~~g~~-~~~~~~~DiT~~~~~~~~~----~~~~~~~~~~~---~~i~~~d~~g~i~~~N 162 (799)
T PRK11359 92 QLEKKDGSKIWTRFALSKV-SAEGKV-YYLALVRDASVEMAQKEQT----RQLIIAVDHLD---RPVIVLDPERRIVQCN 162 (799)
T ss_pred EEecCCcCEEEEEEEeeee-ccCCce-EEEEEEeeccchhhhHHHH----HHHHHHHhcCC---CcEEEEcCCCcEEEEC
Confidence 2347899999999888776 445554 5677889999988776653 45667889998 7889999999999999
Q ss_pred hHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEee
Q 001564 776 PAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKL 855 (1052)
Q Consensus 776 ~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~ 855 (1052)
+++++++||+.++++|+.... ++.. ++........+...+.+...+..++++.+++|..+|+.....|+.
T Consensus 163 ~~~~~l~G~~~~e~~g~~~~~-~~~~---------~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~ 232 (799)
T PRK11359 163 RAFTEMFGYCISEASGMQPDT-LLNI---------PEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVY 232 (799)
T ss_pred hhhHhhhCCCHHHHCCCChHH-hcCC---------CCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeee
Confidence 999999999999999998532 2221 222222333455556666677788889999999999999999999
Q ss_pred CCCCCEEEEeeehHHHHHHHHHHHH
Q 001564 856 DREGAVTGVFCFLQLASHELQQALH 880 (1052)
Q Consensus 856 d~~G~i~g~i~v~~DITerk~~e~e 880 (1052)
+.+|.+.|++++.+|||++++.++.
T Consensus 233 d~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 233 DVLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred cCCCceeEEEEEeehhhhHHHHHHH
Confidence 9999999999999999999876643
No 24
>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=99.78 E-value=4.3e-18 Score=201.97 Aligned_cols=234 Identities=16% Similarity=0.167 Sum_probs=176.6
Q ss_pred HHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEecccc
Q 001564 621 LIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKI 700 (1052)
Q Consensus 621 lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~ 700 (1052)
+++.++++++++|.+|+|++||..+++++||+.++++|+++.+++++++.+.+...+..+..++.. .++++ .....+
T Consensus 1 ~~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~e--~~~~~~ 77 (442)
T TIGR02040 1 LLATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRG-AVRVE--LNHIDP 77 (442)
T ss_pred CCcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCC-cceEe--eccCCC
Confidence 367899999999999999999999999999999999999999999998888777777776665543 12232 233466
Q ss_pred CCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHh-----------HH---HHHHHHHHHHHHHhCCCCCCCCccccC
Q 001564 701 NDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTV-----------MD---KFTRIEGDYKAIVQNPNPLIPPIFGSD 766 (1052)
Q Consensus 701 dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~a-----------E~---~L~~se~~lr~ile~~~~li~~I~~~D 766 (1052)
+|..+|+.++..++.+ + .+++++++|||+++.. |+ +|++++++|+.++++++ +++|++|
T Consensus 78 ~g~~~~~~~~~~~~~~--~--~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l~~~e~r~~~l~e~~~---~~i~~~d 150 (442)
T TIGR02040 78 SSFELPMRFILVRLGA--D--RGVLALGRDLRAVAELQQQLVAAQQAMERDYWTLREMETRYRVVLEVSS---DAVLLVD 150 (442)
T ss_pred CCCccCeEEEEEEeCC--C--CeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC---ceEEEEE
Confidence 6777888877777544 2 2667889999875543 33 67778899999999999 7889999
Q ss_pred C-CCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEE
Q 001564 767 E-FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYA 845 (1052)
Q Consensus 767 ~-~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~ 845 (1052)
. +|+++++|+++++++||++++++|+++. .+.++++...+...+.....++.....++ ..++|...
T Consensus 151 ~~~g~i~~~N~a~~~l~G~~~~el~g~~~~-----------~~~~~~~~~~~~~~l~~~~~~g~~~~~~~--~~~~~~~~ 217 (442)
T TIGR02040 151 MSTGRIVEANSAAAALLGGVGQSLVGRAFP-----------QEFEGRRREELMLTLRNVRATGSAAPVRI--LLRRSQKR 217 (442)
T ss_pred CCCCEEEEEcHHHHHHhCcCHHHHcCCCHH-----------HhCCHHHHHHHHHHHHHHHhcCCCcceEE--EEcCCCeE
Confidence 8 7999999999999999999999999853 34566777777777777776655544444 34555544
Q ss_pred EEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHH
Q 001564 846 ECLLCVNKKLDREGAVTGVFCFLQLASHELQQALH 880 (1052)
Q Consensus 846 ~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~e 880 (1052)
| .+...++.. +|.. ++++.+.|||++++.+.+
T Consensus 218 ~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~ 249 (442)
T TIGR02040 218 L-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDE 249 (442)
T ss_pred E-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHH
Confidence 4 344555543 3433 477888999988766543
No 25
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=99.75 E-value=1.6e-15 Score=185.02 Aligned_cols=275 Identities=14% Similarity=0.173 Sum_probs=177.2
Q ss_pred EEEEeecCCCCEEEEEEEEEccchhhHhHHH--------------------------------------HHHHHHHHHHH
Q 001564 710 NACASRDLHDNVVGVCFVAQDITPQKTVMDK--------------------------------------FTRIEGDYKAI 751 (1052)
Q Consensus 710 ~~~pi~d~~G~v~gvv~i~~DITerk~aE~~--------------------------------------L~~se~~lr~i 751 (1052)
...|+++..|.++|++.+..++.+....-.. +....+.++.+
T Consensus 147 ~~~p~~~~~~~~iG~v~vg~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~l~~l~~~ei~~l~~~~~~i 226 (542)
T PRK11086 147 VFTPVYDENGKQIGVVAVGISLSEVTEQINESRWSIYWSILFGALVGLIGTVILVRVLKRILFGLEPYEISTLFEQRQAM 226 (542)
T ss_pred EEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 5578888899999998777665544332211 23334567889
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCCh---HHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCC
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKR---EEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQ 828 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~---eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~ 828 (1052)
+++++ +||+++|.+|+|+++|+++++++|++. .+.+|+.+. .+ .... .+...+..+
T Consensus 227 l~~~~---~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~-~~----------~~~~-------~~~~~~~~~ 285 (542)
T PRK11086 227 LQSIK---EGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVE-SW----------MPVS-------RLKEVLRTG 285 (542)
T ss_pred HHHhc---CcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHH-Hh----------CCch-------hHHHHHhcC
Confidence 99999 888999999999999999999998763 345555431 11 1111 122233333
Q ss_pred Ccc-eeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 001564 829 DPE-KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPL 907 (1052)
Q Consensus 829 ~~~-~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL 907 (1052)
.+. ..+. ..+|. ++.....|+.+ +|.+.|++++++|+|+.++.+.++... ....++++.++||+||||
T Consensus 286 ~~~~~~~~---~~~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~-----~~~~~~l~~~sHel~npL 354 (542)
T PRK11086 286 TPRRDEEI---NINGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGM-----VNYADALRAQSHEFMNKL 354 (542)
T ss_pred CCccceEE---EECCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHH-----HHHHHHHHhhchhhcCHH
Confidence 322 2222 22454 34566779988 899999999999999987766544332 223456778999999999
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCc
Q 001564 908 SGIIFSRKMMEGTELGAEQKRLLHTS-AQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGI 986 (1052)
Q Consensus 908 ~~I~g~~~lL~~~~l~~e~~~~l~~i-~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i 986 (1052)
++|.+++++... ++..+++..+ .....++..+++++. . .++...+......+.++++
T Consensus 355 ~~I~g~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~--~----------------~~~~~~~~~~~~~~~~~~~ 412 (542)
T PRK11086 355 HVILGLLHLKSY----DQLEDYILKTANNYQEEIGSLLGKIK--S----------------PVIAGFLLGKISRARELGI 412 (542)
T ss_pred HHHHHHHHhCch----HHHHHHHHHHHHHHHHHHHHHHHhcc--C----------------HHHHHHHHHHHHHHHHcCC
Confidence 999999987532 2333343332 333444555554421 0 1222223333445567788
Q ss_pred EEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCC--CCeEEEEEEEccC
Q 001564 987 RIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKD 1038 (1052)
Q Consensus 987 ~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~--~g~I~I~v~~~~~ 1038 (1052)
.+.++.++.+|......+...|.|||.||+.||+||+++ ++.|.|++....+
T Consensus 413 ~~~~~~~~~~~~~~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~I~i~~~~~~~ 466 (542)
T PRK11086 413 TLIISEDSQLPDSGDEDQVHELITILGNLIENALEAVGGEEGGEISVSLHYRNG 466 (542)
T ss_pred EEEEeCCCCCCcccccccHHHHHHHHHHHHHHHHHHhhcCCCcEEEEEEEEcCC
Confidence 888887766654222334457999999999999999743 6788887766544
No 26
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=99.74 E-value=4.2e-17 Score=190.53 Aligned_cols=154 Identities=18% Similarity=0.305 Sum_probs=137.0
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcC--CCCCHH-HHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeE
Q 001564 887 QTALKRLKALAYTKRQIRNPLSGIIFSRKMMEG--TELGAE-QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1052)
Q Consensus 887 ~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~--~~l~~e-~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~ 962 (1052)
+..+.+..+++.+||||||||++|+|.++.|.. ..++++ +.+.+..|.+.+.+|.++|++ ||+.||++|.++++..
T Consensus 655 e~E~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~l~~~ 734 (890)
T COG2205 655 ERERLRSALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKLD 734 (890)
T ss_pred HHHHHHHHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCcccccc
Confidence 334557778999999999999999999999986 556665 788999999999999999999 7999999999999999
Q ss_pred EeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCCC
Q 001564 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQ 1042 (1052)
Q Consensus 963 ~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~~ 1042 (1052)
+..+.+++.+++..+......+. +.++++.++|- +.+|...|+|||.|||.||+||+|++..|.|.+....+
T Consensus 735 ~~~veEvVg~Al~r~~k~~~~~~--i~v~~~~dl~l--i~~D~~LieQVLiNLleNA~Kyap~~s~I~I~~~~~~~---- 806 (890)
T COG2205 735 WVLVEEVVGEALQRLRKRFTGHK--IVVSVPVDLPL--IHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVERE---- 806 (890)
T ss_pred hhhHHHHHHHHHHHhhhhcCCce--EEEecCCCCce--EecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEEEecc----
Confidence 99999999999998888776664 67778888875 99999999999999999999999999999999998887
Q ss_pred ceEEEEEEE
Q 001564 1043 SVHLAYLEL 1051 (1052)
Q Consensus 1043 ~~~~v~lev 1051 (1052)
.+.|+|
T Consensus 807 ---~v~~~V 812 (890)
T COG2205 807 ---NVVFSV 812 (890)
T ss_pred ---eEEEEE
Confidence 666665
No 27
>PRK09303 adaptive-response sensory kinase; Validated
Probab=99.71 E-value=3.5e-16 Score=181.46 Aligned_cols=147 Identities=19% Similarity=0.305 Sum_probs=131.6
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCC-------HHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcee
Q 001564 887 QTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELG-------AEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLD 958 (1052)
Q Consensus 887 ~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~-------~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~ 958 (1052)
+....+.+|++++||||||||++|.++++++.....+ +..+++++.+....++|.+++++ +++++.+.+...
T Consensus 146 e~~~~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~~ 225 (380)
T PRK09303 146 EQLKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEALR 225 (380)
T ss_pred HHHHHHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCce
Confidence 3345678899999999999999999999999853322 33678899999999999999999 799999999999
Q ss_pred eEeEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEE
Q 001564 959 LEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSL 1035 (1052)
Q Consensus 959 l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~ 1035 (1052)
+++.++++.+++.+++..+...+..+++.+.++++.++|. +++|+.+|.|||.|||.||+||++++|.|.|.+..
T Consensus 226 ~~~~~~~l~~ll~~~~~~~~~~~~~~~i~l~~~~~~~~~~--v~~d~~~l~qvl~NLl~NAik~~~~~~~I~i~~~~ 300 (380)
T PRK09303 226 FNPQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLPS--VYADQERIRQVLLNLLDNAIKYTPEGGTITLSMLH 300 (380)
T ss_pred eccccCCHHHHHHHHHHHHHHHHHHcCCEEEEEcCCCCCe--EEeCHHHHHHHHHHHHHHHHhcCCCCceEEEEEEe
Confidence 9999999999999999999999999999999999888775 99999999999999999999999988999888654
No 28
>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=99.71 E-value=2.3e-16 Score=205.94 Aligned_cols=155 Identities=27% Similarity=0.400 Sum_probs=143.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeE
Q 001564 882 QRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLE 960 (1052)
Q Consensus 882 q~~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~ 960 (1052)
+..+++..+.|..|++.|||||||||++|.|+++++.+..++++++++++.|..++++|..++++ +++++++.|...++
T Consensus 454 ~~~~~~~~~~~~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~~~~~~ 533 (968)
T TIGR02956 454 RAEAEEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGHLSIS 533 (968)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeee
Confidence 45667777889999999999999999999999999998888999999999999999999999999 79999999999999
Q ss_pred eEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 961 ~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+++|+|.+++++++..+...+..+++.+.++++++.| ..+.+|+.+|.|||.|||.||+||++ +|.|.|++....+
T Consensus 534 ~~~~~l~~ll~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~~~~d~~~l~~il~nLi~NAik~~~-~g~i~i~~~~~~~ 609 (968)
T TIGR02956 534 PRPFDLNALLDDVHHLMVSRAQLKGIQLRLNIPEQLP-NWWQGDGPRIRQVLINLVGNAIKFTD-RGSVVLRVSLNDD 609 (968)
T ss_pred ecccCHHHHHHHHHHHHHHHHHHcCcEEEEEeCCCCC-ceEeeCHHHHHHHHHHHHHHHHhhCC-CCeEEEEEEEcCC
Confidence 9999999999999999999999999999999987776 36899999999999999999999998 6888888876555
No 29
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=99.67 E-value=1.1e-15 Score=198.66 Aligned_cols=155 Identities=24% Similarity=0.374 Sum_probs=141.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeE
Q 001564 882 QRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLE 960 (1052)
Q Consensus 882 q~~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~ 960 (1052)
++.+++....+.+|++.++|||||||++|.++++++....++++++++++.+..++.+|..++++ +++++++.|.+.++
T Consensus 388 ~~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~ 467 (921)
T PRK15347 388 KQRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMTLS 467 (921)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccce
Confidence 34555666778899999999999999999999999999889999999999999999999999999 79999999999999
Q ss_pred eEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 961 ~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
.+++++.+++++++..+...+..+++.+.+.+++.+| ..+.+|+.+|+|||.|||.||+||++ +|.|.|++...++
T Consensus 468 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~d~~~l~~il~NLl~NAik~~~-~g~I~i~~~~~~~ 543 (921)
T PRK15347 468 LEETALLPLLDQAMLTIQGPAQSKSLTLRTFVGAHVP-LYLHLDSLRLRQILVNLLGNAVKFTE-TGGIRLRVKRHEQ 543 (921)
T ss_pred ecccCHHHHHHHHHHHHHHHHHHCCcEEEEEECCCCC-ceEEECHHHHHHHHHHHHHHHhhcCC-CCCEEEEEEEcCC
Confidence 9999999999999999999999999999998888776 47899999999999999999999998 6778888876554
No 30
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=99.67 E-value=1.5e-15 Score=197.39 Aligned_cols=164 Identities=23% Similarity=0.364 Sum_probs=144.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeE
Q 001564 884 LSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1052)
Q Consensus 884 ~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~ 962 (1052)
.+++..+.|.+|++.+||||||||++|.|+++++....++++++++++.+.++++++..+|++ +++++++.|+..++..
T Consensus 285 ~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~~ 364 (919)
T PRK11107 285 RAQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKLVLENI 364 (919)
T ss_pred HHHHHHHHHHHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEEe
Confidence 445556678899999999999999999999999988888899999999999999999999999 7999999999999999
Q ss_pred EeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCCC
Q 001564 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQ 1042 (1052)
Q Consensus 963 ~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~~ 1042 (1052)
++++.+++++++..+...+..+++.+.+++++++|. .+.+|+.+|.|||.||+.||+||++ +|.|.|++..... .+
T Consensus 365 ~~~l~~~l~~~~~~~~~~~~~~~i~~~~~~~~~~~~-~~~~d~~~l~~vl~NLl~NAik~~~-~g~v~i~v~~~~~--~~ 440 (919)
T PRK11107 365 PFSLRETLDEVVTLLAHSAHEKGLELTLNIDPDVPD-NVIGDPLRLQQIITNLVGNAIKFTE-SGNIDILVELRAL--SN 440 (919)
T ss_pred ecCHHHHHHHHHHHHHHHHHHcCCEEEEEeCCCCCc-eEEeCHHHHHHHHHHHHHHHhhcCC-CCcEEEEEEEEec--CC
Confidence 999999999999999999999999999999887764 6899999999999999999999998 5677777766544 33
Q ss_pred ceEEEEEEE
Q 001564 1043 SVHLAYLEL 1051 (1052)
Q Consensus 1043 ~~~~v~lev 1051 (1052)
+...+.|+|
T Consensus 441 ~~~~~~i~V 449 (919)
T PRK11107 441 TKVQLEVQI 449 (919)
T ss_pred CeeEEEEEE
Confidence 444555655
No 31
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=99.66 E-value=1.5e-13 Score=156.58 Aligned_cols=146 Identities=14% Similarity=0.169 Sum_probs=123.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHH---HcCCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCceeeEeEEeeHHHH
Q 001564 894 KALAYTKRQIRNPLSGIIFSRKM---MEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEV 969 (1052)
Q Consensus 894 ~~la~isHEirnPL~~I~g~~~l---L~~~~l~~e~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l~~~~~dL~~l 969 (1052)
++.+.++||||+||++|..+++- |.+....++....+..|..-.+||.+|...| .|++- -.-...++.+.++
T Consensus 386 QmSA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FArk----~~~a~~~v~l~~a 461 (603)
T COG4191 386 QMSAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFARK----SRDAAGPVSLREA 461 (603)
T ss_pred HHHHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhcc----CccccCCccHHHH
Confidence 34678899999999999976554 4456677889999999999999999999997 88883 3334789999999
Q ss_pred HHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCC--CCeEEEEEEEccCcCCCceEEE
Q 001564 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLA 1047 (1052)
Q Consensus 970 i~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~v 1047 (1052)
|++++..+...++..++.+..+.++.. ..|.+++.+|+|||.|||.||++++.. .++|.|++...++ .|
T Consensus 462 i~~Al~ll~~R~~~~~~~l~~~~~~~~--~~V~~~~iRLeQVLvNLl~NALDA~~~~~~~~i~i~~~~~~~-------~v 532 (603)
T COG4191 462 IEGALELLRGRLRAAGVELELDLPDAP--LWVMANEIRLEQVLVNLLQNALDAMAGQEDRRLSIRAQREGG-------QV 532 (603)
T ss_pred HHHHHHHHHHhhhccCceeeccCCCCC--ceeecchhhHHHHHHHHHHHHHHHhcCCCCCeeEEEEEecCC-------eE
Confidence 999999999999999999999888753 469999999999999999999999864 6788888777666 46
Q ss_pred EEEEC
Q 001564 1048 YLELR 1052 (1052)
Q Consensus 1048 ~levr 1052 (1052)
.+.||
T Consensus 533 ~l~Vr 537 (603)
T COG4191 533 VLTVR 537 (603)
T ss_pred EEEEc
Confidence 66665
No 32
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=99.64 E-value=5.4e-15 Score=191.82 Aligned_cols=153 Identities=22% Similarity=0.364 Sum_probs=137.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccC--ceeeE
Q 001564 884 LSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDG--YLDLE 960 (1052)
Q Consensus 884 ~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g--~~~l~ 960 (1052)
..++..+.|..|++.|||||||||++|.++++++.....+++++++++.+..+++++..++++ +++++++.| ...++
T Consensus 436 ~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~~~~~~~~ 515 (914)
T PRK11466 436 EAEKASQAKSAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVSVS 515 (914)
T ss_pred HHHHHHHHHHHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcceec
Confidence 344556678889999999999999999999999998888889999999999999999999999 799999987 45677
Q ss_pred eEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 961 ~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
.+++++.+++++++..+...+..+++.+.+++++.+| ..+.+|+.+|.|||.|||.||+||++ +|.|.|++....+
T Consensus 516 ~~~~~l~~ll~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~v~~d~~~l~qil~NLl~NAik~~~-~g~I~i~~~~~~~ 591 (914)
T PRK11466 516 DEPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDLP-TALMGDPRRIRQVITNLLSNALRFTD-EGSIVLRSRTDGE 591 (914)
T ss_pred ccccCHHHHHHHHHHHHHHHHHhCCcEEEEEeCCCCC-ceEEECHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEcCC
Confidence 8999999999999999999999999999999988776 37999999999999999999999998 6889988776544
No 33
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=99.64 E-value=2.9e-13 Score=165.29 Aligned_cols=275 Identities=13% Similarity=0.137 Sum_probs=176.9
Q ss_pred EEEEeecCCCCEEEEEEEEEccchhhHhH--------------------------------------HHHHHHHHHHHHH
Q 001564 710 NACASRDLHDNVVGVCFVAQDITPQKTVM--------------------------------------DKFTRIEGDYKAI 751 (1052)
Q Consensus 710 ~~~pi~d~~G~v~gvv~i~~DITerk~aE--------------------------------------~~L~~se~~lr~i 751 (1052)
.+.|+++.+|.++|++.+...+.+..... .++......++.+
T Consensus 148 ~a~PI~~~~g~~iGvi~v~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~~e~~~~~~~~~~~~~i 227 (545)
T PRK15053 148 AKTPIFDDDGKVIGVVSIGYLVSKIDSWRLEFLLPMAGVFVVLLGILMLLSWFFAAHIRRQMMGMEPKQIARVVRQQEAL 227 (545)
T ss_pred EEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 77999999999999987766444332211 1122233456778
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCCh--HHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCC
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKR--EEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD 829 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~--eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~ 829 (1052)
+++.+ +|++.+|.+|+|+++|+++++++|++. ++++|+.+. ++++. ... +. .... ..
T Consensus 228 l~~~~---egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~-~~~~~----------~~~--~~----~~~~-~~ 286 (545)
T PRK15053 228 FSSVY---EGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIA-EVVRP----------ADF--FT----EQID-EK 286 (545)
T ss_pred HHHhC---ceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHH-HhCCC----------chh--hh----hhcC-Cc
Confidence 89988 888999999999999999999999975 568898853 33322 100 00 0111 11
Q ss_pred cceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 001564 830 PEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSG 909 (1052)
Q Consensus 830 ~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~~ 909 (1052)
..... ...+|. .+.....|+.. +|.+.|.+.+++|+|+..+.+.++..... ..+.+..++||++|||++
T Consensus 287 ~~~~~---~~~~~~--~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~-----~~e~l~~~~he~~n~L~~ 355 (545)
T PRK15053 287 RQDVV---ANFNGL--SVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQ-----YVESLRTLRHEHLNWMST 355 (545)
T ss_pred ccceE---EEECCE--EEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhhhHHH
Confidence 11111 223443 34456667664 56778999999999988766544433222 224567789999999999
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEE
Q 001564 910 IIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRI 988 (1052)
Q Consensus 910 I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l 988 (1052)
|.++.++-. ..+.++.+...+..+..+++++ .+-+ ...+ ...+......+.++++.+
T Consensus 356 i~g~l~~~~-------~~~~~~~i~~~s~~~~~l~~~l~~~~~--------------~~~~-~~~l~~~~~~~~~~~i~~ 413 (545)
T PRK15053 356 LNGLLQMKE-------YDRVLEMVQGESQAQQQLIDSLREAFA--------------DRQV-AGLLFGKVQRARELGLKM 413 (545)
T ss_pred HHHHHhhch-------hhHHHHHHHHHHHHHHHHHHHHHHhcc--------------cHHH-HHHHHHHHHHHHHhCCce
Confidence 999877532 2346677777777788887773 3211 0111 122212233455677887
Q ss_pred EeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhcc---CC-CCeEEEEEEEccC
Q 001564 989 VNETAEQIMSETLYGDSIRLQQVLADFLSISINFV---PN-GGQLMVSSSLTKD 1038 (1052)
Q Consensus 989 ~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~---~~-~g~I~I~v~~~~~ 1038 (1052)
.+.....+..+...+|+..|.|||.||+.||+||. ++ ++.|.|++....+
T Consensus 414 ~~~~~~~~~~l~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~~~i~i~~~~~~~ 467 (545)
T PRK15053 414 VIVPGSQLSQLPPGLDSTEFAAIVGNLLDNAFEASLRSDEGNKIVELFLSDEGD 467 (545)
T ss_pred EEcCCCccccccccCCHHHHHHHHHHHHHHHHHHHhhCCCCCceEEEEEEECCC
Confidence 77655443333357799999999999999999995 33 3677777665444
No 34
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=99.54 E-value=1.8e-12 Score=147.21 Aligned_cols=284 Identities=16% Similarity=0.188 Sum_probs=195.3
Q ss_pred EEEEeecCCCCEEEEEEEEEccchhhHhHH--------------------------------------HHHHHHHHHHHH
Q 001564 710 NACASRDLHDNVVGVCFVAQDITPQKTVMD--------------------------------------KFTRIEGDYKAI 751 (1052)
Q Consensus 710 ~~~pi~d~~G~v~gvv~i~~DITerk~aE~--------------------------------------~L~~se~~lr~i 751 (1052)
...|++|++|+++|++.+.--+++-...-. ++...-+...++
T Consensus 141 ~~~PI~d~~g~~IGvVsVG~~l~~i~~~i~~~~~~l~~~~vl~lligl~ga~~la~~ikr~~~glEP~EIa~l~~er~A~ 220 (537)
T COG3290 141 AKVPIFDEDGKQIGVVSVGYLLSEIDDVILEFLRPLALIVVLGLLIGLLGAWILARHIKRQMLGLEPEEIATLLEERQAM 220 (537)
T ss_pred eecceECCCCCEEEEEEEeeEhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 457999999999999998765554332221 123333455688
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCChH--HHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCC
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKRE--EVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD 829 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~e--eliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~ 829 (1052)
++++. +|++.+|..|.++.+|.++++++|+... +.+|+++. ++++ |+. .+...++ .++.
T Consensus 221 l~si~---EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~-~v~~----------p~~--~l~~vl~---~~~~ 281 (537)
T COG3290 221 LQSIK---EGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIV-EVLP----------PDS--DLPEVLE---TGKP 281 (537)
T ss_pred HHHhh---ceEEEECCCCeEeehhHHHHHHhcccCcCcccccccce-Eeec----------ccc--CcHHHHh---cCCc
Confidence 89988 8999999999999999999999999865 68888863 2222 110 0111111 2222
Q ss_pred cceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 001564 830 PEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSG 909 (1052)
Q Consensus 830 ~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~~ 909 (1052)
....++ +-+|. ++.++..|+. .+|+++|.+.++||-|+-++..++|.... .-.+.+...+||+.|-|++
T Consensus 282 ~~~~e~---~~ng~--~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~vr-----~ya~aLRaq~HEfmNkLht 350 (537)
T COG3290 282 QHDEEI---RINGR--LLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGVR-----QYAEALRAQSHEFMNKLHT 350 (537)
T ss_pred ccchhh---hcCCe--EEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHHH-----HHHHHHHHhhHHHHHHHHH
Confidence 223332 23343 4556677775 67899999999999998776664443322 2234467789999999999
Q ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEEE
Q 001564 910 IIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIV 989 (1052)
Q Consensus 910 I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~ 989 (1052)
|.|++++-+- ++..+|+..+.+..+.....+.. ++.+ .++...+---...+++.|+++.
T Consensus 351 I~GLlql~~y----d~a~~~I~~~~~~qq~~~~~l~~----~i~~-------------~~lAg~LlgK~~rArElgv~l~ 409 (537)
T COG3290 351 ILGLLQLGEY----DDALDYIQQESEEQQELIDSLSE----KIKD-------------PVLAGFLLGKISRARELGVSLI 409 (537)
T ss_pred HHHHHhhccH----HHHHHHHHHHHhhhhhhHHHHHH----hccc-------------HHHHHHHHhHHHHHHHcCceEE
Confidence 9999997532 44555665554433333333211 1111 4455555556667889999999
Q ss_pred eeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccC---CCCeEEEEEEEccCcCCCceEEEEEEE
Q 001564 990 NETAEQIMSETLYGDSIRLQQVLADFLSISINFVP---NGGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1052)
Q Consensus 990 ~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~---~~g~I~I~v~~~~~~~~~~~~~v~lev 1051 (1052)
++....+|...-..++..+--|+-|||.||+++.- ++++|.+.++..++ .+++||
T Consensus 410 Id~~S~l~~~p~~~~~~~litIlGNLidNA~eA~~~~~~~k~I~l~i~~~~~-------~lvieV 467 (537)
T COG3290 410 IDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSDRGD-------ELVIEV 467 (537)
T ss_pred EcCCCcCCCCCCccChHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEecCC-------EEEEEE
Confidence 99988888766677899999999999999999976 46788888888777 777776
No 35
>PRK10490 sensor protein KdpD; Provisional
Probab=99.54 E-value=1.5e-13 Score=174.72 Aligned_cols=147 Identities=16% Similarity=0.222 Sum_probs=124.5
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEe
Q 001564 888 TALKRLKALAYTKRQIRNPLSGIIFSRKMMEGT--ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1052)
Q Consensus 888 ~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~--~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~ 964 (1052)
..+.+..+++.++|||||||++|.++++++... ....+..+.++.+.+...++.+++++ +++++++.|...+++.++
T Consensus 660 ~e~lr~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~~~l~~~~~ 739 (895)
T PRK10490 660 REQLRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFNLRKEWL 739 (895)
T ss_pred HHHHHHHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccc
Confidence 344567899999999999999999999988642 22233456788888999999999999 799999999999999999
Q ss_pred eHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++.+++++++..+......+++.+ ++++++|. +.+|+..|.|||.|||.||+||+++++.|.|++....+
T Consensus 740 ~L~eli~~~l~~l~~~~~~~~i~l--~~~~~~~~--v~~D~~~L~qVL~NLL~NAik~s~~g~~I~I~~~~~~~ 809 (895)
T PRK10490 740 TLEEVVGSALQMLEPGLSGHPINL--SLPEPLTL--IHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGE 809 (895)
T ss_pred CHHHHHHHHHHHHHHHhcCCCEEE--EcCCCCeE--EEECHHHHHHHHHHHHHHHHHhCCCCCeEEEEEEEeCC
Confidence 999999999999998887766655 45666654 99999999999999999999999988899998876555
No 36
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=99.54 E-value=1.3e-12 Score=166.64 Aligned_cols=139 Identities=15% Similarity=0.150 Sum_probs=118.7
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEG-TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~-~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
....|++.++|||||||++|.++++++.. ...+++..++++.+...++++..++++ +++++... ....++++.+
T Consensus 449 ~l~~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~~~----~~~~~~~l~~ 524 (828)
T PRK13837 449 AVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRKGE----RNTKPFDLSE 524 (828)
T ss_pred HHHHHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC----CCCcEEcHHH
Confidence 44578999999999999999999998765 344557788999999999999999999 69998544 3567899999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEc
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLT 1036 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~ 1036 (1052)
++++++..+.... .+++.+.++.++..+ .+.+|+.+|.|||.||+.||+||++++|.|.|++...
T Consensus 525 ll~~~~~~~~~~~-~~~i~l~~~~~~~~~--~v~~d~~~L~qvl~NLl~NAik~~~~~g~I~I~~~~~ 589 (828)
T PRK13837 525 LVTEIAPLLRVSL-PPGVELDFDQDQEPA--VVEGNPAELQQVLMNLCSNAAQAMDGAGRVDISLSRA 589 (828)
T ss_pred HHHHHHHHHHHHc-cCCcEEEEEeCCCCc--eEEECHHHHHHHHHHHHHHHHHHcccCCeEEEEEEEe
Confidence 9999999888654 457888888776644 5999999999999999999999999889999988775
No 37
>PRK10364 sensor protein ZraS; Provisional
Probab=99.47 E-value=2e-12 Score=154.29 Aligned_cols=142 Identities=23% Similarity=0.282 Sum_probs=122.8
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEG-TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~-~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
...++.+.++||+||||++|.++++++.+ ....++..++++.+.+..+++..++++ +++++. ......++++.+
T Consensus 236 ~~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~----~~~~~~~~~l~~ 311 (457)
T PRK10364 236 ALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKP----THLALQAVDLND 311 (457)
T ss_pred HHHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCc----CCCcceEecHHH
Confidence 34467889999999999999999999876 344456778889999999999999999 688873 345678899999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+++.++..+...+.++++.+.++.++..+. +.+|+.+|.|++.|||.||+||+++++.|.|++...++
T Consensus 312 ~l~~~~~~~~~~~~~~~i~l~~~~~~~~~~--~~~d~~~l~~il~NLl~NA~k~~~~~~~I~i~~~~~~~ 379 (457)
T PRK10364 312 LINHSLQLVSQDANSREIQLRFTANDTLPE--IQADPDRLTQVLLNLYLNAIQAIGQHGVISVTASESGA 379 (457)
T ss_pred HHHHHHHHHHHHHHhcCeEEEEEcCCCCce--EEECHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEEeCC
Confidence 999999999999999999999998877664 88999999999999999999999878899998887655
No 38
>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=99.44 E-value=8e-13 Score=123.95 Aligned_cols=110 Identities=25% Similarity=0.310 Sum_probs=98.3
Q ss_pred HHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccC
Q 001564 622 IETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKIN 701 (1052)
Q Consensus 622 le~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~d 701 (1052)
++++|++++++|.+|+|+++|+++.+++|++.++++|+++.+++++...+.+...+.+++.++.......... .+
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ 75 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILL-----RD 75 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEEC-----TT
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEe-----ec
Confidence 5899999999999999999999999999999999999999999999899999999999998886544333222 27
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEEEccchhhH
Q 001564 702 DDPITLIVNACASRDLHDNVVGVCFVAQDITPQKT 736 (1052)
Q Consensus 702 g~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~ 736 (1052)
|+.+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 76 ~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 76 GEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp SCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred CCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 99999999999999999999999999999999985
No 39
>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=99.41 E-value=1.9e-12 Score=119.89 Aligned_cols=104 Identities=20% Similarity=0.256 Sum_probs=89.5
Q ss_pred CceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceE
Q 001564 626 TVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPI 705 (1052)
Q Consensus 626 ~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~ 705 (1052)
|+|++++|.+|+|+++|+++++++|++.++++|+++.+++++.........+.+++.++.....++.+. +++|..+
T Consensus 1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~----~~~g~~~ 76 (104)
T PF13426_consen 1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLR----RKDGETF 76 (104)
T ss_dssp -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEE----ETTSEEE
T ss_pred CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEE----cCCCCEE
Confidence 789999999999999999999999999999999999999988877777788888887665544444443 7789999
Q ss_pred EEEEEEEEeecCCCCEEEEEEEEEccch
Q 001564 706 TLIVNACASRDLHDNVVGVCFVAQDITP 733 (1052)
Q Consensus 706 ~v~v~~~pi~d~~G~v~gvv~i~~DITe 733 (1052)
|+.++..|+.+.+|++.+++++++|||+
T Consensus 77 ~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 77 WVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 9999999999999999999999999996
No 40
>PRK10815 sensor protein PhoQ; Provisional
Probab=99.39 E-value=8.8e-12 Score=149.09 Aligned_cols=141 Identities=13% Similarity=0.152 Sum_probs=115.1
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~~~-l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
...+|++.++|||||||+.|.++++.+.... .+.+ +....+.+...++.+++++ ++.++..++...+..+.+++..
