Query 001235
Match_columns 1117
No_of_seqs 610 out of 3801
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 19:28:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4251 Bacteriophytochrome (l 100.0 3E-152 7E-157 1279.0 64.8 708 72-1116 18-744 (750)
2 TIGR02938 nifL_nitrog nitrogen 100.0 4.1E-51 9E-56 494.7 45.2 462 616-1113 4-494 (494)
3 PRK13560 hypothetical protein; 100.0 2.2E-49 4.7E-54 509.8 55.3 476 604-1116 192-806 (807)
4 PRK11091 aerobic respiration c 100.0 7E-45 1.5E-49 465.2 41.4 359 729-1115 138-507 (779)
5 COG5002 VicK Signal transducti 100.0 8.4E-42 1.8E-46 361.5 26.6 344 729-1115 93-450 (459)
6 PRK11006 phoR phosphate regulo 100.0 1.3E-37 2.7E-42 371.2 28.5 338 725-1115 77-425 (430)
7 COG3852 NtrB Signal transducti 100.0 4.4E-36 9.5E-41 314.9 33.2 338 750-1115 11-356 (363)
8 PRK13557 histidine kinase; Pro 100.0 7.5E-35 1.6E-39 357.4 41.0 354 739-1115 23-396 (540)
9 PRK10618 phosphotransfer inter 100.0 5.7E-35 1.2E-39 368.9 37.8 329 735-1115 332-674 (894)
10 PRK11073 glnL nitrogen regulat 100.0 1.9E-34 4.2E-39 334.0 38.0 338 745-1114 6-348 (348)
11 PRK11360 sensory histidine kin 100.0 8.3E-34 1.8E-38 352.3 41.9 347 737-1116 253-604 (607)
12 TIGR02966 phoR_proteo phosphat 100.0 4E-34 8.6E-39 327.8 34.7 320 742-1111 2-333 (333)
13 PRK10841 hybrid sensory kinase 100.0 8.8E-34 1.9E-38 363.7 41.1 330 738-1115 326-669 (924)
14 PF00360 PHY: Phytochrome regi 100.0 1.2E-35 2.7E-40 307.1 13.6 171 411-583 3-178 (182)
15 PRK09959 hybrid sensory histid 100.0 1.4E-32 3.1E-37 367.8 39.9 368 728-1115 558-938 (1197)
16 PRK13559 hypothetical protein; 100.0 1.9E-31 4.2E-36 310.6 34.1 312 743-1114 40-360 (361)
17 COG2205 KdpD Osmosensitive K+ 100.0 1.1E-31 2.5E-36 314.5 26.0 215 888-1115 656-881 (890)
18 PRK11086 sensory histidine kin 100.0 2E-29 4.3E-34 309.8 44.2 345 709-1116 146-538 (542)
19 PRK09303 adaptive-response sen 100.0 4.2E-30 9.1E-35 300.7 29.0 217 889-1115 148-379 (380)
20 COG5000 NtrY Signal transducti 100.0 1.7E-29 3.8E-34 286.3 31.6 330 736-1113 360-708 (712)
21 COG4191 Signal transduction hi 100.0 3.1E-28 6.8E-33 278.3 40.9 205 896-1115 388-603 (603)
22 PRK15053 dpiB sensor histidine 100.0 2.8E-27 6E-32 291.1 44.6 345 709-1116 147-542 (545)
23 TIGR02956 TMAO_torS TMAO reduc 100.0 1.6E-28 3.6E-33 322.4 29.0 223 882-1115 454-685 (968)
24 PRK15347 two component system 100.0 5E-28 1.1E-32 316.3 29.6 222 883-1115 389-616 (921)
25 PRK11466 hybrid sensory histid 100.0 4.2E-27 9.2E-32 307.1 29.7 220 885-1115 437-664 (914)
26 PRK10490 sensor protein KdpD; 100.0 1.2E-26 2.7E-31 296.6 32.5 214 890-1116 662-885 (895)
27 PRK11107 hybrid sensory histid 100.0 5.3E-27 1.1E-31 306.6 29.6 226 884-1115 285-520 (919)
28 PRK13837 two-component VirA-li 99.9 2.1E-25 4.5E-30 286.2 38.4 217 892-1115 450-677 (828)
29 COG3290 CitA Signal transducti 99.9 2E-25 4.3E-30 254.5 31.6 354 702-1116 133-534 (537)
30 PRK10364 sensor protein ZraS; 99.9 2.4E-25 5.1E-30 267.9 29.9 209 892-1115 237-450 (457)
31 PRK10604 sensor protein RstB; 99.9 6.2E-25 1.3E-29 262.0 27.7 207 890-1116 210-426 (433)
32 PRK10815 sensor protein PhoQ; 99.9 7.7E-25 1.7E-29 263.8 28.5 209 892-1116 266-481 (485)
33 PRK10549 signal transduction h 99.9 3.4E-24 7.4E-29 258.4 27.5 215 889-1116 237-461 (466)
34 PRK10755 sensor protein BasS/P 99.9 8.1E-24 1.8E-28 246.1 27.1 208 892-1115 137-352 (356)
35 TIGR03785 marine_sort_HK prote 99.9 1.2E-23 2.5E-28 263.4 29.5 209 891-1112 484-703 (703)
36 PRK09776 putative diguanylate 99.9 2.3E-23 5.1E-28 277.3 28.8 267 604-887 271-537 (1092)
37 PRK09835 sensor kinase CusS; P 99.9 6.4E-23 1.4E-27 248.4 29.9 212 890-1114 260-481 (482)
38 PRK09776 putative diguanylate 99.9 6.3E-23 1.4E-27 273.1 28.7 265 604-885 398-665 (1092)
39 TIGR02916 PEP_his_kin putative 99.9 1.1E-22 2.5E-27 255.7 28.9 199 893-1112 476-679 (679)
40 TIGR01386 cztS_silS_copS heavy 99.9 1.1E-22 2.3E-27 244.4 27.5 207 891-1112 240-457 (457)
41 PRK11100 sensory histidine kin 99.9 3E-22 6.5E-27 241.7 28.1 211 892-1115 256-475 (475)
42 PRK10337 sensor protein QseC; 99.9 3.2E-22 7E-27 240.1 27.5 205 892-1111 237-449 (449)
43 PF08446 PAS_2: PAS fold; Int 99.9 6.1E-24 1.3E-28 201.7 8.8 106 70-185 2-110 (110)
44 PRK09470 cpxA two-component se 99.9 8.2E-22 1.8E-26 237.3 28.6 210 890-1116 241-460 (461)
45 PRK09467 envZ osmolarity senso 99.9 1.1E-21 2.5E-26 234.4 27.8 203 888-1115 225-435 (435)
46 COG0642 BaeS Signal transducti 99.9 3E-21 6.6E-26 219.5 27.5 212 891-1116 114-332 (336)
47 COG4192 Signal transduction hi 99.9 4.1E-21 8.9E-26 210.4 22.1 205 896-1114 455-667 (673)
48 TIGR02040 PpsR-CrtJ transcript 99.9 9.9E-21 2.2E-25 226.6 25.3 243 607-878 124-368 (442)
49 PRK13560 hypothetical protein; 99.9 3.7E-20 8E-25 238.7 30.6 260 606-886 57-332 (807)
50 PRK11644 sensory histidine kin 99.8 3.9E-19 8.5E-24 214.4 25.6 193 890-1113 300-494 (495)
51 PRK11359 cyclic-di-GMP phospho 99.8 1.4E-18 3.1E-23 223.9 25.7 248 616-882 12-259 (799)
52 TIGR02040 PpsR-CrtJ transcript 99.8 3.1E-18 6.6E-23 205.2 21.6 233 621-879 1-248 (442)
53 PF02518 HATPase_c: Histidine 99.7 2.2E-17 4.8E-22 158.2 12.2 103 1003-1114 1-111 (111)
54 PRK10935 nitrate/nitrite senso 99.7 7.3E-15 1.6E-19 181.8 30.5 195 892-1116 360-562 (565)
55 PRK10600 nitrate/nitrite senso 99.7 5.5E-15 1.2E-19 182.8 25.5 190 895-1115 365-558 (569)
56 COG3920 Signal transduction hi 99.6 1E-13 2.2E-18 148.4 25.7 212 869-1115 2-217 (221)
57 PRK10547 chemotaxis protein Ch 99.6 2E-14 4.2E-19 175.5 20.2 139 964-1115 343-525 (670)
58 PF08448 PAS_4: PAS fold; Int 99.5 3E-13 6.4E-18 128.2 12.3 110 622-736 1-110 (110)
59 PF13426 PAS_9: PAS domain; PD 99.5 6.1E-13 1.3E-17 124.5 12.4 104 626-733 1-104 (104)
60 PF00989 PAS: PAS fold; Inter 99.4 8.5E-13 1.8E-17 125.7 12.9 112 616-731 1-113 (113)
61 COG3851 UhpB Signal transducti 99.4 2.9E-11 6.4E-16 130.4 23.6 191 891-1112 302-493 (497)
62 COG4585 Signal transduction hi 99.4 2.4E-11 5.3E-16 141.8 24.0 190 890-1113 169-365 (365)
63 COG0643 CheA Chemotaxis protei 99.4 9.2E-12 2E-16 152.8 20.4 141 961-1114 387-574 (716)
64 COG4564 Signal transduction hi 99.4 1.9E-10 4.1E-15 122.8 26.3 217 868-1115 223-449 (459)
65 smart00387 HATPase_c Histidine 99.3 1.3E-11 2.9E-16 116.4 13.2 103 1003-1114 1-111 (111)
66 PRK11091 aerobic respiration c 99.3 1.8E-11 3.8E-16 157.6 18.1 147 604-754 143-289 (779)
67 PF01590 GAF: GAF domain; Int 99.3 1.1E-11 2.5E-16 125.2 12.6 153 218-394 1-154 (154)
68 PF13426 PAS_9: PAS domain; PD 99.3 7.5E-12 1.6E-16 117.1 9.9 102 761-873 3-104 (104)
69 COG3850 NarQ Signal transducti 99.3 2.7E-10 5.8E-15 130.1 22.2 183 893-1112 370-567 (574)
70 PF00989 PAS: PAS fold; Inter 99.3 3E-11 6.5E-16 115.0 11.3 112 746-871 1-113 (113)
71 PRK04184 DNA topoisomerase VI 99.3 2.2E-11 4.9E-16 143.8 11.9 107 1002-1114 31-153 (535)
72 PF08448 PAS_4: PAS fold; Int 99.2 4.8E-11 1E-15 113.0 8.4 110 752-876 1-110 (110)
73 PRK13559 hypothetical protein; 99.1 4.8E-10 1E-14 130.8 16.1 135 613-751 40-177 (361)
74 PRK10060 RNase II stability mo 99.1 1.3E-09 2.8E-14 137.1 19.2 169 700-887 70-239 (663)
75 COG3275 LytS Putative regulato 99.1 3.7E-09 8E-14 118.9 20.0 130 961-1115 414-553 (557)
76 PRK14868 DNA topoisomerase VI 99.1 4.7E-10 1E-14 134.7 13.3 120 984-1113 23-159 (795)
77 cd00075 HATPase_c Histidine ki 99.1 7.3E-10 1.6E-14 102.7 11.7 95 1008-1111 1-103 (103)
78 KOG0519 Sensory transduction h 99.1 3E-11 6.4E-16 152.2 2.1 217 895-1115 224-490 (786)
79 PRK13558 bacterio-opsin activa 99.1 1.3E-09 2.9E-14 137.7 16.6 138 616-757 148-288 (665)
80 PRK13557 histidine kinase; Pro 99.1 1.2E-09 2.6E-14 134.3 15.4 131 611-745 25-158 (540)
81 TIGR01925 spIIAB anti-sigma F 99.0 1.3E-09 2.9E-14 108.5 12.1 94 1003-1111 35-136 (137)
82 PRK10060 RNase II stability mo 99.0 3.4E-09 7.4E-14 133.2 18.0 163 610-778 105-284 (663)
83 TIGR00229 sensory_box PAS doma 99.0 2.3E-09 4.9E-14 98.9 12.0 120 616-740 3-123 (124)
84 TIGR01052 top6b DNA topoisomer 99.0 1.5E-09 3.2E-14 127.2 12.4 99 1001-1107 22-134 (488)
85 COG3829 RocR Transcriptional r 99.0 1.1E-08 2.4E-13 118.4 18.2 227 619-883 4-231 (560)
86 PRK03660 anti-sigma F factor; 99.0 4.5E-09 9.7E-14 105.9 12.8 99 1003-1116 35-141 (146)
87 PRK14867 DNA topoisomerase VI 99.0 3E-09 6.5E-14 128.1 12.8 105 1002-1114 28-150 (659)
88 smart00065 GAF Domain present 99.0 1.5E-08 3.2E-13 99.4 15.8 139 218-396 1-141 (149)
89 PRK11359 cyclic-di-GMP phospho 98.9 5.2E-08 1.1E-12 126.0 22.3 124 614-741 134-258 (799)
90 PF13596 PAS_10: PAS domain; P 98.9 1.6E-08 3.6E-13 95.8 11.2 106 618-732 1-106 (106)
91 COG2972 Predicted signal trans 98.8 2.1E-07 4.6E-12 111.7 22.2 184 896-1115 263-454 (456)
92 PRK04069 serine-protein kinase 98.8 3.5E-08 7.5E-13 101.1 12.8 98 1003-1114 38-144 (161)
93 PRK13558 bacterio-opsin activa 98.8 6.1E-08 1.3E-12 122.7 17.3 124 747-884 149-275 (665)
94 TIGR02938 nifL_nitrog nitrogen 98.8 1.9E-08 4.2E-13 121.8 11.8 127 745-885 3-129 (494)
95 PF08447 PAS_3: PAS fold; Int 98.8 3.2E-08 6.9E-13 90.6 9.8 90 771-868 1-91 (91)
96 TIGR00229 sensory_box PAS doma 98.8 7.1E-08 1.5E-12 88.7 12.3 120 745-879 2-122 (124)
97 PF08447 PAS_3: PAS fold; Int 98.7 4.9E-08 1.1E-12 89.4 9.9 86 638-728 1-91 (91)
98 PF00512 HisKA: His Kinase A ( 98.7 4.5E-08 9.8E-13 84.7 7.7 64 892-955 2-68 (68)
99 PRK11360 sensory histidine kin 98.7 2.8E-07 6.2E-12 114.6 17.5 134 606-746 252-386 (607)
100 PF14501 HATPase_c_5: GHKL dom 98.7 2.5E-07 5.5E-12 86.7 12.9 96 1004-1112 2-100 (100)
101 TIGR01924 rsbW_low_gc serine-p 98.7 2.2E-07 4.8E-12 94.8 12.6 95 1005-1113 40-143 (159)
102 COG5002 VicK Signal transducti 98.6 3.2E-07 6.9E-12 99.6 12.1 133 601-744 96-228 (459)
103 KOG3558 Hypoxia-inducible fact 98.6 7E-07 1.5E-11 104.5 15.6 224 621-873 124-378 (768)
104 cd00130 PAS PAS domain; PAS mo 98.6 7.3E-07 1.6E-11 77.8 12.6 103 625-731 1-103 (103)
105 TIGR02966 phoR_proteo phosphat 98.5 5.7E-07 1.2E-11 102.9 12.7 113 612-741 2-114 (333)
106 COG2203 FhlA FOG: GAF domain [ 98.5 4.1E-07 8.8E-12 92.3 10.0 152 204-397 6-165 (175)
107 PRK11388 DNA-binding transcrip 98.5 8.9E-06 1.9E-10 102.1 22.7 222 617-876 63-311 (638)
108 PF12860 PAS_7: PAS fold 98.5 6.7E-07 1.5E-11 86.1 9.2 104 622-739 1-115 (115)
109 PF13492 GAF_3: GAF domain; PD 98.4 6.3E-06 1.4E-10 80.3 14.5 128 218-395 1-128 (129)
110 COG2202 AtoS FOG: PAS/PAC doma 98.4 2.7E-05 5.8E-10 79.1 19.8 229 629-877 2-231 (232)
111 PRK11073 glnL nitrogen regulat 98.3 2.8E-06 6E-11 98.5 12.2 118 616-745 7-125 (348)
112 PF13581 HATPase_c_2: Histidin 98.3 5.2E-06 1.1E-10 81.2 11.6 92 1005-1110 29-124 (125)
113 KOG0787 Dehydrogenase kinase [ 98.3 2.6E-05 5.7E-10 86.2 16.8 174 925-1112 172-379 (414)
114 cd00130 PAS PAS domain; PAS mo 98.3 9.6E-06 2.1E-10 70.5 11.2 100 761-871 4-103 (103)
115 PRK11006 phoR phosphate regulo 98.2 8.4E-06 1.8E-10 97.6 13.3 119 605-742 87-205 (430)
116 PF13185 GAF_2: GAF domain; PD 98.1 3.4E-05 7.3E-10 77.1 13.8 137 217-394 2-147 (148)
117 PF13596 PAS_10: PAS domain; P 98.1 7.5E-06 1.6E-10 77.5 8.2 106 748-872 1-106 (106)
118 PRK11086 sensory histidine kin 98.1 2.8E-05 6.1E-10 95.8 14.3 126 609-750 214-342 (542)
119 PRK10820 DNA-binding transcrip 98.0 4.8E-05 1.1E-09 92.7 15.0 113 610-736 74-190 (520)
120 PF14598 PAS_11: PAS domain; P 98.0 7E-05 1.5E-09 71.5 12.3 101 629-733 5-108 (111)
121 TIGR01817 nifA Nif-specific re 98.0 0.00021 4.6E-09 87.8 19.5 151 203-395 6-157 (534)
122 COG1389 DNA topoisomerase VI, 98.0 2.2E-05 4.8E-10 88.6 9.6 100 1005-1112 34-149 (538)
123 COG3829 RocR Transcriptional r 98.0 6.8E-05 1.5E-09 87.6 13.6 126 611-749 112-237 (560)
124 COG3604 FhlA Transcriptional r 97.8 0.00047 1E-08 79.6 17.1 219 217-474 47-272 (550)
125 COG2172 RsbW Anti-sigma regula 97.8 0.00016 3.5E-09 72.3 11.9 88 1002-1104 35-130 (146)
126 PF14598 PAS_11: PAS domain; P 97.8 9.3E-05 2E-09 70.7 8.6 99 763-872 6-107 (111)
127 PRK05022 anaerobic nitric oxid 97.8 0.0022 4.7E-08 78.3 22.4 152 206-397 8-159 (509)
128 COG2202 AtoS FOG: PAS/PAC doma 97.7 0.00056 1.2E-08 69.2 14.6 126 607-737 103-231 (232)
129 PF12860 PAS_7: PAS fold 97.7 6.6E-05 1.4E-09 72.2 7.1 112 753-878 2-114 (115)
130 PRK15429 formate hydrogenlyase 97.7 0.0034 7.5E-08 79.6 23.6 147 216-398 197-345 (686)
131 COG3290 CitA Signal transducti 97.6 0.00035 7.5E-09 81.8 12.2 127 609-751 208-337 (537)
132 PRK15053 dpiB sensor histidine 97.6 0.00075 1.6E-08 83.4 14.9 125 609-750 215-341 (545)
133 PRK10820 DNA-binding transcrip 97.6 0.00055 1.2E-08 83.5 13.2 112 741-876 75-190 (520)
134 TIGR00585 mutl DNA mismatch re 97.5 0.00042 9E-09 79.1 11.0 78 1007-1101 22-113 (312)
135 PF13188 PAS_8: PAS domain; PD 97.5 0.00013 2.8E-09 62.1 4.9 47 616-666 1-47 (64)
136 PRK11061 fused phosphoenolpyru 97.5 0.0017 3.6E-08 82.3 16.6 149 206-395 7-155 (748)
137 smart00388 HisKA His Kinase A 97.5 0.00028 6.1E-09 59.4 6.6 61 893-953 3-64 (66)
138 COG5000 NtrY Signal transducti 97.5 0.001 2.3E-08 78.1 12.6 132 602-745 356-488 (712)
139 KOG3559 Transcriptional regula 97.4 0.0014 3E-08 72.4 11.4 208 620-858 83-313 (598)
140 KOG0501 K+-channel KCNQ [Inorg 97.3 0.0007 1.5E-08 78.0 8.3 122 746-876 14-138 (971)
141 PRK09959 hybrid sensory histid 97.1 0.0056 1.2E-07 83.2 16.5 139 605-748 565-705 (1197)
142 KOG3560 Aryl-hydrocarbon recep 97.0 0.0038 8.2E-08 71.7 10.8 229 619-873 114-385 (712)
143 PRK11388 DNA-binding transcrip 97.0 0.01 2.2E-07 74.8 16.1 114 610-736 197-311 (638)
144 KOG0501 K+-channel KCNQ [Inorg 97.0 0.002 4.4E-08 74.3 8.6 99 635-737 39-139 (971)
145 PRK15429 formate hydrogenlyase 97.0 0.21 4.5E-06 63.5 27.9 201 205-448 12-224 (686)
146 PF13589 HATPase_c_3: Histidin 96.9 0.00084 1.8E-08 66.8 3.8 89 1009-1112 4-106 (137)
147 smart00091 PAS PAS domain. PAS 96.8 0.0031 6.7E-08 49.9 6.2 64 617-680 2-65 (67)
148 cd00082 HisKA Histidine Kinase 96.8 0.0046 1E-07 51.4 7.1 59 892-950 4-64 (65)
149 PF13188 PAS_8: PAS domain; PD 96.7 0.0018 3.9E-08 55.0 3.7 42 746-794 1-42 (64)
150 COG2461 Uncharacterized conser 96.5 0.0052 1.1E-07 68.9 7.2 115 616-740 290-404 (409)
151 PF08670 MEKHLA: MEKHLA domain 96.2 0.054 1.2E-06 54.0 11.7 110 616-731 32-145 (148)
152 PRK00095 mutL DNA mismatch rep 96.2 0.016 3.6E-07 72.1 10.1 55 1007-1073 22-76 (617)
153 COG5385 Uncharacterized protei 96.2 0.46 9.9E-06 47.2 17.2 191 896-1112 19-213 (214)
154 PF07568 HisKA_2: Histidine ki 95.5 0.078 1.7E-06 46.8 8.5 74 898-979 1-74 (76)
155 KOG1229 3'5'-cyclic nucleotide 95.4 0.011 2.3E-07 66.3 3.0 96 761-866 169-264 (775)
156 PRK05559 DNA topoisomerase IV 95.3 0.034 7.5E-07 69.1 7.5 73 1004-1088 34-128 (631)
157 KOG3558 Hypoxia-inducible fact 95.3 0.028 6E-07 67.1 6.3 99 632-734 280-379 (768)
158 TIGR02373 photo_yellow photoac 95.1 0.16 3.5E-06 48.6 9.4 62 621-682 21-83 (124)
159 TIGR02916 PEP_his_kin putative 95.0 0.71 1.5E-05 58.8 18.3 152 204-396 307-459 (679)
160 COG3852 NtrB Signal transducti 94.6 0.21 4.6E-06 54.8 10.1 112 619-740 10-122 (363)
161 PF10090 DUF2328: Uncharacteri 94.4 2.7 5.8E-05 43.9 17.6 175 908-1107 2-180 (182)
162 PRK10841 hybrid sensory kinase 94.3 0.65 1.4E-05 61.1 15.8 119 605-750 323-442 (924)
163 COG3283 TyrR Transcriptional r 94.2 0.15 3.2E-06 57.0 8.0 56 616-671 80-135 (511)
164 TIGR01059 gyrB DNA gyrase, B s 94.0 0.14 3E-06 64.3 8.5 75 1004-1090 27-123 (654)
165 PF08670 MEKHLA: MEKHLA domain 93.9 0.73 1.6E-05 46.1 11.5 111 745-870 31-144 (148)
166 PRK05644 gyrB DNA gyrase subun 93.8 0.15 3.3E-06 63.6 8.2 75 1004-1090 34-130 (638)
167 TIGR01055 parE_Gneg DNA topois 93.7 0.095 2.1E-06 65.1 6.3 75 1004-1090 27-123 (625)
168 KOG1229 3'5'-cyclic nucleotide 93.7 0.059 1.3E-06 60.6 3.8 112 609-725 151-263 (775)
169 TIGR02373 photo_yellow photoac 93.6 0.31 6.8E-06 46.6 8.1 46 752-800 22-67 (124)
170 smart00091 PAS PAS domain. PAS 93.5 0.21 4.6E-06 38.8 6.1 45 747-794 2-46 (67)
171 KOG3753 Circadian clock protei 93.5 0.2 4.3E-06 61.3 8.1 199 628-854 194-418 (1114)
172 COG2461 Uncharacterized conser 93.0 0.26 5.6E-06 55.8 7.6 114 745-878 289-402 (409)
173 COG0323 MutL DNA mismatch repa 92.6 0.14 3E-06 63.9 5.3 54 1008-1073 24-77 (638)
174 COG3284 AcoR Transcriptional a 92.0 2.1 4.5E-05 52.0 13.7 229 550-794 9-268 (606)
175 KOG0519 Sensory transduction h 91.6 0.57 1.2E-05 60.2 9.2 215 885-1100 379-620 (786)
176 smart00086 PAC Motif C-termina 91.5 0.44 9.5E-06 33.1 5.0 40 834-873 3-42 (43)
177 smart00433 TOP2c Topoisomerase 91.3 0.18 3.9E-06 62.6 4.1 47 1008-1066 2-50 (594)
178 PRK14939 gyrB DNA gyrase subun 91.2 0.35 7.7E-06 60.9 6.6 49 1006-1066 36-86 (756)
179 PRK10618 phosphotransfer inter 91.1 1.8 3.9E-05 56.6 13.1 46 606-651 333-379 (894)
180 PRK05218 heat shock protein 90 91.0 0.36 7.8E-06 60.1 6.5 57 1001-1069 23-93 (613)
181 smart00086 PAC Motif C-termina 89.8 1.3 2.8E-05 30.5 6.2 36 699-734 8-43 (43)
182 PRK14083 HSP90 family protein; 89.1 0.39 8.4E-06 59.3 4.5 56 1001-1069 20-83 (601)
183 TIGR02851 spore_V_T stage V sp 88.1 21 0.00047 37.1 15.8 125 218-394 53-179 (180)
184 PF07310 PAS_5: PAS domain; I 87.5 4.9 0.00011 39.8 10.4 86 636-728 51-136 (137)
185 PTZ00272 heat shock protein 83 85.7 0.93 2E-05 56.8 5.0 50 1011-1069 29-92 (701)
186 COG0326 HtpG Molecular chapero 84.8 0.97 2.1E-05 54.9 4.4 48 1011-1067 31-92 (623)
187 KOG3561 Aryl-hydrocarbon recep 83.3 0.76 1.7E-05 57.5 2.8 97 765-872 378-476 (803)
188 TIGR01058 parE_Gpos DNA topois 81.4 2.3 5.1E-05 53.0 6.1 51 1004-1066 31-83 (637)
189 COG5381 Uncharacterized protei 81.3 2.6 5.7E-05 41.1 4.9 42 1008-1059 64-105 (184)
190 KOG3560 Aryl-hydrocarbon recep 80.4 4.5 9.8E-05 47.5 7.3 94 635-733 292-385 (712)
191 KOG3559 Transcriptional regula 79.8 3.9 8.4E-05 46.2 6.3 88 627-718 226-313 (598)
192 COG3283 TyrR Transcriptional r 78.3 2.9 6.3E-05 47.1 4.8 48 745-795 79-126 (511)
193 PTZ00108 DNA topoisomerase 2-l 76.2 5.7 0.00012 53.3 7.5 49 1007-1066 57-111 (1388)
194 PTZ00130 heat shock protein 90 74.3 2.6 5.6E-05 53.3 3.5 47 1012-1067 93-153 (814)
195 COG3887 Predicted signaling pr 72.9 17 0.00036 44.0 9.4 102 613-744 72-173 (655)
196 PLN03237 DNA topoisomerase 2; 72.6 4.2 9.2E-05 54.4 5.0 49 1007-1066 77-128 (1465)
197 PF04340 DUF484: Protein of un 71.8 69 0.0015 34.6 13.5 137 205-395 81-221 (225)
198 PLN03128 DNA topoisomerase 2; 71.8 5 0.00011 53.1 5.4 49 1007-1066 52-103 (1135)
199 COG0187 GyrB Type IIA topoisom 70.6 1.5 3.2E-05 53.2 0.2 80 1006-1101 35-136 (635)
200 PF07310 PAS_5: PAS domain; I 70.1 23 0.00049 35.1 8.6 85 770-868 52-136 (137)
201 PF08446 PAS_2: PAS fold; Int 69.9 3.9 8.5E-05 38.9 2.9 47 629-675 18-68 (110)
202 PRK13837 two-component VirA-li 68.5 1.8E+02 0.0039 38.1 18.8 130 218-395 293-426 (828)
203 KOG1978 DNA mismatch repair pr 68.2 4.9 0.00011 49.1 3.8 52 1008-1071 21-72 (672)
204 PHA02569 39 DNA topoisomerase 67.3 3.1 6.7E-05 51.6 2.1 45 1008-1065 46-95 (602)
205 PF08348 PAS_6: YheO-like PAS 66.4 15 0.00033 35.4 6.2 44 696-741 73-116 (118)
206 KOG1977 DNA mismatch repair pr 65.7 9.1 0.0002 46.6 5.3 54 1007-1073 21-74 (1142)
207 PRK10490 sensor protein KdpD; 64.3 2.5E+02 0.0054 37.2 18.8 48 335-396 596-644 (895)
208 PF08348 PAS_6: YheO-like PAS 64.0 20 0.00042 34.7 6.4 48 829-878 66-113 (118)
209 KOG3561 Aryl-hydrocarbon recep 63.8 4.2 9.1E-05 51.2 2.3 98 632-732 378-476 (803)
210 PF14689 SPOB_a: Sensor_kinase 63.8 46 0.00099 28.1 7.9 46 895-944 15-60 (62)
211 COG3605 PtsP Signal transducti 63.3 1E+02 0.0023 37.4 13.2 145 205-394 6-154 (756)
212 COG1956 GAF domain-containing 62.9 1.8E+02 0.0039 29.5 13.5 122 219-392 34-158 (163)
213 PRK14538 putative bifunctional 62.4 62 0.0013 42.0 12.3 46 616-664 102-148 (838)
214 KOG1979 DNA mismatch repair pr 61.8 8.6 0.00019 46.0 4.1 52 1010-1073 30-81 (694)
215 PF14827 Cache_3: Sensory doma 55.3 40 0.00086 32.2 7.0 74 627-731 40-113 (116)
216 COG3887 Predicted signaling pr 54.2 5.1E+02 0.011 32.0 17.3 39 743-784 72-110 (655)
217 PF07536 HWE_HK: HWE histidine 53.7 80 0.0017 28.4 8.1 81 899-993 2-82 (83)
218 PTZ00109 DNA gyrase subunit b; 53.3 3.1 6.6E-05 53.0 -1.4 49 1006-1066 128-178 (903)
219 KOG3753 Circadian clock protei 49.8 26 0.00056 44.0 5.5 90 633-726 338-431 (1114)
220 PRK10600 nitrate/nitrite senso 48.6 6.2E+02 0.013 31.4 19.1 122 206-396 224-346 (569)
221 COG2865 Predicted transcriptio 45.3 2.4E+02 0.0053 33.9 12.6 89 1010-1113 273-380 (467)
222 PRK14538 putative bifunctional 44.4 8.3E+02 0.018 32.0 18.1 216 746-1032 102-329 (838)
223 PF02743 Cache_1: Cache domain 44.0 26 0.00056 30.9 3.5 58 703-774 10-68 (81)
224 PF13192 Thioredoxin_3: Thiore 39.7 34 0.00074 29.9 3.5 25 445-469 52-76 (76)
225 COG3284 AcoR Transcriptional a 39.0 1.5E+02 0.0032 36.6 9.7 37 741-777 69-105 (606)
226 PRK13719 conjugal transfer tra 38.0 4.2E+02 0.009 28.5 11.7 40 615-654 18-57 (217)
227 COG3275 LytS Putative regulato 37.8 2.6E+02 0.0057 33.5 10.9 119 221-395 225-348 (557)
228 COG5388 Uncharacterized protei 34.8 1.2E+02 0.0027 31.5 6.8 95 626-727 58-155 (209)
229 KOG0020 Endoplasmic reticulum 29.9 62 0.0013 38.1 4.3 46 1011-1065 99-158 (785)
230 PRK13719 conjugal transfer tra 28.8 75 0.0016 34.0 4.4 38 745-785 18-55 (217)
231 PRK04158 transcriptional repre 28.5 8.3E+02 0.018 27.0 12.6 50 334-398 110-159 (256)
232 KOG0387 Transcription-coupled 27.8 33 0.00072 42.9 1.8 16 232-249 614-629 (923)
233 KOG0355 DNA topoisomerase type 25.9 67 0.0014 40.6 3.9 54 1007-1071 53-110 (842)
234 KOG0019 Molecular chaperone (H 24.9 66 0.0014 39.2 3.5 47 1011-1066 61-119 (656)
235 COG0813 DeoD Purine-nucleoside 23.5 75 0.0016 33.9 3.2 52 1000-1062 18-69 (236)
236 COG1098 VacB Predicted RNA bin 23.1 53 0.0011 31.7 1.9 27 80-106 16-42 (129)
237 PF09884 DUF2111: Uncharacteri 23.1 2.3E+02 0.005 25.4 5.6 32 700-732 52-83 (84)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-152 Score=1279.02 Aligned_cols=708 Identities=28% Similarity=0.484 Sum_probs=617.6
Q ss_pred hhccCCCCCCCceeEEEEecCCceEEEEccChhhhhcCCcCCCCCCCCCCccCCCCchhhhcChhHHHHHHHHhccCCcc
Q 001235 72 HHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVS 151 (1117)
Q Consensus 72 ~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~l~~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~l~~~~~~~~~~ 151 (1117)
+|||+||+||||||||++|+.++.|+|+|+|+..+||+.|+. ++|+++.++|+......++.++..+...
T Consensus 18 ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~----------l~~~tl~~vl~~~qv~~l~~~l~~~~~~ 87 (750)
T COG4251 18 EPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPED----------LLGRTLGAVLTSEQVPPLQSALTVGGLT 87 (750)
T ss_pred CCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhh----------hhcCCHHHhcchhhccHHHHhccccCcc
Confidence 689999999999999999999999999999999999998854 7999999999999999999999998888
Q ss_pred ccCcEEEEecCCCCeEEEEEEeeCCeEEEEeeecCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHH
Q 001235 152 LLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVF 231 (1117)
Q Consensus 152 ~~~~~~~~~~~~~~~f~~~~hr~~~~~~~e~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vr 231 (1117)
..||-.+..+..+ .|++++||+++.+|+||||....+. . ..+.+|+++..++.+||+.+ ++.++|+.+++|||
T Consensus 88 ~~np~~~w~~~~~-~fDv~~HR~~~llIlEfEp~~t~e~-~---~~l~f~h~~k~a~~~lq~a~--~l~~l~~~~tqeVr 160 (750)
T COG4251 88 TLNPTKMWTRKGG-SFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDLLSRTTQEVR 160 (750)
T ss_pred cCCchhhhhhcCC-ceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHHHHHHHHHHH
Confidence 8888555434433 7999999999999999999754442 2 23447888889999999955 99999999999999
Q ss_pred hhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCccccccc--CCCCCCc
Q 001235 232 ELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQ--DEKLPFD 309 (1117)
Q Consensus 232 ~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~v~~~~--~~~~~~~ 309 (1117)
++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|+|||+.| +|.+++|
T Consensus 161 ~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavNp~t~~p 240 (750)
T COG4251 161 RMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNEP 240 (750)
T ss_pred HhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccCcccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999 7999999
Q ss_pred ccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCCCchhHHHHHHHHHH
Q 001235 310 LTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQV 389 (1117)
Q Consensus 310 l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~~~~~r~~~~~l~~~ 389 (1117)
+|||+|.|||+||||+|||+||||.||||||||+| |+|||||+|||.|||++||++|.||||++|+
T Consensus 241 ~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~--------------g~LWGLIACHH~sPk~ip~~vR~acef~gq~ 306 (750)
T COG4251 241 LDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD--------------GKLWGLIACHHQSPKVIPYEVRKACEFFGQV 306 (750)
T ss_pred ccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC--------------CeeEEeeeeccCCCccCCHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhcCC-CcccccCCcchhhhccCCEEEEEECCeEEEecCCCCHHHHHHH
Q 001235 390 FAIHVNKELELEYQILEKNILRTQ-TLLCDMLMRDA-PLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDI 467 (1117)
Q Consensus 390 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~g~a~~~~~~~~~~G~~p~~~~~~~l 467 (1117)
+|.+|+.+.+.+...........+ .++..|...++ ..+++...++|++|+.||||+||++|++.++|.||+.+++..|
T Consensus 307 ~s~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~L 386 (750)
T COG4251 307 LSMEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRL 386 (750)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHH
Confidence 999998654433222111122222 34444555554 5788999999999999999999999999999999999999999
Q ss_pred HHHHHhccCCCceEeecccccccCCCccccccccccEEEEEeCC--CCEEEEeccCCccEEeeccCCCCCCCC-CCCCcc
Q 001235 468 VSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISP--KDMIFWFRSQTASEVRWGGAKHEPDEK-DDGRKM 544 (1117)
Q Consensus 468 ~~~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~l~~~~~~--~~~l~wfR~e~~~~v~W~G~p~~~~~~-~~g~~l 544 (1117)
+.||.++... .+|+||+|+.. ||+++.++..||||||++|+. ++||+|||||++++|+|||||+|+... ++|.||
T Consensus 387 l~wl~~~~~~-~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL 464 (750)
T COG4251 387 LQWLAEREEG-DVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRL 464 (750)
T ss_pred HHHHhcCCcc-cEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCccc
Confidence 9999887655 79999999985 999999999999999999998 899999999999999999999999863 557899
Q ss_pred cccchhhhhhhhhccccCCCchHHHHHHHHHHHHHHHHHhhhccccccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 001235 545 HPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIET 624 (1117)
Q Consensus 545 ~PR~SF~~w~e~v~~~s~pW~~~El~aa~sL~liL~~~l~~l~~~~~~~~~~~~~l~~~~~~~~~eL~~~~~~l~~lie~ 624 (1117)
+||+||+.|+|+|++++.||+..|++++..|+..+.+...+- .+++..