T Consensus 265 ~~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~~--~~~~~~~~~i~ri~~~i~~ll~~~~~~~~~~~~~~~~~~l~~ 342 (485)
T PRK10815 265 KYRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSVE--QAEPIMLEQISRISQQIGYYLHRASMRSEHNLLSRELHSVAP 342 (485)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccceecHHH
Confidence 3446899999999999999999999987643 3332 3334556667888899988 6888888888888889999999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++++..+...+..+++.+.+++++++ .+.+|+..|.+|+.||+.||+||++. .|.|++...++
T Consensus 343 ll~~~~~~l~~~~~~~~i~i~~~~~~~~---~v~~d~~~l~~vl~NLi~NAik~~~~--~i~I~~~~~~~ 407 (485)
T PRK10815 343 LLDNLTSALNKVYQRKGVNITLDISPEI---TFVGEKNDFMEVMGNVLDNACKYCLE--FVEISARQTDE 407 (485)
T ss_pred HHHHHHHHHHHHHHHCCcEEEEecCCCc---EEEeCHHHHHHHHHHHHHHHHHhcCC--cEEEEEEEeCC
Confidence 9999999999999999999999887653 48899999999999999999999973 45555555433
No 41
>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=99.39 E-value=3.9e-12 Score=119.91 Aligned_cols=112 Identities=23% Similarity=0.353 Sum_probs=93.5
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCc-cceEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-EQNIQFEIK 694 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~-~~~~e~~~~ 694 (1052)
++|+.+++++++|++++|.+|+|+++|++++++||++.++++|+++.+++++++.......+...+.... .........
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFR 80 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEE
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEE
Confidence 4789999999999999999999999999999999999999999999999988876656666666654443 333333333
Q ss_pred EeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEcc
Q 001564 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDI 731 (1052)
Q Consensus 695 ~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DI 731 (1052)
. ++|+.+|+.+...|+++.+|++.|++++++||
T Consensus 81 ~----~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 81 L----RDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp E----TTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred e----cCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 2 68999999999999999999999999999997
No 42
>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=99.38 E-value=1.8e-11 Score=152.31 Aligned_cols=145 Identities=19% Similarity=0.250 Sum_probs=126.8
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
.....+.+.++||+||||+.|.+.++.+.....+++..++++.+.+.++++..++++ +++++++.+....+.+++++.+
T Consensus 483 ~~l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~~~~~~~~~~~dl~~ 562 (703)
T TIGR03785 483 HYLENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQAIQSAEVEDFDLSE 562 (703)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccceeecHHH
Confidence 344567889999999999999999999988777888888999999999999999999 5899988877778889999999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++++..+......+++.+.++.++ ..+.+|+..|.|||.|||.||+||+++++.|.|++...++
T Consensus 563 ll~~~i~~~~~~~~~~~i~l~i~~~~----~~i~~d~~~L~~il~NLI~NAik~s~~~~~I~I~~~~~~~ 628 (703)
T TIGR03785 563 VLSGCMQGYQMTYPPQRFELNIPETP----LVMRGSPELIAQMLDKLVDNAREFSPEDGLIEVGLSQNKS 628 (703)
T ss_pred HHHHHHHHHHHHhhcCCEEEEecCCC----eEEEECHHHHHHHHHHHHHHHHHHCCCCCeEEEEEEEcCC
Confidence 99999999999888887777765332 3589999999999999999999999988889888776554
No 43
>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=99.37 E-value=4.3e-12 Score=127.00 Aligned_cols=153 Identities=20% Similarity=0.168 Sum_probs=114.7
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCc
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 297 (1052)
|++++++.+++++++++|+||+++|.+++++..-...-.....-.+..+..++.. -+ ...+....+..-.|.|+...|
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~i~d~~~~~ 78 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMD-ES-ICGQVLQSREPIVISDVAADP 78 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETT-SS-HHHHHHHHTSCEEESSSGGST
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccccccccccc-cc-HHHHHHhCCCeEeeccccccc
Confidence 6899999999999999999999999999998776443333222121122222111 11 255666777777888887765
Q ss_pred cceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCC-CCCC
Q 001564 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP-RFVP 376 (1052)
Q Consensus 298 ~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~ 376 (1052)
- ..+.......++..++++.+|+..+|+++.|++||..+ |++||.|+++++.| |.|+
T Consensus 79 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~--------------g~~~G~l~l~~~~~~~~~~ 136 (154)
T PF01590_consen 79 R--------FAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISG--------------GRLIGVLSLYRTRPGRPFT 136 (154)
T ss_dssp T--------SSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEET--------------TEEEEEEEEEEESSSSS--
T ss_pred c--------ccccccccccccccccccccccccccCceeeEeeeecc--------------cCcEEEEEEEECCCCCCcC
Confidence 2 12233344566789999999999999999999999877 99999999999987 9999
Q ss_pred chhHHHHHHHHHHHHHHH
Q 001564 377 FPLRYACEFLAQVFAIHV 394 (1052)
Q Consensus 377 ~~~r~~~~~l~~~~~~~l 394 (1052)
..++.+++.+++++++.|
T Consensus 137 ~~d~~ll~~~a~~~a~ai 154 (154)
T PF01590_consen 137 EEDLALLESFAQQLAIAI 154 (154)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhC
Confidence 999999999999988765
No 44
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=99.35 E-value=2e-11 Score=146.05 Aligned_cols=146 Identities=18% Similarity=0.251 Sum_probs=125.3
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHH
Q 001564 889 ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1052)
Q Consensus 889 ~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~ 967 (1052)
...+.++++.++||++|||+.|.+.++.+.... .+...+.+..+.....++.+++++ +++++.+.+...+...++++.
T Consensus 237 ~~~~~~~~~~~shel~~pL~~i~~~~~~l~~~~-~~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~~~~~~~~~~~~ 315 (466)
T PRK10549 237 EQMRRDFMADISHELRTPLAVLRGELEAIQDGV-RKFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGALAYRKTPVDLV 315 (466)
T ss_pred HHHHHHHHHHHhHHhCChHHHHHHHHHHHHhcc-ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccCCCCHH
Confidence 345667899999999999999999999987632 222345677788888999999999 588888999999999999999
Q ss_pred HHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++.++..++..+..+++.+.+++++.. .+.+|+..|.||+.|||.||++|++++|.|.|.+....+
T Consensus 316 ~~l~~~~~~~~~~~~~~~i~i~~~~~~~~---~~~~d~~~l~qvl~nll~NAi~~~~~~~~I~i~~~~~~~ 383 (466)
T PRK10549 316 PLLEVAGGAFRERFASRGLTLQLSLPDSA---TVFGDPDRLMQLFNNLLENSLRYTDSGGSLHISAEQRDK 383 (466)
T ss_pred HHHHHHHHHHHHHHHHCCcEEEEecCCCc---EEEeCHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEEcCC
Confidence 99999999999999889999999887653 488999999999999999999999988999998877655
No 45
>PRK10604 sensor protein RstB; Provisional
Probab=99.33 E-value=3.2e-11 Score=142.77 Aligned_cols=138 Identities=14% Similarity=0.205 Sum_probs=113.5
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
..+.++++.++||+||||+.|.+.++++... +++..+ .+.+..++|..++++ +.+++++.+......+++++.+
T Consensus 210 ~~~~~l~~~vsHeLrtPL~~i~~~l~~l~~~--~~~~~~---~i~~~~~~l~~li~~ll~~~rl~~~~~~~~~~~~~l~~ 284 (433)
T PRK10604 210 ASKKQLIDGIAHELRTPLVRLRYRLEMSDNL--SAAESQ---ALNRDIGQLEALIEELLTYARLDRPQNELHLSEPDLPA 284 (433)
T ss_pred HHHHHHHHHhhHhhcChHHHHHHHHHHhcCC--CcHHHH---HHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCCCHHH
Confidence 4456789999999999999999999988742 222222 266778899999999 6999999998888999999999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++++..+......+++++.++.++ ..+.+|+..+.+|+.||++||+||+. |.|.|++...++
T Consensus 285 ~l~~~i~~~~~~~~~~~i~~~~~~~~----~~~~~d~~~l~~vl~NLl~NAik~~~--~~I~I~~~~~~~ 348 (433)
T PRK10604 285 WLSTHLADIQAVTPEKTVRLDTPHQG----DYGALDMRLMERVLDNLLNNALRYAH--SRVRVSLLLDGN 348 (433)
T ss_pred HHHHHHHHHHHHhhcCcEEEEecCCC----ceEecCHHHHHHHHHHHHHHHHHhCC--CeEEEEEEEECC
Confidence 99999999998887777777665332 24788999999999999999999985 778888776555
No 46
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=99.32 E-value=3.9e-11 Score=138.31 Aligned_cols=140 Identities=14% Similarity=0.217 Sum_probs=109.5
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeH-HHH
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTL-NEV 969 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL-~~l 969 (1052)
+..|++.++||+||||++|.+.++++.... .++. ..+.+..+++...+++ +++++.+.........++++ .++
T Consensus 137 ~~~~~~~~sHelrtPL~~i~~~~e~l~~~~-~~~~----~~~~~~~~~l~~~i~~ll~~~r~~~~~~~~~~~~~~l~~~~ 211 (356)
T PRK10755 137 ERLFTADVAHELRTPLAGIRLHLELLEKQH-HIDV----APLIARLDQMMHTVEQLLQLARAGQSFSSGHYQTVKLLEDV 211 (356)
T ss_pred HHHHHHHhhHhhcChHHHHHHHHHHHHhcc-chhH----HHHHHHHHHHHHHHHHHHHHHHcccccccccchhhhHHHHH
Confidence 346899999999999999999999886532 2222 2333445678888888 68888776655566678888 899
Q ss_pred HHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 970 i~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+..++..+......+++.+.++.++. ...+.+|+..|.+|+.||++||+||+++++.|.|++...++
T Consensus 212 i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~v~~d~~~l~~il~nLi~NA~k~~~~~~~I~I~~~~~~~ 278 (356)
T PRK10755 212 ILPSQDELSEMLEQRQQTLLLPESAA--DITVQGDATLLRLLLRNLVENAHRYSPEGSTITIKLSQEDG 278 (356)
T ss_pred HHHHHHHHHHHHHHhCCeEEeccCCC--ceEEEECHHHHHHHHHHHHHHHHhhCCCCCcEEEEEEEcCC
Confidence 99988889888888888888753333 24699999999999999999999999888889988766544
No 47
>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=99.31 E-value=4.6e-12 Score=117.37 Aligned_cols=103 Identities=20% Similarity=0.239 Sum_probs=87.7
Q ss_pred CCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEc
Q 001564 760 PPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFA 839 (1052)
Q Consensus 760 ~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~ 839 (1052)
+|++++|.+|+|+++|+++++++||++++++|+++. .+ ..++....+...+.+++.++..+..++.+.+
T Consensus 2 ~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~----------~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 70 (104)
T PF13426_consen 2 DGIFILDPDGRILYVNPAFERLFGYSREELIGKSIS-DF----------FPEEDRPEFEEQIERALEEGGSWSGEVRLRR 70 (104)
T ss_dssp SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGG-GG----------CSTTSCHHHHHHHHHHHHHTSSEEEEEEEEE
T ss_pred EEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcc-cc----------cCcccchhhHHHHHHHHhcCCceeEEEEEEc
Confidence 678999999999999999999999999999999863 33 3334445566677777777777888999999
Q ss_pred cCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHH
Q 001564 840 RNGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1052)
Q Consensus 840 ~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITe 873 (1052)
++|+.+|+.+++.|+.+.+|++.+++++++|||+
T Consensus 71 ~~g~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 71 KDGETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp TTSEEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred CCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 9999999999999999999999999999999996
No 48
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.31 E-value=5.2e-11 Score=151.78 Aligned_cols=142 Identities=17% Similarity=0.134 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcC
Q 001564 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1052)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g 683 (1052)
+.+.++++++.+++++.+++++|++|+++|.+|+|++||+++++++|++.++++|+++.++++++....+.......+.+
T Consensus 143 r~~~~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~ 222 (779)
T PRK11091 143 REETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRH 222 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhc
Confidence 34567788899999999999999999999999999999999999999999999999999999887777666666777766
Q ss_pred CccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHH
Q 001564 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYK 749 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr 749 (1052)
+.....+..+ ..++|..+|+.++..|+++.+|++.|++++++|||++|++++++++..+...
T Consensus 223 ~~~~~~e~~~----~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~~~~~ 284 (779)
T PRK11091 223 NVSLTYEQWL----DYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKASRDKT 284 (779)
T ss_pred CCCeEEEEEE----EcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHHHHHH
Confidence 6544444333 3678999999999999999999999999999999999999999877654333
No 49
>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=99.30 E-value=9.9e-12 Score=117.10 Aligned_cols=112 Identities=29% Similarity=0.349 Sum_probs=90.4
Q ss_pred HHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhh
Q 001564 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAM 825 (1052)
Q Consensus 746 ~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l 825 (1052)
++|+.++++++ +|++++|.+|+|+++|++++++|||++++++|+++. .+.++++.......+...+
T Consensus 1 e~~~~i~~~~~---~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~-----------~~~~~~~~~~~~~~~~~~~ 66 (113)
T PF00989_consen 1 ERYRAILENSP---DGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLF-----------DLIHPEDRRELRERLRQAL 66 (113)
T ss_dssp HHHHHHHHCSS---SEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGG-----------GGCSGGGHHHHHHHHHHHH
T ss_pred CHHHHHHhcCC---ceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHH-----------HhcCchhhHHHHHHHHHHH
Confidence 57999999999 889999999999999999999999999999999975 3444444334455555555
Q ss_pred cCCC-cceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHH
Q 001564 826 SGQD-PEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLA 871 (1052)
Q Consensus 826 ~g~~-~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DI 871 (1052)
.... ....+..+..++|+.+|+.+.+.|+.+.+|++.|++++++||
T Consensus 67 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 67 SQGESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp HHCCHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred HcCCCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 4443 345666666689999999999999999999999999999997
No 50
>PRK09835 sensor kinase CusS; Provisional
Probab=99.30 E-value=1.1e-10 Score=140.33 Aligned_cols=145 Identities=15% Similarity=0.208 Sum_probs=121.7
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHH
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGT-ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~~-~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~ 967 (1052)
..+.+|++.++|||||||+.|.+..+.+... ....+..+.+..+.+...++..++++ +++++.+.+...+...++++.
T Consensus 260 ~~~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~~~~~~~~~~~~l~ 339 (482)
T PRK09835 260 TRQSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADNNQLIPEKKMLDLA 339 (482)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCceeecHH
Confidence 3456789999999999999999988887653 33344566777777888999999999 699999888888888999999
Q ss_pred HHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++.++..+.....++++.+.++.+ . ..+.+|+..|.+|+.||+.||+||+++++.|.|++....+
T Consensus 340 ~~i~~~~~~~~~~~~~~~~~~~~~~~--~--~~v~~d~~~l~~vl~nll~Na~~~~~~~~~I~i~~~~~~~ 406 (482)
T PRK09835 340 DEVGKVFDFFEAWAEERGVELRFVGD--P--CQVAGDPLMLRRAISNLLSNALRYTPAGEAITVRCQEVDH 406 (482)
T ss_pred HHHHHHHHHHHHHHhhCCEEEEEeCC--C--cEEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEeCC
Confidence 99999999999988888888877632 2 2489999999999999999999999888889888776554
No 51
>PRK10337 sensor protein QseC; Provisional
Probab=99.29 E-value=7.2e-11 Score=140.59 Aligned_cols=140 Identities=14% Similarity=0.236 Sum_probs=120.7
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHH
Q 001564 893 LKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE-QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVL 970 (1052)
Q Consensus 893 ~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e-~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li 970 (1052)
.+|++.++||+||||+.+.+..+.+.....+++ ...+++.+...++++..++++ +.+++++.+......+++++.+++
T Consensus 238 ~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~~~~~~~~~~~~l~~~~ 317 (449)
T PRK10337 238 RRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDSLDNLQDVAEIPLEDLL 317 (449)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcccCHHHHH
Confidence 468999999999999999999888765444443 567889999999999999999 699999887666678899999999
Q ss_pred HHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEE
Q 001564 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSS 1034 (1052)
Q Consensus 971 ~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~ 1034 (1052)
++++..+...+..+++.+.++.++..+ .+.+|+..|.+++.||+.||+||+++++.|.|++.
T Consensus 318 ~~~~~~~~~~~~~~~i~~~~~~~~~~~--~~~~~~~~l~~vl~Nli~NA~k~~~~~~~i~i~~~ 379 (449)
T PRK10337 318 QSAVMDIYHTAQQAGIDVRLTLNAHPV--IRTGQPLLLSLLVRNLLDNAIRYSPQGSVVDVTLN 379 (449)
T ss_pred HHHHHHHHHHHHHcCCEEEEecCCCCc--eeecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEE
Confidence 999999999999999999998876533 47999999999999999999999998888888654
No 52
>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=99.29 E-value=9e-11 Score=139.93 Aligned_cols=143 Identities=21% Similarity=0.324 Sum_probs=122.0
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGT-ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~~-~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
....+.+.++||+||||+.+.+..+.+... ...++..++++.+.....++.+++++ +++++++.+...+..+++++.+
T Consensus 240 ~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~~~~~~~~~~~~~ 319 (457)
T TIGR01386 240 RLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQLALERVRLDLAA 319 (457)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCHHH
Confidence 344678899999999999999999887643 33445667888888889999999999 7999999988888999999999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++++..+.....++++++.++.+ ..+.+|+..|.+++.|||.||+||++.++.|.|++...++
T Consensus 320 ~~~~~~~~~~~~~~~~~i~~~~~~~-----~~~~~~~~~l~~~~~nll~Nai~~~~~~~~I~i~~~~~~~ 384 (457)
T TIGR01386 320 ELAKVAEYFEPLAEERGVRIRVEGE-----GLVRGDPQMFRRAISNLLSNALRHTPDGGTITVRIERRSD 384 (457)
T ss_pred HHHHHHHHHHHHHHhCCeEEEecCC-----ceEEECHHHHHHHHHHHHHHHHHcCCCCceEEEEEEecCC
Confidence 9999999999888888888776532 2489999999999999999999999878899988877554
No 53
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=99.26 E-value=2e-10 Score=137.68 Aligned_cols=143 Identities=17% Similarity=0.294 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHH
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVL 970 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li 970 (1052)
..++++.++||+|||++.+.+.++++......++..++++.+....+++..++++ +.+++++.+.......++++.+++
T Consensus 256 ~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~ 335 (475)
T PRK11100 256 VEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQRQELEVLEPVALAALL 335 (475)
T ss_pred HHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCccceeccHHHHH
Confidence 4467899999999999999999999987555667888999999999999999999 699998887777788999999999
Q ss_pred HHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 971 ~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+.++..+......+++++.++.+ + ..+.+|...|.+||.||+.||+||+++++.|.|++...++
T Consensus 336 ~~~~~~~~~~~~~~~i~~~~~~~-~---~~~~~~~~~l~~vl~nli~Na~~~~~~~~~i~i~~~~~~~ 399 (475)
T PRK11100 336 EELVEAREAQAAAKGITLRLRPD-D---ARVLGDPFLLRQALGNLLDNAIDFSPEGGTITLSAEVDGE 399 (475)
T ss_pred HHHHHHHHHHHHhCCceEEEeCC-C---ceEEECHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEEcCC
Confidence 99999999999999999998866 2 3589999999999999999999999878899998876555
No 54
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=99.23 E-value=2.4e-10 Score=125.06 Aligned_cols=134 Identities=14% Similarity=0.202 Sum_probs=109.5
Q ss_pred HHHHHHHhhhHHHHHHHHH---HHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCceeeEeEEeeHHHHHH
Q 001564 896 LAYTKRQIRNPLSGIIFSR---KMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLV 971 (1052)
Q Consensus 896 la~isHEirnPL~~I~g~~---~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l~~~~~dL~~li~ 971 (1052)
+..+||||++||++++.++ .+..+...+.....++++|..-.+|+.+||+.| .|+|-.++.- ...|++|..++.
T Consensus 455 mTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~~--~lqpV~L~~~v~ 532 (673)
T COG4192 455 MTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDE--SLQPVRLNSVVE 532 (673)
T ss_pred HHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC--CcccccHHHHHH
Confidence 6678999999999999654 333345666778899999999999999999997 9999665543 358899999999
Q ss_pred HHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCC-CeEEEEEEE
Q 001564 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNG-GQLMVSSSL 1035 (1052)
Q Consensus 972 ~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~-g~I~I~v~~ 1035 (1052)
++...+....+.+.+++.... +.+ +|.||..+++|||.||+.||++++... .+|.|.+..
T Consensus 533 ~AweLl~~khk~rQ~~Li~pt--D~~--~V~gd~v~ieQVlvNl~~NaldA~~h~~p~i~~~~~~ 593 (673)
T COG4192 533 QAWELLQTKHKRRQIKLINPT--DDL--MVMGDAVSIEQVLVNLIVNALDASTHFAPWIKLIALG 593 (673)
T ss_pred HHHHHHHhhhhhccccccCCc--ccc--eecchhhhHHHHHHHHHHHHHhhhccCCceEEEEeec
Confidence 999999999988888877643 443 599999999999999999999997643 567666544
No 55
>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=99.21 E-value=2.1e-11 Score=114.30 Aligned_cols=110 Identities=21% Similarity=0.288 Sum_probs=94.0
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcc
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPE 831 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~ 831 (1052)
++++| .+++++|.+|+++++|+++.+++|++.++++|+++. +++ ++.....+...+.+++.++...
T Consensus 1 l~~~p---~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~-~~~----------~~~~~~~~~~~~~~~~~~~~~~ 66 (110)
T PF08448_consen 1 LDSSP---DGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLF-DLL----------PPEDREEFQAALRRALAGGEPV 66 (110)
T ss_dssp HHHCS---SEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHH-HHS----------CCGCHHHHHHHHHHHHHHTSEE
T ss_pred CCCCC---ceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccch-hcc----------ccchhhhhHHHHHHhhccCceE
Confidence 46677 788999999999999999999999999999999974 333 3456677888899999988777
Q ss_pred eeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHH
Q 001564 832 KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQ 876 (1052)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~ 876 (1052)
..+..... +|..+|+.++..|+.|.+|++.|++++++|||++|+
T Consensus 67 ~~~~~~~~-~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 67 FFEEILLR-DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp EEEEEECT-TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred EEEEEEee-cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 66655555 999999999999999999999999999999998874
No 56
>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=99.17 E-value=9.2e-10 Score=137.69 Aligned_cols=133 Identities=16% Similarity=0.236 Sum_probs=103.6
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHHHHHHHHHHhhc-cccccccCceeeEeEEeeHHHHH
Q 001564 893 LKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE-QKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVL 970 (1052)
Q Consensus 893 ~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e-~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l~~~~~dL~~li 970 (1052)
.++.+.++||+|||++.+....+..++...+++ ..++++.+.+..++|.++++++ +.. ...++.++++.+++
T Consensus 476 ~~~~a~i~HdLrn~l~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l~~~~------~~~~~~~~~l~~ll 549 (679)
T TIGR02916 476 NRMSAFVVHDLKNLVAQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQLRSKG------LEEEKLCVDLVDLL 549 (679)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc------cccCCccccHHHHH
Confidence 456788999999999999988887765444444 6678899999999999999885 222 24566889999999
Q ss_pred HHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 971 ~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++........ .+.+ +++++ ..+.+|+..|.||+.||+.||+||++++|.|+|++...++
T Consensus 550 ~~~~~~~~~~~~--~~~l--~~~~~---~~v~~d~~~l~~vl~nLl~NAik~~~~~~~I~I~~~~~~~ 610 (679)
T TIGR02916 550 RRAIASKRAQGP--RPEV--SIDTD---LSVRADRERLERVLGHLVQNALEATPGEGRVAIRVERECG 610 (679)
T ss_pred HHHHHHhhhhcC--CceE--EeCCC---ceEEECHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEEcCC
Confidence 999887664332 2333 33444 3499999999999999999999999988899999876554
No 57
>PRK10060 RNase II stability modulator; Provisional
Probab=99.13 E-value=1e-09 Score=136.59 Aligned_cols=168 Identities=14% Similarity=0.108 Sum_probs=123.6
Q ss_pred cCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHH
Q 001564 700 INDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMV 779 (1052)
Q Consensus 700 ~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~ 779 (1052)
.+|.+.|+.....++.+ ....|....+.|+++ ....+......++.++++++ ++|+++|.+|+|+++|++++
T Consensus 70 ~~g~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~~~~---~gI~i~D~~g~I~~~N~a~~ 141 (663)
T PRK10060 70 LDGEPLSVHLVGRKINK--REWAGTASAWHDTPS---VARDLSHGLSFAEQVVSEAN---SVIVILDSRGNIQRFNRLCE 141 (663)
T ss_pred eCCcEEEEEEeeeccCc--ccccchhhHHHHHHH---HHHHHHHHHHHHHHHHhhCC---ceEEEEeCCCCEEEEcHHHH
Confidence 36889998876655433 344455554455555 44455666778889999999 78899999999999999999
Q ss_pred HHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCC
Q 001564 780 KLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREG 859 (1052)
Q Consensus 780 ~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G 859 (1052)
+++||+.++++|+++.. ++ .++++...+...+...+..+..+..+.++.+++|+.+|+.....+ .+.+|
T Consensus 142 ~l~Gy~~~eliG~~~~~-l~---------~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~~-~~~~g 210 (663)
T PRK10060 142 EYTGLKEHDVIGQSVFK-LF---------MSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKFV-HSGSG 210 (663)
T ss_pred HHHCcCHHHHcCCCHHH-Hh---------CChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeEE-EcCCC
Confidence 99999999999998642 22 224444445556666667777788899999999999887665444 44444
Q ss_pred -CEEEEeeehHHHHHHHHHHHHHHHHHH
Q 001564 860 -AVTGVFCFLQLASHELQQALHVQRLSE 886 (1052)
Q Consensus 860 -~i~g~i~v~~DITerk~~e~elq~~ae 886 (1052)
...+++++.+|||++++.+.++++.+.
T Consensus 211 ~~~~~~i~~~~DITe~k~~e~~l~~~a~ 238 (663)
T PRK10060 211 KNEIFLICSGTDITEERRAQERLRILAN 238 (663)
T ss_pred CceEEEEEEEEechHHHHHHHHHHHHhh
Confidence 446688999999999988877666443
No 58
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=99.13 E-value=1.7e-09 Score=129.16 Aligned_cols=141 Identities=14% Similarity=0.237 Sum_probs=113.4
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHH
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~ 968 (1052)
..+.+|++.+|||+||||+.|.+..+++....... ..+..+....+++.+++++ +++++.+.. .....+.+++..
T Consensus 241 ~~~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~---~~~~~i~~~~~~l~~~i~~l~~~~~~~~~-~~~~~~~~~l~~ 316 (461)
T PRK09470 241 TSQQRLLSDISHELRTPLTRLQLATALLRRRQGES---KELERIETEAQRLDSMINDLLVLSRNQQK-NHLERETFKANS 316 (461)
T ss_pred HHHHHHHHhhhHhhCCHHHHHHHHHHHHhhccCCh---HHHHHHHHHHHHHHHHHHHHHHHHHhhcc-cccccceecHHH
Confidence 34456889999999999999999999887543322 2456677889999999999 688887653 456778999999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++++++..+.......++.+.++..++ ...+.+|+..|.+++.||+.||+||++ +.|.|++...++
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~i~~~~~--~~~~~~~~~~l~~~l~nli~NA~~~~~--~~i~i~~~~~~~ 382 (461)
T PRK09470 317 LWSEVLEDAKFEAEQMGKSLTVSAPPG--PWPINGNPNALASALENIVRNALRYSH--TKIEVAFSVDKD 382 (461)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEecCCc--ceEEEECHHHHHHHHHHHHHHHHHhCC--CcEEEEEEEECC
Confidence 999999988887778888888875444 246999999999999999999999986 457777665554
No 59
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=99.11 E-value=2.3e-09 Score=127.13 Aligned_cols=137 Identities=18% Similarity=0.167 Sum_probs=103.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEe
Q 001564 886 EQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1052)
Q Consensus 886 e~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~ 964 (1052)
++..+.+..|++.++|||||||+.|.+.++++... .....+.+.+..++|..++++ +++.+...+ ...+++
T Consensus 223 ~~~~~~~~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~~~---~~~~~~ 294 (435)
T PRK09467 223 KQLEDDRTLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTGQE---MPMEMA 294 (435)
T ss_pred HHHHHHHHHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhcccCC---CCcccc
Confidence 33445566789999999999999999888877432 233455677788899999999 688876543 356789
Q ss_pred eHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++.+++++++.... ..+..+.++++... ..+.+|+..|.+|+.||+.||+||+. |.|.|++....+
T Consensus 295 ~l~~~~~~~~~~~~----~~~~~i~~~~~~~~--~~~~~~~~~l~~il~NLl~NA~k~~~--~~i~i~~~~~~~ 360 (435)
T PRK09467 295 DLNALLGEVIAAES----GYEREIETALQPGP--IEVPMNPIAIKRALANLVVNAARYGN--GWIKVSSGTEGK 360 (435)
T ss_pred CHHHHHHHHHHHhh----hcCCeEEEecCCCC--ceEEECHHHHHHHHHHHHHHHHHhCC--CeEEEEEEecCC
Confidence 99999999887655 34455666665542 25999999999999999999999974 778887766544
No 60
>PRK13559 hypothetical protein; Provisional
Probab=99.08 E-value=1.8e-09 Score=124.78 Aligned_cols=133 Identities=11% Similarity=0.071 Sum_probs=106.1
Q ss_pred HHHHHHHHHHhCCceEEEEcC---CCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEE
Q 001564 614 VTSEMVRLIETATVPILAVDV---DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQ 690 (1052)
Q Consensus 614 ~~~~l~~lle~~~~~I~~~D~---dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e 690 (1052)
+.+.++.+++.++++++++|. +|.|++||+++++++||+.++++|+++..+.++.........+...+.++.....+
T Consensus 41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 120 (361)
T PRK13559 41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVE 120 (361)
T ss_pred hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEE
Confidence 456788899999999999997 66899999999999999999999999887766655555555666666655443333
Q ss_pred EEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKA 750 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ 750 (1052)
+. ..+++|..+|+.++..|+++.+|.+.+++++++|||++|++++..+..+..++.
T Consensus 121 ~~----~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~~~~~l~~~ 176 (361)
T PRK13559 121 LL----NYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEAHERRLARE 176 (361)
T ss_pred EE----EEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHHHHHHHHHH
Confidence 32 347789999999999999999999999999999999999988765554443333
No 61
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=99.05 E-value=5e-09 Score=125.52 Aligned_cols=139 Identities=9% Similarity=0.026 Sum_probs=104.6
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHH
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~~~-l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~ 967 (1052)
..+.++.+.++||++|||++|.+..+++++.. .+++.++..+.+.+.+.++.+.+++ ++..+- ...+++++.
T Consensus 300 ~~r~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~lr~------~~l~~~~L~ 373 (495)
T PRK11644 300 SVRRDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGRLRP------RQLDDLTLE 373 (495)
T ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhccCC------cccccCCHH
Confidence 34556778899999999999999999987633 3345667888898889999999998 554431 234578999
Q ss_pred HHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+.+++++..+.......++++..+.++. + ...+++..+.|++.|+++||+||++ .+.|.|++...++
T Consensus 374 ~~l~~l~~~l~~~~~~~~v~l~~~~~~~-~--l~~~~~~~L~ril~nlL~NAiKha~-~~~I~I~l~~~~~ 440 (495)
T PRK11644 374 QAIRSLMREMELEDRGIVSHLDWRIDES-A--LSETQRVTLFRVCQEGLNNIVKHAD-ASAVTLQGWQQDE 440 (495)
T ss_pred HHHHHHHHHHHHhhcCceEEEEecCCcc-c--CChhHHHHHHHHHHHHHHHHHHhCC-CCEEEEEEEEcCC
Confidence 9999999888765555555555544432 2 3567788899999999999999998 5788888766544
No 62
>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=99.02 E-value=6.5e-09 Score=101.14 Aligned_cols=140 Identities=29% Similarity=0.369 Sum_probs=110.7
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCc
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 297 (1052)
|++++++.+++.+.+++|+||+.||.++++..+........+...+..+..+|..+ ...+.++..+....+.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999888888777665554556677788776 4566777777777777766543
Q ss_pred cceeeCCCCCCcccccCccccCCChhHHHHHHhc-ccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecC-CCCCC
Q 001564 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENM-NSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNT-TPRFV 375 (1052)
Q Consensus 298 ~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nm-gv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~-~pr~~ 375 (1052)
.+ . ..+...+ |+++.+++||..+ |++||+|.+.++ .++.|
T Consensus 79 ~~-----------------------~-~~~~~~~~~~~s~~~~Pl~~~--------------~~~~G~l~~~~~~~~~~~ 120 (149)
T smart00065 79 VF-----------------------A-LDLLGRYQGVRSFLAVPLVAD--------------GELVGVLALHNKDSPRPF 120 (149)
T ss_pred cc-----------------------c-cccccceeceeeEEEeeeeec--------------CEEEEEEEEEecCCCCCC
Confidence 11 1 1122223 3899999999987 999999999998 79999
Q ss_pred CchhHHHHHHHHHHHHHHHHHH
Q 001564 376 PFPLRYACEFLAQVFAIHVNKE 397 (1052)
Q Consensus 376 ~~~~r~~~~~l~~~~~~~l~~~ 397 (1052)
+..++..++.++++++..+...
T Consensus 121 ~~~~~~~l~~~~~~i~~~l~~~ 142 (149)
T smart00065 121 TEEDEELLQALANQLAIALANA 142 (149)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999887654
No 63
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.01 E-value=3.7e-09 Score=132.37 Aligned_cols=136 Identities=17% Similarity=0.172 Sum_probs=113.5
Q ss_pred HHHHHHHhCCceEEEEc---CCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEE
Q 001564 617 EMVRLIETATVPILAVD---VDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEI 693 (1052)
Q Consensus 617 ~l~~lle~~~~~I~~~D---~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~ 693 (1052)
.++.+++.++.+++.+| .+|++++||+++++++||+.++++|+++..+.++.........+...+.++.....++..