T Consensus 465 ~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~~---------------------aeela~----------- 512 (750)
T COG4251 465 TPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRH---------------------AEELAQ----------- 512 (750)
T ss_pred CCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHH-----------
Confidence 999999999999999999999999999999844333222000 000000
Q ss_pred cCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCce
Q 001235 625 ATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDP 704 (1117)
Q Consensus 625 a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~ 704 (1117)
T Consensus 513 -------------------------------------------------------------------------------- 512 (750)
T COG4251 513 -------------------------------------------------------------------------------- 512 (750)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCC
Q 001235 705 ITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGW 784 (1117)
Q Consensus 705 ~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~ 784 (1117)
T Consensus 513 -------------------------------------------------------------------------------- 512 (750)
T COG4251 513 -------------------------------------------------------------------------------- 512 (750)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEE
Q 001235 785 KREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGV 864 (1117)
Q Consensus 785 ~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~ 864 (1117)
T Consensus 513 -------------------------------------------------------------------------------- 512 (750)
T COG4251 513 -------------------------------------------------------------------------------- 512 (750)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred EeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHH
Q 001235 865 FCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGT---ELGAEQKRLLHTSAQCQRQLH 941 (1117)
Q Consensus 865 v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~---~l~~~~~~~l~~i~~~~~~l~ 941 (1117)
+++..++.+....+|...++|++++||+.|.++.++|... .++++.++++..+.+....|.
T Consensus 513 ----------------l~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~ 576 (750)
T COG4251 513 ----------------LRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQ 576 (750)
T ss_pred ----------------HHHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHH
Confidence 0011112222233456667999999999999999999864 578899999999999999999
Q ss_pred HHHhh-ccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHh
Q 001235 942 KILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISI 1020 (1117)
Q Consensus 942 ~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAi 1020 (1117)
.||++ +.++++ |.......+.++.++++.++..+.....+.++++.+.. +| .+.+|+.++.|++.||+.||+
T Consensus 577 ~lidd~l~~s~l--~~~~~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~~---lp--~v~~d~~~l~qv~~NLi~Nai 649 (750)
T COG4251 577 QLIDDLLTYSKL--GLTEAPLQPTDVQKVVDKVLLELSQRIADTGAEIRIAP---LP--VVAADATQLGQVFQNLIANAI 649 (750)
T ss_pred HHHHHHhhhhhh--ccccCCCCCcchHHHHHHHHHhcccccccccceEEecc---cc--eeecCHHHHHHHHHHHHhhhe
Confidence 99999 599987 45555666999999999999999999999999998864 43 799999999999999999999
Q ss_pred hccCC-CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC------CCCCccccHHHHHHHHHHcC
Q 001235 1021 NFVPN-GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG------DTSEEGISLLISRKLVKLMN 1093 (1117)
Q Consensus 1021 k~~~~-~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~------~~~GtGLGL~ivr~iVe~~g 1093 (1117)
||..+ ..+|.|+....++ .+.|.|.|||+||++...++||..|. .+.|+|+||+|||+|++.|+
T Consensus 650 k~~~~e~~~i~I~~~r~ed---------~~t~sV~dng~Gi~~a~~~riF~iFqRl~s~~~y~gtG~GL~I~kkI~e~H~ 720 (750)
T COG4251 650 KFGGPENPDIEISAERQED---------EWTFSVRDNGIGIDPAYFERIFVIFQRLHSRDEYLGTGLGLAICKKIAERHQ 720 (750)
T ss_pred ecCCCCCCceEEeeeccCC---------ceEEEecCCCCCcCHHHHHHHHHHHHhcCchhhhcCCCccHHHHHHHHHHhC
Confidence 99866 4899999777776 79999999999999999999999983 44599999999999999999
Q ss_pred CEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1094 GDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1094 G~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
|+||++|.+|. +||.|++|...+
T Consensus 721 G~i~vEs~~gEgsTF~f~lp~~~~ 744 (750)
T COG4251 721 GRIWVESTPGEGSTFYFTLPVGGE 744 (750)
T ss_pred ceEEEeecCCCceeEEEEeecCCc
Confidence 99999999988 999999998764
No 2
>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=4.1e-51 Score=494.70 Aligned_cols=462 Identities=14% Similarity=0.098 Sum_probs=357.8
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEe
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1117)
+.|+.+++.++++++++|.+|+++++|+++++++||+.++++|++...+.++.........+...+..+.....++
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---- 79 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKL---- 79 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCccccee----
Confidence 5689999999999999999999999999999999999999999987777666555555555555554444332232
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeech
Q 001235 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWN 775 (1117)
Q Consensus 696 ~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N 775 (1117)
...+++|..+|+.....|+++.+|.+.+++++++|||++|++++++++++..++.++++++. +++++|.+|+++++|
T Consensus 80 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~---~i~~~d~~~~i~~~N 156 (494)
T TIGR02938 80 LNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPV---AFVLLDPTGRVILDN 156 (494)
T ss_pred eccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccc---eEEEEcCCCCEEEec
Confidence 23478899999999999999999999999999999999999999999999999999999998 899999999999999
Q ss_pred hhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhc-CCCCceEeEEEEecCCc-EEEEEEEEee
Q 001235 776 PAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMS-GQDPEKVPFGFFARNGK-YAECLLCVNK 853 (1117)
Q Consensus 776 ~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~-g~~~~~~e~~~~~~dG~-~~~v~~~~~p 853 (1117)
+++++++|+...+..+..+.+.+ +++....+ ..... +......+..+...+|. .+|+.....+
T Consensus 157 ~~~~~~~g~~~~~~~~~~~~~~~-----------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (494)
T TIGR02938 157 QEYKKLATDLRVKEPAHTVLDLL-----------REAWREAL----AENWPQQLAFSNREARFDRGGGRPARWLSCTGSV 221 (494)
T ss_pred hhHHHhhchhhhhHHHHHHHHHh-----------hHHhhhhh----hhcchhhhccccceeeeccCCCceeeEEEecCce
Confidence 99999999998877766543221 12222211 11111 11122334455555655 7999998888
Q ss_pred eeCCCCCE---------EEEEeehhHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhhhhhhHHHHHHHHHHH
Q 001235 854 KLDREGAV---------TGVFCFLQLASHELQQALHVQRLSEQTA-------LKRLKALAYTKRQIRNPLSGIIFSRKMM 917 (1117)
Q Consensus 854 i~d~~G~v---------~g~v~i~~DITerk~~e~el~~~ae~~~-------~~k~~~la~isHEIrnPL~~I~~~~~LL 917 (1117)
+.+..|.+ .+++++++|||++|+++++++..+.++. .....++..++|++||||++|.++++++
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~~~al~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~i~~~~~~l 301 (494)
T TIGR02938 222 IGMESDCADSFFCAAEQPYLLLTIADISNLREEQERARLSALQALMAEEERLEAIRETLSAAIHRLQGPMNLISAAISVL 301 (494)
T ss_pred EEeecchhhheeccCCCchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHH
Confidence 87766654 3456689999999999887665433221 1223346778899999999999999999
Q ss_pred hcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCC
Q 001235 918 EGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQI 996 (1117)
Q Consensus 918 ~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~ 996 (1117)
+............+.+......+..++..+ ++.. ........++|+..++++++..++..+..+++.+.++.+..+
T Consensus 302 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~~~~dl~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~ 378 (494)
T TIGR02938 302 QRRGDDAGNPASAAMLQQALSAGREHMEALRQVIP---QSPQEIVVPVNLNQILRDVITLSTPRLLAAGIVVDWQPAATL 378 (494)
T ss_pred HhccccccCHHHHHHHHHHHHHHHHHHHHHHHhhc---cCcccccccccHHHHHHHHHHHhHHHHHhCCCEEEEecCCCC
Confidence 865333222333333333344444444442 2221 222345678999999999999999999999999999988776
Q ss_pred cceeEEecHHHHHHHHHHHHHHHhhccCCC----CeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCC
Q 001235 997 MSETLYGDSIRLQQVLADFLSISINFVPNG----GQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSE 1072 (1117)
Q Consensus 997 ~~~~v~~D~~~L~qVL~nLl~NAik~~~~~----g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f 1072 (1117)
+ .+.+|+.+|+|||.||+.||+||++++ +.|.|.+...++ .+.|+|+|||+|||++.+.+||+||
T Consensus 379 ~--~v~~d~~~l~~vl~Nl~~NAik~~~~~~~~~~~i~i~~~~~~~---------~~~~~V~D~G~Gi~~~~~~~iF~~f 447 (494)
T TIGR02938 379 P--AILGRELQLRSLFKALVDNAIEAMNIKGWKRRELSITTALNGD---------LIVVSILDSGPGIPQDLRYKVFEPF 447 (494)
T ss_pred C--eeecCHHHHHHHHHHHHHHHHHHhhccCCCcceEEEEEEecCC---------EEEEEEEeCCCCCCHHHHHHhcCCC
Confidence 5 689999999999999999999998655 356666665555 8999999999999999999999999
Q ss_pred CCC-----CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEec
Q 001235 1073 GDT-----SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVEL 1113 (1117)
Q Consensus 1073 ~~~-----~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl 1113 (1117)
+++ +|+||||+|||+||+.|||+|+++|++|+ |+|+|+||+
T Consensus 448 ~~~~~~~~~G~GlGL~i~~~iv~~~gG~i~~~s~~~~G~~f~i~lp~ 494 (494)
T TIGR02938 448 FTTKGGSRKHIGMGLSVAQEIVADHGGIIDLDDDYSEGCRIIVEFRV 494 (494)
T ss_pred cccCCCCCCCCcccHHHHHHHHHHcCCEEEEEECCCCCEEEEEEecC
Confidence 755 49999999999999999999999999998 999999996
No 3
>PRK13560 hypothetical protein; Provisional
Probab=100.00 E-value=2.2e-49 Score=509.84 Aligned_cols=476 Identities=14% Similarity=0.146 Sum_probs=377.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcC
Q 001235 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1117)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g 683 (1117)
.++++++|++++++|+.+++++|++++++|.+|+++++|+++++++||+.++++|+++.++.++...+.+.......+..
T Consensus 192 rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 271 (807)
T PRK13560 192 RKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDA 271 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhcc
Confidence 34567788999999999999999999999999999999999999999999999999999998877766665555555554
Q ss_pred CcceeeEEEEEeeccccCCceEEEE--EEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCC
Q 001235 684 QEEQNIQFEIKTHGSKINDDPITLI--VNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPP 761 (1117)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dG~~~~v~--v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~ 761 (1117)
+....++..+ .+++|..+|+. ++..|+.+.+|.+.|++++++|||++|++|++|++++++|+.++++++. +
T Consensus 272 ~~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~---~ 344 (807)
T PRK13560 272 DGSQIIEAEF----QNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPI---A 344 (807)
T ss_pred CCceEEEEEE----EcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcc---c
Confidence 4443334333 47799999655 4556778999999999999999999999999999999999999999998 8
Q ss_pred eeeeCCCCceeec-hhhHHHhcCCChhhHhhcchhhhhcCC---------------------------------------
Q 001235 762 IFGSDEFGWCCEW-NPAMVKLTGWKREEVIDKLLLAEVFGT--------------------------------------- 801 (1117)
Q Consensus 762 I~~~D~~g~i~~~-N~a~~~l~G~~~eEliGk~l~~ei~~~--------------------------------------- 801 (1117)
++.+|.+|+++++ |+++++++||+.++++|+++.+.....
T Consensus 345 i~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 424 (807)
T PRK13560 345 AIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQ 424 (807)
T ss_pred EEEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCc
Confidence 9999999999986 678888999999999987642110000
Q ss_pred --------------------------------------------------------------------------------
Q 001235 802 -------------------------------------------------------------------------------- 801 (1117)
Q Consensus 802 -------------------------------------------------------------------------------- 801 (1117)
T Consensus 425 e~~~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~~ 504 (807)
T PRK13560 425 EVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKNI 504 (807)
T ss_pred eEEEEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecchh
Confidence
Q ss_pred -------------chhhhhccChhHHHHHHHHHHHHhcC-CCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEee
Q 001235 802 -------------NMACCRLKNQEAFVNLGIVLNKAMSG-QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCF 867 (1117)
Q Consensus 802 -------------~~~~~~l~~~d~~~~~~~~l~~~l~g-~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i 867 (1117)
...+..+.+|++...+...+.....+ ...+..++++.+++|.++|+..+..|++|.+|.+.+++++
T Consensus 505 ~~~G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~ 584 (807)
T PRK13560 505 TQFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGI 584 (807)
T ss_pred hhcCCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEE
Confidence 00011123344444444444444443 3456789999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc
Q 001235 868 LQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS 947 (1117)
Q Consensus 868 ~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL 947 (1117)
++|||++|++|+++++. ...+..|++.|+|||||||++|.++++++.....+++...++..+......+..+++.+
T Consensus 585 ~~DITerK~aE~~L~~a----~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 660 (807)
T PRK13560 585 VIDISERKHAEEKIKAA----LTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAMALAHEKL 660 (807)
T ss_pred EechHHHHHHHHHHHHH----HHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999876654 34577899999999999999999999999887777777777777666666666665554
Q ss_pred cccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCC--
Q 001235 948 DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN-- 1025 (1117)
Q Consensus 948 d~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~-- 1025 (1117)
... .....+++..+++.++..+...+......+.+.++.... .....+...+.|||.||++||+||+++
T Consensus 661 ~~~--------~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~il~NLl~NAik~~~~~~ 731 (807)
T PRK13560 661 YQS--------EDLADIDFLDYIESLTAHLKNSFAIDFGRIDCKIDADDG-CLDIDKAIPCGLIISELLSNALKHAFPDG 731 (807)
T ss_pred hcc--------ccchhccHHHHHHHHHHHHHHHhccccCceEEEEecCcc-ccccccccchHHHHHHHHHHHHHhhccCC
Confidence 221 135678999999999999988776666556555544432 134456677899999999999999854
Q ss_pred -CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCe
Q 001235 1026 -GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGK 1104 (1117)
Q Consensus 1026 -~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ 1104 (1117)
.|.|.|++....+ .++.|+|+|||+|||++. ...+++||||+|||+||+.|||+|+++|+ ++
T Consensus 732 ~~~~i~i~~~~~~~--------~~v~i~V~D~G~GI~~~~--------~~~~~~gLGLai~~~iv~~~gG~I~v~S~-~G 794 (807)
T PRK13560 732 AAGNIKVEIREQGD--------GMVNLCVADDGIGLPAGF--------DFRAAETLGLQLVCALVKQLDGEIALDSR-GG 794 (807)
T ss_pred CCceEEEEEEEcCC--------CEEEEEEEeCCCcCCccc--------cccccCCccHHHHHHHHHHcCCEEEEEcC-Cc
Confidence 3678888776522 279999999999999974 23457789999999999999999999996 45
Q ss_pred EEEEEEEeccCC
Q 001235 1105 STFIVSVELAAA 1116 (1117)
Q Consensus 1105 ttF~i~LPl~~a 1116 (1117)
|||+|+||+.++
T Consensus 795 t~F~i~lP~~~~ 806 (807)
T PRK13560 795 ARFNIRFPMSPA 806 (807)
T ss_pred eEEEEEecCCCC
Confidence 999999999876
No 4
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=100.00 E-value=7e-45 Score=465.20 Aligned_cols=359 Identities=22% Similarity=0.281 Sum_probs=325.4
Q ss_pred EccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhc
Q 001235 729 QDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRL 808 (1117)
Q Consensus 729 ~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l 808 (1117)
++|++++++++++++++++++.+++++++ +|++.|.+|++++||+++++++||+.++++|++.. .+
T Consensus 138 ~~i~~r~~~~~~l~~~~~~l~~il~~~~~---~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~-----------~l 203 (779)
T PRK11091 138 NEIKEREETQIELEQQSSLLRSFLDASPD---LVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPK-----------DV 203 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcc---eEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChH-----------Hh
Confidence 69999999999999999999999999999 89999999999999999999999999999999853 22
Q ss_pred cChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHH
Q 001235 809 KNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQT 888 (1117)
Q Consensus 809 ~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~ 888 (1117)
.+++....+.......+.++.....+..+..++|+.+|+.++..|+++.+|.+.|++++++|||++++.++++++.
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a---- 279 (779)
T PRK11091 204 YSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKA---- 279 (779)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHH----
Confidence 3345555566666777778888889999999999999999999999999999999999999999999988765443
Q ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHH
Q 001235 889 ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1117)
Q Consensus 889 ~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~ 967 (1117)
...+..|++.|+|||||||++|.|+.+++.....+++++++++.+..+..++..++++ +++++++.+.+.+...++++.
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 3467789999999999999999999999998888999999999999999999999999 699999999999999999999
Q ss_pred HHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccccccee
Q 001235 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLA 1047 (1117)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~ 1047 (1117)
+++++++..+...+..+++.+.++.+..++ ..+.+|+.+|.|||.||+.||+||++ +|.|.|.+....+ .
T Consensus 360 ~~i~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~v~~d~~~l~qvl~NLl~NAik~~~-~g~v~i~~~~~~~--------~ 429 (779)
T PRK11091 360 DFLADLENLSGLQAEQKGLRFDLEPLLPLP-HKVITDGTRLRQILWNLISNAVKFTQ-QGGVTVRVRYEEG--------D 429 (779)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEEEeCCCCC-ceEEeCHHHHHHHHHHHHHHHHHhCC-CCcEEEEEEEccC--------C
Confidence 999999999999999999999999887765 36899999999999999999999997 6778888777622 1
Q ss_pred EEEEEEeecCCCCChhhhhhccCCCCCCC---------CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1048 YLELRITHAGGGIPEPLLDQMFGSEGDTS---------EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1048 ~l~i~V~D~G~GI~~e~~~~iFe~f~~~~---------GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.+.|+|.|+|+|||++.+++||+||++++ |+||||+|||+||+.|||+|+++|.+|+ |+|+|+||+..
T Consensus 430 ~~~i~V~D~G~Gi~~~~~~~iF~~f~~~~~~~~~~~~~GtGLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~lP~~~ 507 (779)
T PRK11091 430 MLTFEVEDSGIGIPEDELDKIFAMYYQVKDSHGGKPATGTGIGLAVSKRLAQAMGGDITVTSEEGKGSCFTLTIHAPA 507 (779)
T ss_pred EEEEEEEecCCCCCHHHHHHHHHHhhcccCCCCCCCCCCcchHHHHHHHHHHHcCCEEEEEecCCCeEEEEEEEeccc
Confidence 69999999999999999999999997653 8999999999999999999999999988 99999999865
No 5
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=100.00 E-value=8.4e-42 Score=361.53 Aligned_cols=344 Identities=17% Similarity=0.266 Sum_probs=289.5
Q ss_pred Eccchhhh-hhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhh
Q 001235 729 QDITPQKT-VMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCR 807 (1117)
Q Consensus 729 ~DITerK~-aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~ 807 (1117)
.|.|++.+ +++.++....++..++..+.+ |++..|..|+|+.+|..+.+++|.+.|+++|+++.+.+-..
T Consensus 93 n~Lt~~~~~aq~n~e~Er~kL~SvlayMtD---GViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~------ 163 (459)
T COG5002 93 NDLTKRVQEAQANTEQERRKLDSVLAYMTD---GVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIE------ 163 (459)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHcC---ceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCc------
Confidence 35555543 444556666789999999998 99999999999999999999999999999999865332211
Q ss_pred ccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHH
Q 001235 808 LKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQ 887 (1117)
Q Consensus 808 l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~ 887 (1117)
+.+ .+...++..+....+ ..+ .++..-+.++.+.+..+.|-+.|++++++|+||+.+.|++
T Consensus 164 ----d~y-----~~~dL~e~~~s~lld--~~~-~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~E------- 224 (459)
T COG5002 164 ----DTY-----TFEDLVEKNDSLLLD--SSD-EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERE------- 224 (459)
T ss_pred ----cce-----eHHHHHhcCCcEEEe--ecC-CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHH-------
Confidence 111 122333333333333 222 7778888899999999999999999999999998777754
Q ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHH--HHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEe
Q 001235 888 TALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE--QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEF 964 (1117)
Q Consensus 888 ~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~--~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~ 964 (1117)
+..|.+++|||+|+||+++.++++.|+.....+. ..+++........+|.++++| |.++|+.+....++.+.+
T Consensus 225 ----rRefvanvSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~~qln~e~i 300 (459)
T COG5002 225 ----RREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNARYQLNKEWI 300 (459)
T ss_pred ----HHHHHHhcchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchhhhhhHHHH
Confidence 4458999999999999999999999998665544 788999999999999999999 599999999999999999
Q ss_pred eHHHHHHHHHHHHHhhhcccCcE-EEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccc
Q 001235 965 TLNEVLVASISQVMMKSNAKGIR-IVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQS 1043 (1117)
Q Consensus 965 ~L~~li~~v~~~~~~~~~~~~i~-i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~ 1043 (1117)
++...+..++..+...+....+. +..++|.. +.++..|+..+.||+-|+++||+||+|++|.|++++.....
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 99999999999999886655554 66677776 35899999999999999999999999999999999988777
Q ss_pred cceeEEEEEEeecCCCCChhhhhhccCCCC--------CCCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1044 VHLAYLELRITHAGGGIPEPLLDQMFGSEG--------DTSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1044 ~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~--------~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
.+.++|+|.|.|||.+.+++||++|+ +.+||||||+|+|+||+.|||+||.+|+.|+ |+|+|+||..
T Consensus 374 ----~v~iSI~D~G~gIPk~d~~~iFdrfyRvdkARsR~~gGTGLGLaIakeiV~~hgG~iWA~s~~gkgtt~~ftLPy~ 449 (459)
T COG5002 374 ----WVEISISDQGLGIPKEDLEKIFDRFYRVDKARSRKMGGTGLGLAIAKEIVQAHGGRIWAESEEGKGTTFSFTLPYS 449 (459)
T ss_pred ----EEEEEEccCCCCCCchhHHHHHHHHhhhhhhhhhcCCCCchhHHHHHHHHHHhCCeEEEecccCCceEEEEEeccc
Confidence 89999999999999999999999984 4459999999999999999999999999998 9999999975
Q ss_pred C
Q 001235 1115 A 1115 (1117)
Q Consensus 1115 ~ 1115 (1117)
.
T Consensus 450 ~ 450 (459)
T COG5002 450 G 450 (459)
T ss_pred C
Confidence 4
No 6
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=100.00 E-value=1.3e-37 Score=371.20 Aligned_cols=338 Identities=15% Similarity=0.159 Sum_probs=272.0
Q ss_pred EEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchh
Q 001235 725 CFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMA 804 (1117)
Q Consensus 725 ~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~ 804 (1117)
..+.+++++.++.++++++.+++|+.+++++++ +|+++|.+|+|+++|+++++++||+.+++.|+++... +.
T Consensus 77 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~-~~---- 148 (430)
T PRK11006 77 YGLYQMQLRNRKRRRELGNLIKRFRSGAESLPD---AVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNL-LR---- 148 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---eEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHH-hc----
Confidence 345578889999999999999999999999999 8999999999999999999999999999999975322 11
Q ss_pred hhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHH
Q 001235 805 CCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRL 884 (1117)
Q Consensus 805 ~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ 884 (1117)
.+ +.. ..+.. . .......+...+|+. +.++..|..+ + +++.+++|||++++.+..
T Consensus 149 -----~~-~~~---~~~~~----~-~~~~~~~~~~~~~~~--~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~---- 203 (430)
T PRK11006 149 -----YP-EFT---QYLKT----R-DFSRPLTLVLNNGRH--LEIRVMPYTE--G---QLLMVARDVTQMHQLEGA---- 203 (430)
T ss_pred -----CH-HHH---HHHHh----c-ccCCCeEEEcCCCCE--EEEEEEEcCC--C---cEEEEEehhhHHHHHHHH----
Confidence 11 111 11111 1 111223334556654 4555556542 3 246788999987765532
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeE
Q 001235 885 SEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1117)
Q Consensus 885 ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~-l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~ 962 (1117)
+.+|++.++|||||||++|.++++++.... ..+...++++.+.+..++|..++++ +++++++.+.......
T Consensus 204 -------~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~~~~~~~~ 276 (430)
T PRK11006 204 -------RRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAAPTIDLNE 276 (430)
T ss_pred -------HHHHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcccCC
Confidence 336899999999999999999999987654 3456678899999999999999999 5999988877666678
Q ss_pred EeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccc
Q 001235 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQ 1042 (1117)
Q Consensus 963 ~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~ 1042 (1117)
.+++..+++.+........ .+++.+.++.++.+ .+.+|+.+|.|+|.||+.||+||+++++.|.|++....+
T Consensus 277 ~~~~~~~~~~l~~~~~~~~-~~~~~i~~~~~~~~---~i~~d~~~l~~vl~NLl~NAik~~~~~~~I~i~~~~~~~---- 348 (430)
T PRK11006 277 KVDVPMMLRVLEREAQTLS-QGKHTITFEVDNSL---KVFGNEDQLRSAISNLVYNAVNHTPEGTHITVRWQRVPQ---- 348 (430)
T ss_pred ccCHHHHHHHHHHHHHHHh-cCCcEEEEecCCCc---eEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEcCC----
Confidence 8999999988776665544 66788888887764 588999999999999999999999888889998877666
Q ss_pred ccceeEEEEEEeecCCCCChhhhhhccCCCCCC--------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEec
Q 001235 1043 SVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT--------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVEL 1113 (1117)
Q Consensus 1043 ~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~--------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl 1113 (1117)
.+.|+|.|||+|||++.++++|+||+++ +|+||||+|||++++.|||+|+++|.+|+ |+|+|+||.
T Consensus 349 -----~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~~~~~G~GLGL~ivk~iv~~~gG~i~i~s~~~~Gt~f~i~lP~ 423 (430)
T PRK11006 349 -----GAEFSVEDNGPGIAPEHIPRLTERFYRVDKARSRQTGGSGLGLAIVKHALSHHDSRLEIESEVGKGTRFSFVLPE 423 (430)
T ss_pred -----EEEEEEEEcCCCCCHHHHHHhccCcccccCCCCCCCCCCchHHHHHHHHHHHCCCEEEEEecCCCceEEEEEech
Confidence 7899999999999999999999999732 38999999999999999999999999887 999999996
Q ss_pred cC
Q 001235 1114 AA 1115 (1117)
Q Consensus 1114 ~~ 1115 (1117)
..
T Consensus 424 ~~ 425 (430)
T PRK11006 424 RL 425 (430)
T ss_pred Hh
Confidence 53
No 7
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=100.00 E-value=4.4e-36 Score=314.90 Aligned_cols=338 Identities=17% Similarity=0.212 Sum_probs=266.5
Q ss_pred HHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCC
Q 001235 750 AIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD 829 (1117)
Q Consensus 750 ~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~ 829 (1117)
.++++.+. ++.+.|.+|.|.|+|++++.+||.+...+.|.++. ++++.. ......+.+....+.
T Consensus 11 ~~Ln~~~~---pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~-~l~~~g------------s~ll~ll~q~~~~~~ 74 (363)
T COG3852 11 AILNNLIN---PVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLS-ELLPFG------------SLLLSLLDQVLERGQ 74 (363)
T ss_pred hHHhccCC---ceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChH-HHcCCC------------cHHHHHHHHHHHhcC
Confidence 56677766 89999999999999999999999999999998864 333321 113344555554443
Q ss_pred C-ceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHH
Q 001235 830 P-EKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLS 908 (1117)
Q Consensus 830 ~-~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~ 908 (1117)
. .+++..+. .+|....+++.+.|+-...|.+. ..++-+....+..+++.+.+. ..+-..+..+++|||||||.
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---LEFHPRDMQRRLDREQTQHAQ--QRAVKGLVRGLAHEIKNPLG 148 (363)
T ss_pred Ccccceeeee-ecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhHHHHHHHH--HHHHHHHHHHHHHHhcCccc
Confidence 3 45566655 89999999999999988777665 444444443333332222221 12233457789999999999
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEE
Q 001235 909 GIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRI 988 (1117)
Q Consensus 909 ~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i 988 (1117)
+|.|.++||+....++..+.+.+.|.+.++++..+++.+.+.. ...+.+..++|++.+++.|...+...+. .++.+
T Consensus 149 GiRGAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRme~~~---~~rp~~r~~~NIH~VLerV~~lv~~e~~-~~i~l 224 (363)
T COG3852 149 GIRGAAQLLERALPDEALRELTQLIIEEADRLRNLVDRLEVLG---PQRPGDRVPVNIHEVLERVRALVEAEFA-DNVRL 224 (363)
T ss_pred chhhHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCCCcccccchHHHHHHHHHHHHhcccC-CceEE
Confidence 9999999999988888899999999999999999999975554 3445667799999999999998887665 56999
Q ss_pred EEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccC----CCCeEEEEEEeccc-ccccccceeEEEEEEeecCCCCChh
Q 001235 989 VNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP----NGGQLMVSSSLTKD-QLGQSVHLAYLELRITHAGGGIPEP 1063 (1117)
Q Consensus 989 ~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~----~~g~I~I~v~~~~~-~~~~~~~~~~l~i~V~D~G~GI~~e 1063 (1117)
..|.++.+| .+++|+.+|.|+|.||+.||+++.. .+|.|.++.+.... ...+......+.+.|.|||+|+|++
T Consensus 225 ~rdYDPSLP--~v~~d~DqliQv~LNlVrNAaqA~~~~~~~~g~I~LrTR~~~q~~i~g~r~rl~l~leViDNGPGVP~~ 302 (363)
T COG3852 225 IRDYDPSLP--EVLGDRDQLIQVFLNLVRNAAQALGGRADEGGEIILRTRTGIQLTIAGTRYRLALPLEVIDNGPGVPPD 302 (363)
T ss_pred eecCCCCCc--cccCCHHHHHHHHHHHHHHHHHHhcCCCCCCceEEEEeccceEEEccCceeEeeeeeEEecCCCCCChH
Confidence 999999998 6999999999999999999999864 25889888754433 1233444567788899999999999
Q ss_pred hhhhccCCCCCC--CCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEeccC
Q 001235 1064 LLDQMFGSEGDT--SEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAA 1115 (1117)
Q Consensus 1064 ~~~~iFe~f~~~--~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl~~ 1115 (1117)
.++++|.||-++ .|+||||++++++|..|||.|+++|.||+|+|.|.+|+.+
T Consensus 303 L~~~lF~P~Vs~r~~GsGLGLala~~li~qH~G~Ie~~S~Pg~T~FrvllP~~~ 356 (363)
T COG3852 303 LQDHLFYPMVSGREGGTGLGLALAQNLIDQHGGKIEFDSWPGRTVFRVLLPIRK 356 (363)
T ss_pred HhhhccccccccCCCCccccHHHHHHHHHhcCCEEEEeccCCceEEEEEeeccc
Confidence 999999999654 4999999999999999999999999999999999999865
No 8
>PRK13557 histidine kinase; Provisional
Probab=100.00 E-value=7.5e-35 Score=357.39 Aligned_cols=354 Identities=14% Similarity=0.120 Sum_probs=283.7
Q ss_pred hhHhhHHHHHHHHHhCCCCCCCCeeeeCC---CCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHH
Q 001235 739 DKFTRIEGDYKAIVQNPNPLIPPIFGSDE---FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFV 815 (1117)
Q Consensus 739 ~~L~~se~~l~~i~~~~~~li~~I~~~D~---~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~ 815 (1117)
+.....+..|+.++++++. +|++.|. +|+|+++|+++++++||+.+|++|+++. .+.+++...
T Consensus 23 ~~~~~~~~~~~~~~~~~~~---~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~-----------~l~~~~~~~ 88 (540)
T PRK13557 23 DVSDHRSDIFFAAVETTRM---PMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCR-----------FLQGPETDR 88 (540)
T ss_pred hhhhhhhHHHHHHHHhCcC---cEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChH-----------hhcCCCCCH
Confidence 3444567899999999998 8999995 7899999999999999999999999853 222233334
Q ss_pred HHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001235 816 NLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKA 895 (1117)
Q Consensus 816 ~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~ 895 (1117)
.....+...+..+..+..++...+++|..+|+.++..|+++.+|.+++++++.+|||++++.++++++..+. .....+
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~~~--~~l~~~ 166 (540)
T PRK13557 89 ATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQKM--EALGQL 166 (540)
T ss_pred HHHHHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHHHH--HHhhhh
Confidence 445556666666777778888899999999999999999999999999999999999999888766544332 233456
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHhcC-----CCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSRKMMEGT-----ELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~~LL~~~-----~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~l 969 (1117)
+..++|++||||+.|.++++++... ...+...+.++.+....+++..+++++ ++++.. .+....+++..+
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 8889999999999999999987532 234566788888999999999999994 666532 345678999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccc------c
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQ------S 1043 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~------~ 1043 (1117)
+..+...+... ..+++.+.++.++..+ .+.+|+.+|.|+|.||+.||++|++.++.|.|..........+ .
T Consensus 243 i~~~~~~~~~~-~~~~~~i~~~~~~~~~--~~~~d~~~l~~vl~nll~NA~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~ 319 (540)
T PRK13557 243 VSGMGELAERT-LGDAVTIETDLAPDLW--NCRIDPTQAEVALLNVLINARDAMPEGGRVTIRTRNVEIEDEDLAMYHGL 319 (540)
T ss_pred HHHHHHHHHHh-cCCCeEEEEecCCCCC--ceeeCHHHHHHHHHHHHHHHHHhcccCCeEEEEEeeeccCccccccccCC
Confidence 99887766543 3466778877776654 5889999999999999999999998888888776532210000 0
Q ss_pred cceeEEEEEEeecCCCCChhhhhhccCCCCCCC----CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1044 VHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS----EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1044 ~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~----GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.....+.|+|.|||+|||++...++|+||++++ |+||||++||++++.|||+|+++|.+|+ |+|+|+||...
T Consensus 320 ~~~~~~~i~v~D~G~Gi~~~~~~~if~~~~~~~~~~~g~GlGL~i~~~~v~~~gG~i~~~s~~~~G~~f~i~lP~~~ 396 (540)
T PRK13557 320 PPGRYVSIAVTDTGSGMPPEILARVMDPFFTTKEEGKGTGLGLSMVYGFAKQSGGAVRIYSEVGEGTTVRLYFPASD 396 (540)
T ss_pred CCCCEEEEEEEcCCCCCCHHHHHhccCCCcccCCCCCCCCccHHHHHHHHHHCCCEEEEEecCCCceEEEEEeeCCC
Confidence 012378899999999999999999999997654 8999999999999999999999999987 99999999854
No 9
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=100.00 E-value=5.7e-35 Score=368.94 Aligned_cols=329 Identities=16% Similarity=0.193 Sum_probs=263.8
Q ss_pred hhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeC-CCCceeechhhHHHhcCCChhh-HhhcchhhhhcCCchhhhhccChh
Q 001235 735 KTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREE-VIDKLLLAEVFGTNMACCRLKNQE 812 (1117)
Q Consensus 735 K~aE~~L~~se~~l~~i~~~~~~li~~I~~~D-~~g~i~~~N~a~~~l~G~~~eE-liGk~l~~ei~~~~~~~~~l~~~d 812 (1117)
.+...+++..++.++.++++++. |+++.| .+|+++.+|+++++++|...-+ +.... ..+.
T Consensus 332 ~~l~~~L~~~~~l~~~Ii~~lp~---Gilv~D~~~~~Ii~~N~aA~~ll~~~~l~~i~~~~--------------~~~~- 393 (894)
T PRK10618 332 ESMSHELRILRALNEEIVSNLPL---GLLVYDFESNRTVISNKIADHLLPHLNLQKITTMA--------------EQHQ- 393 (894)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCc---eEEEEECCCCeEEEEhHHHHHHhCccchhhHHHHH--------------Hhcc-
Confidence 34556788899999999999999 899999 7899999999999999864211 11000 0000
Q ss_pred HHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHH---HHHHHH
Q 001235 813 AFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQR---LSEQTA 889 (1117)
Q Consensus 813 ~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~---~ae~~~ 889 (1117)
..+... .++...++..... .....+.+.+++|++++...++++++ ..++..
T Consensus 394 ------~~i~~~---------------i~~~~~eir~~~~-----~~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le~~~ 447 (894)
T PRK10618 394 ------GVIQAT---------------INNELYEIRMFRS-----QLAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQ 447 (894)
T ss_pred ------hhhhhh---------------ccCceeEEEEeec-----cccCceEEEEEeehHHHHHHHHHHHHHHHHHHHHH
Confidence 000000 1122222221111 11223467788999988777666554 334456
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~ 968 (1117)
..|.+|++.|+|||||||++|.++++++.....++++.++++.+..+.+++..++++ +++++++.|+..++..++++.+
T Consensus 448 ~~k~~fla~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~~l~~~~~~L~~ 527 (894)
T PRK10618 448 QARKAFLQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDWKPEQELFSLQD 527 (894)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccceeECHHH
Confidence 778899999999999999999999999988777888999999999999999999999 6999999999999999999999
Q ss_pred HHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeE
Q 001235 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAY 1048 (1117)
Q Consensus 969 li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~ 1048 (1117)
++++++..+...+..+++.+.++.+...+ ..+.+|+.+|.|||.||+.||+||++ .|.|.|++..... .+ ..
T Consensus 528 ll~~vl~~~~~~a~~k~i~l~~~~~~~~~-~~v~~D~~~L~QVL~NLL~NAik~t~-~G~I~I~v~~~~~--~~----~~ 599 (894)
T PRK10618 528 LIDEVLPEVLPAIKRKGLQLLIHNHLKAE-QLRIGDRDALRKILLLLLNYAITTTA-YGKITLEVDQDES--SP----DR 599 (894)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEeCCCCC-cEEEecHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEccC--CC----cE
Confidence 99999999999999999999888765443 36899999999999999999999998 6788888776543 11 27
Q ss_pred EEEEEeecCCCCChhhhhhccCCCCCC-------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1049 LELRITHAGGGIPEPLLDQMFGSEGDT-------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1049 l~i~V~D~G~GI~~e~~~~iFe~f~~~-------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
+.|+|+|+|+|||++.+++||+||+++ +|+||||+|||+||+.|||+|++.|.+|+ |+|+|+||+..
T Consensus 600 l~I~V~DtG~GI~~e~l~~IFePF~t~~~~~~~~~GtGLGLaI~k~Lve~~GG~I~v~S~~g~GT~F~I~LPl~~ 674 (894)
T PRK10618 600 LTIRILDTGAGVSIKELDNLHFPFLNQTQGDRYGKASGLTFFLCNQLCRKLGGHLTIKSREGLGTRYSIHLKMLA 674 (894)
T ss_pred EEEEEEECCCCCCHHHHHHhcCccccCCCCCCCCCCcChhHHHHHHHHHHcCCEEEEEECCCCcEEEEEEEEccC
Confidence 999999999999999999999999643 38999999999999999999999999998 99999999854
No 10
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=100.00 E-value=1.9e-34 Score=334.01 Aligned_cols=338 Identities=14% Similarity=0.164 Sum_probs=262.2
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHH
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1117)
...++.+++++++ |++++|.+|+|+++|+++++++||+.++++|+++.. +++.. ..+.. .+...