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 228 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRN 228 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEE
Confidence 34678999999999998 479999999999999999999999999888877766555555566666555443333333
Q ss_pred EEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCC
Q 001564 694 KTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPN 756 (1052)
Q Consensus 694 ~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~ 756 (1052)
.+++|..+|+.++..|+++.+|.+.+++++++|||++|++|+++++.+..++.+++..+
T Consensus 229 ----~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~ 287 (665)
T PRK13558 229 ----YRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVE 287 (665)
T ss_pred ----ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 37899999999999999999999999999999999999999999998888888777654
No 64
>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=99.00 E-value=1.1e-09 Score=93.59 Aligned_cols=65 Identities=26% Similarity=0.431 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcC-CCCCHHH-HHHHHHHHHHHHHHHHHHhh-ccccccccC
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEG-TELGAEQ-KRLLHTSAQCQRQLHKILDD-SDLDSIIDG 955 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~-~~l~~e~-~~~l~~i~~~~~rl~~lI~d-Ld~srie~g 955 (1052)
.|.+|++.++|||||||++|.++++++.+ ...++++ +++++.+..+++++..++++ ++|+++++|
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 36789999999999999999999999999 8888887 99999999999999999999 799999887
No 65
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.00 E-value=1.6e-08 Score=114.03 Aligned_cols=143 Identities=27% Similarity=0.397 Sum_probs=118.2
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCc-eeeEeEEeeHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGY-LDLEMVEFTLNE 968 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~-~~l~~~~~dL~~ 968 (1052)
.+..+++.++||+|||++.+.+..+.+... ..+...+++..+....+++..++++ +++++++.+. .......+++..
T Consensus 114 ~~~~~~~~~~hel~~pl~~i~~~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~ 192 (336)
T COG0642 114 AKREFLANISHELRTPLTAIRGLLELLLEG-LLDPQRELLEIIEEEAERLLRLVNDLLDLSRLEAGTKLKLLLELVDLAE 192 (336)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHhccC-CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccCCCCcCHHH
Confidence 466789999999999999999988866554 2222678888888889999999999 7999987752 344477888999
Q ss_pred HHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 969 li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
++..++..+......+++.+....++ ...+.+|+..|.|||.||+.||+||++ ++.|.|.+....+
T Consensus 193 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~v~~~~~~l~~vl~nLi~NAi~~~~-~~~i~i~~~~~~~ 258 (336)
T COG0642 193 LLEEVVRLLAPLAQEKGIELAVDLPE---LPYVLGDPERLRQVLVNLLSNAIKYTP-GGEITISVRQDDE 258 (336)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEecCC---CceEeeCHHHHHHHHHHHHHHHhccCC-CCeEEEEEEecCC
Confidence 99999999999888888888876652 235899999999999999999999999 8899998877655
No 66
>PRK13557 histidine kinase; Provisional
Probab=99.00 E-value=4.3e-09 Score=128.31 Aligned_cols=131 Identities=13% Similarity=0.131 Sum_probs=106.8
Q ss_pred HHHHHHHHHHHHHhCCceEEEEcC---CCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccc
Q 001564 611 LEAVTSEMVRLIETATVPILAVDV---DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQ 687 (1052)
Q Consensus 611 L~~~~~~l~~lle~~~~~I~~~D~---dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~ 687 (1052)
....+..|+.++++++++|+++|. +|+|+++|+++++++||+.++++|+++..++++++.......+...+..+...
T Consensus 25 ~~~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 104 (540)
T PRK13557 25 SDHRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREI 104 (540)
T ss_pred hhhhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCc
Confidence 344567899999999999999995 88999999999999999999999999998887766555555555555444332
Q ss_pred eEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHH
Q 001564 688 NIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIE 745 (1052)
Q Consensus 688 ~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se 745 (1052)
..++. ..+++|..+|+.+...|+++.+|.+.+++++.+|||+++++++++...+
T Consensus 105 ~~~~~----~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~ 158 (540)
T PRK13557 105 ATEIL----NYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQ 158 (540)
T ss_pred eEEEE----EEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHH
Confidence 22222 2367899999999999999999999999999999999999998876543
No 67
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.97 E-value=1.4e-08 Score=115.96 Aligned_cols=226 Identities=19% Similarity=0.227 Sum_probs=157.5
Q ss_pred HHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEecc
Q 001564 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGS 698 (1052)
Q Consensus 619 ~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~ 698 (1052)
..+++..+++++++|....|..+|..+..+++.....++|+++.+++++...+.+. +++.. .......
T Consensus 4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~-------~~~~~---~~~~~~~-- 71 (560)
T COG3829 4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE-------QSRDK---ELTERLK-- 71 (560)
T ss_pred hhhhhhcccceEEEEcCCceeeechHHHHhhhcceEEEecccceeeccccCcceee-------ccCcc---ceeeeee--
Confidence 44899999999999999999999999999999999999999988887766544332 22221 1111111
Q ss_pred ccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHH-HHHHHHHHHHHhCCCCCCCCccccCCCCcceeechH
Q 001564 699 KINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF-TRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPA 777 (1052)
Q Consensus 699 ~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L-~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a 777 (1052)
.+ ... ..+...++.+..++++|+..++.|+++....-+.. +...+.|+.+++.+. +++++.|.+|+++++|++
T Consensus 72 ~~--~~~-~~~~~~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~---~~l~vvD~~G~~i~~N~~ 145 (560)
T COG3829 72 LK--VKR-IVVVGKTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSID---DGLLVVDEDGIIIYYNKA 145 (560)
T ss_pred cc--cee-EEEcCCceeecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhcc---CceEEEcCCCcEEEEcHH
Confidence 11 233 33344455667899999999999999977666655 667789999999999 888999999999999999
Q ss_pred HHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCC
Q 001564 778 MVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDR 857 (1052)
Q Consensus 778 ~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~ 857 (1052)
+.+++|++.++++|+++. .++.. ..+ .....++..+.+.... ..+..|... ..+..|++ .
T Consensus 146 ~~~~~gl~~e~~~gk~~~-~v~~~---------~~~-----s~~l~vl~~~kp~~~~--~~~~~~~~~--i~~~~pv~-~ 205 (560)
T COG3829 146 YAKLLGLSPEEVLGKHLL-DVVSA---------GED-----STLLEVLRTGKPIRDV--VQTYNGNKI--IVNVAPVY-A 205 (560)
T ss_pred HHHHhCCCHHHHcCCcHH-HHHhc---------cCC-----ceehhhhhcCCcceee--eeeecCCce--eEeeccEe-c
Confidence 999999999999999764 33211 000 0112223333332222 222233332 33444554 6
Q ss_pred CCCEEEEeeehHHHHHHHHHHHHHH
Q 001564 858 EGAVTGVFCFLQLASHELQQALHVQ 882 (1052)
Q Consensus 858 ~G~i~g~i~v~~DITerk~~e~elq 882 (1052)
+|.+.|.+++++|+++-.....++.
T Consensus 206 ~g~l~G~v~~~~~~~~l~~l~~~~~ 230 (560)
T COG3829 206 DGQLIGVVGISKDVSELERLTRELE 230 (560)
T ss_pred CCcEEEEEEeecchHHHHHHHHHHH
Confidence 6799999999999997665554443
No 68
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.96 E-value=1.8e-08 Score=129.28 Aligned_cols=123 Identities=15% Similarity=0.184 Sum_probs=98.1
Q ss_pred HHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCccccccc-CCchHHHHHHHHHHHcCCccceEEEEE
Q 001564 615 TSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVE-DSSIDTVKRMLYLALQGQEEQNIQFEI 693 (1052)
Q Consensus 615 ~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~-~~~~~~~~~~l~~~l~g~~~~~~e~~~ 693 (1052)
++.+..+++.++++++++|.+|+++++|+++++++||+.++++|+++.++++ +.........+.....++.....++..
T Consensus 135 ~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 214 (799)
T PRK11359 135 TRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLL 214 (799)
T ss_pred HHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEE
Confidence 3455678999999999999999999999999999999999999999887764 344444444455555544433333333
Q ss_pred EEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHH
Q 001564 694 KTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1052)
Q Consensus 694 ~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L 741 (1052)
.+++|..+|+.++..|+.+.+|.+.+++++++|||++|++++..
T Consensus 215 ----~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~ 258 (799)
T PRK11359 215 ----LTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLE 258 (799)
T ss_pred ----eCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHH
Confidence 36789999999999999999999999999999999999887654
No 69
>PRK10060 RNase II stability modulator; Provisional
Probab=98.94 E-value=1.1e-08 Score=127.40 Aligned_cols=162 Identities=16% Similarity=0.147 Sum_probs=112.4
Q ss_pred HHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccc-cCCchHHHHHHHHHHHcCCccceE
Q 001564 611 LEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLV-EDSSIDTVKRMLYLALQGQEEQNI 689 (1052)
Q Consensus 611 L~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~-~~~~~~~~~~~l~~~l~g~~~~~~ 689 (1052)
++.....++.+++.++++|+++|.+|+|+++|+++++++||+.++++|+++.+++ ++.+.......+...+.++.....
T Consensus 106 ~~~~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (663)
T PRK10060 106 LSHGLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV 185 (663)
T ss_pred HHHHHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence 3445566788999999999999999999999999999999999999999988765 444555556666666665554333
Q ss_pred EEEEEEeccccCCceEEEEEEEEEeecCCC-CEEEEEEEEEccchhhHhHHHHHHH---------------HHHHHHHHh
Q 001564 690 QFEIKTHGSKINDDPITLIVNACASRDLHD-NVVGVCFVAQDITPQKTVMDKFTRI---------------EGDYKAIVQ 753 (1052)
Q Consensus 690 e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G-~v~gvv~i~~DITerk~aE~~L~~s---------------e~~lr~ile 753 (1052)
+..+ .+++|..+|+.... ++.+.+| ...+++++++|||++|+++++++.. .++++..+.
T Consensus 186 e~~~----~~~~G~~~~~~~~~-~~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~~l~~~l~ 260 (663)
T PRK10060 186 ERWI----KTRKGQRLFLFRNK-FVHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAIN 260 (663)
T ss_pred EEEE----EeCCCCEEEEEeee-EEEcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHHHHHHHHH
Confidence 3333 46788777766544 4444444 4566788899999999999988763 345555543
Q ss_pred CCCCCCCCccccCCCCcceeechHH
Q 001564 754 NPNPLIPPIFGSDEFGWCCEWNPAM 778 (1052)
Q Consensus 754 ~~~~li~~I~~~D~~g~i~~vN~a~ 778 (1052)
.......+++.+|.++- -.+|..+
T Consensus 261 ~~~~~~~~ll~idld~f-k~iNd~~ 284 (663)
T PRK10060 261 AADNNQVGIVYLDLDNF-KKVNDAY 284 (663)
T ss_pred hCCCCcEEEEEEECcch-hHHHHhh
Confidence 32211134666776643 3455443
No 70
>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=98.94 E-value=8.2e-09 Score=94.53 Aligned_cols=120 Identities=21% Similarity=0.347 Sum_probs=97.1
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCcc-ceEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQFEIK 694 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~-~~~e~~~~ 694 (1052)
+.++.+++.++.+++++|.+|+++++|+++++++|++..+++|+++.+++++.+.......+.....++.. ....+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 81 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERRV- 81 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEeee-
Confidence 45678899999999999999999999999999999999999999998888777776666666666653321 1222222
Q ss_pred EeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHH
Q 001564 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1052)
Q Consensus 695 ~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~ 740 (1052)
...+|..+|+.....|+. .+|...+++++++|||++++++++
T Consensus 82 ---~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 82 ---RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred ---EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhc
Confidence 245788899999999988 788999999999999999988764
No 71
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.89 E-value=7.5e-09 Score=96.95 Aligned_cols=106 Identities=23% Similarity=0.312 Sum_probs=81.8
Q ss_pred HHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEec
Q 001564 618 MVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHG 697 (1052)
Q Consensus 618 l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~ 697 (1052)
+.+++++++.++.++|.+++|.++|+++.++|+....+ +|+++.++.++...+.+...+..+..|+.. ..+....
T Consensus 1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~~i~~~~~~~~~-~~~~~~~--- 75 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKKIIEQVRSGKEE-EFEIVIP--- 75 (106)
T ss_dssp HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHHHHHHHHTTSBS-EEEEEEE---
T ss_pred ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHHHHHHHHcCCCc-eEEEEec---
Confidence 46799999999999999999999999999999987766 799999999888888888889888888763 2222232
Q ss_pred cccCCceEEEEEEEEEeecCCCCEEEEEEEEEccc
Q 001564 698 SKINDDPITLIVNACASRDLHDNVVGVCFVAQDIT 732 (1052)
Q Consensus 698 ~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DIT 732 (1052)
.+..|+.+...|+++.+|+..|++.++.|||
T Consensus 76 ----~~~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 76 ----NGGRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp ----ETTEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred ----CCCEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 3346777899999999999999999999998
No 72
>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=98.85 E-value=1.5e-08 Score=91.74 Aligned_cols=90 Identities=12% Similarity=0.234 Sum_probs=73.9
Q ss_pred ceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHh-hhcCCCcceeeEEEEccCCcEEEEEE
Q 001564 771 CCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNK-AMSGQDPEKVPFGFFARNGKYAECLL 849 (1052)
Q Consensus 771 i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~-~l~g~~~~~~e~~~~~~dG~~~~v~~ 849 (1052)
|++||+.+++++||+++++ +.... ..+...+||+|...+...+.. ...++..+..++++++++|+++|+..
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~-------~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~ 72 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDF-------EEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEV 72 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEH-------HHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCH-------HHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEE
Confidence 5899999999999999999 54422 224478899999999999999 78888899999999999999999999
Q ss_pred EeeEeeCCCCCEEEEeeeh
Q 001564 850 CVNKKLDREGAVTGVFCFL 868 (1052)
Q Consensus 850 ~~~pi~d~~G~i~g~i~v~ 868 (1052)
++.+++|.+|++.+++|++
T Consensus 73 ~~~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 73 RGRPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEEEETTTS-EEEEEEEE
T ss_pred EEEEEECCCCCEEEEEEEC
Confidence 9999999999999999873
No 73
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.83 E-value=3.6e-08 Score=123.58 Aligned_cols=125 Identities=18% Similarity=0.148 Sum_probs=101.0
Q ss_pred HHHHHHhCCCCCCCCccccC---CCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHh
Q 001564 747 DYKAIVQNPNPLIPPIFGSD---EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNK 823 (1052)
Q Consensus 747 ~lr~ile~~~~li~~I~~~D---~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~ 823 (1052)
.++.+++..+ .+++..| .+|++++||+++++++||++++++|+.+. . +.+++........+..
T Consensus 149 ~~~~~~~~~~---~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~-~----------l~~~~~~~~~~~~~~~ 214 (665)
T PRK13558 149 LKERALDEAP---VGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCR-F----------LQGEDTNEERVAELRE 214 (665)
T ss_pred HHHHHHhcCC---ccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHH-H----------hcCCCccHHHHHHHHH
Confidence 3467889988 7778887 47999999999999999999999999853 2 2223332333344555
Q ss_pred hhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHH
Q 001564 824 AMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLS 885 (1052)
Q Consensus 824 ~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~a 885 (1052)
.+.++.....++++.+++|..+|+.++..|+.+.+|.+.+++++.+|||++|+.++++++..
T Consensus 215 ~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~ 276 (665)
T PRK13558 215 AIDEERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRER 276 (665)
T ss_pred HHhcCCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHH
Confidence 66666777899999999999999999999999999999999999999999999987766533
No 74
>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=98.82 E-value=1.3e-08 Score=122.34 Aligned_cols=128 Identities=17% Similarity=0.090 Sum_probs=101.0
Q ss_pred HHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhh
Q 001564 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1052)
Q Consensus 745 e~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1052)
.+.|+.++++++ .++|++|.+|+++++|+++++++||++++++|+... .+.. +.........+.+.
T Consensus 3 ~~~~~~i~~~~~---~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~-~~~~----------~~~~~~~~~~~~~~ 68 (494)
T TIGR02938 3 PEAYRQTVDQAP---LAISITDLKANILYANDAFTRITGYTKEEIIGKNES-VLSN----------HTTPPEVYQALWGS 68 (494)
T ss_pred hHHHHHHHHhCC---ceEEEECCCCcEEEEchhheeecCCCHHHHhCCCch-hhcC----------CCCCHHHHHHHHHH
Confidence 357899999999 788999999999999999999999999999998732 1111 11111223333444
Q ss_pred hcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHHHHHHHHH
Q 001564 825 MSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSE 886 (1052)
Q Consensus 825 l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~elq~~ae 886 (1052)
+..+.++..++...+++|+.+|+.....|+.+.+|.+.+++++.+|||++++.+.++++..+
T Consensus 69 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~ 130 (494)
T TIGR02938 69 LAEQKPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKL 130 (494)
T ss_pred HHhCCcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHH
Confidence 45556667777788999999999999999999999999999999999999998877665433
No 75
>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=98.78 E-value=5e-08 Score=89.18 Aligned_cols=119 Identities=20% Similarity=0.231 Sum_probs=92.4
Q ss_pred HHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhh
Q 001564 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAM 825 (1052)
Q Consensus 746 ~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l 825 (1052)
..++.++++.+ .++++.|.+|+++++|+++.+++|++..+++|+.+.. +.+++....+...+...+
T Consensus 3 ~~~~~~~~~~~---~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~ 68 (124)
T TIGR00229 3 ERYRAIFESSP---DAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLE-----------LIPEEDREEVRERIERLL 68 (124)
T ss_pred hHHHHHHhhCC---ceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhh-----------hcChhhhHHHHHHHHHHH
Confidence 46778899998 7789999999999999999999999999999887532 223334444444455555
Q ss_pred cCC-CcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHHH
Q 001564 826 SGQ-DPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQAL 879 (1052)
Q Consensus 826 ~g~-~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e~ 879 (1052)
.+. .....++.+..++|..+|+.....|+. .+|...+++++..|||++++.+.
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 69 EGEREPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred cCCCCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 533 333556666788999999999999988 78889999999999999877653
No 76
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.66 E-value=1e-07 Score=96.03 Aligned_cols=157 Identities=20% Similarity=0.257 Sum_probs=106.7
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCC--ceEEEEeccCCCCCccCCCCCCCCchHH-HHH
Q 001564 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDH--GEVVSEITKSGLEPYLGLHYPATDIPQA-ARF 280 (1052)
Q Consensus 204 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~--G~viaE~~~~~~~~~lg~~~pa~dip~~-ar~ 280 (1052)
+..+...+.. +.+.+++++.+++.+.+.+|.||..+|++++++. +.++++.......+.+.-.+.....|.- ...
T Consensus 6 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (175)
T COG2203 6 LNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLVILPACLIGI 83 (175)
T ss_pred HHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhcccCcchhhhhh
Confidence 3455566666 5699999999999999999999999999999995 7777665544311111111100000000 111
Q ss_pred HHHhCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCc
Q 001564 281 LFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKR 360 (1052)
Q Consensus 281 ly~~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~ 360 (1052)
........++.|+...+. ...+|..++... ++|.+++||+.+ ++
T Consensus 84 ~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~-i~~~l~vPl~~~--------------~~ 127 (175)
T COG2203 84 ALREGRPVVVEDILQDPR---------------------FRDNPLVLLEPP-IRSYLGVPLIAQ--------------GE 127 (175)
T ss_pred hhcCCceEEeeccccCcc---------------------cccCHHHHHHHH-HHHheeeeeeEC--------------CE
Confidence 112233334444443331 122666666665 899999999988 89
Q ss_pred eeeEEEeecCCCC-CCCchhHHHHHHHHHHHHHHHHHHH
Q 001564 361 LWGLVVCHNTTPR-FVPFPLRYACEFLAQVFAIHVNKEL 398 (1052)
Q Consensus 361 LWGLi~~hh~~pr-~~~~~~r~~~~~l~~~~~~~l~~~~ 398 (1052)
+||.+..||+.++ .|+..++...+.+++.++..|....
T Consensus 128 ~~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ai~~~~ 166 (175)
T COG2203 128 LLGLLCVHDSEPRRQWSEEELELLEELAEQVAIAIERAR 166 (175)
T ss_pred eeEEeeeeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999866 6999999999999999999886543
No 77
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.63 E-value=3e-07 Score=106.17 Aligned_cols=226 Identities=12% Similarity=0.124 Sum_probs=149.3
Q ss_pred HHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCc---------cceEEE
Q 001564 621 LIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE---------EQNIQF 691 (1052)
Q Consensus 621 lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~---------~~~~e~ 691 (1052)
+++...-.|++++.||.++|+.+.....+|++.-|+.|.+++|++||-|.+.+.+.+........ ...+-+
T Consensus 124 iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRsFfl 203 (768)
T KOG3558|consen 124 ILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERSFFL 203 (768)
T ss_pred HHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhccccCCCcccccccCccceeEEE
Confidence 45566666788999999999999999999999999999999999999999988887654443111 112222
Q ss_pred EEEEeccccCCceEEEEEEEEEe---------ecCCCC----------EEEEEEEEEccchhhHhHHHHHHHHHHHHHHH
Q 001564 692 EIKTHGSKINDDPITLIVNACAS---------RDLHDN----------VVGVCFVAQDITPQKTVMDKFTRIEGDYKAIV 752 (1052)
Q Consensus 692 ~~~~~~~~~dg~~~~v~v~~~pi---------~d~~G~----------v~gvv~i~~DITerk~aE~~L~~se~~lr~il 752 (1052)
+.+. ...+.|....+......+ ++..+. ..|.+.+..-|---+-.|-.|.
T Consensus 204 RMKs-TLT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL~---------- 272 (768)
T KOG3558|consen 204 RMKS-TLTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPLD---------- 272 (768)
T ss_pred Eeee-eeccCCceeeeeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCcccccccC----------
Confidence 2221 122334333322111111 111111 1122222211111111100000
Q ss_pred hCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcce
Q 001564 753 QNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEK 832 (1052)
Q Consensus 753 e~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~ 832 (1052)
. .. =+...+.|-+|+|+...+.+++||.++|++|+.++ .++|..|...+.......+..+....
T Consensus 273 -~--~~--FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Y-----------e~~Ha~Ds~~v~KSh~dL~~KGQv~T 336 (768)
T KOG3558|consen 273 -C--HM--FVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCY-----------EFVHALDSDRVRKSHHDLLTKGQVVT 336 (768)
T ss_pred -C--ce--eEEeeecceeEEEEchhHHHHhcCCHHHhhchhHH-----------HhhhHhhhhHHHHHHHHHHhcCccch
Confidence 0 00 02335678899999999999999999999999965 78899999999999999998888888
Q ss_pred eeEEEEccCCcEEEEEEEeeEeeCCC-CCEEEEeeehHHHHH
Q 001564 833 VPFGFFARNGKYAECLLCVNKKLDRE-GAVTGVFCFLQLASH 873 (1052)
Q Consensus 833 ~e~~~~~~dG~~~~v~~~~~pi~d~~-G~i~g~i~v~~DITe 873 (1052)
..+|+..++|.+.|+...++.+.+.. ++...++|+..-++.
T Consensus 337 gyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~ 378 (768)
T KOG3558|consen 337 GYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSN 378 (768)
T ss_pred hHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeecc
Confidence 89999999999999999999987643 344556676655553
No 78
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.62 E-value=7.1e-07 Score=110.19 Aligned_cols=131 Identities=19% Similarity=0.285 Sum_probs=102.3
Q ss_pred HHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcC-Ccc
Q 001564 608 MKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG-QEE 686 (1052)
Q Consensus 608 ~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g-~~~ 686 (1052)
.+.++..+..++.++++++++++++|.+|+++++|+++++++|++.++++|+++.+++++... ....+...+.. ...
T Consensus 254 ~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 331 (607)
T PRK11360 254 AQALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP--FASPLLDTLEHGTEH 331 (607)
T ss_pred HHHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh--HHHHHHHHHhcCCCc
Confidence 355666777888999999999999999999999999999999999999999999888765432 22333344433 322
Q ss_pred ceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHH
Q 001564 687 QNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIE 745 (1052)
Q Consensus 687 ~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se 745 (1052)
...++.+. .++|... +.++..|+++.+|++.|++++++|||++|++|+++++.+
T Consensus 332 ~~~~~~~~----~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~ 385 (607)
T PRK11360 332 VDLEISFP----GRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385 (607)
T ss_pred cceEEEEE----cCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHH
Confidence 22233332 4455554 888999999999999999999999999999999988755
No 79
>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=98.62 E-value=2.2e-07 Score=84.01 Aligned_cols=86 Identities=20% Similarity=0.293 Sum_probs=69.4
Q ss_pred EeeccHHHHHHhCCCcchhcCCc----ccccccCCchHHHHHHHHH-HHcCCccceEEEEEEEeccccCCceEEEEEEEE
Q 001564 638 VNGWNTKIAELTGLSVDKAIGKH----FLTLVEDSSIDTVKRMLYL-ALQGQEEQNIQFEIKTHGSKINDDPITLIVNAC 712 (1052)
Q Consensus 638 I~~~N~a~~~l~G~~~eeliG~~----~~~l~~~~~~~~~~~~l~~-~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~~ 712 (1052)
|++||+.+++++||+++++ +.. +..++||++.+.+...+.. ...++.....++++. +++|+.+|+.+.+.
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~----~~~G~~~wi~~~~~ 75 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIR----RKDGEYRWIEVRGR 75 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEE----GTTSTEEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEE----CCCCCEEEEEEEEE
Confidence 6899999999999999998 776 6688999999999999999 676666555555554 78999999999999
Q ss_pred EeecCCCCEEEEEEEE
Q 001564 713 ASRDLHDNVVGVCFVA 728 (1052)
Q Consensus 713 pi~d~~G~v~gvv~i~ 728 (1052)
+++|.+|++.+++|++
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 80
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.54 E-value=1.6e-06 Score=83.67 Aligned_cols=128 Identities=20% Similarity=0.220 Sum_probs=91.1
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCc
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 297 (1052)
|++++++.+++.+++++|+|++.||.++++..--.++.+. . ..+-+...+| .+-| -....+.+++....+|....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~-~~~~~~~~l~-~~~~-~~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW-G-GDPRLSESLP-EDDP-LIGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE-S-S-GCGHHCEE-TTSH-HHHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe-C-CCccccccCC-CCcc-HHHHHHhhCCeEEeccccccc
Confidence 5799999999999999999999999999885444344333 2 2222222555 3333 344666777665555533321
Q ss_pred cceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCCCCc
Q 001564 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPF 377 (1052)
Q Consensus 298 ~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~ 377 (1052)
. .+.++.|++||..+ ++++|+|..+...++.|+.
T Consensus 77 ~--------------------------------~~~~s~~~vPl~~~--------------~~~~Gvl~~~~~~~~~~~~ 110 (129)
T PF13492_consen 77 F--------------------------------LGIRSLLVVPLRSR--------------DRVIGVLCLDSREPEEFSD 110 (129)
T ss_dssp T--------------------------------TTTCEEEEEEEEET--------------TEEEEEEEEEECTTCG-SH
T ss_pred C--------------------------------CCCCEEEEEEEeEC--------------CEEEEEEEEEECCCCCCCH
Confidence 0 55688899999988 8999999998888899999
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 001564 378 PLRYACEFLAQVFAIHVN 395 (1052)
Q Consensus 378 ~~r~~~~~l~~~~~~~l~ 395 (1052)
..+...+.++.++|..|+
T Consensus 111 ~d~~~l~~~a~~~a~ale 128 (129)
T PF13492_consen 111 EDLQLLESLANQLAIALE 128 (129)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhC
Confidence 999999999999998774
No 81
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.54 E-value=8e-07 Score=95.28 Aligned_cols=129 Identities=18% Similarity=0.213 Sum_probs=103.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcC
Q 001564 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1052)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g 683 (1052)
...+++-++....++.+++..+.+|++..|..|+|+.+|+.+.+++|.+.++++|+++.+++.-++.-.+...+. .
T Consensus 99 ~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL~e----~ 174 (459)
T COG5002 99 VQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDLVE----K 174 (459)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHHHh----c
Confidence 344556677777889999999999999999999999999999999999999999999998876665444443332 1
Q ss_pred CccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHH
Q 001564 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTR 743 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~ 743 (1052)
.. ++-+.. +..++...+.++...++-+.|-+.|++.+..|+||+.+.|++.++
T Consensus 175 ~~----s~lld~---~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRe 227 (459)
T COG5002 175 ND----SLLLDS---SDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERRE 227 (459)
T ss_pred CC----cEEEee---cCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHHH
Confidence 11 333332 225777778888888999999999999999999999999988765
No 82
>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=98.51 E-value=2e-06 Score=74.51 Aligned_cols=103 Identities=24% Similarity=0.367 Sum_probs=83.8
Q ss_pred CCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCce
Q 001564 625 ATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDP 704 (1052)
Q Consensus 625 ~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~ 704 (1052)
++++++.+|.+|.++++|+++++++|++..+++|+++.+++++.+...+...+.....++.....++.+. ..+|..
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ 76 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLR----RKDGSV 76 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEE----ccCCCE
Confidence 4678999999999999999999999999999999999888888877777777776665443333333333 456888
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEEcc
Q 001564 705 ITLIVNACASRDLHDNVVGVCFVAQDI 731 (1052)
Q Consensus 705 ~~v~v~~~pi~d~~G~v~gvv~i~~DI 731 (1052)
.|+.+...+..+..|...+++++.+||
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 999999999998888999999998886
No 83
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.44 E-value=9.8e-06 Score=100.70 Aligned_cols=220 Identities=14% Similarity=0.173 Sum_probs=127.6
Q ss_pred HHHHHHHhCCceEEEEcCCCcEeeccHHHHHH-----hCCCcchhcCCcccc-cccCCchHHHHHHHHHHHcCCccceEE
Q 001564 617 EMVRLIETATVPILAVDVDGLVNGWNTKIAEL-----TGLSVDKAIGKHFLT-LVEDSSIDTVKRMLYLALQGQEEQNIQ 690 (1052)
Q Consensus 617 ~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l-----~G~~~eeliG~~~~~-l~~~~~~~~~~~~l~~~l~g~~~~~~e 690 (1052)
.+..++...+..+++.|.+|.|+.++....-+ .|+. .|..+.+ .+... .+-.++..+.+. .
T Consensus 63 ~l~~~l~~~~~~~~l~D~~G~vL~~~g~~~~~~~~~~~~~~----~G~~w~E~~~GTn-------aig~al~~~~pv--~ 129 (638)
T PRK11388 63 DAWEYMADRECALLILDETGCILSRNGDPQTLQQLSALGFN----DGTYCAEGIIGTN-------ALSLAAISGQPV--K 129 (638)
T ss_pred HHHHHhcCCCcEEEEEcCCceEEEEeCCHHHHHHHHHcCCc----cCCccchhccCcC-------HHHHHHhcCCce--E
Confidence 34556677889999999999999875322211 2221 2333221 11111 223333323221 1
Q ss_pred EEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccch------------------hhHhHH---HHHHHHHHHH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITP------------------QKTVMD---KFTRIEGDYK 749 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITe------------------rk~aE~---~L~~se~~lr 749 (1052)
+.... +-......+.+.+.|++|.+|+++|++.+..+... +..... ++......+.
T Consensus 130 v~g~E---H~~~~~~~~~c~aaPI~d~~G~liGvl~l~~~~~~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~~~~~~~ 206 (638)
T PRK11388 130 TMGDQ---HFKQALHNWAFCATPVFDSKGRLTGTIALACPVEQTSAADLPLTLSIAREVGNLLLTDSLLAESNRHLNQLN 206 (638)
T ss_pred EecHH---HHHHhccCceEEeeEEEcCCCCEEEEEEEEecccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11100 00112234567889999999999999987664332 111111 1222233445
Q ss_pred HHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCC
Q 001564 750 AIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD 829 (1052)
Q Consensus 750 ~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~ 829 (1052)
.++++.+ +||+++|.+|+|+++|+++++++|++.++++|+.+ .++++. +.. +..++..+.
T Consensus 207 ~il~~~~---~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i-~~l~~~---------~~~-------l~~vl~~~~ 266 (638)
T PRK11388 207 ALLESMD---DGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAI-TELLTL---------PAV-------LQQAIKQAH 266 (638)
T ss_pred HHHhccC---CcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcH-HHHhcc---------chH-------HHHHHhcCC
Confidence 6888888 88999999999999999999999999999999985 333332 111 122222333
Q ss_pred cc-eeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHH
Q 001564 830 PE-KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHEL 875 (1052)
Q Consensus 830 ~~-~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk 875 (1052)
.. ..+..+ ..+|..+++.+...|+.+..|. +++.++++++..+
T Consensus 267 ~~~~~~~~l-~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~ 310 (638)
T PRK11388 267 PLKHVEVTF-ESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMR 310 (638)
T ss_pred ceeeEEEEE-ecCCceEEEEEEEEeecccCce--EEEEEehhhHHHH
Confidence 22 223232 3457777888999998754443 3566677877644
No 84
>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=98.44 E-value=1.5e-06 Score=98.53 Aligned_cols=113 Identities=15% Similarity=0.194 Sum_probs=85.3
Q ss_pred HHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEE
Q 001564 612 EAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQF 691 (1052)
Q Consensus 612 ~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~ 691 (1052)
++..++|+.+++++++|++++|.+|+|++||+++++++|++.++.+|+++.++.++.+ +...+..... .. .+
T Consensus 2 ~~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~---~~~~l~~~~~---~~--~~ 73 (333)
T TIGR02966 2 SALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE---FVEYLAAGRF---SE--PL 73 (333)
T ss_pred hhHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH---HHHHHHhccc---CC--Ce
Confidence 3456778999999999999999999999999999999999999999999988866432 2222222221 11 22
Q ss_pred EEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHH
Q 001564 692 EIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1052)
Q Consensus 692 ~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L 741 (1052)
.+. .+.+...|+.+...|+.+.. ++++++|||++++.++..
T Consensus 74 ~~~----~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~ 114 (333)
T TIGR02966 74 ELP----SPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMR 114 (333)
T ss_pred Eee----cCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHH
Confidence 222 35677889999999987642 667789999998887654
No 85
>PF12860 PAS_7: PAS fold
Probab=98.43 E-value=9.7e-07 Score=83.92 Aligned_cols=104 Identities=22% Similarity=0.319 Sum_probs=71.2
Q ss_pred HHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchh-cCCcccccc---------cCCch-HHHHHHHHHHHcCCccceEE
Q 001564 622 IETATVPILAVDVDGLVNGWNTKIAELTGLSVDKA-IGKHFLTLV---------EDSSI-DTVKRMLYLALQGQEEQNIQ 690 (1052)
Q Consensus 622 le~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eel-iG~~~~~l~---------~~~~~-~~~~~~l~~~l~g~~~~~~e 690 (1052)
+++++.||+++|.+|++++||+++.+++|++.+.+ .|.++.+++ .+.+. ..+...+..... .... .