T Consensus 6 ~~~~~~il~~~~~---gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~-~~~~~--------~~~~~----~~~~~ 69 (348)
T PRK11073 6 LPDAGQILNSLIN---SILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPE-LLSYF--------SLNIE----LMRES 69 (348)
T ss_pred cchHHHHHhcCcC---eEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHH-HcCcc--------hhhHH----HHHHH
Confidence 3467899999999 899999999999999999999999999999998643 32210 11111 22233
Q ss_pred hcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 001235 825 MSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIR 904 (1117)
Q Consensus 825 l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIr 904 (1117)
+..+.....+......+|+.+|+.++..|+. + .+++..++|+|++++.+.++.+.++. ....++++.++||+|
T Consensus 70 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~~~--~~~~~~~~~iaHelr 142 (348)
T PRK11073 70 LQAGQGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHAQQ--VAARDLVRGLAHEIK 142 (348)
T ss_pred HHcCCcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHHHH--HHHHHHHHhhhHhhc
Confidence 3333333222334456999999999999987 2 34567799999988877665543333 234567889999999
Q ss_pred hhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHHHHHHHHHHHhhhcc
Q 001235 905 NPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNA 983 (1117)
Q Consensus 905 nPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~ 983 (1117)
|||++|.++++++.+...++...++++.+...++++..+++++ .+.+.. ....+++..+++.+...+.....
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 9999999999999877667788899999999999999999994 555422 24567999999998887776553
Q ss_pred cCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhcc-CCCCeEEEEEEeccccc-ccccceeEEEEEEeecCCCCC
Q 001235 984 KGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV-PNGGQLMVSSSLTKDQL-GQSVHLAYLELRITHAGGGIP 1061 (1117)
Q Consensus 984 ~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~-~~~g~I~I~v~~~~~~~-~~~~~~~~l~i~V~D~G~GI~ 1061 (1117)
+++.+.++.++..+ .+.+|+.+|.|||.||+.||++|+ ++++.|.|++....... .+......+.++|.|||+|||
T Consensus 216 ~~i~i~~~~~~~~~--~i~~d~~~l~~vl~nLl~NA~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~~i~v~D~G~Gi~ 293 (348)
T PRK11073 216 DNVRLIRDYDPSLP--ELAHDPDQIEQVLLNIVRNALQALGPEGGTITLRTRTAFQLTLHGERYRLAARIDIEDNGPGIP 293 (348)
T ss_pred CCcEEEEecCCCCC--ceeeCHHHHHHHHHHHHHHHHHHhccCCCeEEEEEccccccccCCccCCceEEEEEEeCCCCCC
Confidence 56888888777654 689999999999999999999998 66888888765432100 111112257899999999999
Q ss_pred hhhhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEecc
Q 001235 1062 EPLLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELA 1114 (1117)
Q Consensus 1062 ~e~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl~ 1114 (1117)
++..+++|+||++++ |+||||++||++++.|||+|+++|.+|+|+|+|+||+.
T Consensus 294 ~~~~~~iF~~~~~~~~~g~GlGL~i~~~iv~~~gG~i~~~s~~~~~~f~i~lP~~ 348 (348)
T PRK11073 294 PHLQDTLFYPMVSGREGGTGLGLSIARNLIDQHSGKIEFTSWPGHTEFSVYLPIR 348 (348)
T ss_pred HHHHhhccCCcccCCCCCccCCHHHHHHHHHHcCCeEEEEecCCceEEEEEEecC
Confidence 999999999997555 89999999999999999999999998889999999973
No 11
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=100.00 E-value=8.3e-34 Score=352.29 Aligned_cols=347 Identities=18% Similarity=0.265 Sum_probs=291.7
Q ss_pred hhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHH
Q 001235 737 VMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVN 816 (1117)
Q Consensus 737 aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~ 816 (1117)
+.+.++..+..++.++++.++ +++++|.+|+++++|+++++++|+++++++|+.+. .+++. +. .
T Consensus 253 ~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~-~~~~~----------~~--~ 316 (607)
T PRK11360 253 LAQALRETRSLNELILESIAD---GVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYS-ELFPP----------NT--P 316 (607)
T ss_pred HHHHHHHHHHHHHHHHHhccC---eEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHH-HHcCC----------ch--h
Confidence 446677788889999999998 89999999999999999999999999999999853 23321 11 1
Q ss_pred HHHHHHHHhc-CCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001235 817 LGIVLNKAMS-GQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKA 895 (1117)
Q Consensus 817 ~~~~l~~~l~-g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~ 895 (1117)
+...+...+. +......++.+..++|... +.++..|+.+.+|++.|++++++|||++++.+.++++..+.+. ..++
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~~~~--l~~~ 393 (607)
T PRK11360 317 FASPLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQERLAA--LGEL 393 (607)
T ss_pred HHHHHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHHHHH--HHHH
Confidence 1222233333 3444566788888899877 8999999999999999999999999999999988776654433 4467
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASI 974 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v~ 974 (1117)
++.++||++|||+.|.++++++.....+++..+.++.+.+..+++..++++ +++++... ....++++..+++.+.
T Consensus 394 ~~~~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~~----~~~~~~~~~~~~~~~~ 469 (607)
T PRK11360 394 VAGVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPRE----SQWQPVSLNALVEEVL 469 (607)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc----CccceecHHHHHHHHH
Confidence 899999999999999999999887766777889999999999999999999 47777543 2467899999999999
Q ss_pred HHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEe
Q 001235 975 SQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRIT 1054 (1117)
Q Consensus 975 ~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~ 1054 (1117)
..+......+++.+.++++++.+ .+.+|+..|.+++.|++.||++|.+.+|.|+|++....+ ..+.|.|.
T Consensus 470 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~nli~na~~~~~~~~~i~v~~~~~~~--------~~~~i~v~ 539 (607)
T PRK11360 470 QLFQTAGVQARVDFETELDNELP--PIWADPELLKQVLLNILINAVQAISARGKIRIRTWQYSD--------GQVAVSIE 539 (607)
T ss_pred HHHHHhhhccCcEEEEEcCCCCC--eEEECHHHHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCC--------CEEEEEEE
Confidence 99888877788999888877764 588999999999999999999998878899998876655 02899999
Q ss_pred ecCCCCChhhhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1055 HAGGGIPEPLLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1055 D~G~GI~~e~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
|||+|||++..+++|+||++++ |+|+||++||++++.|||+|+++|.+|+ |+|+|+||+...
T Consensus 540 D~G~G~~~~~~~~~f~~~~~~~~~g~glGL~~~~~~~~~~~G~i~~~s~~~~Gt~~~i~lp~~~~ 604 (607)
T PRK11360 540 DNGCGIDPELLKKIFDPFFTTKAKGTGLGLALSQRIINAHGGDIEVESEPGVGTTFTLYLPINPQ 604 (607)
T ss_pred eCCCCCCHHHHhhhcCCceeCCCCCCchhHHHHHHHHHHcCCEEEEEEcCCCceEEEEEecCCCC
Confidence 9999999999999999997444 8999999999999999999999999986 999999998653
No 12
>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=100.00 E-value=4e-34 Score=327.82 Aligned_cols=320 Identities=17% Similarity=0.172 Sum_probs=269.0
Q ss_pred hhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHH
Q 001235 742 TRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVL 821 (1117)
Q Consensus 742 ~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l 821 (1117)
++..++|+.+++++++ +|+.+|.+|++++||+++++++|+++++++|+++....+ +++ +...+
T Consensus 2 ~~~~~~l~~~~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~-----------~~~---~~~~l 64 (333)
T TIGR02966 2 SALLSRFRAAAQALPD---AVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIR-----------HPE---FVEYL 64 (333)
T ss_pred hhHHHHHHHHHHhCcC---cEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHcc-----------CHH---HHHHH
Confidence 4567889999999999 999999999999999999999999999999988643322 222 12222
Q ss_pred HHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 001235 822 NKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKR 901 (1117)
Q Consensus 822 ~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isH 901 (1117)
. +... ..++.+..++|..+|+.++..|+.+.+ ++++++|||+.++.+.. +.++++.++|
T Consensus 65 ~----~~~~-~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~-----------~~~~~~~l~h 123 (333)
T TIGR02966 65 A----AGRF-SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQM-----------RRDFVANVSH 123 (333)
T ss_pred H----hccc-CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHH-----------HHHHHHhhhh
Confidence 2 2211 223556668899999999999987653 67888999987765532 2357889999
Q ss_pred hhhhhHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHHHHHHHHH
Q 001235 902 QIRNPLSGIIFSRKMMEGT--ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1117)
Q Consensus 902 EIrnPL~~I~~~~~LL~~~--~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v~~~~~ 978 (1117)
+++|||++|.++.+++... ..++...++++.+....+++..++++ +++.+++.+.......++++.+++..++..+.
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 9999999999999988654 45566778899999999999999999 48899888778888899999999999999999
Q ss_pred hhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCC
Q 001235 979 MKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGG 1058 (1117)
Q Consensus 979 ~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~ 1058 (1117)
.....+++.+.++.++. ..+.+|+..|.++|.||+.||++|++.++.|.|++...++ .+.|.|.|+|+
T Consensus 204 ~~~~~~~i~i~~~~~~~---~~~~~d~~~l~~vl~nll~Nai~~~~~~~~i~i~~~~~~~---------~~~i~i~d~G~ 271 (333)
T TIGR02966 204 ALSQGKNHQITFEIDGG---VDVLGDEDELRSAFSNLVSNAIKYTPEGGTITVRWRRDGG---------GAEFSVTDTGI 271 (333)
T ss_pred HHHHHcCcEEEEcCCCC---ceEEECHHHHHHHHHHHHHHhheeCCCCCeEEEEEEEcCC---------EEEEEEEecCC
Confidence 99999999999988443 3799999999999999999999999888899998887766 78999999999
Q ss_pred CCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEE
Q 001235 1059 GIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSV 1111 (1117)
Q Consensus 1059 GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~L 1111 (1117)
|||++..+++|++|+. .+|+|+||++|+.+++.|||+|++.|.+++ |+|+|+|
T Consensus 272 gi~~~~~~~if~~~~~~~~~~~~~~~g~glGL~~~~~~~~~~gG~i~~~s~~~~Gt~~~i~l 333 (333)
T TIGR02966 272 GIAPEHLPRLTERFYRVDKSRSRDTGGTGLGLAIVKHVLSRHHARLEIESELGKGSTFSFIF 333 (333)
T ss_pred CCCHHHHhhhccCceecCcccccCCCCCcccHHHHHHHHHHCCCEEEEEecCCCCeEEEEEC
Confidence 9999999999999862 248899999999999999999999999887 9999975
No 13
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=100.00 E-value=8.8e-34 Score=363.67 Aligned_cols=330 Identities=23% Similarity=0.297 Sum_probs=269.6
Q ss_pred hhhHhhHHHHHHHHHhCCCCCCCCeeeeC-CCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHH
Q 001235 738 MDKFTRIEGDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVN 816 (1117)
Q Consensus 738 E~~L~~se~~l~~i~~~~~~li~~I~~~D-~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~ 816 (1117)
..+++++++.++.+++.+|. ++++++ .+|.++.+|+.+..++|+...+...+
T Consensus 326 ~~~L~e~e~~~r~iv~~~p~---gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~~~~------------------------ 378 (924)
T PRK10841 326 ALRLEEHEQFNRKIVASAPV---GICILRTSDGTNILSNELAHNYLNMLTHEDRQR------------------------ 378 (924)
T ss_pred HHHHHHHHHHHHHHHHhCCc---cEEEEEcCCCcEEEehHHHHHHhccCChhHHHH------------------------
Confidence 34688889999999999998 888886 79999999999999998754322111
Q ss_pred HHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHH---HHHHHHHH
Q 001235 817 LGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLS---EQTALKRL 893 (1117)
Q Consensus 817 ~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~a---e~~~~~k~ 893 (1117)
+. .......... ......++....+........ ++. ..++++.|||++++.++++++.. ++....|.
T Consensus 379 ~~----~~~~~~~~~~--~~~~~~~~~~~~i~~~~~~~~---~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~a~~~k~ 448 (924)
T PRK10841 379 LT----QIICGQQVNF--VDVLTSNNTNLQISFVHSRYR---NEN-VAICVLVDVSARVKMEESLQEMAQAAEQASQSKS 448 (924)
T ss_pred HH----HHHhccccce--eeEEcCCCcEEEEEEEeeeec---Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 10 0111111111 122234444444433333322 222 36788999999999998877644 34456677
Q ss_pred HHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHHH
Q 001235 894 KALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVA 972 (1117)
Q Consensus 894 ~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~ 972 (1117)
.|++.|+|||||||++|.++++++.....+++++++++.+..+.++|..++++ +++++++.+...++..+|++.+++++
T Consensus 449 ~fla~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~~l~~~~~~l~~li~~ 528 (924)
T PRK10841 449 MFLATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLKIEPREFSPREVINH 528 (924)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeeeEEecHHHHHHH
Confidence 89999999999999999999999998888899999999999999999999999 69999999999999999999999999
Q ss_pred HHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEE
Q 001235 973 SISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELR 1052 (1117)
Q Consensus 973 v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~ 1052 (1117)
++..+...+..+++.+.++++++.+ ..+.+|+.+|.|||.||+.||+||++ .|.|.|++...++ .+.|+
T Consensus 529 v~~~~~~~~~~k~i~l~~~i~~~~~-~~v~~D~~~L~qvl~NLl~NAik~t~-~G~I~I~v~~~~~---------~l~i~ 597 (924)
T PRK10841 529 ITANYLPLVVKKRLGLYCFIEPDVP-VALNGDPMRLQQVISNLLSNAIKFTD-TGCIVLHVRVDGD---------YLSFR 597 (924)
T ss_pred HHHHHHHHHHHcCcEEEEEeCCCCC-cEEEECHHHHHHHHHHHHHHHHhhCC-CCcEEEEEEEeCC---------EEEEE
Confidence 9999999999999999998887765 36999999999999999999999997 6778888877655 89999
Q ss_pred EeecCCCCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1053 ITHAGGGIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1053 V~D~G~GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
|.|+|+|||++.++++|+||+. .+|+||||+||+++++.|||+|+++|++|+ |+|+|+||+..
T Consensus 598 V~DtG~GI~~e~~~~lFepF~~~~~~~~~~~~GtGLGL~I~k~lv~~~gG~I~v~S~~g~Gt~F~i~LP~~~ 669 (924)
T PRK10841 598 VRDTGVGIPAKEVVRLFDPFFQVGTGVQRNFQGTGLGLAICEKLINMMDGDISVDSEPGMGSQFTIRIPLYG 669 (924)
T ss_pred EEEcCcCCCHHHHHHHhcccccCCCCCCCCCCCeehhHHHHHHHHHHCCCEEEEEEcCCCcEEEEEEEECCc
Confidence 9999999999999999999963 238999999999999999999999999988 99999999854
No 14
>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=1.2e-35 Score=307.07 Aligned_cols=171 Identities=33% Similarity=0.645 Sum_probs=141.8
Q ss_pred HHHHHHHHhhhc-CC-CcccccCCcchhhhccCCEEEEEECCeEEEecCCCCHHHHHHHHHHHHhccCCCceEeeccccc
Q 001235 411 RTQTLLCDMLMR-DA-PLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYD 488 (1117)
Q Consensus 411 ~~~~~~~~~~~~-~~-~~~~~~~~~~~~~l~~~~g~a~~~~~~~~~~G~~p~~~~~~~l~~~l~~~~~~~~~~~t~~l~~ 488 (1117)
++++.|..++.. .. ..++..+.++||+|++|||+||+++|+++++|.||++.+|.+|++||...... .+|+||+|++
T Consensus 3 ~~~~~L~~~~~~~~~~~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~~~-~v~~T~~L~~ 81 (182)
T PF00360_consen 3 RLQQRLLEALSSSRDLLEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQADG-EVFATDSLSE 81 (182)
T ss_dssp -HHHHHHHHHHCSSSHHHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTTT--SEEEESBGGG
T ss_pred HHHHHHHHHHccCCChhHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhCCC-ccchhhhHhH
Confidence 334444455444 33 46788899999999999999999999999999999999999999999977544 7999999998
Q ss_pred ccCCCccccccccccEEEEEeCC--CCEEEEeccCCccEEeeccCCCCCCCCC-CCCcccccchhhhhhhhhccccCCCc
Q 001235 489 AGYLGALALGDVVCGMAAVRISP--KDMIFWFRSQTASEVRWGGAKHEPDEKD-DGRKMHPRSSFKAFLEVVKTRSLPWK 565 (1117)
Q Consensus 489 ~~~p~~~~~~~~~~g~l~~~~~~--~~~l~wfR~e~~~~v~W~G~p~~~~~~~-~g~~l~PR~SF~~w~e~v~~~s~pW~ 565 (1117)
. ||+++++.+.+||||+++|++ ++||+|||+|+.++|+|||||+|+...+ ++.+++||+||+.|+|+|+++|.||+
T Consensus 82 ~-~p~~~~~~~~aaGvLai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~ 160 (182)
T PF00360_consen 82 D-YPDAAALAERAAGVLAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWS 160 (182)
T ss_dssp T-SGGGGGGCCCHSEEEEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---
T ss_pred h-ChhhhhhcccCCCcEEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCC
Confidence 5 999999999999999999986 6899999999999999999999998654 47899999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 001235 566 DYEMDAIHSLQLILRNAF 583 (1117)
Q Consensus 566 ~~El~aa~sL~liL~~~l 583 (1117)
..|++++..|+..|.+.+
T Consensus 161 ~~d~~~A~~lr~~l~~~~ 178 (182)
T PF00360_consen 161 DADLEAAERLRRALLEVI 178 (182)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999977666555
No 15
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=100.00 E-value=1.4e-32 Score=367.78 Aligned_cols=368 Identities=17% Similarity=0.198 Sum_probs=273.4
Q ss_pred EEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhh
Q 001235 728 AQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCR 807 (1117)
Q Consensus 728 ~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~ 807 (1117)
.++++.++.++.+++..+..++.++++++. +|++.|.+|+|+++|+++++++|.......+....... ..+
T Consensus 558 ~~~i~~r~~~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~----~~~-- 628 (1197)
T PRK09959 558 LRSVRRRKVIQGDLENQISFRKALSDSLPN---PTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLENSD----SPF-- 628 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---cEEEEcCCCcEEEehHHHHHHhCccccccccccccccc----Cch--
Confidence 478899999999999999999999999999 89999999999999999999999874332222210000 000
Q ss_pred ccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEE-EeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHH
Q 001235 808 LKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLC-VNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSE 886 (1117)
Q Consensus 808 l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~-~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae 886 (1117)
.+..............+...+ ...+...+|....+... ..+.....+...++++.++|||++++.+.++++..+
T Consensus 629 ---~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~ 703 (1197)
T PRK09959 629 ---KDVFSNAHEVTAETKENRTIY--TQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERN 703 (1197)
T ss_pred ---hhhHhHHHHHHHHHhhccccc--eeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHH
Confidence 011100001111111111111 22233344433222222 222222344456688889999998888776654333
Q ss_pred ---HHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHH-HHHHHHHHHHHHHHHHHHHhh-ccccccccCccccee
Q 001235 887 ---QTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE-QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEM 961 (1117)
Q Consensus 887 ---~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~-~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~ 961 (1117)
+....+.+|++.|+|||||||++|.++++++.....+++ ..+.++.+..+.+++..++++ +++++++.+...+..
T Consensus 704 ~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~~~~~ 783 (1197)
T PRK09959 704 KAINATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQLQP 783 (1197)
T ss_pred HHHHHHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCceeee
Confidence 344567889999999999999999999999976554444 457888888899999999999 699999999999999
Q ss_pred EEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccc
Q 001235 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLG 1041 (1117)
Q Consensus 962 ~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~ 1041 (1117)
.++++.+++++++..+...+..+++.+.+...... ...+.+|+.+|.|||.||+.||+||++ .|.+.|.+.......+
T Consensus 784 ~~~~l~~~i~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~v~~d~~~l~qvl~NLl~NAik~~~-~g~i~i~~~~~~~~~~ 861 (1197)
T PRK09959 784 QWVDIPTLVQNTCHSFGAIAASKSIALSCSSTFPD-HYLVKIDPQAFKQVLSNLLSNALKFTT-EGAVKITTSLGHIDDN 861 (1197)
T ss_pred eeeCHHHHHHHHHHHHHHHHHhcCcEEEEecCCCC-ceEEEECHHHHHHHHHHHHHHHHHhCC-CCCEEEEEEEeeecCC
Confidence 99999999999999999999999988887653221 136899999999999999999999998 4555555443211001
Q ss_pred cccceeEEEEEEeecCCCCChhhhhhccCCCCCC------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1042 QSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1042 ~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
...+.|+|.|+|+|||++.+++||+||+++ +|+||||+|||+|++.|||+|++.|.+|+ |+|+|+||+.
T Consensus 862 ----~~~~~i~V~D~G~Gi~~~~~~~iF~~f~~~~~~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~~ 937 (1197)
T PRK09959 862 ----HAVIKMTIMDSGSGLSQEEQQQLFKRYSQTSAGRQQTGSGLGLMICKELIKNMQGDLSLESHPGIGTTFTITIPVE 937 (1197)
T ss_pred ----ceEEEEEEEEcCCCCCHHHHHHhhccccccccCCCCCCcCchHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEEcc
Confidence 126889999999999999999999999644 48999999999999999999999999987 9999999985
Q ss_pred C
Q 001235 1115 A 1115 (1117)
Q Consensus 1115 ~ 1115 (1117)
.
T Consensus 938 ~ 938 (1197)
T PRK09959 938 I 938 (1197)
T ss_pred c
Confidence 3
No 16
>PRK13559 hypothetical protein; Provisional
Probab=100.00 E-value=1.9e-31 Score=310.62 Aligned_cols=312 Identities=13% Similarity=0.101 Sum_probs=245.0
Q ss_pred hHHHHHHHHHhCCCCCCCCeeeeCC---CCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHH
Q 001235 743 RIEGDYKAIVQNPNPLIPPIFGSDE---FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGI 819 (1117)
Q Consensus 743 ~se~~l~~i~~~~~~li~~I~~~D~---~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~ 819 (1117)
.++..|+.++++.++ +|++.|. +|.+++||+++++++||+.++++|+.+. .+ .+++.......
T Consensus 40 ~~~~~~~~~~e~~~~---~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~l----------~~~~~~~~~~~ 105 (361)
T PRK13559 40 ASGRLFEQAMEQTRM---AMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCR-FL----------QGAATDPIAVA 105 (361)
T ss_pred hhhhHHHHHHHhCCC---cEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChh-hh----------cCCCCCHHHHH
Confidence 456778999999998 8999997 5689999999999999999999999742 11 11222233344
Q ss_pred HHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001235 820 VLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYT 899 (1117)
Q Consensus 820 ~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~i 899 (1117)
.+...+.++..+..++...+++|..+|+.++..|+++.+|.+.+++++++|||++++.+++.+ .+.+++..+
T Consensus 106 ~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~--------~~~~l~~~l 177 (361)
T PRK13559 106 KIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEA--------HERRLAREV 177 (361)
T ss_pred HHHHHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHH--------HHHHHHHHH
Confidence 556677777778888889999999999999999999999999999999999999988764322 234578889
Q ss_pred HhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHHHHHHHHH
Q 001235 900 KRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1117)
Q Consensus 900 sHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v~~~~~ 978 (1117)
+|++||||+.|.++..++... .+..++++.+......|..++++ ++..+ ..++++.++++.++..+.
T Consensus 178 ~H~~~n~L~~i~~~~~l~~~~---~~~~~~~~~i~~~~~~l~~~~~~ll~~~~---------~~~v~l~~~~~~~~~~~~ 245 (361)
T PRK13559 178 DHRSKNVFAVVDSIVRLTGRA---DDPSLYAAAIQERVQALARAHETLLDERG---------WETVEVEELIRAQVAPYA 245 (361)
T ss_pred HHhhhhHHHHHHHHHHhhccC---CCHHHHHHHHHHHHHHHHHHHHHHhccCC---------cCcccHHHHHHHHHHhhc
Confidence 999999999999999988732 23455677777778888888877 45543 568999999999887665
Q ss_pred hhhcccCcEEEEeecCCCcceeEEec-HHHHHHHHHHHHHHHhhc---cCCCCeEEEEEEecccccccccceeEEEEEEe
Q 001235 979 MKSNAKGIRIVNETAEQIMSETLYGD-SIRLQQVLADFLSISINF---VPNGGQLMVSSSLTKDQLGQSVHLAYLELRIT 1054 (1117)
Q Consensus 979 ~~~~~~~i~i~~~~~~~~~~~~v~~D-~~~L~qVL~nLl~NAik~---~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~ 1054 (1117)
.. +.++.++.++ + .+..+ ...|.|||.||+.||+|| ++++|.|.|++..... + ..+.+.|.
T Consensus 246 ~~----~~~i~~~~~~-~---~~~~~~~~~l~~vl~nLi~NA~k~~~~~~~~g~i~v~~~~~~~--~-----~~~~i~v~ 310 (361)
T PRK13559 246 PR----ATRVAFEGPG-I---RLGAASVQPLGLVLHELAVNAIKHGALSADQGRISISWKPSPE--G-----AGFRIDWQ 310 (361)
T ss_pred CC----CceEEEECCC-e---eeCHHHHHHHHHHHHHHHHhHHHhccccCCCcEEEEEEEecCC--C-----CeEEEEEE
Confidence 32 4556665432 1 23333 357999999999999999 4557899998732221 1 27899999
Q ss_pred ecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHH-cCCEEEEEeeCCeEEEEEEEecc
Q 001235 1055 HAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKL-MNGDVQYLREAGKSTFIVSVELA 1114 (1117)
Q Consensus 1055 D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~-~gG~I~v~s~~g~ttF~i~LPl~ 1114 (1117)
|+|+|++++ ..|+|+||.+|+++++. |||+|++++.+++|+|+|+||+.
T Consensus 311 d~G~~~~~~-----------~~~~g~Gl~i~~~~v~~~~gG~i~~~~~~~G~~~~l~~P~~ 360 (361)
T PRK13559 311 EQGGPTPPK-----------LAKRGFGTVIIGAMVESQLNGQLEKTWSDDGLLARIEIPSR 360 (361)
T ss_pred CCCCCCCCC-----------CCCCCcHHHHHHHHHHHHcCCeEEEEEcCCeEEEEEEEeCC
Confidence 999998764 35789999999999997 99999999998789999999975
No 17
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-31 Score=314.53 Aligned_cols=215 Identities=20% Similarity=0.359 Sum_probs=194.5
Q ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhc--CCCCHH-HHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEE
Q 001235 888 TALKRLKALAYTKRQIRNPLSGIIFSRKMMEG--TELGAE-QKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVE 963 (1117)
Q Consensus 888 ~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~--~~l~~~-~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~ 963 (1117)
....+..+++.|||+|||||++|.|.++.|.. ..++++ ..+++..|.+.+.++..++.+ ||+.|+++|.+.++..+
T Consensus 656 ~E~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~l~~~~ 735 (890)
T COG2205 656 RERLRSALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKLDW 735 (890)
T ss_pred HHHHHHHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCcccccch
Confidence 34557778999999999999999999999875 345544 788999999999999999999 69999999999999999
Q ss_pred eeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccc
Q 001235 964 FTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQS 1043 (1117)
Q Consensus 964 ~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~ 1043 (1117)
..+.+++.+++..+......+ .+.++++.+++ .+.+|...|.|||.||+.||+||+|++..|.|.+....+
T Consensus 736 ~~veEvVg~Al~r~~k~~~~~--~i~v~~~~dl~--li~~D~~LieQVLiNLleNA~Kyap~~s~I~I~~~~~~~----- 806 (890)
T COG2205 736 VLVEEVVGEALQRLRKRFTGH--KIVVSVPVDLP--LIHVDSPLIEQVLINLLENALKYAPPGSEIRINAGVERE----- 806 (890)
T ss_pred hhHHHHHHHHHHHhhhhcCCc--eEEEecCCCCc--eEecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEEEecc-----
Confidence 999999999999888777666 47777888876 899999999999999999999999999999999999887
Q ss_pred cceeEEEEEEeecCCCCChhhhhhccCCCCC------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1044 VHLAYLELRITHAGGGIPEPLLDQMFGSEGD------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1044 ~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.+.|.|.|+|+|||++..++||++|+. +.|+||||+||+.||+.|||+|++.+.+++ ++|+|+||+.+
T Consensus 807 ----~v~~~V~DeGpGIP~~~~~~IFD~F~r~~~~~~~~G~GLGLsIc~~iv~ahgG~I~a~~~~~gGa~f~~~LP~~~ 881 (890)
T COG2205 807 ----NVVFSVIDEGPGIPEGELERIFDKFYRGNKESATRGVGLGLAICRGIVEAHGGTISAENNPGGGAIFVFTLPVEE 881 (890)
T ss_pred ----eEEEEEEeCCCCCChhHHHHhhhhhhcCCCCCCCCCccccHHHHHHHHHHcCCeEEEEEcCCCceEEEEEeecCC
Confidence 899999999999999999999999953 339999999999999999999999998766 99999999875
No 18
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=99.98 E-value=2e-29 Score=309.79 Aligned_cols=345 Identities=15% Similarity=0.217 Sum_probs=244.7
Q ss_pred EEEEEeecCCCCEEEEEEEEEccchhhhhh--------------------------------------hhHhhHHHHHHH
Q 001235 709 VNACASRDLHDNVVGVCFVAQDITPQKTVM--------------------------------------DKFTRIEGDYKA 750 (1117)
Q Consensus 709 v~~~pi~d~~G~v~gv~~v~~DITerK~aE--------------------------------------~~L~~se~~l~~ 750 (1117)
....|+++..|.++|++.++.++.+-...- .++....+.+++
T Consensus 146 ~~~~p~~~~~~~~iG~v~vg~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~l~~l~~~ei~~l~~~~~~ 225 (542)
T PRK11086 146 RVFTPVYDENGKQIGVVAVGISLSEVTEQINESRWSIYWSILFGALVGLIGTVILVRVLKRILFGLEPYEISTLFEQRQA 225 (542)
T ss_pred EEEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 355789999999999988877665543322 123344466789
Q ss_pred HHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCC---hhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcC
Q 001235 751 IVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWK---REEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSG 827 (1117)
Q Consensus 751 i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~---~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g 827 (1117)
+++++++ ||+..|.+|+|++||+++++++|++ .++.+|+.+.. ++ ... .+...+..
T Consensus 226 il~~~~~---gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~-~~----------~~~-------~~~~~~~~ 284 (542)
T PRK11086 226 MLQSIKE---GVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVES-WM----------PVS-------RLKEVLRT 284 (542)
T ss_pred HHHHhcC---cEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHH-hC----------Cch-------hHHHHHhc
Confidence 9999998 8999999999999999999999875 33455554321 11 111 12333434
Q ss_pred CCCc-eEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 001235 828 QDPE-KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNP 906 (1117)
Q Consensus 828 ~~~~-~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnP 906 (1117)
+.+. ..+. ..+|. ++.....|+.+ +|.+.|++++++|+|+.++.++++.... ...++++.++||+|||
T Consensus 285 ~~~~~~~~~---~~~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~-----~~~~~l~~~sHel~np 353 (542)
T PRK11086 285 GTPRRDEEI---NINGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMV-----NYADALRAQSHEFMNK 353 (542)
T ss_pred CCCccceEE---EECCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHH-----HHHHHHHhhchhhcCH
Confidence 3332 2222 22453 45566789988 8999999999999999887776554432 2334567789999999
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHH-HHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccC
Q 001235 907 LSGIIFSRKMMEGTELGAEQKRLLHT-SAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKG 985 (1117)
Q Consensus 907 L~~I~~~~~LL~~~~l~~~~~~~l~~-i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~ 985 (1117)
|++|.+++++... ++..+++.. +......+..+++++.- .++...+......+..++
T Consensus 354 L~~I~g~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~~ 411 (542)
T PRK11086 354 LHVILGLLHLKSY----DQLEDYILKTANNYQEEIGSLLGKIKS------------------PVIAGFLLGKISRARELG 411 (542)
T ss_pred HHHHHHHHHhCch----HHHHHHHHHHHHHHHHHHHHHHHhccC------------------HHHHHHHHHHHHHHHHcC
Confidence 9999999887532 223333322 23334445555554310 112222223334556678
Q ss_pred cEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccC--CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChh
Q 001235 986 IRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP--NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEP 1063 (1117)
Q Consensus 986 i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~--~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e 1063 (1117)
+.+.++.++.++......+...|.|||.||+.||++|++ +++.|.|++...++ .+.|+|+|||+|||++
T Consensus 412 ~~~~~~~~~~~~~~~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~I~i~~~~~~~---------~~~i~V~D~G~gi~~~ 482 (542)
T PRK11086 412 ITLIISEDSQLPDSGDEDQVHELITILGNLIENALEAVGGEEGGEISVSLHYRNG---------WLHCEVSDDGPGIAPD 482 (542)
T ss_pred CEEEEeCCCCCCcccccccHHHHHHHHHHHHHHHHHHhhcCCCcEEEEEEEEcCC---------EEEEEEEECCCCCCHH
Confidence 888887766554322334456899999999999999974 36788888877666 7999999999999999
Q ss_pred hhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1064 LLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1064 ~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
.++++|+||++++ |+||||++||++++.|||+|+++|.+|+ |+|+|+||+...
T Consensus 483 ~~~~iF~~~~~~~~~g~GlGL~iv~~iv~~~~G~i~v~s~~~~G~~f~i~lP~~~~ 538 (542)
T PRK11086 483 EIDAIFDKGYSTKGSNRGVGLYLVKQSVENLGGSIAVESEPGVGTQFFVQIPWDGE 538 (542)
T ss_pred HHHHHHhCCCccCCCCCcCcHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEEeCCCC
Confidence 9999999998655 8999999999999999999999999887 999999998753
No 19
>PRK09303 adaptive-response sensory kinase; Validated
Probab=99.97 E-value=4.2e-30 Score=300.75 Aligned_cols=217 Identities=21% Similarity=0.346 Sum_probs=193.7
Q ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCC-------HHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccce
Q 001235 889 ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELG-------AEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLE 960 (1117)
Q Consensus 889 ~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~-------~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~ 960 (1117)
...+.++++.++||+||||++|.++++++.....+ +..+++++.+.+..++|..++++ +++++.+.+...++
T Consensus 148 ~~~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~~~~ 227 (380)
T PRK09303 148 LKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEALRFN 227 (380)
T ss_pred HHHHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCceec
Confidence 34577889999999999999999999999854322 33678889999999999999999 69999998888889
Q ss_pred eEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccc
Q 001235 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQL 1040 (1117)
Q Consensus 961 ~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~ 1040 (1117)
..++++.+++.+++..+...+..+++.+.++++.+.+ .+++|+.+|.|||.||+.||+||++++|.|.|.+....+
T Consensus 228 ~~~~~l~~ll~~~~~~~~~~~~~~~i~l~~~~~~~~~--~v~~d~~~l~qvl~NLl~NAik~~~~~~~I~i~~~~~~~-- 303 (380)
T PRK09303 228 PQKLDLGSLCQEVILELEKRWLAKSLEIQTDIPSDLP--SVYADQERIRQVLLNLLDNAIKYTPEGGTITLSMLHRTT-- 303 (380)
T ss_pred cccCCHHHHHHHHHHHHHHHHHHcCCEEEEEcCCCCC--eEEeCHHHHHHHHHHHHHHHHhcCCCCceEEEEEEecCC--
Confidence 9999999999999999999999999999999988765 699999999999999999999999988899988755333
Q ss_pred ccccceeEEEEEEeecCCCCChhhhhhccCCCCC------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEec
Q 001235 1041 GQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVEL 1113 (1117)
Q Consensus 1041 ~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl 1113 (1117)
..+.|+|.|||+|||++..++||+||++ .+|+||||+|||++++.|||+|++.|.+|+ |+|+|+||+
T Consensus 304 ------~~v~i~V~D~G~GI~~~~~~~iF~pf~~~~~~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~~~Gt~f~i~lP~ 377 (380)
T PRK09303 304 ------QKVQVSICDTGPGIPEEEQERIFEDRVRLPRDEGTEGYGIGLSVCRRIVRVHYGQIWVDSEPGQGSCFHFTLPV 377 (380)
T ss_pred ------CEEEEEEEEcCCCCCHHHHHHHccCceeCCCCCCCCcccccHHHHHHHHHHcCCEEEEEecCCCccEEEEEEec
Confidence 2799999999999999999999999973 348999999999999999999999999887 999999998
Q ss_pred cC
Q 001235 1114 AA 1115 (1117)
Q Consensus 1114 ~~ 1115 (1117)
-.
T Consensus 378 ~~ 379 (380)
T PRK09303 378 YR 379 (380)
T ss_pred CC
Confidence 54
No 20
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=99.97 E-value=1.7e-29 Score=286.31 Aligned_cols=330 Identities=15% Similarity=0.177 Sum_probs=249.7
Q ss_pred hhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHH
Q 001235 736 TVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFV 815 (1117)
Q Consensus 736 ~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~ 815 (1117)
++.+++.+....++.++...+. |++..|.+|++.-+|+++++|+|.+-++++|.++. .+ ..
T Consensus 360 ~ak~~~e~rr~f~E~VLsgvta---GVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~ls-a~---------------ap 420 (712)
T COG5000 360 RAKDALEQRRRFLEAVLSGLTA---GVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLS-AI---------------AP 420 (712)
T ss_pred HHHHHHHHHHHHHHHHHhcCce---eEEEEcCCCeeEeecchHHHHhcCChhHhhcchhh-hh---------------hh
Confidence 3345566667778889999988 99999999999999999999999999999999852 11 12
Q ss_pred HHHHHHHHHhcC-CCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001235 816 NLGIVLNKAMSG-QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLK 894 (1117)
Q Consensus 816 ~~~~~l~~~l~g-~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~ 894 (1117)
.+...+...-.. +.....+..+ .+.|+.+.+.+..+....+ .--|++.++.|||+--.+++.... ..
T Consensus 421 ~~~~vf~~~~a~~~~~~~~ev~~-~r~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~AQRs~AW---------~d 488 (712)
T COG5000 421 ELEEVFAEAGAAARTDKRVEVKL-AREGEERTLNVQATREPED--NGNGYVVTFDDITDLVIAQRSAAW---------GD 488 (712)
T ss_pred HHHHHHHHhhhhcCCCccceeec-ccCCCceeeeeeeeecccc--cCCceEEEecchHHHHHHHHHHHH---------HH
Confidence 233333333322 2333444444 4455556666666554332 233578899999987766633222 22
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHhc---CCCCH---HHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHH
Q 001235 895 ALAYTKRQIRNPLSGIIFSRKMMEG---TELGA---EQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLN 967 (1117)
Q Consensus 895 ~la~isHEIrnPL~~I~~~~~LL~~---~~l~~---~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~ 967 (1117)
....|+|||||||+.|...++-|++ ...++ ...++.++|.+....+.+++++. .|++. ..+.++..||.