T Consensus 1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~~--~ 77 (115)
T PF12860_consen 1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRR-RQPR--S 77 (115)
T ss_pred CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhc-CCCc--e
Confidence 47899999999999999999999999999999987 788876554 11222 222233322222 2222 2
Q ss_pred EEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMD 739 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~ 739 (1052)
++.. ..+| +|+.+...|..+ | |++.++.|||++|++|+
T Consensus 78 ~~~~----~~dg--r~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 78 FELR----LPDG--RWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred eEEE----CCCC--EEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 3333 2344 566677777644 4 77888999999999874
No 86
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=98.34 E-value=1.3e-07 Score=118.27 Aligned_cols=149 Identities=28% Similarity=0.354 Sum_probs=132.9
Q ss_pred HHHHHHHHH--HHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeE
Q 001564 886 EQTALKRLK--ALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1052)
Q Consensus 886 e~~~~~k~~--~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~ 962 (1052)
+++...+.+ +.+.++||||+|+++ +....+-.+..+.+++.+++....++.....++++ +|.++++.|...+.-.
T Consensus 213 e~~~~~~sq~~~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g~~~l~~~ 290 (786)
T KOG0519|consen 213 EAAVWSPSQKGFLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESGKGELVAK 290 (786)
T ss_pred hhcccCccchhhcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccccceeeee
Confidence 333344445 899999999999998 66666667888999999999999999999999999 7999999999999999
Q ss_pred EeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 963 ~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+|++..+++.++..+...+..+++.+....+...|. .+.+|..++.||+.|++.||+|++. .|.|.+++.....
T Consensus 291 rf~l~~ll~~~~~~~~e~~~~~~~~l~~~~~~~~p~-~v~~de~~~~qv~~n~v~naik~t~-~~~i~~~~~~~~~ 364 (786)
T KOG0519|consen 291 RFDLRTLLNFVISLLSELSQAKYAILVLDLSSGVPR-NVRGDEARLRQVIANLVSNAIKFTH-AGHLEESVIAREE 364 (786)
T ss_pred ecchHhhhhhhhhhhHHHhhcCCeEEEEecCCCCcc-eeeccceeeeeeehhhccceecccc-cceEEEEEEeehh
Confidence 999999999999999999999999999999888775 7899999999999999999999998 7888888877654
No 87
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.31 E-value=5.3e-05 Score=80.41 Aligned_cols=150 Identities=14% Similarity=0.119 Sum_probs=103.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccc
Q 001564 870 LASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDL 949 (1052)
Q Consensus 870 DITerk~~e~elq~~ae~~~~~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~ 949 (1052)
++|.+++.+..+... .+.-++..+.|.+||-|+.|.+++.+-.+...++ ..+++.....-...|..+-+.|.-
T Consensus 3 ~~~~~~~~e~~~~~~------~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~~~Ri~sla~~He~L~~ 75 (221)
T COG3920 3 LTTARKETEERLAES------EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRESQNRIQSLALIHELLYK 75 (221)
T ss_pred hHHHHHHHHHHHHHH------HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 556665555332221 4556688999999999999999999987755554 555555554444444444433422
Q ss_pred cccccCceeeEeEEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEc-HHHHHHHHHHHHHhHhhccCC---
Q 001564 950 DSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGD-SIRLQQVLADFLSISINFVPN--- 1025 (1052)
Q Consensus 950 srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D-~~~L~QVL~NLL~NAik~~~~--- 1025 (1052)
+ ....++...+++.+...+.+....+++.+..+..+. +.+..| ..-|--|+.+|++||+||...
T Consensus 76 s---------~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~---~~l~~d~A~~Lgliv~EL~tNa~Khaf~~~~ 143 (221)
T COG3920 76 S---------GDDTWDFASYLELLASNLFPSYGGKDIRLILDSGPN---VFLDPDTAVPLGLIVHELVTNALKHAFLSRP 143 (221)
T ss_pred C---------CcceEcHHHHHHHHHHHHHHhcCCCCceEEEecCCc---eEECchhhHHHHHHHHHHHHHHHHhcCCCCC
Confidence 1 235678889999998888887655567788776664 123334 455899999999999999855
Q ss_pred CCeEEEEEEEccC
Q 001564 1026 GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1026 ~g~I~I~v~~~~~ 1038 (1052)
+|.|.|++....+
T Consensus 144 ~G~I~I~~~~~~~ 156 (221)
T COG3920 144 GGEIRITLSREGD 156 (221)
T ss_pred CCEEEEEEEEcCC
Confidence 7899999888766
No 88
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.30 E-value=4.6e-06 Score=95.76 Aligned_cols=117 Identities=15% Similarity=0.141 Sum_probs=86.5
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCcc-ceEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQFEIK 694 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~-~~~e~~~~ 694 (1052)
..+..+++++++|++++|.+|+|+++|+++++++|++.++++|+++.++++..... ...+...+..+.. ...++.+
T Consensus 7 ~~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~- 83 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLN--IELMRESLQAGQGFTDNEVTL- 83 (348)
T ss_pred chHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchhh--HHHHHHHHHcCCcccccceEE-
Confidence 35678999999999999999999999999999999999999999999887654321 1223333333221 1112222
Q ss_pred EeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHH
Q 001564 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRI 744 (1052)
Q Consensus 695 ~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~s 744 (1052)
..+|..+|+.++..|+.. .+++..++|+|++++.++++.+.
T Consensus 84 ----~~~g~~~~~~~~~~~~~~-----~~~~~~~~dit~~~~~~~~~~~~ 124 (348)
T PRK11073 84 ----VIDGRSHILSLTAQRLPE-----GMILLEMAPMDNQRRLSQEQLQH 124 (348)
T ss_pred ----EECCceEEEEEEEEEccC-----ceeEEEEechhHHHHHHHHHHHH
Confidence 347889999999999872 35667789999999988776543
No 89
>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=98.30 E-value=4.8e-06 Score=72.02 Aligned_cols=101 Identities=26% Similarity=0.295 Sum_probs=80.7
Q ss_pred CCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEc
Q 001564 760 PPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFA 839 (1052)
Q Consensus 760 ~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~ 839 (1052)
.+++.+|.+|.++++|+++.+++|++.++++|+.+. .+.++++...+...+.....+......++.+..
T Consensus 3 ~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (103)
T cd00130 3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLL-----------DLIHPEDREELRERLENLLSGGEPVTLEVRLRR 71 (103)
T ss_pred ceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHH-----------HhcCCccchHHHHHHHHHHhcCcCeEEEEEEEc
Confidence 567899999999999999999999999999998754 223333444455555555555556677888888
Q ss_pred cCCcEEEEEEEeeEeeCCCCCEEEEeeehHHH
Q 001564 840 RNGKYAECLLCVNKKLDREGAVTGVFCFLQLA 871 (1052)
Q Consensus 840 ~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DI 871 (1052)
.+|..+|+.....+..+.+|...+++++.+||
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 72 KDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred cCCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 99999999999999999889999999888774
No 90
>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=98.27 E-value=1.1e-05 Score=79.83 Aligned_cols=136 Identities=17% Similarity=0.170 Sum_probs=88.0
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCC--CCC--CchHHHH-----HHHHhCCee
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHY--PAT--DIPQAAR-----FLFMKNKVR 288 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~--pa~--dip~~ar-----~ly~~~~~r 288 (1052)
+++++++.+++.+.+++|+|...||-+|+++.=..++-+..+ ...++..+ |.. .-|...+ .++..++..
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDP--SEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEPI 80 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSS--CTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-E
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCc--hhhhhhhcccCcccccccchhhhhHHHHHHhcCceE
Confidence 789999999999999999999999999877722222322222 22222221 111 1111110 014455544
Q ss_pred EEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEee
Q 001564 289 MIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCH 368 (1052)
Q Consensus 289 ~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~h 368 (1052)
++. .... ...+ .......|+++.+++||+.+ |++||.|...
T Consensus 81 ~~~-~~~~----------------------~~~~--~~~~~~~~~~s~l~vPl~~~--------------~~~~Gvl~l~ 121 (148)
T PF13185_consen 81 IIN-DDDS----------------------SFPP--WELARHPGIRSILCVPLRSG--------------GEVIGVLSLY 121 (148)
T ss_dssp EES-CCCG----------------------GGST--THHHCCTT-SEEEEEEEEET--------------TEEEEEEEEE
T ss_pred EEe-Cccc----------------------cccc--hhhhccccCCEEEEEEEeEC--------------CEEEEEEEEe
Confidence 444 0000 0111 36789999999999999988 9999999999
Q ss_pred cCCCCCCCchhHHHHHHHHHHHHHHH
Q 001564 369 NTTPRFVPFPLRYACEFLAQVFAIHV 394 (1052)
Q Consensus 369 h~~pr~~~~~~r~~~~~l~~~~~~~l 394 (1052)
+..++.++...+..++.++.++|..|
T Consensus 122 ~~~~~~f~~~~~~~l~~la~~~a~ai 147 (148)
T PF13185_consen 122 SKEPNAFSEEDLELLEALADQIAIAI 147 (148)
T ss_dssp ESSTT---HHHHHHHHHHHHHHHHHH
T ss_pred eCCCCCcCHHHHHHHHHHHHHHHHHh
Confidence 89899999999999999999998876
No 91
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.27 E-value=5.5e-05 Score=76.36 Aligned_cols=228 Identities=22% Similarity=0.275 Sum_probs=142.4
Q ss_pred EEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEEEEE
Q 001564 630 LAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIV 709 (1052)
Q Consensus 630 ~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v 709 (1052)
+..+..+.+...|......+++......+ .......................... ...........+...++..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~ 76 (232)
T COG2202 3 LVLDRDGRIIYANEAAEELLGYSAEELLG--LLLALHPEDRDRLRELLRRLLAGEEL----LSEELRLVRKDGEERWVEL 76 (232)
T ss_pred EEEcccccEEEecccchhhcCCChHHhhh--hhhccCccchhhhHHHHHHHhccCCc----chhhHHhhhcCCcEEEEEe
Confidence 45667788888888888888877776555 11111111111111111111111111 0111111122344444443
Q ss_pred EEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHH
Q 001564 710 NACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEV 789 (1052)
Q Consensus 710 ~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eel 789 (1052)
.........+........ .|++..+..++.++..+.+++.++++.+ .+++..|.+|.+.++|+++.+++|++..+.
T Consensus 77 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~ 152 (232)
T COG2202 77 SAAPLRDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASP---DGIWVLDEDGRILYANPAAEELLGYSPEEE 152 (232)
T ss_pred cceEEEcCCCCEEEEEee-eecchHHHHHHHHHHHHHHHHHHHhhCC---ceEEEEeCCCCEEEeCHHHHHHhCCChHHh
Confidence 333334445555555556 8999999999999999999999999999 788999999999999999999999998887
Q ss_pred hhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcE-EEEEEEeeEeeCCCCCEEEEeeeh
Q 001564 790 IDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKY-AECLLCVNKKLDREGAVTGVFCFL 868 (1052)
Q Consensus 790 iG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~-~~v~~~~~pi~d~~G~i~g~i~v~ 868 (1052)
.+..... .... ...+.. ..................++....++|.. .+......+... +|.+.++.+..
T Consensus 153 ~~~~~~~-~~~~-------~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~ 222 (232)
T COG2202 153 LGRGLSD-LIHP-------EDEERR-ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIA 222 (232)
T ss_pred cCCChhh-eEec-------CCCchh-hHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEEE
Confidence 7666321 1111 111100 01111222223334567888999999996 877777777654 78899899999
Q ss_pred HHHHHHHHH
Q 001564 869 QLASHELQQ 877 (1052)
Q Consensus 869 ~DITerk~~ 877 (1052)
.|++++++.
T Consensus 223 ~d~~~~~~~ 231 (232)
T COG2202 223 RDITERKQA 231 (232)
T ss_pred echHHHhhc
Confidence 999987653
No 92
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.22 E-value=1.3e-05 Score=94.91 Aligned_cols=119 Identities=14% Similarity=0.143 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCC
Q 001564 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQ 684 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~ 684 (1052)
++..++|++.+++++.+++++|+|++++|.+|+|+++|+++++++||+.++.+|+++.+++.+.+. ...+.. ..
T Consensus 87 ~~~~~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~---~~~~~~---~~ 160 (430)
T PRK11006 87 RKRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEF---TQYLKT---RD 160 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHH---HHHHHh---cc
Confidence 345567888889999999999999999999999999999999999999999999998877654322 111111 11
Q ss_pred ccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHH
Q 001564 685 EEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFT 742 (1052)
Q Consensus 685 ~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~ 742 (1052)
... ..... ..++ .++.+...|..+ + +++.+.+|||++++.+++.+
T Consensus 161 ~~~--~~~~~----~~~~--~~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~~~ 205 (430)
T PRK11006 161 FSR--PLTLV----LNNG--RHLEIRVMPYTE--G---QLLMVARDVTQMHQLEGARR 205 (430)
T ss_pred cCC--CeEEE----cCCC--CEEEEEEEEcCC--C---cEEEEEehhhHHHHHHHHHH
Confidence 111 12222 1223 345555556543 2 35567899999998876544
No 93
>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=98.21 E-value=4.5e-05 Score=92.68 Aligned_cols=153 Identities=9% Similarity=0.048 Sum_probs=107.9
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHH
Q 001564 202 KLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFL 281 (1052)
Q Consensus 202 ~~~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~l 281 (1052)
+.+.++...+.. +.+++++++.+++.+.+++|+||..||-+++++...+++ +....-+..-...|+... --....
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 344455566666 669999999999999999999999999998887544333 322111111113333221 234566
Q ss_pred HHhCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCce
Q 001564 282 FMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRL 361 (1052)
Q Consensus 282 y~~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~L 361 (1052)
+..+..-+|.|+...|-.. .++. +...|+++.|+|||..+ |+.
T Consensus 80 ~~~~~pvii~Dv~~d~~~~---------------------~~~~--~~~~~~~S~l~VPL~~~--------------g~v 122 (534)
T TIGR01817 80 VATGNSLVVPDVAAEPLFL---------------------DRLS--LYDPGPVPFIGVPIKAD--------------SET 122 (534)
T ss_pred HhcCCeEEecccccCchhh---------------------hccc--cccCCcceEEEEEEcCC--------------CEE
Confidence 7778888888887664211 0000 23467899999999977 999
Q ss_pred eeEEEeecCC-CCCCCchhHHHHHHHHHHHHHHHHH
Q 001564 362 WGLVVCHNTT-PRFVPFPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 362 WGLi~~hh~~-pr~~~~~~r~~~~~l~~~~~~~l~~ 396 (1052)
+|.|..++.. ++.+......+++.+|.+++..|..
T Consensus 123 iGvL~v~s~~~~~~ft~~d~~lL~~lA~~ia~aI~~ 158 (534)
T TIGR01817 123 IGVLAADRDFRSRERLEEEVRFLEMVANLIGQTVRL 158 (534)
T ss_pred EEEEEEEeccccccccHHHHHHHHHHHHHHHHHHHH
Confidence 9999998875 6777889999999999999998853
No 94
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=98.14 E-value=0.00017 Score=88.62 Aligned_cols=133 Identities=16% Similarity=0.172 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHH----HcC--CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEe
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKM----MEG--TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~l----L~~--~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~ 964 (1052)
..+....++||+++|++.+..+... +.. ....++..+.+..+.....++.+.+.+ +...+ ....++
T Consensus 360 ~~~~~~~la~el~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~l~~~~~-------~~~~~~ 432 (565)
T PRK10935 360 LMEERATIARELHDSLAQVLSYLKIQLTLLKRSLDEDNAKAQSIIAEFDQALSDAYRQLRELLTTFR-------LTIQEA 432 (565)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-------CCCCCC
Confidence 3445567899999998888766543 332 223455666777777777777777777 43322 244678
Q ss_pred eHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEc
Q 001564 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLT 1036 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~ 1036 (1052)
++.+++.+++..+...... .+.+..+.|+.. ...+++.++.||+.|++.||+||++ .|.|.|.+...
T Consensus 433 ~l~~~l~~~~~~~~~~~~~-~i~~~~~~~~~~---~~~~~~~~l~qv~~nll~NA~k~~~-~~~i~i~~~~~ 499 (565)
T PRK10935 433 NLGSALEEMLDQLRNQTDA-KITLDCRLPSQA---LDAQQQVHLLQIIREATLNAIKHAN-ASEIAVSCVTN 499 (565)
T ss_pred CHHHHHHHHHHHHHHhhCC-eEEEEeeCCCCC---CCHHHHHHHHHHHHHHHHHHHhcCC-CCeEEEEEEEc
Confidence 9999999999988865322 244444333321 1234456799999999999999987 67888887665
No 95
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.12 E-value=3.5e-05 Score=92.85 Aligned_cols=112 Identities=19% Similarity=0.245 Sum_probs=81.0
Q ss_pred HHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEE
Q 001564 611 LEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQ 690 (1052)
Q Consensus 611 L~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e 690 (1052)
+++...++..+++++++||+++|.+|+|+++|++++++||++.++++|+++.++++... +...+..+......
T Consensus 75 ~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~~ 147 (520)
T PRK10820 75 SEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSHN 147 (520)
T ss_pred HHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccce
Confidence 44555678999999999999999999999999999999999999999999998887543 22233333221112
Q ss_pred EEEEEeccccCCceEEEEEEEEEee--cCCCCE--EEEEEEEEccchhhH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASR--DLHDNV--VGVCFVAQDITPQKT 736 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~--d~~G~v--~gvv~i~~DITerk~ 736 (1052)
..+. .+|.. +.+...|+. +.+|.. .|++.+++|+++..+
T Consensus 148 ~~v~-----~~g~~--~~v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 148 EHVV-----INGQD--FLMEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred EEEE-----ECCEE--EEEEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 2222 12443 335667776 656654 899999999998643
No 96
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.11 E-value=3.4e-06 Score=78.89 Aligned_cols=106 Identities=19% Similarity=0.208 Sum_probs=74.6
Q ss_pred HHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcC
Q 001564 748 YKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSG 827 (1052)
Q Consensus 748 lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g 827 (1052)
++.++++++ .++.++|.++++.++|+++.++|+..+. .+|+++. .+..+...+.+...+.....|
T Consensus 1 L~~il~s~~---~~i~~vD~~~~I~~~n~~a~~~f~~~~~-~iGr~l~-----------~~~~~~~~~~l~~~i~~~~~~ 65 (106)
T PF13596_consen 1 LNNILDSMP---IGIIFVDRNLRIRYFNPAAARLFNLSPS-DIGRPLF-----------DIHPPLSYPNLKKIIEQVRSG 65 (106)
T ss_dssp HHHHHHHSS---SEEEEEETTSBEEEE-SCGC-SS---GG-GTTSBCC-----------CSS-HHHHHHHHHHHHHHHTT
T ss_pred ChHHHhcCC---CCEEEEcCCCeEEEeChhHhhhcCCChH-HCCCCHH-----------HcCCccchHHHHHHHHHHHcC
Confidence 467889999 8899999999999999999999997754 4798864 445556667777778777777
Q ss_pred CCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHH
Q 001564 828 QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLAS 872 (1052)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DIT 872 (1052)
+... .+... ..+| +|+.+...|+++.+|+..|++.++.|||
T Consensus 66 ~~~~-~~~~~-~~~~--~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 66 KEEE-FEIVI-PNGG--RWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp SBSE-EEEEE-EETT--EEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred CCce-EEEEe-cCCC--EEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 6532 22222 2444 4557789999999999999999999997
No 97
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=98.02 E-value=0.00014 Score=82.68 Aligned_cols=205 Identities=19% Similarity=0.137 Sum_probs=124.0
Q ss_pred CCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHH-HHHhCC-eeEE-ecC
Q 001564 217 GSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARF-LFMKNK-VRMI-VDC 293 (1052)
Q Consensus 217 ~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~-ly~~~~-~r~i-~d~ 293 (1052)
.+++.++..+++.+..+.|||+++++++|.+. .+..+.+.-..+.+|.+-+....|.+.-+ .+..+. ++++ .|+
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 47999999999999999999999999999987 45555554455666664444444444433 333443 4441 222
Q ss_pred CCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCC
Q 001564 294 RARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR 373 (1052)
Q Consensus 294 ~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr 373 (1052)
... ++..+ + +--.+|+++.|.|.+||.++ +++||.+.--|+.|-
T Consensus 124 ~~~------~~~~~---------l-------~~~~~~~~~~a~i~~PL~~~--------------~~~~G~Ltld~~~~~ 167 (550)
T COG3604 124 LFP------DPYDG---------L-------LPDTEGNKKHACIGVPLKSG--------------DKLIGALTLDHTEPD 167 (550)
T ss_pred ccC------Ccccc---------c-------ccCccCCcceeEEeeeeeeC--------------CeeeeeEEeeeeccc
Confidence 111 11110 0 11145678899999999998 999999999999888
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhcc--CCCcccccCCcchhhhcCCCEEEEEECC
Q 001564 374 FVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQ-TLLCDMLMR--DAPLGIVTQSPNIMDLVKCDGAALLYKN 450 (1052)
Q Consensus 374 ~~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~l~~l~~~dg~~~~~~~ 450 (1052)
...+..-...++|+...++.+......+.-...++.+..+ ..+..-+.. ....+|+.++|.++++++.--.+--.+-
T Consensus 168 ~f~~~~~~~lr~La~~a~la~~~~~l~~~l~~~~~~l~~e~~~~~~~~~~~~~~~~~iIG~S~am~~ll~~i~~VA~Sd~ 247 (550)
T COG3604 168 QFDEDLDEELRFLAALAALAVANALLHRELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDS 247 (550)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccchhcccccceecCHHHHHHHHHHHHHhcCCC
Confidence 7777777888888888877765433222222221111111 111111111 1234677777776666654444444445
Q ss_pred eEEEecCCCC
Q 001564 451 KIWRLGVTPN 460 (1052)
Q Consensus 451 ~~~~~g~~p~ 460 (1052)
.+...|+|=+
T Consensus 248 tVLi~GETGt 257 (550)
T COG3604 248 TVLIRGETGT 257 (550)
T ss_pred eEEEecCCCc
Confidence 5555566554
No 98
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.02 E-value=5.4e-05 Score=92.48 Aligned_cols=123 Identities=19% Similarity=0.233 Sum_probs=88.4
Q ss_pred HHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCC---cchhcCCcccccccCCchHHHHHHHHHHHcCCc
Q 001564 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLS---VDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE 685 (1052)
Q Consensus 609 ~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~---~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~ 685 (1052)
.|+....++++.+++++++||+++|.+|+|+++|+++++++|++ ..+.+|+.+.++.+.. .+..++..+.
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~ 286 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVS-------RLKEVLRTGT 286 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCch-------hHHHHHhcCC
Confidence 45566667789999999999999999999999999999999865 3456677766555432 2333444333
Q ss_pred cceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHH
Q 001564 686 EQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGD 747 (1052)
Q Consensus 686 ~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~ 747 (1052)
... ..... .+| .++.++..|+.+ +|.+.|++.+++|+|+.++.++++......
T Consensus 287 ~~~-~~~~~-----~~g--~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~~~ 339 (542)
T PRK11086 287 PRR-DEEIN-----ING--RLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMVNY 339 (542)
T ss_pred Ccc-ceEEE-----ECC--EEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHHHH
Confidence 221 11111 123 345567789998 899999999999999999998887665543
No 99
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=98.01 E-value=0.00026 Score=85.29 Aligned_cols=154 Identities=12% Similarity=0.059 Sum_probs=106.4
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhC
Q 001564 206 KAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKN 285 (1052)
Q Consensus 206 ~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~ 285 (1052)
++...|-+ +.+++++++.+++.+++++++|.+-|+.++++ .....+..+.-....+..|+..+-|.-...+ ..+
T Consensus 8 eis~~L~~--s~d~~e~L~~vl~~l~~~l~~~~~~l~l~~~~---~l~~~as~gl~~~~~~~~~~~geGP~l~av~-~~g 81 (509)
T PRK05022 8 PIALDLSR--GLPHQDRFQRLLTTLRQVLPCDASALLRLDGD---QLVPLAIDGLSPDVLGRRFALEEHPRLEAIL-RAG 81 (509)
T ss_pred HHHHHHhc--CCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC---cEEEEEEcCCChHhhCCccCCCcchHHHHHH-hcC
Confidence 44555666 77999999999999999999999999999753 3333333333334456678777766433333 325
Q ss_pred CeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEE
Q 001564 286 KVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLV 365 (1052)
Q Consensus 286 ~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi 365 (1052)
++..|+|...-|.++ + |-.. ....++|++|.|+|||.++ |+.+|.|
T Consensus 82 ~~v~v~~~~~~p~~~-~---------------~~~~----~~~~~~gi~S~l~vPL~~~--------------~~~~GvL 127 (509)
T PRK05022 82 DPVRFPADSELPDPY-D---------------GLIP----GVQESLPVHDCMGLPLFVD--------------GRLIGAL 127 (509)
T ss_pred CeEEEecCCCCCccc-c---------------cccc----cccccCCcceEEEEEEEEC--------------CEEEEEE
Confidence 444555443333211 0 0000 0134579999999999998 9999999
Q ss_pred EeecCCCCCCCchhHHHHHHHHHHHHHHHHHHHH
Q 001564 366 VCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELE 399 (1052)
Q Consensus 366 ~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~~ 399 (1052)
.++...|..++.....+++.++.+++..+.....
T Consensus 128 ~l~~~~~~~f~~~~~~~l~~~a~~~a~Al~~a~~ 161 (509)
T PRK05022 128 TLDALDPGQFDAFSDEELRALAALAAATLRNALL 161 (509)
T ss_pred EEeeCCCCcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9998888888888889999999999998875443
No 100
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=98.01 E-value=0.00016 Score=88.99 Aligned_cols=128 Identities=14% Similarity=0.150 Sum_probs=86.1
Q ss_pred HHHHHhhhHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHHHHHHH
Q 001564 898 YTKRQIRNPLSGIIFSRKMMEG--TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASI 974 (1052)
Q Consensus 898 ~isHEirnPL~~I~g~~~lL~~--~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~li~~v~ 974 (1052)
.+.+.+.++|+.+......+.. ...+++..+.+..+....+++...+.+ +...+. ...+.++.+.+..++
T Consensus 368 elhd~i~~~L~~l~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~~~~~lr~ll~~~r~-------~~~~~~l~~~l~~~~ 440 (569)
T PRK10600 368 ELHDSIAQSLSCMKMQVSCLQMQGDALPESSRELLSQIRNELNASWRQLRELLTTFRL-------QLTEPGLRPALEASC 440 (569)
T ss_pred HhccHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-------CcccCCHHHHHHHHH
Confidence 4444455566666655544432 445677888999999999999999988 555443 335678899999998
Q ss_pred HHHHhhccccCcEEEeeecCCCcceeEE-EcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 975 SQVMMKSNAKGIRIVNETAEQIMSETLY-GDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 975 ~~~~~~~~~~~i~l~~~~~~~lp~~~v~-~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
..+..... ..+.+.++.++. .+. .++..|.||+.|+|+||+||++ .+.|.|++...++
T Consensus 441 ~~~~~~~~-~~i~~~~~~~~~----~~~~~~~~~l~~il~ell~NA~kha~-a~~i~V~~~~~~~ 499 (569)
T PRK10600 441 EEFSARFG-FPVKLDYQLPPR----LVPSHQAIHLLQIAREALSNALKHAQ-ASEVVVTVAQNQN 499 (569)
T ss_pred HHHHHHhC-CeEEEEecCCcc----cCCHHHHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEcCC
Confidence 88776542 224444333332 122 2345699999999999999997 5788888765544
No 101
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=97.96 E-value=1.9e-05 Score=65.96 Aligned_cols=63 Identities=30% Similarity=0.436 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-cccccccc
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIID 954 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~ 954 (1052)
+.++++.++||+||||++|.++++.+.....+++...+++.+..+++++..++++ +++++.+.
T Consensus 2 ~~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~ 65 (66)
T smart00388 2 KREFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIEA 65 (66)
T ss_pred HHHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3468899999999999999999999887666677788999999999999999999 68887543
No 102
>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=97.95 E-value=4.7e-05 Score=71.68 Aligned_cols=96 Identities=11% Similarity=0.107 Sum_probs=77.6
Q ss_pred cccCCCCcceeechH-HHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHh-hHHHHHhhhcCCCcceeeEEEEcc
Q 001564 763 FGSDEFGWCCEWNPA-MVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVN-LGIVLNKAMSGQDPEKVPFGFFAR 840 (1052)
Q Consensus 763 ~~~D~~g~i~~vN~a-~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~-~~~~l~~~l~g~~~~~~e~~~~~~ 840 (1052)
...+.+|+|+++.+. ...++||.++|++|+.++ .+.||+|... +.......+..+.....-+|+..+
T Consensus 6 trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y-----------~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k 74 (111)
T PF14598_consen 6 TRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIY-----------DFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTK 74 (111)
T ss_dssp EEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGG-----------GGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-T
T ss_pred EEECCCcEEEEEcCccChhhcCCCcHHHcCCchH-----------HhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEec
Confidence 346789999999999 699999999999999976 7889999997 777788887777777778999999
Q ss_pred CCcEEEEEEEeeEeeCC-CCCEEEEeeehH
Q 001564 841 NGKYAECLLCVNKKLDR-EGAVTGVFCFLQ 869 (1052)
Q Consensus 841 dG~~~~v~~~~~pi~d~-~G~i~g~i~v~~ 869 (1052)
+|.++|+...+....+. .+++..++|+-.
T Consensus 75 ~g~~vwvqt~~~~~~n~~~~~~~~Iv~~n~ 104 (111)
T PF14598_consen 75 NGGYVWVQTKATLFYNPWTSKPEFIVCTNT 104 (111)
T ss_dssp TSSEEEEEEEEEEEEETTTTCEEEEEEEEE
T ss_pred CCcEEEEEEEEEEEECCCCCCccEEEEEEE
Confidence 99999999999999864 456555555543
No 103
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.93 E-value=0.0008 Score=84.35 Aligned_cols=150 Identities=8% Similarity=0.033 Sum_probs=102.4
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEec--cCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecC
Q 001564 216 SGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEIT--KSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDC 293 (1052)
Q Consensus 216 ~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~--~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~ 293 (1052)
..++++++..+++.+++++|+|++.|+-++++...-++.-+. ..+.....|...|... --+-..+..+...++.|.
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 669999999999999999999999999998886554442222 2222223333333221 123456666777777665
Q ss_pred CCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCC
Q 001564 294 RARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR 373 (1052)
Q Consensus 294 ~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr 373 (1052)
...+.... .....+ +..-++++.|+||++.+ |+.=|.|..-++.++
T Consensus 275 ~~d~~~~~-------------------~~~~~~-~~~~~~~s~l~vPL~~~--------------~~v~GvL~l~~~~~~ 320 (686)
T PRK15429 275 ERDDLAPY-------------------ERMLFD-TWGNQIQTLCLLPLMSG--------------DTMLGVLKLAQCEEK 320 (686)
T ss_pred cCcccchh-------------------hhhhhh-cccccceEEEEEeEEEC--------------CEEEEEEEEeeCCCC
Confidence 54431000 000001 12335789999999988 999999999888888
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHH
Q 001564 374 FVPFPLRYACEFLAQVFAIHVNKELELE 401 (1052)
Q Consensus 374 ~~~~~~r~~~~~l~~~~~~~l~~~~~~~ 401 (1052)
.++......+..+|.++++.|......+
T Consensus 321 ~F~~~dl~lL~~iA~~~A~Aie~a~~~~ 348 (686)
T PRK15429 321 VFTTTNLKLLRQIAERVAIAVDNALAYQ 348 (686)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 8999999999999999999987654433
No 104
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=97.88 E-value=0.00014 Score=68.40 Aligned_cols=101 Identities=11% Similarity=0.152 Sum_probs=78.7
Q ss_pred EEEEcCCCcEeeccHH-HHHHhCCCcchhcCCcccccccCCchHH-HHHHHHHHHcCCccceEEEEEEEeccccCCceEE
Q 001564 629 ILAVDVDGLVNGWNTK-IAELTGLSVDKAIGKHFLTLVEDSSIDT-VKRMLYLALQGQEEQNIQFEIKTHGSKINDDPIT 706 (1052)
Q Consensus 629 I~~~D~dg~I~~~N~a-~~~l~G~~~eeliG~~~~~l~~~~~~~~-~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~ 706 (1052)
+.-.+.+|+|+++-++ ...++||.++|++|+++.+++||+|... +......+++.+.....-+++. .++|+.+|
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~----~k~g~~vw 80 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFR----TKNGGYVW 80 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-----TTSSEEE
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEE----ecCCcEEE
Confidence 3456889999999999 6999999999999999999999999996 8888888887666433334444 67899999
Q ss_pred EEEEEEEeecC-CCCEEEEEEEEEccch
Q 001564 707 LIVNACASRDL-HDNVVGVCFVAQDITP 733 (1052)
Q Consensus 707 v~v~~~pi~d~-~G~v~gvv~i~~DITe 733 (1052)
+...+.++.++ .+++..++++-+=|++
T Consensus 81 vqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 81 VQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 99999998874 4566677766554444
No 105
>PF12860 PAS_7: PAS fold
Probab=97.87 E-value=2.3e-05 Score=74.47 Aligned_cols=113 Identities=10% Similarity=0.035 Sum_probs=70.5
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHH-hhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCc
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEV-IDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP 830 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eel-iG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~ 830 (1052)
+++++ .||+++|.+|++++||+++.+++|++.+.+ .|.++ .+++..... .....+.+................
T Consensus 1 Ld~l~---~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~-~~l~~~~~~-~g~~~~~~~~~~~~~~~~~~~~~~- 74 (115)
T PF12860_consen 1 LDSLP---QGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASF-RDLLRRLAE-RGEFPPGDPEAWVRQRLARLRRRQ- 74 (115)
T ss_pred CCCcC---ceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCH-HHHHHHHHH-cCCCCCCCHHHHHHHHHHHHhcCC-
Confidence 35677 888999999999999999999999999998 67764 444432110 011222222222222222222222
Q ss_pred ceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHH
Q 001564 831 EKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1052)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e 878 (1052)
...+.+...||.++ .++..|.- +| |++.+..|||+++++|
T Consensus 75 -~~~~~~~~~dgr~l--~~~~~~~~--~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 75 -PRSFELRLPDGRWL--EVRAQPLP--DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred -CceeEEECCCCEEE--EEEeEECC--CC---CEEEEEEeCCHHHHhc
Confidence 22344566888765 45555653 34 5788999999998776
No 106
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.87 E-value=8.8e-05 Score=85.57 Aligned_cols=126 Identities=24% Similarity=0.390 Sum_probs=91.2
Q ss_pred HHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEE
Q 001564 611 LEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQ 690 (1052)
Q Consensus 611 L~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e 690 (1052)
|....+.|..+++.+.++++++|.+|.++++|+++..++|++.++++|+++.+++..... .....++..+.+. .
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~--~ 185 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPI--R 185 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCcc--e
Confidence 456668899999999999999999999999999999999999999999998888611110 1223334333321 1
Q ss_pred EEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYK 749 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr 749 (1052)
....+. .+... ..+..|++. +|.+.|.+++++|+++.+.+..++++++..++
T Consensus 186 ~~~~~~----~~~~~--i~~~~pv~~-~g~l~G~v~~~~~~~~l~~l~~~~~~~~~~~~ 237 (560)
T COG3829 186 DVVQTY----NGNKI--IVNVAPVYA-DGQLIGVVGISKDVSELERLTRELEESEGLLR 237 (560)
T ss_pred eeeeee----cCCce--eEeeccEec-CCcEEEEEEeecchHHHHHHHHHHHHHhhhhc
Confidence 111111 12222 445566655 67999999999999999999998887776555
No 107
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=97.70 E-value=0.00069 Score=84.66 Aligned_cols=150 Identities=10% Similarity=0.025 Sum_probs=106.0
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhC
Q 001564 206 KAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKN 285 (1052)
Q Consensus 206 ~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~ 285 (1052)
++...+.+ +.+++++++.+++.+++++|+|++.||-+++++..-+++-+...+-+..-..+||-..=+ ....+..+
T Consensus 7 eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~geGi--~G~Va~tg 82 (748)
T PRK11061 7 EIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDEGI--VGLVGRLA 82 (748)
T ss_pred HHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCcch--HHHHhccC
Confidence 34445555 569999999999999999999999999999997665555443322122222344432211 23455556
Q ss_pred CeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEE
Q 001564 286 KVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLV 365 (1052)
Q Consensus 286 ~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi 365 (1052)
..-.|.|+...|--. +...+...+++|.|++||+.+ |++-|.|
T Consensus 83 ~pV~V~Dv~~dprf~-----------------------~~~~~~~~~~~S~L~VPL~~~--------------geVIGVL 125 (748)
T PRK11061 83 EPINLADAQKHPSFK-----------------------YIPSVKEERFRAFLGVPIIYR--------------RQLLGVL 125 (748)
T ss_pred ceEEECCcccCcccc-----------------------cCccccCccceEEEEEEEeeC--------------CEEEEEE
Confidence 666777777654110 000112468899999999976 9999999
Q ss_pred EeecCCCCCCCchhHHHHHHHHHHHHHHHHH
Q 001564 366 VCHNTTPRFVPFPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 366 ~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~ 396 (1052)
.+++..|+.++......++.|+.+.+..|..
T Consensus 126 ~v~~~~~~~Fs~~d~~lL~~LA~~aAiAL~n 156 (748)
T PRK11061 126 VVQQRELRQFDESEESFLVTLATQLAAILSQ 156 (748)
T ss_pred EEeeCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999988887753
No 108
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.68 E-value=0.00032 Score=81.00 Aligned_cols=122 Identities=20% Similarity=0.322 Sum_probs=90.8
Q ss_pred HHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcc--hhcCCcccccccCCchHHHHHHHHHHHcCCcc
Q 001564 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVD--KAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE 686 (1052)
Q Consensus 609 ~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~e--eliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~ 686 (1052)
.|+...-++..++++++..|++.+|..|.|..+|.++++|+|+... +.+|+++.++++|+.. +..+++.+.+
T Consensus 208 ~EIa~l~~er~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~ 281 (537)
T COG3290 208 EEIATLLEERQAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKP 281 (537)
T ss_pred HHHHHHHHHHHHHHHHhhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCc
Confidence 3455555666889999999999999999999999999999998765 6899999999987321 2222322222
Q ss_pred -ceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHH
Q 001564 687 -QNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEG 746 (1052)
Q Consensus 687 -~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~ 746 (1052)
+..++.+. | .++.++..|++- +|+++|.+.++||-||-++.-++|.....
T Consensus 282 ~~~~e~~~n-------g--~~~i~nr~pI~~-~~~~~GaI~tFRdktei~~L~eqLt~vr~ 332 (537)
T COG3290 282 QHDEEIRIN-------G--RLLVANRVPIRS-GGQIVGAIITFRDKTEIKKLTEQLTGVRQ 332 (537)
T ss_pred ccchhhhcC-------C--eEEEEEeccEEE-CCEEeEEEEEEecHHHHHHHHHHHHHHHH
Confidence 22222221 2 456678888876 79999999999999999999888876553
No 109
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.63 E-value=0.0012 Score=66.43 Aligned_cols=126 Identities=21% Similarity=0.321 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHH-HHHHHHHHHcC-C
Q 001564 607 GMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDT-VKRMLYLALQG-Q 684 (1052)
Q Consensus 607 ~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~-~~~~l~~~l~g-~ 684 (1052)
...++.....+++.+++..+++++.+|.+|.+.++|+++.+++|++..+..+....++........ ..........+ .
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (232)
T COG2202 103 AEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRG 182 (232)
T ss_pred HHHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCC
Confidence 345556666669999999999999999999999999999999999988877887776554333221 12222222222 2
Q ss_pred ccceEEEEEEEeccccCCce-EEEEEEEEEeecCCCCEEEEEEEEEccchhhHh
Q 001564 685 EEQNIQFEIKTHGSKINDDP-ITLIVNACASRDLHDNVVGVCFVAQDITPQKTV 737 (1052)
Q Consensus 685 ~~~~~e~~~~~~~~~~dg~~-~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~a 737 (1052)
.....++... .++|.. .+......+... .|.+.++.....|+|++++.
T Consensus 183 ~~~~~~~~~~----~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 183 GPLEIEYRVR----RKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred CCcceEEEEE----ecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 2222233333 456775 666666655544 78999999999999998864
No 110
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.58 E-value=0.0009 Score=81.93 Aligned_cols=122 Identities=20% Similarity=0.311 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCc--chhcCCcccccccCCchHHHHHHHHHHHcCCcc
Q 001564 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSV--DKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE 686 (1052)
Q Consensus 609 ~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~--eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~ 686 (1052)
.++.....+++.++++.++|++++|.+|+|+++|+++++++|++. ++++|+++.+++++... . ..... ...
T Consensus 215 ~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~--~----~~~~~-~~~ 287 (545)
T PRK15053 215 KQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF--F----TEQID-EKR 287 (545)
T ss_pred HHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh--h----hhhcC-Ccc
Confidence 334445566788999999999999999999999999999999865 46899998887764321 1 11111 111
Q ss_pred ceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHH
Q 001564 687 QNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGD 747 (1052)
Q Consensus 687 ~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~ 747 (1052)
. ..... .+| ..+.++..|+.. +|++.|++.+++|+|+.++.+.++...+..
T Consensus 288 ~--~~~~~-----~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~~ 338 (545)
T PRK15053 288 Q--DVVAN-----FNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQY 338 (545)
T ss_pred c--ceEEE-----ECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHHH
Confidence 1 11111 123 345567778775 677889999999999999988887766543
No 111
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.54 E-value=0.00012 Score=61.43 Aligned_cols=46 Identities=26% Similarity=0.291 Sum_probs=37.8
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccc
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLV 665 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~ 665 (1052)
++|+.+++++|+||+++| +++|+++|+++++++||+ ..|+.+..++
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~~~~ 46 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIGQLF 46 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHHCTS
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHHHhC
Confidence 478999999999999999 889999999999999998 5566655443
No 112
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.52 E-value=0.00072 Score=78.44 Aligned_cols=125 Identities=16% Similarity=0.224 Sum_probs=90.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHH-c
Q 001564 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLAL-Q 682 (1052)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l-~ 682 (1052)
.+++.+++++..+.++.+++..+.|++.+|.+|+|.-+|++++.|+|.+.++++|+++..+-+. +.+.+...- .
T Consensus 358 l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap~-----~~~vf~~~~a~ 432 (712)
T COG5000 358 LERAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSAIAPE-----LEEVFAEAGAA 432 (712)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhhhhhH-----HHHHHHHhhhh
Confidence 3456678888889999999999999999999999999999999999999999999997765432 222222222 1
Q ss_pred CCccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHH
Q 001564 683 GQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1052)
Q Consensus 683 g~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~ 740 (1052)
++..+..++.+. ..|+.+.+.+..+--.. .+-.|++.++.|||+...++..
T Consensus 433 ~~~~~~~ev~~~-----r~g~~rtl~Vq~t~~~~--d~~~gyVvt~DDITdLV~AQRs 483 (712)
T COG5000 433 ARTDKRVEVKLA-----REGEERTLNVQATREPE--DNGNGYVVTFDDITDLVIAQRS 483 (712)
T ss_pred cCCCccceeecc-----cCCCceeeeeeeeeccc--ccCCceEEEecchHHHHHHHHH
Confidence 233334444443 23667777766643222 2445788999999999888765
No 113
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.50 E-value=0.00055 Score=82.60 Aligned_cols=112 Identities=14% Similarity=0.125 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHH
Q 001564 741 FTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIV 820 (1052)
Q Consensus 741 L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~ 820 (1052)
+++.+..+++++++++ +||+.+|.+|+|+++|++++++||++.++++|+++. ++++. .. +..
T Consensus 75 ~e~e~~~L~aIL~sm~---eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~-eli~~----------~~---l~~- 136 (520)
T PRK10820 75 SEREHRALSALLEALP---EPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAA-QLING----------FN---FLR- 136 (520)
T ss_pred HHHHHHHHHHHHHhCC---CcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHH-HHcCc----------ch---HHH-
Confidence 3445567889999999 899999999999999999999999999999999863 33332 11 111
Q ss_pred HHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEee--CCCCCE--EEEeeehHHHHHHHH
Q 001564 821 LNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKL--DREGAV--TGVFCFLQLASHELQ 876 (1052)
Q Consensus 821 l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~--d~~G~i--~g~i~v~~DITerk~ 876 (1052)
.+......... .....+|..++ +...|+. +.+|.. .|.+.+++|+++..+
T Consensus 137 ---~le~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 137 ---WLESEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred ---HHHcCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 22222221111 12344576554 5556776 666654 899999999997533
No 114
>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=97.40 E-value=0.0005 Score=56.71 Aligned_cols=59 Identities=24% Similarity=0.342 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHhh-cccc
Q 001564 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGT-ELGAEQKRLLHTSAQCQRQLHKILDD-SDLD 950 (1052)
Q Consensus 892 k~~~la~isHEirnPL~~I~g~~~lL~~~-~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~s 950 (1052)
+.++.+.++||+||||++|.+.++.+.+. ...++...+++.+..+++++..++++ ++++
T Consensus 4 ~~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 64 (65)
T cd00082 4 KGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLS 64 (65)
T ss_pred HHHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999988763 33667788999999999999999999 4665
No 115
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=97.26 E-value=0.001 Score=75.15 Aligned_cols=229 Identities=12% Similarity=0.092 Sum_probs=145.3
Q ss_pred HHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCc------cc-----
Q 001564 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE------EQ----- 687 (1052)
Q Consensus 619 ~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~------~~----- 687 (1052)
+-++++..-.++++..+|.|.|++...+..+|+...+++-+++.+++|.+|++.+.+.+.-++.-.. ..
T Consensus 114 e~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~~ppq~~~s~q~~~e~~~ 193 (712)
T KOG3560|consen 114 ELLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAMDPPQVVFSQQPPLETGD 193 (712)
T ss_pred HHHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhccCCchhhccCCCcccccc
Confidence 4467788888889999999999999999999999999999999999999999998887765432110 00
Q ss_pred eEEEEEEEe--ccccCCc---eEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHH---------------------
Q 001564 688 NIQFEIKTH--GSKINDD---PITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF--------------------- 741 (1052)
Q Consensus 688 ~~e~~~~~~--~~~~dg~---~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L--------------------- 741 (1052)
......... +...+.. .+.+.++...+.|.. .|+.. .|+-.+-+.-.-.
T Consensus 194 ~~~~~~~~~~d~~ppens~yleRcficR~RCLLDnT---sGFLa--mdfqGklk~LhGqkkk~~~g~~lpP~LaLf~iat 268 (712)
T KOG3560|consen 194 DAILRAQEWGDGTPPENSAYLERCFICRFRCLLDNT---SGFLA--MDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIAT 268 (712)
T ss_pred ccceeeeccCccCCcccchHHhhhheeeEEEeecCC---cceee--eecccceeeecCCcccCCCCccCCCceeEEEEec
Confidence 000000000 0000010 123334444444432 33333 3544322111000
Q ss_pred -----HHHHHHHH-HHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHH
Q 001564 742 -----TRIEGDYK-AIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFV 815 (1052)
Q Consensus 742 -----~~se~~lr-~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~ 815 (1052)
..+|-+.+ .|+..-. -.|+..+.+......++||...|+.|...+ .++|-+|..
T Consensus 269 P~~pPS~lEi~~k~~i~rtKh---------klDfa~vs~Dak~k~~lgy~eaEL~~m~gY-----------~lvH~~D~~ 328 (712)
T KOG3560|consen 269 PFLPPSALEIKMKSAILRTKH---------KLDFALVSMDAKVKATLGYCEAELHGMPGY-----------NLVHVEDKV 328 (712)
T ss_pred CCCCchhhhhhhhhhhhhccc---------ccccceeccchhhhhhhccchhhccCCCcc-----------ceeehhhhh
Confidence 00000000 1111110 125556667788889999999999986633 788888887
Q ss_pred hhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHH
Q 001564 816 NLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1052)
Q Consensus 816 ~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITe 873 (1052)
-+.+.-.+.++.++..-.-+|+.+++|++.|+..++.-++ .+|++--+++.-+-.++
T Consensus 329 y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 329 YMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred hhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee-ecCCCCEEEecCCCccc
Confidence 7777778888888888899999999999999998887665 56777656766665554
No 116
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.22 E-value=0.00064 Score=73.96 Aligned_cols=208 Identities=18% Similarity=0.144 Sum_probs=122.7
Q ss_pred HHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHH--cC-CccceEEEEEEEe
Q 001564 620 RLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLAL--QG-QEEQNIQFEIKTH 696 (1052)
Q Consensus 620 ~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l--~g-~~~~~~e~~~~~~ 696 (1052)
.+++...-.|++++++|.|+++++.+.--+|++.-|+.|..+.+.+|+.|.+.+...+...- +. +.++.+-++....
T Consensus 83 hlLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~H~qeyeIErsfflrmkCv 162 (598)
T KOG3559|consen 83 HLLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQHLQEYEIERSFFLRMKCV 162 (598)
T ss_pred hHHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHhhhhhhhhhhhhhhhhhhhhhh
Confidence 45677777889999999999999999999999999999999999999999887665543322 10 0011111111100
Q ss_pred ccccC------Cc-eEE----EEEEEEEeec-CCC---CEEEEEEEEE-----ccchhhHhHHHHHHHHHHHHHHHhCCC
Q 001564 697 GSKIN------DD-PIT----LIVNACASRD-LHD---NVVGVCFVAQ-----DITPQKTVMDKFTRIEGDYKAIVQNPN 756 (1052)
Q Consensus 697 ~~~~d------g~-~~~----v~v~~~pi~d-~~G---~v~gvv~i~~-----DITerk~aE~~L~~se~~lr~ile~~~ 756 (1052)
...++ |. .+. +.+...++.- ..| ..+|++.+.. -||+.|. - .+
T Consensus 163 lakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteikl---------------~--sN 225 (598)
T KOG3559|consen 163 LAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIKL---------------H--SN 225 (598)
T ss_pred heeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEEe---------------c--cc
Confidence 00111 11 010 1111112111 111 3345555533 2333221 1 11
Q ss_pred CCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEE
Q 001564 757 PLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFG 836 (1052)
Q Consensus 757 ~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~ 836 (1052)
.-+|....|-++++......+++||++.++++++++.- +|.-|...+...-.-.+..+....--+|
T Consensus 226 ---mFmfraslDlkliF~D~rv~qltgYepqdliektLY~~-----------ih~~D~~~lr~~H~~ll~kGqvtTkYYR 291 (598)
T KOG3559|consen 226 ---MFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHH-----------IHGCDSFHLRCAHHLLLVKGQVTTKYYR 291 (598)
T ss_pred ---eEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHH-----------hhhhhHHHHHHHHHHHHhccccccHHHH
Confidence 11466778999999999999999999999999998733 3333322222222222222222233357
Q ss_pred EEccCCcEEEEEEEeeEeeCCC
Q 001564 837 FFARNGKYAECLLCVNKKLDRE 858 (1052)
Q Consensus 837 ~~~~dG~~~~v~~~~~pi~d~~ 858 (1052)
+..+.|.+.|+.-...-+.+..
T Consensus 292 ~l~k~ggwvwvqsyat~vHnSr 313 (598)
T KOG3559|consen 292 FLLKQGGWVWVQSYATFVHNSR 313 (598)
T ss_pred HHHcCCceEEEEEeeEEEeccc
Confidence 7889999999988777665543
No 117
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.11 E-value=0.24 Score=62.27 Aligned_cols=204 Identities=10% Similarity=0.031 Sum_probs=117.2
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHH
Q 001564 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFM 283 (1052)
Q Consensus 204 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~ 283 (1052)
+..+...+.+ ..+++++++.+-..++++.-+|||-|.-+|+.. +.+.-=....+-++. ..+ ....+.
T Consensus 11 l~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~--~~~--------~~~~~~ 77 (686)
T PRK15429 11 LFDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV--KYE--------DETVLA 77 (686)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch--hcc--------chhhhc
Confidence 3344444555 459999999999999999999999999999976 555321111111110 000 011111
Q ss_pred hCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHH--HHHHhcccceeEEEEEEEcCCcccCCCCCcccCCce
Q 001564 284 KNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHL--QYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRL 361 (1052)
Q Consensus 284 ~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~--~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~L 361 (1052)
.+++.++ -.+++|+-+++...+-..|--. .+-..| ++.+.|||.+. |+.
T Consensus 78 ~g~~g~v-------------l~~~~~l~~~~~~~~~~~~~l~~~~~~~~~--~~~lgvPl~~~--------------~~v 128 (686)
T PRK15429 78 HGPVRRI-------------LSRPDTLHCSYEEFCETWPQLAAGGLYPKF--GHYCLMPLAAE--------------GHI 128 (686)
T ss_pred cCcceEE-------------eecCceEEEchHHhhhccHHHhhcccccCc--cceEEeceeeC--------------Cee
Confidence 1211111 1234455444333322221111 122344 55889999998 999
Q ss_pred eeEEEeecCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH---HHHHHHHHHHh----ccCCCcccccC-C
Q 001564 362 WGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQIL-EKNI---LRTQTLLCDML----MRDAPLGIVTQ-S 432 (1052)
Q Consensus 362 WGLi~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~-~~~~---~~~~~~~~~~~----~~~~~~~~~~~-~ 432 (1052)
+|-|..-.+.+..++........+|+++.+..++.....+.... +... ...+..+.++. ....+..+... .
T Consensus 129 ~G~l~l~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~eIs~~l~s~~dl~ell~~I~ 208 (686)
T PRK15429 129 FGGCEFIRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVAITNAVLSRLDMDELVSEVA 208 (686)
T ss_pred EEEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 99999877778999999999999999999999975433221111 1111 11122233322 22222333332 4
Q ss_pred cchhhhcCCCEEEEEEC
Q 001564 433 PNIMDLVKCDGAALLYK 449 (1052)
Q Consensus 433 ~~l~~l~~~dg~~~~~~ 449 (1052)
..+..++++|.+.|+.-
T Consensus 209 ~~i~~~~~a~~~~I~L~ 225 (686)
T PRK15429 209 KEIHYYFDIDAISIVLR 225 (686)
T ss_pred HHHHHHhCCCEEEEEEE
Confidence 57888999999888753
No 118
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.08 E-value=0.0074 Score=81.29 Aligned_cols=137 Identities=12% Similarity=-0.062 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHH-cC
Q 001564 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLAL-QG 683 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l-~g 683 (1052)
...+.+++...+.++.+++++|+||+++|.+|+|+++|+++++++|.+.....+.+.....+ ...+.+........ ..
T Consensus 565 ~~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 643 (1197)
T PRK09959 565 KVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSDS-PFKDVFSNAHEVTAETK 643 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccccccccccC-chhhhHhHHHHHHHHHh
Confidence 34566788888889999999999999999999999999999999997654333322221111 11111111111111 01
Q ss_pred CccceEEEEEEEeccccCCceEE-EEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHH
Q 001564 684 QEEQNIQFEIKTHGSKINDDPIT-LIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEG 746 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~-v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~ 746 (1052)
........... ..+|...+ +.....+.....+...++++.++|||++++.+++++....
T Consensus 644 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~ 703 (1197)
T PRK09959 644 ENRTIYTQVFE----IDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERN 703 (1197)
T ss_pred hccccceeeEe----eecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHH
Confidence 11011111111 11222222 1111222222345556777888999999998887765433
No 119
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.06 E-value=0.0081 Score=74.86 Aligned_cols=112 Identities=13% Similarity=0.186 Sum_probs=76.9
Q ss_pred HHHHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCcc-ceEE
Q 001564 612 EAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQ 690 (1052)
Q Consensus 612 ~~~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~-~~~e 690 (1052)
......+..++++.++||+++|.+|+|+++|+++++++|++.++++|+++.++++... .+..++..+.. ...+
T Consensus 199 ~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~~------~l~~vl~~~~~~~~~~ 272 (638)
T PRK11388 199 NRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLTLPA------VLQQAIKQAHPLKHVE 272 (638)
T ss_pred HHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhccch------HHHHHHhcCCceeeEE
Confidence 3344556678999999999999999999999999999999999999999988774321 12233333321 1112
Q ss_pred EEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhH
Q 001564 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKT 736 (1052)
Q Consensus 691 ~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~ 736 (1052)
..+ ..+|..+++.+...|+.+..| .+++.+.+|++..++
T Consensus 273 ~~l-----~~~g~~~~~~v~~~Pi~~~~g--~~~v~~l~~~~~~~~ 311 (638)
T PRK11388 273 VTF-----ESQGQFIDAVITLKPIIEGQG--TSFILLLHPVEQMRQ 311 (638)
T ss_pred EEE-----ecCCceEEEEEEEEeecccCc--eEEEEEehhhHHHHH
Confidence 222 223566678888888865434 345666788887654
No 120
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.96 E-value=0.0017 Score=71.74 Aligned_cols=115 Identities=20% Similarity=0.214 Sum_probs=94.1
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEE
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1052)
+++.+++++.|.-|-.+|.++++.+.|+. .++|-.++.. +|+++..+-+|.+...+...+.....|..... ++-+.
T Consensus 290 ~e~naif~~lP~Ditfvdk~diV~ffs~~-~rif~rt~sv-iGr~v~~chpPksv~iv~ki~~~fksG~kd~~-efw~~- 365 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKNDIVRFFSGG-ERIFPRTPSV-IGRRVQLCHPPKSVHIVEKILKDFKSGEKDFA-EFWIN- 365 (409)
T ss_pred HHHHHHHhhCCCceEEecccceEEecCCc-ceecccChHh-hCCcccCCCCCchHHHHHHHHHHhhcCCcchH-HHhcc-
Confidence 56788999999888889999999999988 8899888776 79999988899998888888888887765432 33222
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHH
Q 001564 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1052)
Q Consensus 696 ~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~ 740 (1052)
.+..++.++..+++|.+|+..|++-++||||.-|..+-+
T Consensus 366 ------~~~~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ge 404 (409)
T COG2461 366 ------MGDKFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELEGE 404 (409)
T ss_pred ------CCCceEEEEEEEEEcCCCceeeeehhhhhhHHHHhccch
Confidence 334556678889999999999999999999998876543
No 121
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=96.93 E-value=0.0027 Score=72.43 Aligned_cols=98 Identities=24% Similarity=0.268 Sum_probs=73.3
Q ss_pred CCcEeeccHHHHHHhCCCcchhcCCccc-ccccCC--chHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEEEEEEE
Q 001564 635 DGLVNGWNTKIAELTGLSVDKAIGKHFL-TLVEDS--SIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNA 711 (1052)
Q Consensus 635 dg~I~~~N~a~~~l~G~~~eeliG~~~~-~l~~~~--~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~ 711 (1052)
|.-|+|+|+.+|++.||.+.|++.++.. .+.+.+ +...+ +.++..+...+... +++.. .+++..++|+.+..
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti-~k~~~t~eN~~~~q--fEill--yKKN~TPvW~~vqi 113 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTI-EKVRQTLENYETNQ--FEILL--YKKNRTPVWLLVQI 113 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhH-HHHHHHHHhhhhcc--eeeEe--eecCCCceEEEEEe
Confidence 6678999999999999999999999875 444433 22222 23444444433333 33332 26788999999999
Q ss_pred EEeecCCCCEEEEEEEEEccchhhHh
Q 001564 712 CASRDLHDNVVGVCFVAQDITPQKTV 737 (1052)
Q Consensus 712 ~pi~d~~G~v~gvv~i~~DITerk~a 737 (1052)
.|++++.+.++-+.+.+.|||..|+-
T Consensus 114 APIrNe~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 114 APIRNEKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred ecccCCCceEEEEEeecccchhhcCC
Confidence 99999999999999999999998864
No 122
>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]
Probab=96.85 E-value=0.083 Score=57.93 Aligned_cols=141 Identities=11% Similarity=0.080 Sum_probs=100.3
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEeEEeeHHHH
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~~~~dL~~l 969 (1052)
.|.+.+..+..||-+.+++|..-+.+.++...++..++....|++-+.++-.-+.. |.--| .....+..+...
T Consensus 302 iRk~vARELHDeIGQnITAIr~Qa~ivkR~~~~~q~kqaas~Ie~LslrI~~svrqLL~rLR------P~~LDdL~l~qa 375 (497)
T COG3851 302 IRKDVARELHDEIGQNITAIRTQAGIVKRAADNAQVKQAASLIEQLSLRIYDSVRQLLGRLR------PRQLDDLTLEQA 375 (497)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHhccCCHhHHhHHHHHHHHHHHHHHHHHHHHHhcC------CcccccccHHHH
Confidence 34455778899999999999999999998777777788888887777777776666 32111 112345567777
Q ss_pred HHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcH---HHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCCCceEE
Q 001564 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDS---IRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHL 1046 (1052)
Q Consensus 970 i~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~---~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~~~~~~ 1046 (1052)
+..++..+. ..++||.+.++...+- -.-|+ .-|.++..++++|-+||++ ...|+|.+...++ .
T Consensus 376 i~~l~~Em~--~~ergihcq~~~~~n~----~~ldet~rvTLyRl~QE~LNNI~KHA~-AS~V~i~l~~~~e-------~ 441 (497)
T COG3851 376 IRSLLREME--LEERGIHCQLDWRINE----TALDETQRVTLYRLCQELLNNICKHAD-ASAVTIQLWQQDE-------R 441 (497)
T ss_pred HHHHHHHhh--hhhcCeEEEeccccCc----ccCCcceeEeHHHHHHHHHHHHHhccc-cceEEEEEeeCCc-------E
Confidence 777777655 4566777776654321 12222 3388999999999999998 7889999888777 5
Q ss_pred EEEEE
Q 001564 1047 AYLEL 1051 (1052)
Q Consensus 1047 v~lev 1051 (1052)
++++|
T Consensus 442 l~Lei 446 (497)
T COG3851 442 LMLEI 446 (497)
T ss_pred EEEEE
Confidence 66665
No 123
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=96.81 E-value=0.00098 Score=55.77 Aligned_cols=42 Identities=24% Similarity=0.307 Sum_probs=35.2
Q ss_pred HHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhh
Q 001564 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLL 794 (1052)
Q Consensus 746 ~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l 794 (1052)
++|+.++++++ .||+++| +++|+++|+++++++||+ ..|+.+
T Consensus 1 e~~~~l~~~~~---~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSP---DGILIID-GGRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSS---SEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCc---cceEEEE-CCChHHhhHHHHHHhCCC---CCCCCH
Confidence 47899999999 8899999 889999999999999998 555553
No 124
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=96.80 E-value=0.0015 Score=74.42 Aligned_cols=100 Identities=14% Similarity=0.160 Sum_probs=78.4
Q ss_pred CCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEE
Q 001564 768 FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAEC 847 (1052)
Q Consensus 768 ~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v 847 (1052)
|.-|+|+|..|+++.||.+.|+..++..-.+... .+.+.+...++. ..+...+...+|+-+..|+...+|+
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyG-----Eltdk~ti~k~~----~t~eN~~~~qfEillyKKN~TPvW~ 109 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYG-----ELTDKGTIEKVR----QTLENYETNQFEILLYKKNRTPVWL 109 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeec-----cccchhhHHHHH----HHHHhhhhcceeeEeeecCCCceEE
Confidence 5678999999999999999999998742111111 233344444444 4455556678999999999999999
Q ss_pred EEEeeEeeCCCCCEEEEeeehHHHHHHHH
Q 001564 848 LLCVNKKLDREGAVTGVFCFLQLASHELQ 876 (1052)
Q Consensus 848 ~~~~~pi~d~~G~i~g~i~v~~DITerk~ 876 (1052)
.+...|++++...++-++|.+.|||.-||
T Consensus 110 ~vqiAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 110 LVQIAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred EEEeecccCCCceEEEEEeecccchhhcC
Confidence 99999999999999999999999997664
No 125
>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins. The fold of this domain consists of two layers, alpha/beta, which contains an 8-stranded mixed beta-sheet. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0005524 ATP binding; PDB: 3JZ3_A 3DGE_A 2C2A_A 2BU5_A 2BU8_A 2BU6_A 2BU7_A 2BU2_A 2BTZ_A 3K99_D ....
Probab=96.75 E-value=0.0017 Score=60.98 Aligned_cols=42 Identities=31% Similarity=0.578 Sum_probs=37.1
Q ss_pred EcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcCCCceEEEEEEE
Q 001564 1003 GDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1052)
Q Consensus 1003 ~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~~~~~~~v~lev 1051 (1052)
||+.+|.+||.||+.||++|+++++.|.|.+....+ .+.|+|
T Consensus 1 gd~~~l~~il~~ll~Na~~~~~~~~~I~i~~~~~~~-------~~~i~i 42 (111)
T PF02518_consen 1 GDPDRLRQILSELLDNAIKHSPEGGKIDITIEEDDD-------HLSIEI 42 (111)
T ss_dssp ETHHHHHHHHHHHHHHHHHHHHHTSEEEEEEEEETT-------EEEEEE
T ss_pred CcHHHHHHHHHHHHHHHHHHhcCCCEEEEEEEEecC-------eEEEEE
Confidence 799999999999999999999988999999998876 555555
No 126
>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]
Probab=96.67 E-value=0.051 Score=62.86 Aligned_cols=133 Identities=16% Similarity=0.229 Sum_probs=82.1
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHH----HcC---CCCCHHHHHHHHHHHHHHHHHHHHHhh-c-cccccccCceeeEe
Q 001564 891 KRLKALAYTKRQIRNPLSGIIFSRKM----MEG---TELGAEQKRLLHTSAQCQRQLHKILDD-S-DLDSIIDGYLDLEM 961 (1052)
Q Consensus 891 ~k~~~la~isHEirnPL~~I~g~~~l----L~~---~~l~~e~~~~l~~i~~~~~rl~~lI~d-L-d~srie~g~~~l~~ 961 (1052)
.-.+.-+.|+.|+..-|+-..+++++ |+. ....++..+.+..++...+---+-+.. | .|. +..
T Consensus 368 llmEERatIAReLHDSiAQsLS~LkiQvt~L~~~~~~~~~e~s~~~i~~~r~~Ln~~Y~QLRELLtTFR--------ltL 439 (574)
T COG3850 368 LLMEERATIARELHDSIAQSLSFLKIQVTLLKTAIPEELPEKAREIIAQIRQGLNDAYRQLRELLTTFR--------LTL 439 (574)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------Hhc
Confidence 34445578888888888877777665 333 244455666666655544433333333 2 232 122
Q ss_pred EEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEc-HHHHHHHHHHHHHhHhhccCCCCeEEEEEEEcc
Q 001564 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGD-SIRLQQVLADFLSISINFVPNGGQLMVSSSLTK 1037 (1052)
Q Consensus 962 ~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D-~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~ 1037 (1052)
.+-+|...+.+++..+..+ .|+++++++. +|+..+..+ ..++-||+.+-++||+||+. +..|+|++....
T Consensus 440 ~e~~L~~AL~~~~~~f~~q---tg~~~~l~~q--lp~~~lpa~qqvHlLqIvREAlsNa~KHa~-As~i~V~~~~~~ 510 (574)
T COG3850 440 QEAELPPALEQMLAEFSNQ---TGITVTLDYQ--LPPRALPAHQQVHLLQIVREALSNAIKHAQ-ASEIKVTVSQND 510 (574)
T ss_pred ccCchHHHHHHHHHHHHhc---cCCeEEEecc--CCCCCCCHHHHHHHHHHHHHHHHHHHHhcc-cCeEEEEEEecC
Confidence 3346777888888777765 4566665542 334223333 46688999999999999998 677777766653
No 127
>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=96.67 E-value=0.0054 Score=48.00 Aligned_cols=63 Identities=27% Similarity=0.384 Sum_probs=53.4
Q ss_pred HHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHH
Q 001564 617 EMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYL 679 (1052)
Q Consensus 617 ~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~ 679 (1052)
+++.+++.++++++.+|.++.+.++|+.+.+++|++..++.|+.+.+++++.+...+...+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (67)
T smart00091 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQR 64 (67)
T ss_pred hHHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHH
Confidence 356788999999999999999999999999999999999999988888887776655555443
No 128
>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=96.49 E-value=0.041 Score=53.95 Aligned_cols=109 Identities=16% Similarity=0.081 Sum_probs=83.9
Q ss_pred HHHHHHHHhCCceEEEEcC--CCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceE-EEE
Q 001564 616 SEMVRLIETATVPILAVDV--DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNI-QFE 692 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~--dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~-e~~ 692 (1052)
...+.+++ +|.+|+..|. +-.++|.|.++.+||+++-+++++.+..--..+..++.....+.++.+.+-...+ .++
T Consensus 32 ~~~~~L~~-ap~ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~GiR 110 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIR 110 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeEE
Confidence 34455666 9999998774 5689999999999999999999999988666777777788888888866543222 233
Q ss_pred EEEeccccCCceEEEE-EEEEEeecCCCCEEEEEEEEEc
Q 001564 693 IKTHGSKINDDPITLI-VNACASRDLHDNVVGVCFVAQD 730 (1052)
Q Consensus 693 ~~~~~~~~dg~~~~v~-v~~~pi~d~~G~v~gvv~i~~D 730 (1052)
+ .+.|.++++. ..+-.+.|.+|+..|...++.+
T Consensus 111 i-----ss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 111 I-----SSTGRRFRIERATVWNLIDEDGNYCGQAAMFSN 144 (148)
T ss_pred E-----cCCCCeEEEeceEEEEEEcCCCCEEEEEEEEee
Confidence 3 4568888776 5566789999999999888765
No 129
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=96.03 E-value=0.19 Score=58.21 Aligned_cols=138 Identities=14% Similarity=0.105 Sum_probs=74.3
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHcC--CCCCHHHHHHHH----HHHHHHHHHHHHHhhccccccccCceeeEeEE
Q 001564 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEG--TELGAEQKRLLH----TSAQCQRQLHKILDDSDLDSIIDGYLDLEMVE 963 (1052)
Q Consensus 890 ~~k~~~la~isHEirnPL~~I~g~~~lL~~--~~l~~e~~~~l~----~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~ 963 (1052)
..|.+....++..+-+-|+++.....+... ....++.++.+. .++++.+.+..+|.+|. +..