T Consensus 489 VArRIAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afARm----P~p~~e~~dL~ 564 (712)
T COG5000 489 VARRIAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFARM----PAPKLEKSDLR 564 (712)
T ss_pred HHHHHHHHhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCCCCCcchHH
Confidence 4567899999999999988888764 22333 34778899999999999999994 88874 35577899999
Q ss_pred HHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCC-------CCeEEEEEEeccccc
Q 001235 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN-------GGQLMVSSSLTKDQL 1040 (1117)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~-------~g~I~I~v~~~~~~~ 1040 (1117)
.++.+++...+. ....+.+..+++.+ +.....|+..|.|+|.||+.||.++... .+.|+++....++
T Consensus 565 ~ll~e~~~L~e~--~~~~i~f~~e~g~e--pl~~~~D~~~l~Qvf~NliKNA~EAi~~~~~~e~~~~~i~~~~~~~~g-- 638 (712)
T COG5000 565 ALLKEVSFLYEI--GNDHIVFAAEFGGE--PLIGMADATLLGQVFGNLLKNAAEAIEAVEAEERRTALIRVSLDDADG-- 638 (712)
T ss_pred HHHHHHHHHHhc--cCCCeEEEeecCCC--ceeeecCHHHHHHHHHHHHHhHHHHhhhcccccCCcceEEEEEecCCC--
Confidence 999999876553 33567888888887 3467789999999999999999988521 3346666555555
Q ss_pred ccccceeEEEEEEeecCCCCChhhhhhccCCCCCC--CCccccHHHHHHHHHHcCCEEEEEeeCC--eEEEEEEEec
Q 001235 1041 GQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT--SEEGISLLISRKLVKLMNGDVQYLREAG--KSTFIVSVEL 1113 (1117)
Q Consensus 1041 ~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~--~GtGLGL~ivr~iVe~~gG~I~v~s~~g--~ttF~i~LPl 1113 (1117)
.+++.|.|||.|+|.|...++||||-++ |||||||+|||+|+|.|||.|.+...|+ ++++.+.||.
T Consensus 639 -------~i~v~V~DNGkG~p~e~r~r~~EPYvTtr~KGTGLGLAiVKkIvEeHGG~leL~da~d~~GA~i~i~fp~ 708 (712)
T COG5000 639 -------RIVVDVIDNGKGFPRENRHRALEPYVTTREKGTGLGLAIVKKIVEEHGGRLELHNAPDFDGAMIRIKFPL 708 (712)
T ss_pred -------eEEEEEecCCCCCChHHhhhhccCceecccccccccHHHHHHHHHhcCCeEEecCCCCCCCcEEEEEccc
Confidence 8999999999999999999999999544 5999999999999999999999998753 4899999997
No 21
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=99.97 E-value=3.1e-28 Score=278.31 Aligned_cols=205 Identities=17% Similarity=0.234 Sum_probs=181.2
Q ss_pred HHHHHhhhhhhHHHHHHHHH---HHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSRK---MMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLV 971 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~~---LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~li~ 971 (1117)
.+.|+||||+||++|..+.+ ++-++...++....+..|..-.++|..|...| .|++-- .-...++.+.++|+
T Consensus 388 SA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FArk~----~~a~~~v~l~~ai~ 463 (603)
T COG4191 388 SAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFARKS----RDAAGPVSLREAIE 463 (603)
T ss_pred HHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhccC----ccccCCccHHHHHH
Confidence 56789999999999996643 44456667888999999999999999999998 677632 22377999999999
Q ss_pred HHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccC--CCCeEEEEEEecccccccccceeEE
Q 001235 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP--NGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 972 ~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~--~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
.++..+...++..++.+..+.++.. ..|.+++.+|+|||.|||.||++++. +.++|.|.....++ .+
T Consensus 464 ~Al~ll~~R~~~~~~~l~~~~~~~~--~~V~~~~iRLeQVLvNLl~NALDA~~~~~~~~i~i~~~~~~~---------~v 532 (603)
T COG4191 464 GALELLRGRLRAAGVELELDLPDAP--LWVMANEIRLEQVLVNLLQNALDAMAGQEDRRLSIRAQREGG---------QV 532 (603)
T ss_pred HHHHHHHHhhhccCceeeccCCCCC--ceeecchhhHHHHHHHHHHHHHHHhcCCCCCeeEEEEEecCC---------eE
Confidence 9999999999999999999988753 38999999999999999999999974 37899999888877 89
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCCC----CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDTS----EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~~----GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.|+|.|||+||++|...++|+|||++| |.||||+||++|++.+||+|.+.+.+++ +.|+|+||.++
T Consensus 533 ~l~VrDnGpGi~~e~~~~lFePF~TtK~~~~GLGLGLaIS~~i~~d~GGsL~v~n~~~~Ga~F~i~L~~a~ 603 (603)
T COG4191 533 VLTVRDNGPGIAPEALPHLFEPFFTTKPVGKGLGLGLAISQNIARDLGGSLEVANHPEGGASFTIELRRAA 603 (603)
T ss_pred EEEEccCCCCCCHHHHHhhcCCccccCcccCCcchhHHHHHHHHHHhCCeEEeecCCCCceEEEEEeecCC
Confidence 999999999999999999999999888 7899999999999999999999998666 99999999653
No 22
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=99.97 E-value=2.8e-27 Score=291.13 Aligned_cols=345 Identities=14% Similarity=0.179 Sum_probs=242.4
Q ss_pred EEEEEeecCCCCEEEEEEEEEccchhhhhh--------------------------------------hhHhhHHHHHHH
Q 001235 709 VNACASRDLHDNVVGVCFVAQDITPQKTVM--------------------------------------DKFTRIEGDYKA 750 (1117)
Q Consensus 709 v~~~pi~d~~G~v~gv~~v~~DITerK~aE--------------------------------------~~L~~se~~l~~ 750 (1117)
..+.|+++++|.++|++.+...+.+..... .++......++.
T Consensus 147 ~~a~PI~~~~g~~iGvi~v~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~~e~~~~~~~~~~~~~ 226 (545)
T PRK15053 147 RAKTPIFDDDGKVIGVVSIGYLVSKIDSWRLEFLLPMAGVFVVLLGILMLLSWFFAAHIRRQMMGMEPKQIARVVRQQEA 226 (545)
T ss_pred EEEeeeEcCCCCEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 378999999999999987777544432211 112233355677
Q ss_pred HHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCCh--hhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCC
Q 001235 751 IVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKR--EEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQ 828 (1117)
Q Consensus 751 i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~--eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~ 828 (1117)
+++++++ |++.+|.+|+|+.+|+++++++|+.. ++++|+.+. ++++. ... +..... .
T Consensus 227 il~~~~e---gii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~-~~~~~----------~~~------~~~~~~-~ 285 (545)
T PRK15053 227 LFSSVYE---GLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIA-EVVRP----------ADF------FTEQID-E 285 (545)
T ss_pred HHHHhCc---eEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHH-HhCCC----------chh------hhhhcC-C
Confidence 8888888 99999999999999999999999975 568898753 22221 000 000111 1
Q ss_pred CCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHH
Q 001235 829 DPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLS 908 (1117)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~ 908 (1117)
.....+ ...+| ..+..+..|+.. +|++.|++.+++|+|+.++.+.++.+.... .+.+..++||++|||+
T Consensus 286 ~~~~~~---~~~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~~-----~e~l~~~~he~~n~L~ 354 (545)
T PRK15053 286 KRQDVV---ANFNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQY-----VESLRTLRHEHLNWMS 354 (545)
T ss_pred cccceE---EEECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHHH-----HHHHHHHHHHHhhhHH
Confidence 111111 22344 345566777764 567889999999999987776555443322 2346678999999999
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcE
Q 001235 909 GIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIR 987 (1117)
Q Consensus 909 ~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~ 987 (1117)
+|.+++++-+ ..+.++.+......+..+++++ ...+ ... +...+......+.++++.
T Consensus 355 ~i~g~l~~~~-------~~~~~~~i~~~s~~~~~l~~~l~~~~~--------------~~~-~~~~l~~~~~~~~~~~i~ 412 (545)
T PRK15053 355 TLNGLLQMKE-------YDRVLEMVQGESQAQQQLIDSLREAFA--------------DRQ-VAGLLFGKVQRARELGLK 412 (545)
T ss_pred HHHHHHhhch-------hhHHHHHHHHHHHHHHHHHHHHHHhcc--------------cHH-HHHHHHHHHHHHHHhCCc
Confidence 9999877532 2345556666666777777764 2211 011 112222223445567777
Q ss_pred EEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhcc---CC-CCeEEEEEEecccccccccceeEEEEEEeecCCCCChh
Q 001235 988 IVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV---PN-GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEP 1063 (1117)
Q Consensus 988 i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~---~~-~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e 1063 (1117)
+.+.....+.......|+..|.|+|.||+.||++|. ++ ++.|.|.+...++ .+.|.|+|||+|||++
T Consensus 413 ~~~~~~~~~~~l~~~~~~~~l~~vl~nLl~NAi~~~~~~~~~~~~i~i~~~~~~~---------~~~i~V~D~G~Gi~~~ 483 (545)
T PRK15053 413 MVIVPGSQLSQLPPGLDSTEFAAIVGNLLDNAFEASLRSDEGNKIVELFLSDEGD---------DVVIEVADQGCGVPES 483 (545)
T ss_pred eEEcCCCccccccccCCHHHHHHHHHHHHHHHHHHHhhCCCCCceEEEEEEECCC---------EEEEEEEeCCCCcCHH
Confidence 777654433222356799999999999999999995 33 4678888776655 7899999999999999
Q ss_pred hhhhccCCCCCCC-----CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1064 LLDQMFGSEGDTS-----EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1064 ~~~~iFe~f~~~~-----GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
..+++|++|++++ |+|+||+|||++++.|||+|+++|.+|+ |+|+|+||....
T Consensus 484 ~~~~iF~~~~~tk~~~~~g~GlGL~ivk~iv~~~~G~i~v~s~~~~Gt~f~i~lP~~~~ 542 (545)
T PRK15053 484 LRDKIFEQGVSTRADEPGEHGIGLYLIASYVTRCGGVITLEDNDPCGTLFSIFIPKVKP 542 (545)
T ss_pred HHHHHhCCCCCCCCCCCCCceeCHHHHHHHHHHcCCEEEEEECCCCeEEEEEEECCCCC
Confidence 9999999998665 6899999999999999999999999887 999999998764
No 23
>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=99.96 E-value=1.6e-28 Score=322.41 Aligned_cols=223 Identities=27% Similarity=0.414 Sum_probs=205.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccce
Q 001235 882 QRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLE 960 (1117)
Q Consensus 882 ~~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~ 960 (1117)
+..+++....|..|++.|+|||||||++|.++++++.+...+++++++++.+.....+|..++++ +++++++.+...++
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 44566677788999999999999999999999999999888999999999999999999999999 69999999999999
Q ss_pred eEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccc
Q 001235 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQL 1040 (1117)
Q Consensus 961 ~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~ 1040 (1117)
..++++.+++++++..+...+..+++.+.+++++..+ ..+.+|+.+|.|||.||+.||+||++ .|.|.|.+....+
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 9999999999999999999999999999999987664 37899999999999999999999997 6789888877665
Q ss_pred ccccceeE-EEEEEeecCCCCChhhhhhccCCCCCC------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEe
Q 001235 1041 GQSVHLAY-LELRITHAGGGIPEPLLDQMFGSEGDT------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVE 1112 (1117)
Q Consensus 1041 ~~~~~~~~-l~i~V~D~G~GI~~e~~~~iFe~f~~~------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LP 1112 (1117)
. +.|+|.|+|+|||++.++++|+||+.. +|+||||+|||++++.|||+|++.|.+|+ |+|+|+||
T Consensus 610 -------~~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~~~g~GLGL~i~~~l~~~~gG~i~~~s~~~~Gt~f~~~lp 682 (968)
T TIGR02956 610 -------SSLLFEVEDTGCGIAEEEQATLFDAFTQADGRRRSGGTGLGLAISQRLVEAMDGELGVESELGVGSCFWFTLP 682 (968)
T ss_pred -------CeEEEEEEeCCCCCCHHHHHHHHhhhhccCCCCCCCCccHHHHHHHHHHHHcCCEEEEEecCCCcEEEEEEEE
Confidence 4 999999999999999999999999644 58999999999999999999999999987 99999999
Q ss_pred ccC
Q 001235 1113 LAA 1115 (1117)
Q Consensus 1113 l~~ 1115 (1117)
+..
T Consensus 683 ~~~ 685 (968)
T TIGR02956 683 LTR 685 (968)
T ss_pred cCC
Confidence 865
No 24
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=99.96 E-value=5e-28 Score=316.31 Aligned_cols=222 Identities=24% Similarity=0.382 Sum_probs=203.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCccccee
Q 001235 883 RLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEM 961 (1117)
Q Consensus 883 ~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~ 961 (1117)
+.+++....+..+++.++|||||||++|.++++++.....+++++++++.+..+..+|..++++ +++++++.+.+.+..
T Consensus 389 ~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~ 468 (921)
T PRK15347 389 QRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMTLSL 468 (921)
T ss_pred HHHHHHHHHHHHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccee
Confidence 3445556678889999999999999999999999999888999999999999999999999999 699999999999999
Q ss_pred EEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccc
Q 001235 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLG 1041 (1117)
Q Consensus 962 ~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~ 1041 (1117)
.++++.+++++++..+......+++.+.+.+++.++ ..+.+|+.+|+|||.||+.||+||++ .|.|.|++...++
T Consensus 469 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~d~~~l~~il~NLl~NAik~~~-~g~I~i~~~~~~~--- 543 (921)
T PRK15347 469 EETALLPLLDQAMLTIQGPAQSKSLTLRTFVGAHVP-LYLHLDSLRLRQILVNLLGNAVKFTE-TGGIRLRVKRHEQ--- 543 (921)
T ss_pred cccCHHHHHHHHHHHHHHHHHHCCcEEEEEECCCCC-ceEEECHHHHHHHHHHHHHHHhhcCC-CCCEEEEEEEcCC---
Confidence 999999999999999999999999999998887765 37899999999999999999999997 6779998887666
Q ss_pred cccceeEEEEEEeecCCCCChhhhhhccCCCCCC----CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1042 QSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT----SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1042 ~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~----~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.+.|+|.|+|+|||++.++++|+||+.+ +|+||||+||+++++.|||+|+++|++|+ |+|+|+||+..
T Consensus 544 ------~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~g~GLGL~i~~~~~~~~gG~i~i~s~~~~Gt~f~i~lp~~~ 616 (921)
T PRK15347 544 ------QLCFTVEDTGCGIDIQQQQQIFTPFYQADTHSQGTGLGLTIASSLAKMMGGELTLFSTPGVGSCFSLVLPLNE 616 (921)
T ss_pred ------EEEEEEEEcCCCCCHHHHHHHhcCcccCCCCCCCCchHHHHHHHHHHHcCCEEEEEecCCCceEEEEEEECCC
Confidence 8999999999999999999999999643 48999999999999999999999999988 99999999864
No 25
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=99.95 E-value=4.2e-27 Score=307.06 Aligned_cols=220 Identities=22% Similarity=0.365 Sum_probs=199.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccC--ccccee
Q 001235 885 SEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDG--YLDLEM 961 (1117)
Q Consensus 885 ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g--~~~l~~ 961 (1117)
.++....+..|++.|+|||||||++|.++++++.....+++.+++++.+..+.+++..++++ +++++++.+ ...++.
T Consensus 437 ~~~~~~~~~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~~~~~~~~~ 516 (914)
T PRK11466 437 AEKASQAKSAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAGGKNVSVSD 516 (914)
T ss_pred HHHHHHHHHHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcceecc
Confidence 33445677889999999999999999999999998888889999999999999999999999 699999877 456677
Q ss_pred EEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccc
Q 001235 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLG 1041 (1117)
Q Consensus 962 ~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~ 1041 (1117)
.++++.++++.++..+...+..+++.+.+++++..+ ..+.+|+.+|.|||.||+.||+||++ .|.|.|++...++
T Consensus 517 ~~~~l~~ll~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~v~~d~~~l~qil~NLl~NAik~~~-~g~I~i~~~~~~~--- 591 (914)
T PRK11466 517 EPFEPRPLLESTLQLMSGRVKGRPIRLATDIADDLP-TALMGDPRRIRQVITNLLSNALRFTD-EGSIVLRSRTDGE--- 591 (914)
T ss_pred cccCHHHHHHHHHHHHHHHHHhCCcEEEEEeCCCCC-ceEEECHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEcCC---
Confidence 899999999999999999999999999999887765 36899999999999999999999997 6889998877665
Q ss_pred cccceeEEEEEEeecCCCCChhhhhhccCCCCC----CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1042 QSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD----TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1042 ~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~----~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.+.|.|.|+|+|||++.++++|+||+. .+|+||||+|||++++.|||+|++.|.+|+ |+|+|+||+..
T Consensus 592 ------~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~g~GLGL~i~~~l~~~~gG~i~v~s~~~~Gt~f~i~lP~~~ 664 (914)
T PRK11466 592 ------QWLVEVEDSGCGIDPAKLAEIFQPFVQVSGKRGGTGLGLTISSRLAQAMGGELSATSTPEVGSCFCLRLPLRV 664 (914)
T ss_pred ------EEEEEEEECCCCCCHHHHHHHhchhhcCCCCCCCCcccHHHHHHHHHHcCCEEEEEecCCCCeEEEEEEEccc
Confidence 789999999999999999999999963 348999999999999999999999999887 99999999864
No 26
>PRK10490 sensor protein KdpD; Provisional
Probab=99.95 E-value=1.2e-26 Score=296.56 Aligned_cols=214 Identities=18% Similarity=0.263 Sum_probs=185.7
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTE--LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTL 966 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~--l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L 966 (1117)
..+..+++.++|||||||++|.++.+++.... ......+.++.+.+...++..++++ +++++++.+...+...++++
T Consensus 662 ~lr~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~~~l~~~~~~L 741 (895)
T PRK10490 662 QLRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFNLRKEWLTL 741 (895)
T ss_pred HHHHHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccccCH
Confidence 44567899999999999999999999886432 2233446678888888899999999 59999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccce
Q 001235 967 NEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHL 1046 (1117)
Q Consensus 967 ~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~ 1046 (1117)
.+++++++..+......+++.+ +++.+.+ .+.+|+..|.|||.||+.||+||+++++.|.|++...++
T Consensus 742 ~eli~~~l~~l~~~~~~~~i~l--~~~~~~~--~v~~D~~~L~qVL~NLL~NAik~s~~g~~I~I~~~~~~~-------- 809 (895)
T PRK10490 742 EEVVGSALQMLEPGLSGHPINL--SLPEPLT--LIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGE-------- 809 (895)
T ss_pred HHHHHHHHHHHHHHhcCCCEEE--EcCCCCe--EEEECHHHHHHHHHHHHHHHHHhCCCCCeEEEEEEEeCC--------
Confidence 9999999999988877665555 5556553 799999999999999999999999888899999887766
Q ss_pred eEEEEEEeecCCCCChhhhhhccCCCCCC------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1047 AYLELRITHAGGGIPEPLLDQMFGSEGDT------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1047 ~~l~i~V~D~G~GI~~e~~~~iFe~f~~~------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
.+.|+|.|+|+|||++..+++|+||+++ +|+||||+|||++++.|||+|+++|.+|+ |+|+|+||+..+
T Consensus 810 -~v~I~V~D~G~GI~~e~~~~IFepF~~~~~~~~~~G~GLGL~Ivk~ive~hGG~I~v~s~~~~Gt~f~i~LPl~~~ 885 (895)
T PRK10490 810 -RLQLDVWDNGPGIPPGQEQLIFDKFARGNKESAIPGVGLGLAICRAIVEVHGGTIWAENRPEGGACFRVTLPLETP 885 (895)
T ss_pred -EEEEEEEECCCCCCHHHHHHhcCCCccCCCCCCCCCccHHHHHHHHHHHHcCCEEEEEECCCCeEEEEEEeECCCC
Confidence 7999999999999999999999999643 38899999999999999999999999887 999999999754
No 27
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=99.95 E-value=5.3e-27 Score=306.60 Aligned_cols=226 Identities=26% Similarity=0.419 Sum_probs=199.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeE
Q 001235 884 LSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1117)
Q Consensus 884 ~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~ 962 (1117)
.+++....|.+|++.|+|||||||++|.++++++.....++.++++++.+.++.+++..++++ +++++++.++..++..