T Consensus 169 ~ER~RIARdLHDsv~q~L~~i~m~~~~~~~~~~~~~e~~~~~l~~i~~~~~e~l~evR~~v~~Lr------------p~~ 236 (365)
T COG4585 169 EERNRIARDLHDSVGQSLTAISMLLALLLLLADEDAEKAQEELKEIEKLLREALQEVRALVRDLR------------PVE 236 (365)
T ss_pred HHHHHHHHHHhhHHhhHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC------------Cch
Confidence 334444445555555556666652222211 222233444333 34444445555554442 122
Q ss_pred eeHHHHHHHHHHHHHhhccccCcEEEeeecC---CCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccCcC
Q 001564 964 FTLNEVLVASISQVMMKSNAKGIRIVNETAE---QIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQL 1040 (1052)
Q Consensus 964 ~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~---~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~~~ 1040 (1052)
.+-..+...+...+.......++.+..+... .+|+ .-...+..++++.|+||+||+. ...+.|++...++
T Consensus 237 l~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~L~~----~~e~~l~rivQEaltN~~rHa~-A~~v~V~l~~~~~-- 309 (365)
T COG4585 237 LEGLGLVEALRALLADFEERTGITVDLSLGSELERLPP----EAEDALFRIVQEALTNAIRHAQ-ATEVRVTLERTDD-- 309 (365)
T ss_pred hhcchHHHHHHHHHHHHHhhcCeEEEEecCcccccCCh----hHHHHHHHHHHHHHHHHHhccC-CceEEEEEEEcCC--
Confidence 2222233344334444444455666665543 2332 3467799999999999999998 6788888888777
Q ss_pred CCceEEEEEEE
Q 001564 1041 GQSVHLAYLEL 1051 (1052)
Q Consensus 1041 ~~~~~~v~lev 1051 (1052)
.+.++|
T Consensus 310 -----~l~l~V 315 (365)
T COG4585 310 -----ELRLEV 315 (365)
T ss_pred -----EEEEEE
Confidence 455555
No 130
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=95.87 E-value=0.008 Score=66.40 Aligned_cols=116 Identities=13% Similarity=0.079 Sum_probs=88.5
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhh
Q 001564 738 MDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNL 817 (1052)
Q Consensus 738 E~~L~~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~ 817 (1052)
.-+++.-...| +.++... .+|-+.|.+..|.|+|+++++++|+-+.|++|+...+ +.. ....+..+
T Consensus 150 afkiRAcnalF-aaLD~c~---eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~ad-lpk---------kdknradl 215 (775)
T KOG1229|consen 150 AFKIRACNALF-AALDECD---EAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEAD-LPK---------KDKNRADL 215 (775)
T ss_pred HHHHhhhHHHH-HHHhhhh---hhheeccchhHHHHhcHHHHhhhcchhhhhcCCchhh-ccc---------cccchhhh
Confidence 33445544444 3455555 6778899999999999999999999999999998531 111 12344557
Q ss_pred HHHHHhhhcCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeee
Q 001564 818 GIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCF 867 (1052)
Q Consensus 818 ~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v 867 (1052)
...++..+..+..+..+..-+++.|......+..+|+....|++..++..
T Consensus 216 ldtintcikkgke~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfvsl 265 (775)
T KOG1229|consen 216 LDTINTCIKKGKEAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFVSL 265 (775)
T ss_pred hhhhhHhhhcCccccchHHHhhccCCcccceEEEeeecCCCCceeeehhh
Confidence 77888888888888888888999999888889999999999998876643
No 131
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=95.39 E-value=0.023 Score=66.95 Aligned_cols=82 Identities=13% Similarity=0.098 Sum_probs=68.4
Q ss_pred EcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEEEEEEE
Q 001564 632 VDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNA 711 (1052)
Q Consensus 632 ~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~ 711 (1052)
...|-+|+|+.+++.+++||.+++++|+++.+++|..|.+.+.+.....+..|....-.++ ...++|+.+|+...+
T Consensus 280 hs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR----~lak~GGyvWlQTqA 355 (768)
T KOG3558|consen 280 HSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYR----LLAKNGGYVWLQTQA 355 (768)
T ss_pred eecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHH----HHHhcCCeEEEEeee
Confidence 5678999999999999999999999999999999999999999998888866543222222 247889999999888
Q ss_pred EEeecC
Q 001564 712 CASRDL 717 (1052)
Q Consensus 712 ~pi~d~ 717 (1052)
+.+.+.
T Consensus 356 TVi~~t 361 (768)
T KOG3558|consen 356 TVIYNT 361 (768)
T ss_pred EEEecC
Confidence 887764
No 132
>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=95.39 E-value=0.52 Score=59.41 Aligned_cols=153 Identities=14% Similarity=0.053 Sum_probs=90.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHH
Q 001564 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFM 283 (1052)
Q Consensus 204 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~ 283 (1052)
..+.+++|.+ +.+.+++++.+++.+.+++++++..+|-.++++ |........ +++. .+...|..+-..+ .+-.
T Consensus 307 ~l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~~-~~~~~~~~~-~~~~-~~~~~~~~~~~~~--~~~~ 379 (679)
T TIGR02916 307 WLRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGND-GLYRPAARW-NQPL-AQAFEPSDSAFCQ--FLQE 379 (679)
T ss_pred HHHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCCC-CEEeeehhc-CCCC-cccCCCCCCHHHH--HHHh
Confidence 3467777877 568899999999999999999999999665544 444433321 1111 1212222211111 2222
Q ss_pred hCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceee
Q 001564 284 KNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWG 363 (1052)
Q Consensus 284 ~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWG 363 (1052)
.+++--+.+....|.. .++.+..+..+..-++.+.+||..+ |++.|
T Consensus 380 ~~~v~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~l~vPL~~~--------------~~~~G 425 (679)
T TIGR02916 380 SGWIINLEEARSEPDH--------------------YSGLVLPEWLREIPNAWLIVPLISG--------------EELVG 425 (679)
T ss_pred CCCcccchhhcCCccc--------------------ccccccchhhhcCCCceEEEEeccC--------------CEEEE
Confidence 2332111111111100 0000111122223356899999977 99999
Q ss_pred EEEeecC-CCCCCCchhHHHHHHHHHHHHHHHHHH
Q 001564 364 LVVCHNT-TPRFVPFPLRYACEFLAQVFAIHVNKE 397 (1052)
Q Consensus 364 Li~~hh~-~pr~~~~~~r~~~~~l~~~~~~~l~~~ 397 (1052)
.+.+-+. +++.++.+++...+.++.+.+..+...
T Consensus 426 ~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~~~ 460 (679)
T TIGR02916 426 FVVLARPRTAGEFNWEVRDLLKTAGRQAASYLAQM 460 (679)
T ss_pred EEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9988665 677888899999999999988887653
No 133
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=95.24 E-value=1.1 Score=48.92 Aligned_cols=135 Identities=11% Similarity=0.060 Sum_probs=77.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCceee-EeEEeeHHHHHH
Q 001564 894 KALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDL-EMVEFTLNEVLV 971 (1052)
Q Consensus 894 ~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dL-d~srie~g~~~l-~~~~~dL~~li~ 971 (1052)
+....+..-|.+.|-+....++++.+.-.++.. .....+.+++..++.-|+.. .+|. .+.+ -...+.|...++
T Consensus 253 rlaRELHDGIsQ~LVs~k~~lela~~ql~~p~~-~a~~aieKaa~aL~~Ai~EVRRiSH----~LRP~~LDDLGL~aALe 327 (459)
T COG4564 253 RLARELHDGISQNLVSVKCALELAARQLNPPKG-GAHPAIEKAADALNGAIKEVRRISH----DLRPRALDDLGLTAALE 327 (459)
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHhccCCCCCC-CCchhhhhHHHHHHHHHHHHHHhcc----ccChhhhhhhhHHHHHH
Confidence 334455555667777777778887663222221 11233444455555555552 3332 1111 112334555566
Q ss_pred HHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 972 ~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
..++.++ ...|+.+.+.... .|......-..-|..|.++-++|-=+|+. ..+|+|.+....+
T Consensus 328 ~L~~~f~---~~tg~~itle~~~-~p~~l~~e~~talyRv~QEaltNIErHa~-Atrv~ill~~~~d 389 (459)
T COG4564 328 ALLEDFK---ERTGIEITLEFDT-QPGKLKPEVATALYRVVQEALTNIERHAG-ATRVTILLQQMGD 389 (459)
T ss_pred HHHHHhh---hccCeEEEEEecC-CcccCCcHHHHHHHHHHHHHHHHHHhhcC-CeEEEEEeccCCc
Confidence 6666655 5567777765532 12111223457799999999999999995 7788888777666
No 134
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=95.08 E-value=0.19 Score=54.38 Aligned_cols=112 Identities=13% Similarity=0.123 Sum_probs=79.5
Q ss_pred HHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCcc-ceEEEEEEEec
Q 001564 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQFEIKTHG 697 (1052)
Q Consensus 619 ~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~-~~~e~~~~~~~ 697 (1052)
..++++.+.+++++|.+|.|.|+|++++.+||.+...+.|..+.++++..+ .....+.++...+.. ..+++.+.
T Consensus 10 ~~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs--~ll~ll~q~~~~~~~~~~~~v~l~--- 84 (363)
T COG3852 10 GAILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPFGS--LLLSLLDQVLERGQPVTEYEVTLV--- 84 (363)
T ss_pred HhHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCc--HHHHHHHHHHHhcCCcccceeeee---
Confidence 357899999999999999999999999999999999999999999887655 334455555543332 22233332
Q ss_pred cccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHH
Q 001564 698 SKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1052)
Q Consensus 698 ~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~ 740 (1052)
..|....+.....|+....|.+ +..++-+....+..++
T Consensus 85 --~~g~~~~v~~~v~~v~~~~G~v---lle~~~~~~~~ridre 122 (363)
T COG3852 85 --ILGRSHIVDLTVAPVPEEPGSV---LLEFHPRDMQRRLDRE 122 (363)
T ss_pred --ecCccceEEEEEeeccCCCCeE---EEEechhHHHhHhhHH
Confidence 3588888998898887655544 3344555444444333
No 135
>PRK10547 chemotaxis protein CheA; Provisional
Probab=95.07 E-value=0.19 Score=62.02 Aligned_cols=70 Identities=14% Similarity=0.106 Sum_probs=52.4
Q ss_pred eHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHH---HHHHHHhHhhcc------------CCCCeE
Q 001564 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQV---LADFLSISINFV------------PNGGQL 1029 (1052)
Q Consensus 965 dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QV---L~NLL~NAik~~------------~~~g~I 1029 (1052)
.+..+++..-..++..+...+.++.+.+... . +..|+..+.++ |.||+.||++|. |.+|.|
T Consensus 344 p~~~~~~~~~rlvrdla~~~gk~v~l~~~g~--~--~~lD~~~l~~l~dpL~hLirNAidHgie~p~~R~~~gkp~~G~I 419 (670)
T PRK10547 344 PMEYVFSRFPRLVRDLAGKLGKQVELTLVGS--S--TELDKSLIERIIDPLTHLVRNSLDHGIELPEKRLAAGKNSVGNL 419 (670)
T ss_pred cHHHHHHHHHHHHHHHHHHcCCcEEEEEeCC--c--eecCHHHHHHHHHHHHHHHHHHHHhhccchhhHHhcCCCCCCce
Confidence 4567777777777777776666666665543 2 67899999998 689999999995 446888
Q ss_pred EEEEEEccC
Q 001564 1030 MVSSSLTKD 1038 (1052)
Q Consensus 1030 ~I~v~~~~~ 1038 (1052)
.|++...++
T Consensus 420 ~l~a~~~~~ 428 (670)
T PRK10547 420 ILSAEHQGG 428 (670)
T ss_pred EEEEEEcCC
Confidence 888776554
No 136
>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=94.96 E-value=0.11 Score=48.94 Aligned_cols=46 Identities=24% Similarity=0.204 Sum_probs=41.9
Q ss_pred HhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhc
Q 001564 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFG 800 (1052)
Q Consensus 752 le~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~ 800 (1052)
++..| .|++-+|.+|+|+..|.+-.++.|++++.++|++++.++-+
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 67777 89999999999999999999999999999999998766655
No 137
>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=94.94 E-value=0.24 Score=46.64 Aligned_cols=72 Identities=14% Similarity=0.321 Sum_probs=54.0
Q ss_pred HHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCccc-ccccCCchHHHHHHHHHHH-cCCccceEEEEE
Q 001564 622 IETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFL-TLVEDSSIDTVKRMLYLAL-QGQEEQNIQFEI 693 (1052)
Q Consensus 622 le~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~-~l~~~~~~~~~~~~l~~~l-~g~~~~~~e~~~ 693 (1052)
++..|-|++-+|.+|.|+..|.+-.++.|++++.++|+++. ++-|-.....+...+.... +|.-...+++.+
T Consensus 22 lD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~Ld~~f~yvf 95 (124)
T TIGR02373 22 FDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGTLNAMFDYVF 95 (124)
T ss_pred hhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCCCceEEEEEE
Confidence 78999999999999999999999999999999999999998 4545445555555555533 333333333333
No 138
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=94.76 E-value=0.083 Score=63.64 Aligned_cols=201 Identities=14% Similarity=0.120 Sum_probs=112.8
Q ss_pred eEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCc-------------cceEEEEEE
Q 001564 628 PILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-------------EQNIQFEIK 694 (1052)
Q Consensus 628 ~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~-------------~~~~e~~~~ 694 (1052)
.+++-+.+|+|+++...+..++|+.++-+.|..+.|++++.|...+...+....--.. .....+..+
T Consensus 194 ~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~vF~sfta~~~lp~ws~~s~~ds~~~~c~~~ks~fcR 273 (1114)
T KOG3753|consen 194 VVAVSFLDGRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGVFYSFTARYKLPLWSMGSSADSFTQECAEEKSFFCR 273 (1114)
T ss_pred EEEEeccCCcEEEeechhhhhccCchhhhccchhhhhcchhhhhhhhhccccccCccccccccccchhhhhhhhcceeee
Confidence 4555678999999999999999999999999999999999988776654433210000 000011111
Q ss_pred Eeccc-cCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHH--HHHHHHHHHHhCC---CCCCCCcccc--C
Q 001564 695 THGSK-INDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFT--RIEGDYKAIVQNP---NPLIPPIFGS--D 766 (1052)
Q Consensus 695 ~~~~~-~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~--~se~~lr~ile~~---~~li~~I~~~--D 766 (1052)
..+.. ......+ .+..++-.+..+-++..++.+.- ...++...-.+.. ++ --||.. .
T Consensus 274 isgr~~~~~~~~y-------------~PFRl~pyl~ev~~~~~~~s~~ccLllaerihSgYeAPrIps~--KriFtT~HT 338 (1114)
T KOG3753|consen 274 ISGRKDRENEIRY-------------HPFRLTPYLVEVRDQQGAESQPCCLLLAERIHSGYEAPRIPSN--KRIFTTTHT 338 (1114)
T ss_pred eecccCCcCcccc-------------CcccccceeEEeccccccCcCcceeehhhhhhcccccCcCCcc--cceeEeccC
Confidence 11100 0000000 11111111122222222222110 0000111111111 10 013433 3
Q ss_pred CCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcC-CCc-c-eeeEEEEccCCc
Q 001564 767 EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSG-QDP-E-KVPFGFFARNGK 843 (1052)
Q Consensus 767 ~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g-~~~-~-~~e~~~~~~dG~ 843 (1052)
..+-+..+..++.-++||-+.+++|+.++ .+.|++|+..+.+.-.+.+.. +.+ + .-.+|+...+|.
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~sil-----------~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~ 407 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTSIL-----------AFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGS 407 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccchh-----------hhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCc
Confidence 45667789999999999999999999976 667788877666666666543 333 2 556799999999
Q ss_pred EEEEEEEeeEe
Q 001564 844 YAECLLCVNKK 854 (1052)
Q Consensus 844 ~~~v~~~~~pi 854 (1052)
++.+.....-.
T Consensus 408 yv~ldTeWSsF 418 (1114)
T KOG3753|consen 408 YVRLDTEWSSF 418 (1114)
T ss_pred EEEEechhhhc
Confidence 98776554433
No 139
>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]
Probab=94.52 E-value=0.75 Score=54.89 Aligned_cols=116 Identities=16% Similarity=0.230 Sum_probs=63.4
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHh-hc-cccccccCceeeEeEEeeHH-HHHHH
Q 001564 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILD-DS-DLDSIIDGYLDLEMVEFTLN-EVLVA 972 (1052)
Q Consensus 896 la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~-dL-d~srie~g~~~l~~~~~dL~-~li~~ 972 (1052)
...-.|.+.|-|++|..++..-. .+...+.+ ..+.+++. ++ ...++ .+.... .+++.
T Consensus 263 sqi~pHfL~NtL~~I~~~~~~~~-------~~~~~~~v----~~l~~llR~~l~~~~~~---------~~l~~E~~~~~k 322 (456)
T COG2972 263 SQINPHFLYNTLETIRMLAEEDD-------PEEAAKVV----KALSKLLRYSLSNLDNI---------VTLEIELLLIEK 322 (456)
T ss_pred hhcchHHHHhHHHHHHHHHHhcC-------HHHHHHHH----HHHHHHHHHHhhCCCCe---------eeHHHHHHHHHH
Confidence 44668999999999998877421 12222222 22333333 12 22221 111111 23333
Q ss_pred HHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhcc----CCCCeEEEEEEEccC
Q 001564 973 SISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV----PNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 973 v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~----~~~g~I~I~v~~~~~ 1038 (1052)
-+..-+.....+ +++..++++...+ ..||. -+|+.|+.||++|. .++|+|.|.+...++
T Consensus 323 yl~iq~~r~~~~-le~~~~i~~~~~~---l~~p~---l~lqpLvENAi~hgi~~~~~~~~I~i~~~~~~~ 385 (456)
T COG2972 323 YLEIQKLRIGDR-LEVPLPIDEELEP---LIDPK---LVLQPLVENAIEHGIEPKRPGGSIAISAKKQDD 385 (456)
T ss_pred HHHHHHhccCcc-eEEEeccCccccc---ccCch---HHHhHHHHHHHHHhcccCCCCCEEEEEEEEcCC
Confidence 343333333332 5555555554332 35654 78888999999997 337899988877654
No 140
>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=94.52 E-value=0.084 Score=40.84 Aligned_cols=45 Identities=36% Similarity=0.372 Sum_probs=38.9
Q ss_pred HHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhh
Q 001564 747 DYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLL 794 (1052)
Q Consensus 747 ~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l 794 (1052)
+++.+++..+ .+++..|.++.+.++|+.+.+++|++..++.|..+
T Consensus 2 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (67)
T smart00091 2 RLRAILESLP---DGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46 (67)
T ss_pred hHHHHHhhCC---ceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcH
Confidence 3567788888 77799999999999999999999999988888764
No 141
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=94.49 E-value=2.4 Score=48.91 Aligned_cols=118 Identities=12% Similarity=0.080 Sum_probs=69.9
Q ss_pred HHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHHHHh
Q 001564 900 KRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMM 979 (1052)
Q Consensus 900 sHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~~~~ 979 (1052)
.|=+=|-||+|+.... ..++..++++-.+.. -+... |+-+ ..+.+.|.+=++++-..+..
T Consensus 373 PHFLFNaLNTIsa~IR-----~npdkAreLil~LS~---yfR~N---L~~~---------~~~~v~L~kEl~~v~AYl~I 432 (557)
T COG3275 373 PHFLFNALNTISAVIR-----RNPDKARELILYLST---YFRYN---LENN---------TQEIVTLSKELEHVNAYLSI 432 (557)
T ss_pred hHHHHHHHHHHHHHhc-----CChHHHHHHHHHHHH---HHHHH---hcCC---------cceEeehHHHHHHHHHHHHH
Confidence 7888888888866543 123334444333311 22222 2221 13567777777777665554
Q ss_pred h---ccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccC----CCCeEEEEEEEccCcCCCceEEEEEEE
Q 001564 980 K---SNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP----NGGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1052)
Q Consensus 980 ~---~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~----~~g~I~I~v~~~~~~~~~~~~~v~lev 1051 (1052)
. ... ..++.+++++++-+ +.. |. -+++=|+.|||||.- +.|.|+|+|...+. .++++|
T Consensus 433 EkARF~~-rL~v~i~id~~l~~--~~i-P~---filQPLVENAIKHG~~~~~~~g~V~I~V~~~d~-------~l~i~V 497 (557)
T COG3275 433 EKARFGD-RLDVVIDIDEELRQ--VQI-PS---FILQPLVENAIKHGISQLKDTGRVTISVEKEDA-------DLRIEV 497 (557)
T ss_pred HHHhcCC-ceEEEEecCHHHhh--ccC-ch---hhhhHHHHHHHHhcccchhcCCceEEEEEEeCC-------eEEEEE
Confidence 3 323 37777888777654 222 22 256668999999963 37899999988777 466665
No 142
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=94.29 E-value=0.16 Score=56.02 Aligned_cols=54 Identities=26% Similarity=0.364 Sum_probs=49.4
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCc
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSS 669 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~ 669 (1052)
-.+.+++++.|++++.+|..|.+..+|++++++||.+.+++.|++...++...+
T Consensus 80 l~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n 133 (511)
T COG3283 80 LALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN 133 (511)
T ss_pred HHHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence 356889999999999999999999999999999999999999999988876655
No 143
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=94.25 E-value=0.042 Score=60.96 Aligned_cols=104 Identities=10% Similarity=0.068 Sum_probs=77.2
Q ss_pred HHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCC-chHHHHHHHHHHHcCCccceEEEEEEEec
Q 001564 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDS-SIDTVKRMLYLALQGQEEQNIQFEIKTHG 697 (1052)
Q Consensus 619 ~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~-~~~~~~~~l~~~l~g~~~~~~e~~~~~~~ 697 (1052)
-+.++....+|-+.|.+..|.|+|++++.++|+-..|++|++..++-..+ .+..+...+..++..+. +++.....
T Consensus 160 FaaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgk----e~qG~~~a 235 (775)
T KOG1229|consen 160 FAALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGK----EAQGEEEA 235 (775)
T ss_pred HHHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCc----cccchHHH
Confidence 34577788899999999999999999999999999999999998774332 33444555566665444 33333334
Q ss_pred cccCCceEEEEEEEEEeecCCCCEEEEEE
Q 001564 698 SKINDDPITLIVNACASRDLHDNVVGVCF 726 (1052)
Q Consensus 698 ~~~dg~~~~v~v~~~pi~d~~G~v~gvv~ 726 (1052)
+++.|......+...|+....|++..++.
T Consensus 236 RRksgdS~dqh~~itP~~gqggkirhfvs 264 (775)
T KOG1229|consen 236 RRKSGDSCDQHFIITPFAGQGGKIRHFVS 264 (775)
T ss_pred hhccCCcccceEEEeeecCCCCceeeehh
Confidence 57778787788888999988888877653
No 144
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=94.05 E-value=0.91 Score=59.16 Aligned_cols=117 Identities=14% Similarity=0.114 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEc-CCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcC
Q 001564 605 IEGMKELEAVTSEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1052)
Q Consensus 605 ~~~~~eL~~~~~~l~~lle~~~~~I~~~D-~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g 683 (1052)
.+..++|++.++.++.+++++|.|+++++ .+|.++..|+.+..++|+...+. ...+. .....
T Consensus 323 ~~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~-------------~~~~~----~~~~~ 385 (924)
T PRK10841 323 ESNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHED-------------RQRLT----QIICG 385 (924)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChhH-------------HHHHH----HHHhc
Confidence 34456788888999999999999999997 69999999999999998644321 11111 11111
Q ss_pred CccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHH
Q 001564 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDY 748 (1052)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~l 748 (1052)
.... ..... ..++.. +.+...+.+. .+.. ..++++.|||++++++++|++..+.+
T Consensus 386 ~~~~--~~~~~----~~~~~~--~~i~~~~~~~-~~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~ 440 (924)
T PRK10841 386 QQVN--FVDVL----TSNNTN--LQISFVHSRY-RNEN-VAICVLVDVSARVKMEESLQEMAQAA 440 (924)
T ss_pred cccc--eeeEE----cCCCcE--EEEEEEeeee-cCce-EEEEEEEEhhHHHHHHHHHHHHHHHH
Confidence 1111 11111 112322 3333333332 2333 34567789999999999887654433
No 145
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=93.48 E-value=0.86 Score=44.87 Aligned_cols=109 Identities=13% Similarity=-0.003 Sum_probs=73.3
Q ss_pred HHHHHHHhCCCCCCCCccccC--CCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHh
Q 001564 746 GDYKAIVQNPNPLIPPIFGSD--EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNK 823 (1052)
Q Consensus 746 ~~lr~ile~~~~li~~I~~~D--~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~ 823 (1052)
..++.+.+ .| ++|+..+ .+-.++|.|.++.++++++-+++++.+.. .-..+.++......+.+
T Consensus 32 ~~~~~L~~-ap---~ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr-----------~sae~~~r~er~~lL~~ 96 (148)
T PF08670_consen 32 ELAKALWH-AP---FAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSR-----------LSAEEPERKERQSLLAQ 96 (148)
T ss_pred HHHHHHHc-CC---CEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHh-----------hccChhhHHHHHHHHHH
Confidence 45566666 56 5566654 45689999999999999999999998842 22234444445555666
Q ss_pred hhcCCCcceeeEEEEccCCcEEEEE-EEeeEeeCCCCCEEEEeeehH
Q 001564 824 AMSGQDPEKVPFGFFARNGKYAECL-LCVNKKLDREGAVTGVFCFLQ 869 (1052)
Q Consensus 824 ~l~g~~~~~~e~~~~~~dG~~~~v~-~~~~pi~d~~G~i~g~i~v~~ 869 (1052)
+...+-.....-.-..+.|+.+++. ..+=.+.|++|...|...++.
T Consensus 97 v~~qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~ 143 (148)
T PF08670_consen 97 VMQQGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAMFS 143 (148)
T ss_pred HHHhCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEe
Confidence 6555443333333356778877665 455678899999988766554
No 146
>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=93.05 E-value=0.69 Score=40.19 Aligned_cols=73 Identities=12% Similarity=0.128 Sum_probs=57.4
Q ss_pred HHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHHHH
Q 001564 899 TKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1052)
Q Consensus 899 isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~~~ 978 (1052)
+.|.+||-|+.|.+++.+-.+...+++.+..+..+..-..-|..+-+.|.-+. ....+++.+.+++++..+.
T Consensus 2 ~~HRVkNnLq~i~sll~lq~~~~~~~e~~~~L~~~~~RI~aia~vh~~L~~~~--------~~~~v~l~~yl~~L~~~l~ 73 (76)
T PF07568_consen 2 LHHRVKNNLQIISSLLRLQARRSEDPEAREALEDAQNRIQAIALVHEQLYQSE--------DLSEVDLREYLEELCEDLR 73 (76)
T ss_pred hHHhHHhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCC--------CCCeecHHHHHHHHHHHHH
Confidence 68999999999999999988877788888888888777766666655552222 3467899999999998775
Q ss_pred h
Q 001564 979 M 979 (1052)
Q Consensus 979 ~ 979 (1052)
.
T Consensus 74 ~ 74 (76)
T PF07568_consen 74 Q 74 (76)
T ss_pred H
Confidence 4
No 147
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=92.57 E-value=0.26 Score=60.32 Aligned_cols=57 Identities=11% Similarity=0.104 Sum_probs=40.5
Q ss_pred cccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCC---eEEEEEEEccC
Q 001564 982 NAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSLTKD 1038 (1052)
Q Consensus 982 ~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g---~I~I~v~~~~~ 1038 (1052)
..+.+.+...+..+.+.+-+..|...|.++|.|||.||++|++.+| .|.|.+...++
T Consensus 21 ~~~~iS~aEfF~kN~~~lgfD~d~r~L~tVLkNLIeNALDAs~~~gilp~I~V~Ie~~g~ 80 (795)
T PRK14868 21 SQREISIAEFFEKNKHMLGFDSGARGLVTAVKEAVDNALDATEEAGILPDIYVEIEEVGD 80 (795)
T ss_pred hccccceeeecccCcceeeccCCHHHHHHHHHHHHHHHHHhCcccCCCceEEEEEEECCC
Confidence 3455777766666655433444677899999999999999998655 57777655433
No 148
>smart00387 HATPase_c Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Probab=92.44 E-value=0.28 Score=44.69 Aligned_cols=36 Identities=39% Similarity=0.704 Sum_probs=30.7
Q ss_pred EcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 1003 GDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 1003 ~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+|+..|.+++.|++.||++|...++.|.|++.....
T Consensus 1 ~~~~~l~~~~~~l~~n~~~~~~~~~~v~i~~~~~~~ 36 (111)
T smart00387 1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGD 36 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEcCC
Confidence 477889999999999999999876888888776554
No 149
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=91.98 E-value=0.33 Score=54.24 Aligned_cols=113 Identities=12% Similarity=0.039 Sum_probs=79.0
Q ss_pred HHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhh
Q 001564 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAM 825 (1052)
Q Consensus 746 ~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l 825 (1052)
+.+.+++.+.| .-|-.+|.++++.+.|+. .++|-+++. ++|+.+. .+.+|..... ...+.+.+
T Consensus 290 ~e~naif~~lP---~Ditfvdk~diV~ffs~~-~rif~rt~s-viGr~v~-----------~chpPksv~i-v~ki~~~f 352 (409)
T COG2461 290 EELNAIFKHLP---VDITFVDKNDIVRFFSGG-ERIFPRTPS-VIGRRVQ-----------LCHPPKSVHI-VEKILKDF 352 (409)
T ss_pred HHHHHHHhhCC---CceEEecccceEEecCCc-ceecccChH-hhCCccc-----------CCCCCchHHH-HHHHHHHh
Confidence 45778999998 445788999999999998 888888765 5677742 2223444443 33444455
Q ss_pred cCCCcceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHH
Q 001564 826 SGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1052)
Q Consensus 826 ~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e 878 (1052)
..+.....++. .+..+.+ +.++..++.|.+|+..|++-+.+|||+-++-+
T Consensus 353 ksG~kd~~efw-~~~~~~~--i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 353 KSGEKDFAEFW-INMGDKF--IHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred hcCCcchHHHh-ccCCCce--EEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 55555666666 3344444 45677789999999999999999999765443
No 150
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.87 E-value=1.4 Score=43.23 Aligned_cols=126 Identities=15% Similarity=0.171 Sum_probs=78.6
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHH
Q 001564 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASIS 975 (1052)
Q Consensus 896 la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~ 975 (1052)
.+.+.|+|-.|..+|..-++||++..-+++...+ |..++......+ .|.|+-=|-.--.-..+|-.+.=.....
T Consensus 19 csRvCHDiISPvgAInnGLeLLdeg~addDAm~L---IrsSArnas~rL---qFaR~AFGAsgSag~~iDtgeaek~A~~ 92 (214)
T COG5385 19 CSRVCHDIISPVGAINNGLELLDEGGADDDAMDL---IRSSARNASVRL---QFARLAFGASGSAGASIDTGEAEKAAQD 92 (214)
T ss_pred HHHHHhhccCcHHHhhchhhhhccCCccHHHHHH---HHHHhhhHHHHH---HHHHHHhcccccccccccchhHHHHHHH
Confidence 5678999999999999999999987777665554 444454444433 3444433322222245555554333333
Q ss_pred HHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 976 QVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 976 ~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
.+.. ++ -++.++.+..+ +.-+.. ..+.||+.-|--+.|-||.+.++++.-..
T Consensus 93 ~~a~---ek-pe~~W~g~r~~----~~Kn~v---kllLNl~lia~~aiPrGG~~~vtle~~e~ 144 (214)
T COG5385 93 FFAN---EK-PELTWNGPRAI----LPKNRV---KLLLNLFLIAYGAIPRGGSLVVTLENPET 144 (214)
T ss_pred HHhc---cC-CcccccCChhh----cCcchH---HHHHHHHHHHcccCCCCCeeEEEeecCCc
Confidence 3322 22 45666655432 333433 56789999999999999999988876544
No 151
>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=91.22 E-value=8 Score=39.68 Aligned_cols=125 Identities=10% Similarity=0.151 Sum_probs=87.8
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCc
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 297 (1052)
++...++.+++-+.+.||+ -|+|- ..-.|+|=+-.+ -.. |-|.+ +.+..++.+..+++.+..+.+...
T Consensus 53 ~~~~~A~~~aeII~~~t~~-aVaIT-----Dr~~ILA~~G~g-~d~----~~~~~-is~~t~~~i~~gk~~~~~~~~~~~ 120 (180)
T TIGR02851 53 ELGDFAKEYAESLYQSLGH-IVLIT-----DRDTVIAVAGVS-KKE----YLNKP-ISDELEDTMEERKTVILSDTKDGP 120 (180)
T ss_pred chHHHHHHHHHHHHHHhCC-EEEEE-----CCCcEEEEECCC-hhh----cCCCc-cCHHHHHHHHcCCEEEecCCccce
Confidence 5566667777778889999 88885 244566655332 222 34444 999999999999998888654221
Q ss_pred cceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCC--CC
Q 001564 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR--FV 375 (1052)
Q Consensus 298 ~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr--~~ 375 (1052)
++.... ..| ...+.+++||+.+ |+.=|.|.-. ...+ .+
T Consensus 121 i~c~~~-----------------~~~--------~l~s~ii~Pl~~~--------------g~viGtLkly-~k~~~~~~ 160 (180)
T TIGR02851 121 IEIIDG-----------------QEF--------EYTSQVIAPIIAE--------------GDPIGAVIIF-SKEPGEKL 160 (180)
T ss_pred eccccC-----------------CCC--------CcceEEEEEEEEC--------------CeEEEEEEEE-ECCccCCC
Confidence 221100 111 1278899999988 9999966665 6666 78
Q ss_pred CchhHHHHHHHHHHHHHHH
Q 001564 376 PFPLRYACEFLAQVFAIHV 394 (1052)
Q Consensus 376 ~~~~r~~~~~l~~~~~~~l 394 (1052)
+..++.+.+-||+.||.||
T Consensus 161 ~~~e~~la~glA~lLS~QL 179 (180)
T TIGR02851 161 GEVEQKAAETAAAFLGKQM 179 (180)
T ss_pred CHHHHHHHHHHHHHHHHhh
Confidence 8899999999999999987
No 152
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=91.20 E-value=3.5 Score=49.48 Aligned_cols=185 Identities=17% Similarity=0.153 Sum_probs=92.6
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHH---hCCceEEEEcCCCcEeeccHHHHHHhCCCcc-hhcCCcccccccCCchHHH
Q 001564 598 SKLCDLKIEGMKELEAVTSEMVRLIE---TATVPILAVDVDGLVNGWNTKIAELTGLSVD-KAIGKHFLTLVEDSSIDTV 673 (1052)
Q Consensus 598 ~~l~~~~~~~~~eL~~~~~~l~~lle---~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~e-eliG~~~~~l~~~~~~~~~ 673 (1052)
.++.+...+...-|......|..++. ..+..+++.|.+|.++..+-.-......+.- =..|..+.+-...
T Consensus 56 ~el~~~rE~~~~LL~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WSE~~~G------ 129 (606)
T COG3284 56 TELREARERAEALLTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWSEPREG------ 129 (606)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecChhhhhhhhhhcccccccccccccc------
Confidence 33344444444445555555666555 4677889999999999764332111111110 0112222211100
Q ss_pred HHHHHHHHcCCccceEEEEEEEeccccCCceEEEEEEEEEeecCCCCEEEEEEEE---EccchhhHh------HHHHHHH
Q 001564 674 KRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVA---QDITPQKTV------MDKFTRI 744 (1052)
Q Consensus 674 ~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~---~DITerk~a------E~~L~~s 744 (1052)
.+.+-.++..++. +.+.-. -|-....+.+.+++.|++|.+|++.|+.-+. .|+++.-.. ...-+..
T Consensus 130 TNgIGTcLve~~a--VtI~~~---qHF~~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~~~~~~s~~~~~~iV~~~ar~I 204 (606)
T COG3284 130 TNGIGTCLVEGEA--VTIHGD---QHFIQAHHGLSCSAAPIFDEQGELVGVLDISSCRSDLSEASQPLTLAIVTDAARRI 204 (606)
T ss_pred ccchhhhhccCcc--eEEehh---hhHhhcccCceeeeeccccCCCcEEEEEEeccCCcchhhhhhHHHHHHHHHHHHHH
Confidence 1122223322221 111111 1112344567889999999999999986654 233332210 0011111
Q ss_pred HH-HHHH--------HHhCCCC----CCCCccccCCCCcceeechHHHHHhCCC-hHHHhhhh
Q 001564 745 EG-DYKA--------IVQNPNP----LIPPIFGSDEFGWCCEWNPAMVKLTGWK-REEVIDKL 793 (1052)
Q Consensus 745 e~-~lr~--------ile~~~~----li~~I~~~D~~g~i~~vN~a~~~i~G~~-~eeliG~~ 793 (1052)
|. .+.. .+-..|. .-.+.+.+|.+|+++-.|+++..+++.+ ..-++|.+
T Consensus 205 E~~~~~~~~~~~~~lr~~~~p~~~d~~~~~~lavd~~grvl~at~aA~~~La~~~~~~l~g~p 267 (606)
T COG3284 205 EAELFLAAFEGHWLLRIALAPDYLDSQSEALLAVDQDGRVLGATRAARQLLALTDRQRLIGQP 267 (606)
T ss_pred HHHHHHHhcCcchHHHHhcCccccCcccceeeeecCcchhhhccHHHHHhhccchhhHhhcCC
Confidence 11 1111 1111111 1145788999999999999999999988 44555555
No 153
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=90.94 E-value=1.7 Score=56.14 Aligned_cols=45 Identities=13% Similarity=0.020 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHhCCceEEEEc-CCCcEeeccHHHHHHhCC
Q 001564 607 GMKELEAVTSEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGL 651 (1052)
Q Consensus 607 ~~~eL~~~~~~l~~lle~~~~~I~~~D-~dg~I~~~N~a~~~l~G~ 651 (1052)
..++++..++.++.+++++|+|++++| .+|+|+.+|+++.+++|.
T Consensus 334 l~~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 334 MSHELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHHHHhCc
Confidence 346788888999999999999999999 689999999999999984
No 154
>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=90.91 E-value=0.44 Score=32.71 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=34.6
Q ss_pred eEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHH
Q 001564 834 PFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1052)
Q Consensus 834 e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITe 873 (1052)
++.+...+|..+|+.....++.+.+|.+.+++++..|+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 4566788999999999999999888999999999999884
No 155
>TIGR01925 spIIAB anti-sigma F factor. This model describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter. SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex. The SpoIIE phosphatase dephosphorylates SpoIIAA.
Probab=88.79 E-value=0.85 Score=44.43 Aligned_cols=36 Identities=8% Similarity=0.173 Sum_probs=28.2
Q ss_pred EcHHHHHHHHHHHHHhHhhccC---CCCeEEEEEEEccC
Q 001564 1003 GDSIRLQQVLADFLSISINFVP---NGGQLMVSSSLTKD 1038 (1052)
Q Consensus 1003 ~D~~~L~QVL~NLL~NAik~~~---~~g~I~I~v~~~~~ 1038 (1052)
.+...+.+++.|++.||++|+. .++.|.|++....+
T Consensus 35 ~~~~~l~~~l~eli~Nai~h~~~~~~~~~I~v~~~~~~~ 73 (137)
T TIGR01925 35 EELTDIKTAVSEAVTNAIIHGYEENCEGVVYISATIEDH 73 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEeCC
Confidence 3566799999999999999863 25788888776555
No 156
>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=87.01 E-value=1.8 Score=29.35 Aligned_cols=35 Identities=31% Similarity=0.372 Sum_probs=29.9
Q ss_pred ccCCceEEEEEEEEEeecCCCCEEEEEEEEEccch
Q 001564 699 KINDDPITLIVNACASRDLHDNVVGVCFVAQDITP 733 (1052)
Q Consensus 699 ~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITe 733 (1052)
.++|...|+.....++.+.+|.+.+++++.+|||+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 8 RKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred ecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 45677888888888888888999999999999986
No 157
>PF14501 HATPase_c_5: GHKL domain
Probab=85.15 E-value=1.7 Score=39.93 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=26.4
Q ss_pred cHHHHHHHHHHHHHhHhhccCC---CCeEEEEEEEccC
Q 001564 1004 DSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1004 D~~~L~QVL~NLL~NAik~~~~---~g~I~I~v~~~~~ 1038 (1052)
|+.-|-.+|.|||.||+++... ...|.|.+....+
T Consensus 2 ~~~dl~~il~nlldNAiea~~~~~~~~~I~i~~~~~~~ 39 (100)
T PF14501_consen 2 DDLDLCRILGNLLDNAIEACKKYEDKRFISISIREENG 39 (100)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEEecCC
Confidence 3456789999999999999754 4467777666555
No 158
>PF10090 DUF2328: Uncharacterized protein conserved in bacteria (DUF2328); InterPro: IPR018762 Members of this family of hypothetical bacterial proteins have no known function.
Probab=84.93 E-value=9.2 Score=39.34 Aligned_cols=113 Identities=12% Similarity=0.081 Sum_probs=72.4
Q ss_pred HHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh--ccccccccCceeeEeEEeeHHHHHHHHHHHHHhhccccC
Q 001564 908 SGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD--SDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKG 985 (1052)
Q Consensus 908 ~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d--Ld~srie~g~~~l~~~~~dL~~li~~v~~~~~~~~~~~~ 985 (1052)
.+|...+++|.+...+++.. .++.|.++++....-+.- +.|..-.+ -..+++.++-. .++.......
T Consensus 2 GAI~NGLELL~~~~~~~~~~-~~~LI~~Sa~~A~aRl~F~RlAFGaag~------~~~i~~~e~~~----~~~~~~~~~r 70 (182)
T PF10090_consen 2 GAINNGLELLDDEGDPEMRP-AMELIRESARNASARLRFFRLAFGAAGS------GQQIDLGEARS----VLRGYFAGGR 70 (182)
T ss_pred cchhhhHHHHcCCCCccchH-HHHHHHHHHHHHHHHHHHHHHHcCCCCC------CCCCCHHHHHH----HHHHHHhCCc
Confidence 46788889998755433322 777787777777766655 34443211 24566555443 3333334445
Q ss_pred cEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 986 IRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 986 i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+++.+..+.... +...-+++.||+.-|..+.|-||.|+|.+....+
T Consensus 71 ~~l~W~~~~~~~-------~k~~vklllnl~l~a~~alprGG~i~V~~~~~~~ 116 (182)
T PF10090_consen 71 ITLDWQVERDLL-------PKPEVKLLLNLLLCAEDALPRGGEITVSIEGSEG 116 (182)
T ss_pred eEEEccCccccC-------CHHHHHHHHHHHHHHHhhcCCCCEEEEEEeccCC
Confidence 777777666521 2234489999999999999999999998555444
No 159
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=84.66 E-value=6.7 Score=38.34 Aligned_cols=92 Identities=16% Similarity=0.090 Sum_probs=71.0
Q ss_pred EEEcCCC--cEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEEE
Q 001564 630 LAVDVDG--LVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITL 707 (1052)
Q Consensus 630 ~~~D~dg--~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v 707 (1052)
+.++.+| ++..+=.++++++|. |+.|+++.+++.+.....+...+..+.....+........ ..+|....+
T Consensus 43 le~~~~~~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~----~~~g~~~~~ 115 (137)
T PF07310_consen 43 LEVDDPGDFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAE----DADGRYLEY 115 (137)
T ss_pred EEEeCCCceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEe----cCCCCeeEE
Confidence 3344434 455788999999996 4579999999999999999999999997776544443333 456778888
Q ss_pred EEEEEEeecCCCCEEEEEEEE
Q 001564 708 IVNACASRDLHDNVVGVCFVA 728 (1052)
Q Consensus 708 ~v~~~pi~d~~G~v~gvv~i~ 728 (1052)
+.-..|+.+.+|.+..++|+.
T Consensus 116 e~l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 116 ERLLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred EEEEcccCCCCCCccEEEEec
Confidence 888999999999998888764
No 160
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=84.26 E-value=1.7 Score=52.05 Aligned_cols=36 Identities=8% Similarity=0.178 Sum_probs=28.2
Q ss_pred EEEcHHHHHHHHHHHHHhHhhccCCCC---eEEEEEEEc
Q 001564 1001 LYGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSLT 1036 (1052)
Q Consensus 1001 v~~D~~~L~QVL~NLL~NAik~~~~~g---~I~I~v~~~ 1036 (1052)
+.++...|.|++.|||.||++|++.+| .|.|.+...
T Consensus 30 f~~p~~~L~qVLkNLIeNAIDa~~~~gilp~I~I~I~~~ 68 (535)
T PRK04184 30 FDNPARALYTTVKELVDNSLDACEEAGILPDIKIEIKRV 68 (535)
T ss_pred ecCCHHHHHHHHHHHHHHHHHHhhhcCCCceEEEEEEEc
Confidence 445567899999999999999998655 577776553
No 161
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=84.15 E-value=0.66 Score=57.39 Aligned_cols=98 Identities=11% Similarity=0.087 Sum_probs=67.8
Q ss_pred ccCCCCcceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCC-cceeeEEEEccCC
Q 001564 764 GSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD-PEKVPFGFFARNG 842 (1052)
Q Consensus 764 ~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~-~~~~e~~~~~~dG 842 (1052)
-.+.+|.++++-.....+.||...++.|+..+ ...|+++...+...+........ ....-++++.++|
T Consensus 377 r~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~-----------~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~ 445 (803)
T KOG3561|consen 377 RSSSDGSFTFVDQRASAILGYQPQELLGRSSY-----------ESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNG 445 (803)
T ss_pred ccCcCCceeccccccccccccCchhhcCcccc-----------cccCccccchhhchHHHHHHhcccccccccccccCCC
Confidence 34568899999999999999999999999854 44556665555555544433332 3356678889999
Q ss_pred cEEEEEEEeeEeeCC-CCCEEEEeeehHHHH
Q 001564 843 KYAECLLCVNKKLDR-EGAVTGVFCFLQLAS 872 (1052)
Q Consensus 843 ~~~~v~~~~~pi~d~-~G~i~g~i~v~~DIT 872 (1052)
.+.|.........+. ...+.+++|....+.
T Consensus 446 ~~~~~~~~~~~~~n~~s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 446 SSIPNKSSAYLFSNPGSDEVEYIVCTNSNVP 476 (803)
T ss_pred CccccccccccccCCCccccceeeecccccc
Confidence 999887776665543 345556677666555
No 162
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=84.11 E-value=2.4 Score=47.07 Aligned_cols=45 Identities=22% Similarity=0.268 Sum_probs=42.2
Q ss_pred HHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhh
Q 001564 747 DYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLL 794 (1052)
Q Consensus 747 ~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l 794 (1052)
.+.+++++.+ ++++.+|..|.+...|++++++||.+.+++.|.+.
T Consensus 81 ~L~aLL~al~---~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~ 125 (511)
T COG3283 81 ALSALLEALP---EPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTA 125 (511)
T ss_pred HHHHHHHhCC---CceEEecccCceeecCHHHHHHhCCChhhhcCccH
Confidence 4678999999 89999999999999999999999999999999985
No 163
>cd00075 HATPase_c Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins
Probab=84.01 E-value=1.9 Score=38.29 Aligned_cols=31 Identities=42% Similarity=0.649 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhHhhccCC-CCeEEEEEEEccC
Q 001564 1008 LQQVLADFLSISINFVPN-GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1008 L~QVL~NLL~NAik~~~~-~g~I~I~v~~~~~ 1038 (1052)
|.+++.+|+.||++|... ++.|.|++....+
T Consensus 1 l~~~~~~ll~Na~~~~~~~~~~v~i~~~~~~~ 32 (103)
T cd00075 1 LQQVLLNLLSNAIKHTPEGGGRITISVERDGD 32 (103)
T ss_pred CHHHHHHHHHHHHHhCcCCCCeEEEEEEecCC
Confidence 468999999999999985 6778877766543
No 164
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=83.88 E-value=44 Score=43.30 Aligned_cols=134 Identities=13% Similarity=0.049 Sum_probs=79.5
Q ss_pred CHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCc
Q 001564 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1052)
Q Consensus 218 ~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~ 297 (1052)
..+..++.+.+.+.+++|.+++.++-|+.++...+... + |.. |..+.+...+.+-.. ....+
T Consensus 293 ~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---~------~~~-~~~~~~~~~~~~~~~--------~~~~~ 354 (828)
T PRK13837 293 ELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---P------GLT-PDPVWPDRLRALAST--------VKAAE 354 (828)
T ss_pred hhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---C------ccC-CCCCchHHHHHHHHH--------HhccC
Confidence 34689999999999999999999999988765443221 1 111 233344333333111 00000
Q ss_pred cceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCC-CCCC
Q 001564 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP-RFVP 376 (1052)
Q Consensus 298 ~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~ 376 (1052)
-.++.. .+...+....++...+....+++|+..+ ++++|++.+....+ ..++
T Consensus 355 ~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~g~l~~~~~~~~~~~~ 407 (828)
T PRK13837 355 RDVVFV-------------DRNGPVRKRSCLTRRGPALWACLAFKSG--------------DRIVALLGLGRQRYGLRPP 407 (828)
T ss_pred CceEEe-------------ecccchhhhcccccCCcceEEEEEeccC--------------CceEEEEEecccccCCCCC
Confidence 000000 0111223333444667888999999877 99999999877643 2334
Q ss_pred chhHHHHHHHHHHHHHHHHH
Q 001564 377 FPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 377 ~~~r~~~~~l~~~~~~~l~~ 396 (1052)
..+...++.++..++..+..
T Consensus 408 ~~~~~~l~~~~~~~~~~~~~ 427 (828)
T PRK13837 408 AGELQLLELALDCLAHAIER 427 (828)
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 56677777777777766643
No 165
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=83.74 E-value=2.3 Score=54.16 Aligned_cols=152 Identities=17% Similarity=0.210 Sum_probs=121.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCceeeEe
Q 001564 884 LSEQTALKRLKALAYTKRQIRNPLSGIIFSRK-MMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEM 961 (1052)
Q Consensus 884 ~ae~~~~~k~~~la~isHEirnPL~~I~g~~~-lL~~~~l~~e~~~~l~~i~~~~~rl~~lI~d-Ld~srie~g~~~l~~ 961 (1052)
.+.....++..++..+.|..++|.+.+.+... +++...+.+++.-.++...+....+..++.. .+.++...|....+.
T Consensus 378 e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~~~~~~~~~gt~~~~~ 457 (786)
T KOG0519|consen 378 EAHMAGKARIDFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPDSGLEIQTVMRSSNVFTSLIQADPDITRLYGGTGLGES 457 (786)
T ss_pred hhhhccchhhhHHHHhccccccccccccccchhhHhheEeccCCceeEehhhhhhhHHHHHhccccccccccCCCcccch
Confidence 33333444555666677999999999998887 4455667777777888888888889999999 899998888888888
Q ss_pred EEeeHHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHHHHHHHHhHhh--ccCCCCeEEEEEEEc
Q 001564 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISIN--FVPNGGQLMVSSSLT 1036 (1052)
Q Consensus 962 ~~~dL~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QVL~NLL~NAik--~~~~~g~I~I~v~~~ 1036 (1052)
..+.|..++.............+...+.+.+....|+ .+.+|..++.|++.++..++.+ ++..+....+.+...
T Consensus 458 i~~~l~~l~~~~~~~~~~~~~~~t~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~ 533 (786)
T KOG0519|consen 458 IVFSLVELMSGEISDISCISLGKTFSFTLDLLTNLPK-SVVGDEKRLFQIILDFNGMLALLIDTKLGREQIFQVLAE 533 (786)
T ss_pred hhccHHHHHHHHhhhhhhhccCceeeEEEEeccCCCc-cchhhhhhhhhhhhhhcchhhhhhccccCcceeEEEEec
Confidence 9999999999999999998888888888888888775 6888888899999999999998 777565544455444
No 166
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=83.35 E-value=3.5 Score=47.76 Aligned_cols=94 Identities=10% Similarity=-0.066 Sum_probs=72.7
Q ss_pred CCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEEEEEEEEEe
Q 001564 635 DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACAS 714 (1052)
Q Consensus 635 dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~v~v~~~pi 714 (1052)
|+..+.+..+...++||...|+.|.+..+++|-+|.-.+.....+.++.++..-+.++.. .++|++.|+..++..+
T Consensus 292 Dfa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~q----tk~grw~wvqssarll 367 (712)
T KOG3560|consen 292 DFALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQ----TKAGRWAWVQSSARLL 367 (712)
T ss_pred ccceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEe----ecCCcEEEeeccceee
Confidence 555666677888899999999999999999999998777777778887777655555554 5688888888666544
Q ss_pred ecCCCCEEEEEEEEEccch
Q 001564 715 RDLHDNVVGVCFVAQDITP 733 (1052)
Q Consensus 715 ~d~~G~v~gvv~i~~DITe 733 (1052)
+ .+|++..++.+-+-.++
T Consensus 368 y-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 368 Y-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred e-ecCCCCEEEecCCCccc
Confidence 4 58888888877666665
No 167
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=83.16 E-value=7.4 Score=32.29 Aligned_cols=47 Identities=17% Similarity=0.095 Sum_probs=36.7
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 001564 894 KALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKIL 944 (1052)
Q Consensus 894 ~~la~isHEirnPL~~I~g~~~lL~~~~l~~e~~~~l~~i~~~~~rl~~lI 944 (1052)
..+....||+.|-|+.|.|++++= -.++..+|+..+....+....++
T Consensus 14 ~~lR~~RHD~~NhLqvI~gllqlg----~~~~a~eYi~~~~~~~~~~s~l~ 60 (62)
T PF14689_consen 14 DSLRAQRHDFLNHLQVIYGLLQLG----KYEEAKEYIKELSKDLQQESELL 60 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677999999999999999963 34667888888888777776654
No 168
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=80.52 E-value=12 Score=44.39 Aligned_cols=146 Identities=16% Similarity=0.168 Sum_probs=99.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCc-eEEEEeccCCCCCccCCCCCCCCchHHHHHHH
Q 001564 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHG-EVVSEITKSGLEPYLGLHYPATDIPQAARFLF 282 (1052)
Q Consensus 204 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G-~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly 282 (1052)
+.++...+.+ ..++.+-++..|++|..-...+=+-||=-+.|++- +..| ..|+.+.-|.
T Consensus 5 Lr~i~E~va~--~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~A---TeGLnk~av~--------------- 64 (756)
T COG3605 5 LRRIVEKVAS--ALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELMA---TEGLNKPAVH--------------- 64 (756)
T ss_pred HHHHHHHHhc--ccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEe---ccccCccccc---------------
Confidence 3456667777 56999999999999999999999999999988742 2222 2333322221
Q ss_pred HhCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcc---cceeEEEEEEEcCCcccCCCCCcccCC
Q 001564 283 MKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMN---SIASLVMAVVVNDEEEEGDNTLPQKRK 359 (1052)
Q Consensus 283 ~~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmg---v~asl~~~i~~~~~~~~~~~~~~~~~~ 359 (1052)
.+++-. ...-|.++ ....+|++|+++. -||-. .|+..-| -.|.|.+||+.. |
T Consensus 65 ---~~~l~~--~eGLVG~v--~~~aePlNLsdAq---sHPsF-~Y~petgEE~Y~sFLGvPIi~~--------------~ 119 (756)
T COG3605 65 ---LVQLAF--GEGLVGLV--GRSAEPLNLADAQ---SHPSF-KYLPETGEERYHSFLGVPIIRR--------------G 119 (756)
T ss_pred ---eEEecC--CCchhhhh--hhccCCCChhhhh---hCCcc-ccccccchHHHHHhhccceeec--------------C
Confidence 011111 11111111 2346888888773 35543 3666555 367899999977 9
Q ss_pred ceeeEEEeecCCCCCCCchhHHHHHHHHHHHHHHH
Q 001564 360 RLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHV 394 (1052)
Q Consensus 360 ~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~~~~l 394 (1052)
++-|.++.++.++|.....+..+.+.++.+++--+
T Consensus 120 r~lGVLVVQqk~~R~y~E~Eve~L~T~A~~lA~iv 154 (756)
T COG3605 120 RLLGVLVVQQRELRQYDEDEVEFLVTLAMQLAEIV 154 (756)
T ss_pred ceeEEEEEecccccccchHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999888888877666544
No 169
>PRK03660 anti-sigma F factor; Provisional
Probab=80.19 E-value=3.4 Score=40.66 Aligned_cols=35 Identities=6% Similarity=0.204 Sum_probs=26.9
Q ss_pred cHHHHHHHHHHHHHhHhhccCC---CCeEEEEEEEccC
Q 001564 1004 DSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1004 D~~~L~QVL~NLL~NAik~~~~---~g~I~I~v~~~~~ 1038 (1052)
|...+.+++.|++.||++|... ++.|.|++....+
T Consensus 36 ~~~~l~~~l~eli~Nai~h~~~~~~~~~i~i~~~~~~~ 73 (146)
T PRK03660 36 ELTEIKTAVSEAVTNAIIHGYENNPDGVVYIEVEIEEE 73 (146)
T ss_pred HHHhHHHHHHHHHHHHHHHhcCCCCCCEEEEEEEECCC
Confidence 5677899999999999998643 3678887765444
No 170
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=79.96 E-value=6.8 Score=48.97 Aligned_cols=69 Identities=13% Similarity=0.143 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHhhccccCcEEEeeecCCCcceeEEEcHHHHHHH---HHHHHHhHhhcc------------CCCCeEE
Q 001564 966 LNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQV---LADFLSISINFV------------PNGGQLM 1030 (1052)
Q Consensus 966 L~~li~~v~~~~~~~~~~~~i~l~~~~~~~lp~~~v~~D~~~L~QV---L~NLL~NAik~~------------~~~g~I~ 1030 (1052)
+..++...-..++..+++.|-++.+.+..+ . ...|..-|+++ |..|+.||++|. |+.|.|+
T Consensus 392 ~~~vf~RfpR~VRdla~~lgK~V~L~ieG~--~--telDksIlE~l~dPL~HLvRNAvDHGIE~pE~R~a~GKp~~G~I~ 467 (716)
T COG0643 392 FEQVFSRFPRMVRDLARKLGKQVELVIEGE--D--TELDKSILERLGDPLTHLVRNAVDHGIETPEERRAAGKPEEGTIT 467 (716)
T ss_pred HHHHHhhccHHHHHHHHHhCCeeEEEEecC--C--eeehHHHHHHhcccHHHHHhcchhccCCCHHHHHHcCCCCcceEE
Confidence 447777777777777776666666666554 2 67898888877 899999999993 4478999
Q ss_pred EEEEEccC
Q 001564 1031 VSSSLTKD 1038 (1052)
Q Consensus 1031 I~v~~~~~ 1038 (1052)
++....++
T Consensus 468 L~A~~~gn 475 (716)
T COG0643 468 LSAYHEGN 475 (716)
T ss_pred EEEEcCCC
Confidence 88877666
No 171
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=79.58 E-value=15 Score=43.72 Aligned_cols=101 Identities=14% Similarity=0.201 Sum_probs=61.2
Q ss_pred HHHHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEE
Q 001564 614 VTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEI 693 (1052)
Q Consensus 614 ~~~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~ 693 (1052)
.+.-+..++.++|.||+.+|.++.+.|+|+-+..+|+- ++ +|....++ +.+.+.....+.+.. .+.+
T Consensus 73 ~~~~~~~al~nmPiGii~~~e~~~veW~Npf~~~if~~--~~-~~~~~~~~--------~~~il~~~~~~~~~~--~~~i 139 (655)
T COG3887 73 AEKSLEEALTNMPIGIILFNETNKVEWVNPFASKIFNK--NE-IGESLSEL--------IPEILKQLARNDEKQ--YIKI 139 (655)
T ss_pred HHHHHHHHHHhCCceEEEEcCCCceEEecHHHHHhcCh--hh-hhhhHHHH--------hHHHHHHHhcCCcce--EEEE
Confidence 34557788999999999999999999999999999972 22 34333322 333444444333221 2222
Q ss_pred EEeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHH
Q 001564 694 KTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRI 744 (1052)
Q Consensus 694 ~~~~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~s 744 (1052)
. +..+ .+ ..+.+.++ ..+-|+|++.+.+++++.+
T Consensus 140 ~--------e~~y-~~----~~~~~~~l----iYf~DvT~~~~~~~~~~~~ 173 (655)
T COG3887 140 N--------EKKY-DV----YFDSDKRL----IYFFDVTEEEAIEEEYENS 173 (655)
T ss_pred c--------ceEE-EE----EEecCCCE----EEEEeccHHHHHHHHHhcc
Confidence 1 1112 21 23334443 3357999999888776543
No 172
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=79.24 E-value=4.2 Score=45.33 Aligned_cols=87 Identities=10% Similarity=0.020 Sum_probs=63.5
Q ss_pred ceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCceEE
Q 001564 627 VPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPIT 706 (1052)
Q Consensus 627 ~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~~~ 706 (1052)
..+|....|.++++...++.+++||++.+++|+.+...++..|...+..+-...+..+....--++ ...+.|+++|
T Consensus 226 mFmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR----~l~k~ggwvw 301 (598)
T KOG3559|consen 226 MFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYR----FLLKQGGWVW 301 (598)
T ss_pred eEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHH----HHHcCCceEE
Confidence 345666778999999999999999999999999999999988888777766666544422111111 2355689999
Q ss_pred EEEEEEEeecC
Q 001564 707 LIVNACASRDL 717 (1052)
Q Consensus 707 v~v~~~pi~d~ 717 (1052)
+...+.-+.+.
T Consensus 302 vqsyat~vHnS 312 (598)
T KOG3559|consen 302 VQSYATFVHNS 312 (598)
T ss_pred EEEeeEEEecc
Confidence 98776655443
No 173
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=78.76 E-value=41 Score=35.93 Aligned_cols=137 Identities=15% Similarity=0.061 Sum_probs=71.6
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHh
Q 001564 205 AKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMK 284 (1052)
Q Consensus 205 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~ 284 (1052)
.++.-+|-. +.+++++++++.+.+++..+.|-|-+--|++++.- +++.. .++..+ .........
T Consensus 81 ~~l~l~LL~--a~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~~---~~~~~--------~~~~~~---~~~~~~~~~ 144 (225)
T PF04340_consen 81 HRLVLALLA--ARSLQELLQALDDGLREDFDVDAVRLRLFDDDAAP---GPSLT--------DHVWLS---RDAFAQVFI 144 (225)
T ss_dssp HHHHHHHHC----SHHHHHHHHHHHHHHTS--SEEEEEEE-SS------SEE--------------E----HHHHHHHHC
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHhcCCCeEEEEeecccccc---ccchh--------hccccc---HHHHHHHHH
Confidence 344555555 56999999999999999999999999999987662 11110 111111 111000000
Q ss_pred CCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHH---hcccceeEEEEEEEcCCcccCCCCCcccCCce
Q 001564 285 NKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYME---NMNSIASLVMAVVVNDEEEEGDNTLPQKRKRL 361 (1052)
Q Consensus 285 ~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~---nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~L 361 (1052)
..+ ..+.|. +--++..-...|= --+|+|...+|+. . ++.
T Consensus 145 ~~l-----------------~~~~p~------~G~~~~~~~~~lF~~~~~~v~S~AlipL~-~--------------~~~ 186 (225)
T PF04340_consen 145 DLL-----------------GLQQPY------CGRLSEEEAALLFGDEAAQVGSVALIPLG-S--------------GRP 186 (225)
T ss_dssp CCH-----------------TT---C------CCS--HHHHHHHHHHCHCC-SEEEEEEEE-S--------------SSE
T ss_pred HHh-----------------CCCCce------eCCCCcchhHHhcCCCCccccchheeecc-C--------------CCc
Confidence 000 000111 1111222222222 2457888899997 5 899
Q ss_pred eeEEEeecCC-CCCCCchhHHHHHHHHHHHHHHHH
Q 001564 362 WGLVVCHNTT-PRFVPFPLRYACEFLAQVFAIHVN 395 (1052)
Q Consensus 362 WGLi~~hh~~-pr~~~~~~r~~~~~l~~~~~~~l~ 395 (1052)
+|+|+-=... -|+-|---=.+.++|+.+++..|.
T Consensus 187 ~G~LalGS~D~~rF~p~mgT~fL~~La~vv~~~L~ 221 (225)
T PF04340_consen 187 IGLLALGSRDPDRFQPDMGTDFLEQLAEVVSAALE 221 (225)
T ss_dssp EEEEEEEESSTTCCCSTTTTHHHHHHHHHHHHHGG
T ss_pred eEEEEecCCChhhCCCCccHHHHHHHHHHHHHHHh
Confidence 9999865554 455554557788888888887653
No 174
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=77.52 E-value=4.7 Score=40.62 Aligned_cols=41 Identities=7% Similarity=0.130 Sum_probs=31.1
Q ss_pred cHHHHHHHHHHHHHhHhhccCC---CCeEEEEEEEccCcCCCceEEEEEEE
Q 001564 1004 DSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1052)
Q Consensus 1004 D~~~L~QVL~NLL~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~v~lev 1051 (1052)
+...+..++.+++.|||+|... +|.|.|++....+ .++++|
T Consensus 39 ~~~~l~lav~Ea~~Nai~Hg~~~~~~~~I~I~~~~~~~-------~l~i~V 82 (161)
T PRK04069 39 DIEDMKIAVSEACTNAVQHAYKEDEVGEIHIRFEIYED-------RLEIVV 82 (161)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCCeEEEEEEEECC-------EEEEEE
Confidence 4566888999999999999864 4678888777655 555555
No 175
>PRK10490 sensor protein KdpD; Provisional
Probab=76.53 E-value=1e+02 Score=40.27 Aligned_cols=49 Identities=8% Similarity=0.165 Sum_probs=38.2
Q ss_pred ceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCC-CCCCchhHHHHHHHHHHHHHHHHH
Q 001564 334 IASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP-RFVPFPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 334 ~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~p-r~~~~~~r~~~~~l~~~~~~~l~~ 396 (1052)
.+.+.+|+... ++++|.+.+..+.+ +.++.+.+...+.++.+++..+..
T Consensus 595 ~~~~~lPl~~~--------------~~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler 644 (895)
T PRK10490 595 VPYQILPLKSA--------------QKTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALER 644 (895)
T ss_pred CceEEEEEEEC--------------CEEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 34668999977 99999998877654 456777788888888888877754
No 176
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=76.07 E-value=5.6 Score=37.85 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=31.8
Q ss_pred cHHHHHHHHHHHHHhHhhccCCC---CeEEEEEEEccCcCCCceEEEEEEE
Q 001564 1004 DSIRLQQVLADFLSISINFVPNG---GQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1052)
Q Consensus 1004 D~~~L~QVL~NLL~NAik~~~~~---g~I~I~v~~~~~~~~~~~~~v~lev 1051 (1052)
+...+.-++.+++.||++|...+ +.|.|++....+ .++++|
T Consensus 28 ~~~~~~lav~E~~~Nav~H~~~~~~~~~v~v~~~~~~~-------~l~i~v 71 (125)
T PF13581_consen 28 DRDDLELAVSEALTNAVEHGYPGDPDGPVDVRLEVDPD-------RLRISV 71 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCCcEEEEEEEEcCC-------EEEEEE
Confidence 34578899999999999998753 578888777776 566665
No 177
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.48 E-value=5.1 Score=38.49 Aligned_cols=30 Identities=13% Similarity=0.395 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhHhhccCCCCeEEEEEEEccC
Q 001564 1008 LQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1052)
Q Consensus 1008 L~QVL~NLL~NAik~~~~~g~I~I~v~~~~~ 1038 (1052)
+.-+..+||.||+||.. +|.|+|+++....
T Consensus 64 vgYl~NELiENAVKfra-~geIvieasl~s~ 93 (184)
T COG5381 64 VGYLANELIENAVKFRA-TGEIVIEASLYSH 93 (184)
T ss_pred HHHHHHHHHHhhhcccC-CCcEEEEEEeccc
Confidence 44567789999999998 7899999887665
No 178
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=73.80 E-value=4.8 Score=47.72 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=28.8
Q ss_pred EEEcHHHHHHHHHHHHHhHhhccCCCC---eEEEEEEE
Q 001564 1001 LYGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSL 1035 (1052)
Q Consensus 1001 v~~D~~~L~QVL~NLL~NAik~~~~~g---~I~I~v~~ 1035 (1052)
+.++...|.|++.||+.||++|+..+| .|.|.+..
T Consensus 22 f~~~~~~L~~VlkELVeNAIDA~~~~g~~p~I~V~i~~ 59 (488)
T TIGR01052 22 YSGKIRSLTTVIHELVTNSLDACEEAGILPDIKVEIEK 59 (488)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhhccCCCceEEEEEEE
Confidence 567889999999999999999987655 67766654
No 179
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=72.53 E-value=7.6 Score=39.05 Aligned_cols=34 Identities=12% Similarity=0.190 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHhHhhccCC---CCeEEEEEEEccC
Q 001564 1005 SIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1005 ~~~L~QVL~NLL~NAik~~~~---~g~I~I~v~~~~~ 1038 (1052)
...+..++.+++.||++|... +|.|.|++....+
T Consensus 40 ~~~l~lav~Ea~~Nai~ha~~~~~~~~I~I~~~~~~~ 76 (159)
T TIGR01924 40 IEDLKIAVSEACTNAVKHAYKEGENGEIGISFHIYED 76 (159)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCeEEEEEEEeCC
Confidence 345888999999999999853 4688888776555
No 180
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=71.33 E-value=31 Score=44.06 Aligned_cols=46 Identities=9% Similarity=0.051 Sum_probs=38.9
Q ss_pred HHHHHHHHhCCceEEEEc-CCCcEeeccHHHHHHhCCCcchhcCCccccc
Q 001564 616 SEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGLSVDKAIGKHFLTL 664 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D-~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l 664 (1052)
+....++...|.|++++| .+|.|.|+|+.+.+++| .+ ++|+++.++
T Consensus 102 ~~~~~~l~~~p~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 102 QIGEEVLNELPIGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HHHHHHHHhCCceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 445667889999999999 79999999999999988 33 789998864
No 181
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=71.06 E-value=17 Score=35.49 Aligned_cols=85 Identities=15% Similarity=0.086 Sum_probs=68.5
Q ss_pred cceeechHHHHHhCCChHHHhhhhhhhhhhcCchhhhhccchhhHHhhHHHHHhhhcCCCcceeeEEEEccCCcEEEEEE
Q 001564 770 WCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLL 849 (1052)
Q Consensus 770 ~i~~vN~a~~~i~G~~~eeliG~~l~~~v~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~ 849 (1052)
++-.+-...++++|++ +.|+.+. ++..++....+...+..++....+..........+|....++.
T Consensus 52 r~RLaGt~i~~~~G~d---~tG~~~~-----------el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~ 117 (137)
T PF07310_consen 52 RYRLAGTRIVELFGRD---LTGRRLS-----------ELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYER 117 (137)
T ss_pred EEEEecHHHHHHhCCC---CCCCCHH-----------HhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEE
Confidence 4556788899999874 5577653 3444666777888899999998888888888899999999999
Q ss_pred EeeEeeCCCCCEEEEeeeh
Q 001564 850 CVNKKLDREGAVTGVFCFL 868 (1052)
Q Consensus 850 ~~~pi~d~~G~i~g~i~v~ 868 (1052)
..-|+.+.+|.+..++|.+
T Consensus 118 l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 118 LLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred EEcccCCCCCCccEEEEec
Confidence 9999999999888888764
No 182
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=69.43 E-value=2.5 Score=52.45 Aligned_cols=47 Identities=11% Similarity=0.208 Sum_probs=39.6
Q ss_pred HHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCChHHHhhhhhhhhh
Q 001564 749 KAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEV 798 (1052)
Q Consensus 749 r~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~~eeliG~~l~~~v 798 (1052)
..|++.+..++ |++..+|+|+||+.....++||..+|++|+++++.+
T Consensus 98 ~LmLeAlDGF~---fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~il 144 (803)
T KOG3561|consen 98 HLILEALDGFL---FVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDIL 144 (803)
T ss_pred HHHHHHhcCeE---EEEecCceEEEEecchHHhhCcCHHHHhcchHHHhc
Confidence 45777776444 788889999999999999999999999999987444
No 183
>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=67.63 E-value=6.1 Score=37.00 Aligned_cols=47 Identities=26% Similarity=0.410 Sum_probs=38.1
Q ss_pred eEEEEcC-CCcEeeccHHHHHHhCCC---cchhcCCcccccccCCchHHHH
Q 001564 628 PILAVDV-DGLVNGWNTKIAELTGLS---VDKAIGKHFLTLVEDSSIDTVK 674 (1052)
Q Consensus 628 ~I~~~D~-dg~I~~~N~a~~~l~G~~---~eeliG~~~~~l~~~~~~~~~~ 674 (1052)
.++++|. +++|+.++..+.+++|.+ .++++|+++.+++.+.....+.
T Consensus 17 ~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~ 67 (110)
T PF08446_consen 17 ALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLR 67 (110)
T ss_dssp EEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHH
T ss_pred EEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHH
Confidence 3456775 689999999999999999 9999999999999877655433
No 184
>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]
Probab=63.20 E-value=13 Score=36.74 Aligned_cols=36 Identities=17% Similarity=0.251 Sum_probs=30.3
Q ss_pred EcHHHHHHHHHHHHHhHhhccCC----CCeEEEEEEEccC
Q 001564 1003 GDSIRLQQVLADFLSISINFVPN----GGQLMVSSSLTKD 1038 (1052)
Q Consensus 1003 ~D~~~L~QVL~NLL~NAik~~~~----~g~I~I~v~~~~~ 1038 (1052)
.+..++.-++.+++.||++|+-. .|.|.|.+....+
T Consensus 36 ~~~~~l~~av~E~~~N~v~Ha~~~~~~~g~I~i~~~~~~~ 75 (146)
T COG2172 36 VDIADLAIAVSEALTNAVKHAYKLDPSEGEIRIEVSLDDG 75 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCceEEEEEEEcCC
Confidence 46788999999999999999753 4889988888766
No 185
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=60.42 E-value=27 Score=33.14 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=34.3
Q ss_pred ccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHH
Q 001564 697 GSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1052)
Q Consensus 697 ~~~~dg~~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L 741 (1052)
...++| ..+..+...++|.+|+++|+.++-.|+|....+..-|
T Consensus 74 ~~~~~G--k~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~~~L 116 (118)
T PF08348_consen 74 TKTKDG--KILRSSTFFIRDENGKLIGALCINFDISALEQAQNFL 116 (118)
T ss_pred ccCCCC--CEEEEEEEEEECCCCCEEEEEEEEeccHHHHHHHHHH
Confidence 445666 4466677789999999999999999999988776554
No 186
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=60.00 E-value=4e+02 Score=32.64 Aligned_cols=125 Identities=12% Similarity=0.092 Sum_probs=76.2
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHH
Q 001564 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFM 283 (1052)
Q Consensus 204 ~~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~ 283 (1052)
+-.+..+|.. +....+.|+.+.+++.+++|.+.+.+.-+++++......=...+ +.+.+ +
T Consensus 222 ly~~~~~l~~--~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~----~------------ 281 (569)
T PRK10600 222 LWQANRRLHS--RAPLCERLSPVLNGLQNLTLLRDIELRVYETDDEENHQEFTCQS--DMTCD----D------------ 281 (569)
T ss_pred HHHHHHHHhc--CcchHHHHHHHHHHHHHhcCCCceEEEEeccccccceeeccCCC--ccCcc----c------------
Confidence 3344566666 45788899999999999999999999987766544221111111 00000 0
Q ss_pred hCCeeEEecCCCCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceee
Q 001564 284 KNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWG 363 (1052)
Q Consensus 284 ~~~~r~i~d~~~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWG 363 (1052)
..|...+... .|.. .+ ...+.+||..+ ++.-|
T Consensus 282 -------~~~~~~~~~~--------------------~~~~------~~-~~~~~~~l~~~--------------~~~~G 313 (569)
T PRK10600 282 -------KGCQLCPRGV--------------------LPVG------DR-GTTLKWRLSDK--------------HGQYG 313 (569)
T ss_pred -------cccccccccC--------------------CCcC------CC-CceEEEEeecC--------------CcceE
Confidence 0011111000 0000 00 25678899866 88889
Q ss_pred EEEeecCCCCCCCchhHHHHHHHHHHHHHHHHH
Q 001564 364 LVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 364 Li~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~ 396 (1052)
.+...-..++.++.+.+..++.++.+++..+..
T Consensus 314 ~~~~~~~~~~~l~~~~~~ll~~l~~~l~~~l~~ 346 (569)
T PRK10600 314 ILLATLPQGRHLSHDQQQLVDTLVEQLTATLAL 346 (569)
T ss_pred EEEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 887654456778888999999999988876644
No 187
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=56.64 E-value=2.8e+02 Score=33.72 Aligned_cols=38 Identities=18% Similarity=0.022 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhC
Q 001564 743 RIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTG 783 (1052)
Q Consensus 743 ~se~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G 783 (1052)
+.+.-++.++.++| .||+.+|.++++.|+||-+..+|+
T Consensus 72 ~~~~~~~~al~nmP---iGii~~~e~~~veW~Npf~~~if~ 109 (655)
T COG3887 72 QAEKSLEEALTNMP---IGIILFNETNKVEWVNPFASKIFN 109 (655)
T ss_pred HHHHHHHHHHHhCC---ceEEEEcCCCceEEecHHHHHhcC
Confidence 34556778999999 889999999999999999999986
No 188
>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=56.52 E-value=31 Score=32.78 Aligned_cols=47 Identities=17% Similarity=0.116 Sum_probs=36.5
Q ss_pred cceeeEEEEccCCcEEEEEEEeeEeeCCCCCEEEEeeehHHHHHHHHHH
Q 001564 830 PEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1052)
Q Consensus 830 ~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~i~g~i~v~~DITerk~~e 878 (1052)
.....+.-..++|+.. ..+...++|.+|+++|++|+-.|+|.-.+..
T Consensus 67 ~~~~nY~~~~~~Gk~l--rSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~ 113 (118)
T PF08348_consen 67 DYIINYKTKTKDGKIL--RSSTFFIRDENGKLIGALCINFDISALEQAQ 113 (118)
T ss_pred CccccccccCCCCCEE--EEEEEEEECCCCCEEEEEEEEeccHHHHHHH
Confidence 3455566778899654 5677788999999999999999999765443
No 189
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=54.14 E-value=21 Score=43.98 Aligned_cols=35 Identities=11% Similarity=0.223 Sum_probs=25.5
Q ss_pred EEcHHH---HHHHHHHHHHhHhhccCCCC---eEEEEEEEc
Q 001564 1002 YGDSIR---LQQVLADFLSISINFVPNGG---QLMVSSSLT 1036 (1052)
Q Consensus 1002 ~~D~~~---L~QVL~NLL~NAik~~~~~g---~I~I~v~~~ 1036 (1052)
.|++.. |.+|+.||+.||++|...+| .|.|.+...
T Consensus 28 lGf~~~~r~L~~VVkELVeNAIDA~~~~g~~p~I~V~I~~~ 68 (659)
T PRK14867 28 LGYSGKLRSMTTIIHELVTNSLDACEEAEILPDIKVEIEKL 68 (659)
T ss_pred eechhHHHHHHHHHHHHHHHHHHHhhccCCCceEEEEEEEC
Confidence 444444 55999999999999987543 677776553
No 190
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=47.11 E-value=85 Score=29.48 Aligned_cols=76 Identities=21% Similarity=0.247 Sum_probs=42.9
Q ss_pred CCceEEEEcCCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccCCce
Q 001564 625 ATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDP 704 (1052)
Q Consensus 625 ~~~~I~~~D~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dg~~ 704 (1052)
--+-+++.|.+|.++.-+ ..+.+|+++.+ - + ...+++|+. +.... ...+
T Consensus 38 ~~~~i~v~D~~g~~l~~s----------~~~~iG~~~~~-~---~-------~~~aL~G~~-----~~~~~---~~~~-- 86 (116)
T PF14827_consen 38 DIDYIVVTDRDGIVLAHS----------DPERIGDRYSD-E---D-------VRKALQGKS-----YTSVS---QGTG-- 86 (116)
T ss_dssp T-SEEEEECTTSBECE-S----------SCCCTTSB-SS-C---C-------HCHHCCT-------EEEEE---ECTT--
T ss_pred CCeEEEEEcCCCCEEEcC----------ChHHcCCcccC-C---C-------hhhhhcCCc-----eEEee---ecCC--
Confidence 345688899999987653 34557887663 1 1 234555532 11111 1223
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEEcc
Q 001564 705 ITLIVNACASRDLHDNVVGVCFVAQDI 731 (1052)
Q Consensus 705 ~~v~v~~~pi~d~~G~v~gvv~i~~DI 731 (1052)
-+......|++|.+|+++|++.+...+
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 334456789999999999999887543
No 191
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=46.90 E-value=33 Score=42.53 Aligned_cols=80 Identities=14% Similarity=0.094 Sum_probs=58.3
Q ss_pred CCCcEeeccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccc---eEEEEEEEeccccCCceEEEEEE
Q 001564 634 VDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQ---NIQFEIKTHGSKINDDPITLIVN 710 (1052)
Q Consensus 634 ~dg~I~~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~---~~e~~~~~~~~~~dg~~~~v~v~ 710 (1052)
..+.|..+..++..++||-+.++||+++..++|++|+..+.+....+++.+... ...+++. ..+|..+.+...
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~----aqNG~yv~ldTe 414 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFC----AQNGSYVRLDTE 414 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeee----ecCCcEEEEech
Confidence 466678899999999999999999999999999999998888888777543211 1123333 346777777665
Q ss_pred EEEeecC
Q 001564 711 ACASRDL 717 (1052)
Q Consensus 711 ~~pi~d~ 717 (1052)
...+.+.
T Consensus 415 WSsFVNP 421 (1114)
T KOG3753|consen 415 WSSFVNP 421 (1114)
T ss_pred hhhccCh
Confidence 5555444
No 192
>PF07536 HWE_HK: HWE histidine kinase; InterPro: IPR011102 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. The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as IPR003661 from INTERPRO []. In [], the HWE family was defined by the presence of conserved a H residue and a WXE motifs and was limited to members of the proteobacteria. However, many homologues of this domain are lack the WXE motif. Furthermore, homologues are found in a wide range of Gram-positive and Gram-negative bacteria as well as in several archaea.; GO: 0004673 protein histidine kinase activity
Probab=43.90 E-value=1.2e+02 Score=26.89 Aligned_cols=68 Identities=10% Similarity=0.137 Sum_probs=42.8
Q ss_pred HHHHhhhHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHHHHHHHHHHhhccccccccCceeeEeEEeeHHHHHHHHHHH
Q 001564 899 TKRQIRNPLSGIIFSRKMMEGTELGAE--QKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQ 976 (1052)
Q Consensus 899 isHEirnPL~~I~g~~~lL~~~~l~~e--~~~~l~~i~~~~~rl~~lI~dLd~srie~g~~~l~~~~~dL~~li~~v~~~ 976 (1052)
+.|.+||-|+.|.++...-.+...+.+ ...+..++..-+ +...++.+ -....++|.++++..+.-
T Consensus 2 L~HRvKN~lavv~ai~~~t~r~~~s~~~~~~~~~~Rl~ALa-~a~~ll~~------------~~~~~~~L~~lv~~~l~p 68 (83)
T PF07536_consen 2 LNHRVKNLLAVVQAIARQTARSAASVEEFAEAFSGRLQALA-RAHDLLSR------------SDWEGVSLRDLVEAELAP 68 (83)
T ss_pred chhHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHH-HHHHHHhc------------CCCCCccHHHHHHHHHHh
Confidence 689999999999999998876433332 344444443322 22233211 123567899999988776
Q ss_pred HHh
Q 001564 977 VMM 979 (1052)
Q Consensus 977 ~~~ 979 (1052)
+..
T Consensus 69 ~~~ 71 (83)
T PF07536_consen 69 YGS 71 (83)
T ss_pred ccC
Confidence 554
No 193
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=42.18 E-value=3.7e+02 Score=26.96 Aligned_cols=109 Identities=20% Similarity=0.207 Sum_probs=75.6
Q ss_pred hhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHH---HHHHHHhCCeeEEecCCCCccceeeCCCCCC
Q 001564 232 ELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQA---ARFLFMKNKVRMIVDCRARHVKVLQDEKLPF 308 (1052)
Q Consensus 232 ~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~---ar~ly~~~~~r~i~d~~~~~~~~~~~~~~~~ 308 (1052)
.+..+|=|=.|.++ +++-| +.||-|. -+=.+||-- =..--.+|++-.|.||++-|=.+-=++
T Consensus 47 ~l~~~nW~GFYl~~---~~~Lv-------LgPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~ghiaCD~---- 111 (163)
T COG1956 47 RLPDVNWVGFYLLE---GDELV-------LGPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHAFPGHIACDA---- 111 (163)
T ss_pred hccCCceEEEEEec---CCeEE-------EecccCC-cceEEeccCcchhHHHHhcCCeEEecccccCCCcccccc----
Confidence 34448888888888 55555 3566665 333455521 112346789999999998874332111
Q ss_pred cccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCCCCchhHHHHHHHHH
Q 001564 309 DLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQ 388 (1052)
Q Consensus 309 ~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~ 388 (1052)
-++|-+++||+.+ |++-|-|=.-..+|-+.+...+...+.++.
T Consensus 112 -----------------------as~SEIVvPi~~~--------------g~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~ 154 (163)
T COG1956 112 -----------------------ASNSEIVVPIFKD--------------GKLIGVLDIDSPTPGRFDEEDEAGLEKLAA 154 (163)
T ss_pred -----------------------ccCceEEEEEEEC--------------CEEEEEEecCCCCcccCCHHHHHHHHHHHH
Confidence 2478899999988 999999988888888888888887777776
Q ss_pred HHHH
Q 001564 389 VFAI 392 (1052)
Q Consensus 389 ~~~~ 392 (1052)
.+..
T Consensus 155 ~l~~ 158 (163)
T COG1956 155 LLEK 158 (163)
T ss_pred HHHH
Confidence 6543
No 194
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=42.07 E-value=3.9e+02 Score=28.28 Aligned_cols=38 Identities=13% Similarity=0.063 Sum_probs=34.3
Q ss_pred HHHHHHHHhCCceEEEEcCCCcEeeccHHHHHHhCCCc
Q 001564 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSV 653 (1052)
Q Consensus 616 ~~l~~lle~~~~~I~~~D~dg~I~~~N~a~~~l~G~~~ 653 (1052)
+.+..+++..|.|+++-+.+|.+++.|.++.++|.-..
T Consensus 19 ~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcC
Confidence 46788999999999999999999999999999997443
No 195
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.58 E-value=1e+02 Score=31.50 Aligned_cols=98 Identities=13% Similarity=0.089 Sum_probs=70.3
Q ss_pred CCceEE-EEcCCCcEe--eccHHHHHHhCCCcchhcCCcccccccCCchHHHHHHHHHHHcCCccceEEEEEEEeccccC
Q 001564 625 ATVPIL-AVDVDGLVN--GWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKIN 701 (1052)
Q Consensus 625 ~~~~I~-~~D~dg~I~--~~N~a~~~l~G~~~eeliG~~~~~l~~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~d 701 (1052)
.++-++ ..|.+|.+. .+-...|.+|| .|+-|..+..++.+.+......++..+.+...+.-+..+ +....
T Consensus 57 L~d~FiL~~~~~G~~~FRLAGTriC~LfG---RELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~d----g~s~~ 129 (209)
T COG5388 57 LPDVFILERDGRGKLPFRLAGTRICDLFG---RELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTAD----GRSHG 129 (209)
T ss_pred cCceEEEeccCCCCceEEecccchhhhhc---hhhcCCchhHhccccchHHHHHHHHHHhhccCceEEecc----hhhcc
Confidence 444333 344556544 56788889998 578899999999999999999988888876665433333 33556
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEEE
Q 001564 702 DDPITLIVNACASRDLHDNVVGVCFVAQ 729 (1052)
Q Consensus 702 g~~~~v~v~~~pi~d~~G~v~gvv~i~~ 729 (1052)
|...-+++-..|.....|+...+.|.+.
T Consensus 130 G~sl~fEmLl~PL~~~~g~~~R~LGais 157 (209)
T COG5388 130 GRSLGFEMLLAPLQGASGETDRFLGAIS 157 (209)
T ss_pred CcccceeeeeecccCCCCCccchhhhcc
Confidence 7778888899999988888666666543
No 196
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=33.64 E-value=7.9e+02 Score=29.26 Aligned_cols=121 Identities=19% Similarity=0.268 Sum_probs=80.6
Q ss_pred HHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccC----CCCCCCCchHHH-HHHHHhCCeeEEecCC
Q 001564 220 ERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLG----LHYPATDIPQAA-RFLFMKNKVRMIVDCR 294 (1052)
Q Consensus 220 ~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg----~~~pa~dip~~a-r~ly~~~~~r~i~d~~ 294 (1052)
.+=+..+++-|.+.+|.+=|.+ .-+..+-.|.| +|.|-++|-... |.--..|.+ +..|-.
T Consensus 224 ~es~~~va~Ii~~~~~~~AVai--------------Td~e~ilA~vg~g~dhhi~g~~i~s~~t~~ai~~g~v-v~~~~~ 288 (557)
T COG3275 224 EESLMKVAEIIYEELGAGAVAI--------------TDREKLLAFVGIGDDHHIPGKPIISSLTRKAIKTGEV-VYADGN 288 (557)
T ss_pred hhhHHHHHHHHHHHhCCCeEEe--------------cCHHHHHHhhcccccccCCCCeeccHHHHHHHhhCCE-EEEccc
Confidence 3445667777888899887754 33444444444 577888775444 333344443 222222
Q ss_pred CCccceeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCC
Q 001564 295 ARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRF 374 (1052)
Q Consensus 295 ~~~~~~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~ 374 (1052)
.. +. | +-.-||+ .|.+++|+--+ |+.-|-|--.-+.|+-
T Consensus 289 e~----~~------------c---sh~~c~l--------~s~lViPL~~~--------------g~ViGTiK~y~~~~~l 327 (557)
T COG3275 289 EV----YE------------C---SHPTCKL--------GSALVIPLRGK--------------GRVIGTIKLYEAKARL 327 (557)
T ss_pred hh----hc------------c---CCCCCCc--------CCceEeecccC--------------CceeeeEEEEeccHhH
Confidence 22 00 0 1123444 88899999744 8889999888899999
Q ss_pred CCchhHHHHHHHHHHHHHHHHH
Q 001564 375 VPFPLRYACEFLAQVFAIHVNK 396 (1052)
Q Consensus 375 ~~~~~r~~~~~l~~~~~~~l~~ 396 (1052)
++.-+|++.+-+++.+|.|+..
T Consensus 328 is~~~r~la~Gia~l~SaQie~ 349 (557)
T COG3275 328 ISSINRELAEGIAQLLSAQIEA 349 (557)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999863
No 197
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=32.47 E-value=1.2e+03 Score=30.14 Aligned_cols=57 Identities=14% Similarity=-0.013 Sum_probs=41.0
Q ss_pred hhhHhHHHHHH-------HHHHHHHHHhCCCCCCCCccccC-CCCcceeechHHHHHhCCChHHHhhhhhh
Q 001564 733 PQKTVMDKFTR-------IEGDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREEVIDKLLL 795 (1052)
Q Consensus 733 erk~aE~~L~~-------se~~lr~ile~~~~li~~I~~~D-~~g~i~~vN~a~~~i~G~~~eeliG~~l~ 795 (1052)
+-|+.+.+|.. ....-+.++...| .|++++| .+|.|.|.|+.|.+++| .+ ++|+++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~p---~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 82 QIKRLQNKLSLWSKLSFHVSQIGEEVLNELP---IGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHhCC---ceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 34556655532 2333456777888 7889999 79999999999999987 23 7888753
No 198
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=32.42 E-value=25 Score=43.42 Aligned_cols=27 Identities=41% Similarity=0.567 Sum_probs=21.8
Q ss_pred hhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHH
Q 001564 232 ELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARF 280 (1052)
Q Consensus 232 ~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ 280 (1052)
.|||++||+| |||||| |.+|-.+.-|.
T Consensus 614 NLTgAnRVII--fDPdWN--------------------PStD~QAreRa 640 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN--------------------PSTDNQARERA 640 (923)
T ss_pred ccccCceEEE--ECCCCC--------------------CccchHHHHHH
Confidence 6899999999 689987 67887666655
No 199
>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=32.39 E-value=37 Score=29.45 Aligned_cols=57 Identities=16% Similarity=0.075 Sum_probs=35.8
Q ss_pred eEEEEEEEEEeecCCCCEEEEEEEEEccchhhHhHHHHHHHHHHHHHHHhCCCCCCC-CccccCCCCcceee
Q 001564 704 PITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIP-PIFGSDEFGWCCEW 774 (1052)
Q Consensus 704 ~~~v~v~~~pi~d~~G~v~gvv~i~~DITerk~aE~~L~~se~~lr~ile~~~~li~-~I~~~D~~g~i~~v 774 (1052)
..++...+.|+++.+|++.|++++-.++.. +..++......-. -++++|.+|.+++-
T Consensus 11 ~~~vi~~s~pi~~~~g~~~Gvv~~di~l~~--------------l~~~i~~~~~~~~g~~~ivd~~G~ii~h 68 (81)
T PF02743_consen 11 GQPVITISVPIYDDDGKIIGVVGIDISLDQ--------------LSEIISNIKFGNNGYAFIVDKNGTIIAH 68 (81)
T ss_dssp TEEEEEEEEEEEETTTEEEEEEEEEEEHHH--------------HHHHHTTSBBTTTBEEEEEETTSBBCE-
T ss_pred CcEEEEEEEEEECCCCCEEEEEEEEeccce--------------eeeEEEeeEECCCEEEEEEECCCCEEEe
Confidence 355666788999999999999987444322 2233443321111 26788888888753
No 200
>PRK10963 hypothetical protein; Provisional
Probab=29.33 E-value=5.2e+02 Score=27.48 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=31.0
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHhhhCCCEEEEEeecCC
Q 001564 205 AKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHED 247 (1052)
Q Consensus 205 ~~~~~~l~~~~~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d 247 (1052)
.+..-+|-. +.+++++++++. ..++..+.|.|-+-=|.+.
T Consensus 78 ~~l~l~Ll~--a~~~~~l~~~L~-~~~~~f~~~~v~l~L~~~~ 117 (223)
T PRK10963 78 LPLQSRLAA--ADSLQDMLMRLH-RWARDLGLAGAKIRLFPDR 117 (223)
T ss_pred HHHHHHHhc--CCCHHHHHHHHH-HHHHHcCCCceEEEEeccc
Confidence 344555545 669999999996 6899999999888777654
No 201
>TIGR00585 mutl DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.21 E-value=64 Score=36.31 Aligned_cols=27 Identities=15% Similarity=0.155 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhHhhccCCCCeEEEEEEE
Q 001564 1007 RLQQVLADFLSISINFVPNGGQLMVSSSL 1035 (1052)
Q Consensus 1007 ~L~QVL~NLL~NAik~~~~~g~I~I~v~~ 1035 (1052)
.+.+++.|||.||+++.. ..|.|.+..
T Consensus 22 ~~~~~l~eLi~Na~dA~a--~~I~i~~~~ 48 (312)
T TIGR00585 22 RPASVVKELVENSLDAGA--TRIDVEIEE 48 (312)
T ss_pred hHHHHHHHHHHHHHHCCC--CEEEEEEEe
Confidence 467999999999999865 567666543
No 202
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=28.24 E-value=1.4e+02 Score=28.01 Aligned_cols=52 Identities=17% Similarity=0.338 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCch
Q 001564 216 SGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIP 275 (1052)
Q Consensus 216 ~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip 275 (1052)
..+....++..++.+++.++.|-|+| -|-+|.+++-+ .+ ..+|.+|...|+.
T Consensus 19 ~~~~~~~lq~~~~~~~~~~~~~~i~v----~D~~g~~l~~s-~~---~~iG~~~~~~~~~ 70 (116)
T PF14827_consen 19 QGDPEAELQALLEQLRKESDIDYIVV----TDRDGIVLAHS-DP---ERIGDRYSDEDVR 70 (116)
T ss_dssp TTGHHSCCCCHHHHHHHHCT-SEEEE----ECTTSBECE-S-SC---CCTTSB-SSCCHC
T ss_pred cCCccHHHHHHHHHHHhhcCCeEEEE----EcCCCCEEEcC-Ch---HHcCCcccCCChh
Confidence 44666566889999999999998876 58899999987 33 3499999876643
No 203
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=27.41 E-value=40 Score=31.94 Aligned_cols=28 Identities=25% Similarity=0.407 Sum_probs=21.4
Q ss_pred CCCCcceEEEEecCCceEEEEccChhhh
Q 001564 79 LIQPFGCLLALDEKTFKVIAYSENAPEL 106 (1052)
Q Consensus 79 ~iQ~~G~ll~~~~~~~~i~~~S~N~~~~ 106 (1052)
-|||||+.+.++..+-=.+++||=+..+
T Consensus 15 gI~~yGAFV~l~~g~tGLVHISEIa~~f 42 (129)
T COG1098 15 GITPYGAFVELEGGKTGLVHISEIADGF 42 (129)
T ss_pred eeEecceEEEecCCCcceEEehHhhhhh
Confidence 4899999999998644478899744443
No 204
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=27.36 E-value=70 Score=33.71 Aligned_cols=38 Identities=16% Similarity=0.061 Sum_probs=33.3
Q ss_pred HHHHHHHHhCCCCCCCCccccCCCCcceeechHHHHHhCCC
Q 001564 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWK 785 (1052)
Q Consensus 745 e~~lr~ile~~~~li~~I~~~D~~g~i~~vN~a~~~i~G~~ 785 (1052)
.+.+.++++..+ .|+++.+.+|.+++.|.+|.+.|.-.
T Consensus 18 ~~~~~~~i~~~~---~P~CiR~~~g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 18 PESLTAFIDDYS---YPACIRNESGKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHHHcCC---CCeEEECCCCCeeecchHHHHHHHhc
Confidence 346778999999 89999999999999999999998644
No 205
>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=26.30 E-value=2.2e+02 Score=25.01 Aligned_cols=30 Identities=20% Similarity=0.139 Sum_probs=23.9
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEEEccc
Q 001564 702 DDPITLIVNACASRDLHDNVVGVCFVAQDIT 732 (1052)
Q Consensus 702 g~~~~v~v~~~pi~d~~G~v~gvv~i~~DIT 732 (1052)
|...=+-+...|+++.+|++++.++++ |+|
T Consensus 54 G~Y~G~PViV~PI~~~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 54 GPYKGVPVIVAPIKDEDGEVIAAIGVV-DLT 83 (84)
T ss_pred cccCCeeEEEEEEEcCCCCEEEEEEEE-Ecc
Confidence 444445567789999999999999985 776
No 206
>PRK04158 transcriptional repressor CodY; Validated
Probab=24.38 E-value=6.3e+02 Score=27.45 Aligned_cols=49 Identities=10% Similarity=0.095 Sum_probs=37.8
Q ss_pred eeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCCCCchhHHHHHHHHHHHHHHHHHHH
Q 001564 335 ASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEL 398 (1052)
Q Consensus 335 asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~~ 398 (1052)
=.+++||..+ |..-|-|+.-.+.. .+......++|..|.+++++|.+..
T Consensus 111 ~~tIvPI~gg--------------GeRLGTLvl~r~~~-~f~~dDliL~EyaATVVgLEIlR~~ 159 (256)
T PRK04158 111 LTTIVPIIGG--------------GERLGTLILARFDK-EFTDDDLILAEYAATVVGMEILREK 159 (256)
T ss_pred eEEEEEEecC--------------CeEEEEEEEEecCC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678999987 88889888877653 3345568899999999999986543
No 207
>PRK13870 transcriptional regulator TraR; Provisional
Probab=22.76 E-value=7.7e+02 Score=26.38 Aligned_cols=111 Identities=7% Similarity=0.074 Sum_probs=68.2
Q ss_pred CCCHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCC
Q 001564 216 SGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRA 295 (1052)
Q Consensus 216 ~~~~~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~ 295 (1052)
+++.+.+++.. ..+.+.+|||.+.+-.... ...+..+..|...++.|..+..-.+
T Consensus 15 ~~~~~~~~~~l-~~~~~~~Gf~~~~y~~~~~-------------------~~~~~~~nyP~~W~~~Y~~~~y~~~----- 69 (234)
T PRK13870 15 EGDECILKTGL-ADIADHFGFTGYAYLHIQH-------------------RHITAVTNYHREWQSVYFDKKFDAL----- 69 (234)
T ss_pred hCCHHHHHHHH-HHHHHHcCCCcEEEEecCC-------------------CCeeEeCCCCHHHHHHHHHCCCccc-----
Confidence 56777777754 4555666999995543211 1223356778999999999986443
Q ss_pred Cccceee-CCCCCCcccccCccc-cCCChhHH---HHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEe
Q 001564 296 RHVKVLQ-DEKLPFDLTLCGSTL-RAPHSCHL---QYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVC 367 (1052)
Q Consensus 296 ~~~~~~~-~~~~~~~~~l~~~~l-r~~~~~h~---~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~ 367 (1052)
.| ++. ......|++=+.... ...++... +..+.+|++.-+++||.-. +.-+|++++
T Consensus 70 DP--vv~~~~~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~tiPi~~~--------------~g~~~~lS~ 130 (234)
T PRK13870 70 DP--VVKRARSRKHIFTWSGEQERPRLSKDERAFYAHAADFGIRSGITIPIKTA--------------NGSMSMFTL 130 (234)
T ss_pred Ch--HHHHHhcCCCCeecCcccccccCCHHHHHHHHHHHHcCCCCceEEEEECC--------------CCCEEEEEE
Confidence 22 221 112234554443221 23455555 4567889999999999733 456898886
No 208
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=22.36 E-value=7.3e+02 Score=24.15 Aligned_cols=110 Identities=14% Similarity=0.311 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCCCCCCCchHHHHHHHHhCCeeEEecCCCCccc
Q 001564 220 ERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVK 299 (1052)
Q Consensus 220 ~~l~~~~v~~vr~~~g~dRV~iY~F~~d~~G~viaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~~~~r~i~d~~~~~~~ 299 (1052)
.++.|..|+++.+.+||+ |-|. |.+|.+||-+-... +| .+-..|++.-..++.-.
T Consensus 3 ~~~Aq~Iv~~~~~~i~~~-inim----d~~G~IIAStd~~R----IG------~~HegA~~~i~~~~~~~---------- 57 (135)
T PF05651_consen 3 KELAQKIVDEIMEIIGYN-INIM----DENGIIIASTDPER----IG------TFHEGAKEVIRTNKEIE---------- 57 (135)
T ss_pred HHHHHHHHHHHHHHcCCC-EEEE----CCCcEEEecCChhh----cC------ccCHHHHHHHHcCCccc----------
Confidence 478899999999999998 4432 68899999765544 44 22345555544443211
Q ss_pred eeeCCCCCCcccccCccccCCChhHHHHHHhcccceeEEEEEEEcCCcccCCCCCcccCCceeeEEEeecCCCCCCCchh
Q 001564 300 VLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPL 379 (1052)
Q Consensus 300 ~~~~~~~~~~~~l~~~~lr~~~~~h~~yl~nmgv~asl~~~i~~~~~~~~~~~~~~~~~~~LWGLi~~hh~~pr~~~~~~ 379 (1052)
++....+-+. |++.-..+||.++ |+.=|-|.-=-. |.+.
T Consensus 58 --------------------i~~~~~~~~~--g~k~GinlPI~~~--------------g~~iGviGItG~-----p~eV 96 (135)
T PF05651_consen 58 --------------------ITEEDAEQYP--GVKPGINLPIIFN--------------GEVIGVIGITGE-----PEEV 96 (135)
T ss_pred --------------------ccHhHHhhcc--CCCcceeeeEEEC--------------CEEEEEEEEecC-----HHHH
Confidence 1111121222 7888889999998 999999865322 2334
Q ss_pred HHHHHHHHHHHHHHHH
Q 001564 380 RYACEFLAQVFAIHVN 395 (1052)
Q Consensus 380 r~~~~~l~~~~~~~l~ 395 (1052)
+...+.+..+.-+-|.
T Consensus 97 ~~~~~lvk~~~Elll~ 112 (135)
T PF05651_consen 97 RPYAQLVKKMAELLLE 112 (135)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4455544444444343
No 209
>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=20.98 E-value=1.1e+02 Score=26.12 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=18.8
Q ss_pred EEEECCeEEEecCCCCHHHHHHHH
Q 001564 445 ALLYKNKIWRLGVTPNDFQLHDIV 468 (1052)
Q Consensus 445 ~~~~~~~~~~~g~~p~~~~~~~l~ 468 (1052)
+++.+|+....|..|+.+++..++
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 568899999999999999888665
Done!