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 334455667789999999999999999999999988888899999999999999999999999 6999999999999999
Q ss_pred EeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccc
Q 001235 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQ 1042 (1117)
Q Consensus 963 ~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~ 1042 (1117)
++++.+++++++..+...+..+++.+.+++++..+ ..+.+|+.+|.|||.||+.||+||++ .|.|.|.+.......
T Consensus 365 ~~~l~~~l~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~~~~d~~~l~~vl~NLl~NAik~~~-~g~v~i~v~~~~~~~-- 440 (919)
T PRK11107 365 PFSLRETLDEVVTLLAHSAHEKGLELTLNIDPDVP-DNVIGDPLRLQQIITNLVGNAIKFTE-SGNIDILVELRALSN-- 440 (919)
T ss_pred ecCHHHHHHHHHHHHHHHHHHcCCEEEEEeCCCCC-ceEEeCHHHHHHHHHHHHHHHhhcCC-CCcEEEEEEEEecCC--
Confidence 99999999999999999999999999999887765 36899999999999999999999997 566666665433210
Q ss_pred ccceeEEEEEEeecCCCCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEec
Q 001235 1043 SVHLAYLELRITHAGGGIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVEL 1113 (1117)
Q Consensus 1043 ~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl 1113 (1117)
....+.|+|.|+|+|||++.++++|+||+. .+|+||||+|||++++.|||+|++.|.+|+ |+|+|+||+
T Consensus 441 --~~~~~~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~~~~~g~GLGL~i~~~i~~~~gG~i~v~s~~~~Gt~f~i~lp~ 518 (919)
T PRK11107 441 --TKVQLEVQIRDTGIGISERQQSQLFQAFRQADASISRRHGGTGLGLVITQKLVNEMGGDISFHSQPNRGSTFWFHLPL 518 (919)
T ss_pred --CeeEEEEEEEEeCCCcCHHHHHHHhhhhccCCCCCCCCCCCcchhHHHHHHHHHHhCCEEEEEecCCCCEEEEEEEEe
Confidence 123689999999999999999999999962 248999999999999999999999999987 999999998
Q ss_pred cC
Q 001235 1114 AA 1115 (1117)
Q Consensus 1114 ~~ 1115 (1117)
..
T Consensus 519 ~~ 520 (919)
T PRK11107 519 DL 520 (919)
T ss_pred cc
Confidence 54
No 28
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=99.95 E-value=2.1e-25 Score=286.22 Aligned_cols=217 Identities=18% Similarity=0.213 Sum_probs=181.8
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEG-TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~-~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~l 969 (1117)
...|++.|+|||||||++|.++.+++.. ....++..++++.+....+++..++++ +++++... ....++++.++
T Consensus 450 l~~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~~~----~~~~~~~l~~l 525 (828)
T PRK13837 450 VGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRKGE----RNTKPFDLSEL 525 (828)
T ss_pred HHHHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC----CCCcEEcHHHH
Confidence 3468899999999999999999998764 334567788999999999999999999 58888543 34678999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccc------
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQS------ 1043 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~------ 1043 (1117)
+++++..+.... .+++.+.++.++..+ .+.+|+..|.|||.||+.||+||++++|.|.|++..........
T Consensus 526 l~~~~~~~~~~~-~~~i~l~~~~~~~~~--~v~~d~~~L~qvl~NLl~NAik~~~~~g~I~I~~~~~~~~~~~~~~~~~~ 602 (828)
T PRK13837 526 VTEIAPLLRVSL-PPGVELDFDQDQEPA--VVEGNPAELQQVLMNLCSNAAQAMDGAGRVDISLSRAKLRAPKVLSHGVL 602 (828)
T ss_pred HHHHHHHHHHHc-cCCcEEEEEeCCCCc--eEEECHHHHHHHHHHHHHHHHHHcccCCeEEEEEEEeecccccccccccC
Confidence 999998887654 467888888766543 79999999999999999999999988899999887652100000
Q ss_pred cceeEEEEEEeecCCCCChhhhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1044 VHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1044 ~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
....++.|+|.|||+|||++..+++|+||++++ |+||||+|||++++.|||+|++.|.+|+ |+|+|+||+..
T Consensus 603 ~~~~~v~i~V~D~G~GI~~e~~~~iFe~F~~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~LP~~~ 677 (828)
T PRK13837 603 PPGRYVLLRVSDTGAGIDEAVLPHIFEPFFTTRAGGTGLGLATVHGIVSAHAGYIDVQSTVGRGTRFDVYLPPSS 677 (828)
T ss_pred CCCCEEEEEEEECCCCCCHHHHHHhhCCcccCCCCCCcchHHHHHHHHHHCCCEEEEEecCCCeEEEEEEEeCCC
Confidence 112379999999999999999999999998664 9999999999999999999999999887 99999999864
No 29
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=99.95 E-value=2e-25 Score=254.45 Aligned_cols=354 Identities=16% Similarity=0.207 Sum_probs=259.0
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhh--------------------------------------hhHhh
Q 001235 702 DDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVM--------------------------------------DKFTR 743 (1117)
Q Consensus 702 G~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE--------------------------------------~~L~~ 743 (1117)
|+--+-.--..|++|++|+++|++.++.-+++--..- .++..
T Consensus 133 Gslg~s~R~~~PI~d~~g~~IGvVsVG~~l~~i~~~i~~~~~~l~~~~vl~lligl~ga~~la~~ikr~~~glEP~EIa~ 212 (537)
T COG3290 133 GSLGKSLRAKVPIFDEDGKQIGVVSVGYLLSEIDDVILEFLRPLALIVVLGLLIGLLGAWILARHIKRQMLGLEPEEIAT 212 (537)
T ss_pred ccchhhheeecceECCCCCEEEEEEEeeEhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence 4444444556899999999999999988666543322 22333
Q ss_pred HHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChh--hHhhcchhhhhcCCchhhhhccChhHHHHHHHHH
Q 001235 744 IEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKRE--EVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVL 821 (1117)
Q Consensus 744 se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~e--EliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l 821 (1117)
.-+...++++++.. |++.+|..|.+..+|.++++|+|+... +.+|+++...+.+. . + +.
T Consensus 213 l~~er~A~l~si~E---GviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~-~---------~---l~--- 273 (537)
T COG3290 213 LLEERQAMLQSIKE---GVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPD-S---------D---LP--- 273 (537)
T ss_pred HHHHHHHHHHHhhc---eEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeeccc-c---------C---cH---
Confidence 44455677777777 999999999999999999999999854 68888865444321 0 0 11
Q ss_pred HHHhcC-CCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001235 822 NKAMSG-QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTK 900 (1117)
Q Consensus 822 ~~~l~g-~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~is 900 (1117)
..++. ++....+++ -+| .++.++..|+. .+|+++|++.+++|-||-++..+++.....- ...+...+
T Consensus 274 -~vl~~~~~~~~~e~~---~ng--~~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~vr~y-----a~aLRaq~ 341 (537)
T COG3290 274 -EVLETGKPQHDEEIR---ING--RLLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGVRQY-----AEALRAQS 341 (537)
T ss_pred -HHHhcCCcccchhhh---cCC--eEEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHHHHH-----HHHHHHhh
Confidence 11222 222222222 223 35667777776 6899999999999999988777665543332 23466788
Q ss_pred hhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHHhh
Q 001235 901 RQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMK 980 (1117)
Q Consensus 901 HEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~~~ 980 (1117)
||..|-|++|.|++++-+- ++..+++.......+.....+.. ++. ..++...+---...
T Consensus 342 HEfmNkLhtI~GLlql~~y----d~a~~~I~~~~~~qq~~~~~l~~----~i~-------------~~~lAg~LlgK~~r 400 (537)
T COG3290 342 HEFMNKLHTILGLLQLGEY----DDALDYIQQESEEQQELIDSLSE----KIK-------------DPVLAGFLLGKISR 400 (537)
T ss_pred HHHHHHHHHHHHHHhhccH----HHHHHHHHHHHhhhhhhHHHHHH----hcc-------------cHHHHHHHHhHHHH
Confidence 9999999999999887543 34556665554333333222221 100 13344444455568
Q ss_pred hcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccC---CCCeEEEEEEecccccccccceeEEEEEEeecC
Q 001235 981 SNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVP---NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAG 1057 (1117)
Q Consensus 981 ~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~---~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G 1057 (1117)
+++.++.+.++....++.....-++..+--|+-||+.||+++.- ++++|.+++...++ .+.++|.|+|
T Consensus 401 ArElgv~l~Id~~S~l~~~p~~~~~~~litIlGNLidNA~eA~~~~~~~k~I~l~i~~~~~---------~lvieV~D~G 471 (537)
T COG3290 401 ARELGVSLIIDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSDRGD---------ELVIEVADTG 471 (537)
T ss_pred HHHcCceEEEcCCCcCCCCCCccChHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEecCC---------EEEEEEeCCC
Confidence 89999999999988887666777899999999999999999874 36799999988887 9999999999
Q ss_pred CCCChhhhhhccCCCCCCC---CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1058 GGIPEPLLDQMFGSEGDTS---EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1058 ~GI~~e~~~~iFe~f~~~~---GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
+|||++..+++|+..++++ +.|+||++||+.|+.+||.|+++|+++. |+|.+.+|....
T Consensus 472 ~GI~~~~~~~iFe~G~Stk~~~~rGiGL~Lvkq~V~~~~G~I~~~s~~~~Gt~F~i~iP~~~~ 534 (537)
T COG3290 472 PGIPPEVRDKIFEKGVSTKNTGGRGIGLYLVKQLVERLGGSIEVESEKGQGTRFSIYIPKVKE 534 (537)
T ss_pred CCCChHHHHHHHhcCccccCCCCCchhHHHHHHHHHHcCceEEEeeCCCCceEEEEECCCCcc
Confidence 9999999999999987666 5799999999999999999999998666 999999998653
No 30
>PRK10364 sensor protein ZraS; Provisional
Probab=99.94 E-value=2.4e-25 Score=267.87 Aligned_cols=209 Identities=23% Similarity=0.327 Sum_probs=184.4
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGT-ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~-~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~l 969 (1117)
..++.+.++||+||||++|.++++++.+. ...++..++++.+....+++..++++ +++.+.. .....++++.++
T Consensus 237 ~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~~----~~~~~~~~l~~~ 312 (457)
T PRK10364 237 LGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKPT----HLALQAVDLNDL 312 (457)
T ss_pred HHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCcC----CCcceEecHHHH
Confidence 34567889999999999999999998754 33456677888888899999999999 5777632 346779999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
++.++..+...+.++++.+.++.++..+ .+.+|+..|.|++.||+.||+||++.++.|.|++...++ .+
T Consensus 313 l~~~~~~~~~~~~~~~i~l~~~~~~~~~--~~~~d~~~l~~il~NLl~NA~k~~~~~~~I~i~~~~~~~---------~~ 381 (457)
T PRK10364 313 INHSLQLVSQDANSREIQLRFTANDTLP--EIQADPDRLTQVLLNLYLNAIQAIGQHGVISVTASESGA---------GV 381 (457)
T ss_pred HHHHHHHHHHHHHhcCeEEEEEcCCCCc--eEEECHHHHHHHHHHHHHHHHHhcCCCCeEEEEEEEeCC---------eE
Confidence 9999999999999999999999887654 688999999999999999999998878899999888766 79
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.|.|.|||+|||++..+++|++|++++ |+||||++||++++.|||+|+++|.+|+ |+|+|+||+.+
T Consensus 382 ~i~V~D~G~Gi~~~~~~~if~~~~~~k~~g~GlGL~iv~~~v~~~gG~i~i~s~~~~Gt~f~i~lP~~~ 450 (457)
T PRK10364 382 KISVTDSGKGIAADQLEAIFTPYFTTKAEGTGLGLAVVHNIVEQHGGTIQVASQEGKGATFTLWLPVNI 450 (457)
T ss_pred EEEEEECCCCCCHHHHHHHhCccccCCCCCCcccHHHHHHHHHHCCCEEEEEeCCCCcEEEEEEecCCC
Confidence 999999999999999999999997655 8999999999999999999999999887 99999999864
No 31
>PRK10604 sensor protein RstB; Provisional
Probab=99.94 E-value=6.2e-25 Score=262.05 Aligned_cols=207 Identities=17% Similarity=0.207 Sum_probs=176.6
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~ 968 (1117)
..+.++++.++||+||||+.|.+.+++++... ++..+ .+.+..++|..++++ +.+++++.+..++...++++..
T Consensus 210 ~~~~~l~~~vsHeLrtPL~~i~~~l~~l~~~~--~~~~~---~i~~~~~~l~~li~~ll~~~rl~~~~~~~~~~~~~l~~ 284 (433)
T PRK10604 210 ASKKQLIDGIAHELRTPLVRLRYRLEMSDNLS--AAESQ---ALNRDIGQLEALIEELLTYARLDRPQNELHLSEPDLPA 284 (433)
T ss_pred HHHHHHHHHhhHhhcChHHHHHHHHHHhcCCC--cHHHH---HHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCCCHHH
Confidence 34567899999999999999999999887432 22222 266677899999999 5999999888888899999999
Q ss_pred HHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeE
Q 001235 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAY 1048 (1117)
Q Consensus 969 li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~ 1048 (1117)
++++++..+......+++++.++.++. .+.+|+..+.+++.||+.||++|+. +.|.|++...++ .
T Consensus 285 ~l~~~i~~~~~~~~~~~i~~~~~~~~~----~~~~d~~~l~~vl~NLl~NAik~~~--~~I~I~~~~~~~---------~ 349 (433)
T PRK10604 285 WLSTHLADIQAVTPEKTVRLDTPHQGD----YGALDMRLMERVLDNLLNNALRYAH--SRVRVSLLLDGN---------Q 349 (433)
T ss_pred HHHHHHHHHHHHhhcCcEEEEecCCCc----eEecCHHHHHHHHHHHHHHHHHhCC--CeEEEEEEEECC---------E
Confidence 999999999888777777776654332 5778999999999999999999984 788888887766 7
Q ss_pred EEEEEeecCCCCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1049 LELRITHAGGGIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1049 l~i~V~D~G~GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
+.|+|.|||+|||++..+++|+||+. ++|.||||+|||++++.|||+|.+++.+++ |+|++++|+..+
T Consensus 350 ~~I~V~D~G~Gi~~e~~~~if~~f~r~~~~~~~~~~g~GLGL~ivk~i~~~~gG~i~v~s~~~~G~~f~i~lP~~~~ 426 (433)
T PRK10604 350 ACLIVEDDGPGIPPEERERVFEPFVRLDPSRDRATGGCGLGLAIVHSIALAMGGSVNCDESELGGARFSFSWPVWHN 426 (433)
T ss_pred EEEEEEEcCCCCCHHHHhhcCCCCccCCCCCCCCCCCccchHHHHHHHHHHCCCEEEEEecCCCeeEEEEEEeCCCC
Confidence 99999999999999999999999963 348999999999999999999999999876 999999998764
No 32
>PRK10815 sensor protein PhoQ; Provisional
Probab=99.94 E-value=7.7e-25 Score=263.79 Aligned_cols=209 Identities=14% Similarity=0.196 Sum_probs=175.7
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~~-l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~l 969 (1117)
..++++.++|||||||++|.++++.+.... ...+ +....+.+...++..++++ ++.++...+...+....+++..+
T Consensus 266 ~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~~--~~~~~~~~~i~ri~~~i~~ll~~~~~~~~~~~~~~~~~~l~~l 343 (485)
T PRK10815 266 YRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSVE--QAEPIMLEQISRISQQIGYYLHRASMRSEHNLLSRELHSVAPL 343 (485)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccccceecHHHH
Confidence 445799999999999999999999887543 2222 2233445556677777877 57777777777788889999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
+++++..+...+..+++.+.++++++. .+.+|+..|.+++.||+.||+||++. .|.|++...++ .+
T Consensus 344 l~~~~~~l~~~~~~~~i~i~~~~~~~~---~v~~d~~~l~~vl~NLi~NAik~~~~--~i~I~~~~~~~---------~v 409 (485)
T PRK10815 344 LDNLTSALNKVYQRKGVNITLDISPEI---TFVGEKNDFMEVMGNVLDNACKYCLE--FVEISARQTDE---------HL 409 (485)
T ss_pred HHHHHHHHHHHHHHCCcEEEEecCCCc---EEEeCHHHHHHHHHHHHHHHHHhcCC--cEEEEEEEeCC---------EE
Confidence 999999999999999999999887654 57899999999999999999999973 46666666555 79
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCC----CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDT----SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~----~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
.|+|+|+|+|||++.++++|+||+.. +|+||||+||+++++.|||+|.+.|.+++ |+|+|+||..++
T Consensus 410 ~I~V~D~G~GI~~e~~~~iF~~f~~~~~~~~G~GLGL~Ivk~iv~~~gG~i~v~s~~~~Gt~f~i~lp~~~~ 481 (485)
T PRK10815 410 HIVVEDDGPGIPESKRELIFDRGQRADTLRPGQGLGLSVAREITEQYEGKISAGDSPLGGARMEVIFGRQHS 481 (485)
T ss_pred EEEEEECCCCcCHHHHHHHhCCcccCCCCCCCcchhHHHHHHHHHHcCCEEEEEECCCCEEEEEEEEcCCCC
Confidence 99999999999999999999998643 38999999999999999999999999876 999999998654
No 33
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=99.93 E-value=3.4e-24 Score=258.44 Aligned_cols=215 Identities=19% Similarity=0.259 Sum_probs=187.4
Q ss_pred HHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHH
Q 001235 889 ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLN 967 (1117)
Q Consensus 889 ~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~ 967 (1117)
...+..+++.++||+++||+.|.+.++.+..... +...+.+..+.....++..+++++ ++++.+.+...+....+++.
T Consensus 237 ~~~~~~~~~~~shel~~pL~~i~~~~~~l~~~~~-~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~~~~~~~~~~~~ 315 (466)
T PRK10549 237 EQMRRDFMADISHELRTPLAVLRGELEAIQDGVR-KFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGALAYRKTPVDLV 315 (466)
T ss_pred HHHHHHHHHHHhHHhCChHHHHHHHHHHHHhccc-cCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccccCCCCHH
Confidence 3445668899999999999999999988875432 223345666777788999999984 78888888888899999999
Q ss_pred HHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccccccee
Q 001235 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLA 1047 (1117)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~ 1047 (1117)
++++.++..+......+++++.+++++.. .+.+|+..|.|++.||+.||++|++++|.|.|.+...++
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 99999999999998889999999887764 578999999999999999999999888999999888776
Q ss_pred EEEEEEeecCCCCChhhhhhccCCCCCC--------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1048 YLELRITHAGGGIPEPLLDQMFGSEGDT--------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1048 ~l~i~V~D~G~GI~~e~~~~iFe~f~~~--------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
.+.|.|.|||+|||++.++++|+||++. +|+||||++|+++++.|||++.+++.+++ |+|+|.||+..+
T Consensus 384 ~~~i~V~D~G~Gi~~e~~~~lf~~~~~~~~~~~~~~~g~GlGL~iv~~i~~~~~G~l~~~s~~~~G~~~~i~lP~~~~ 461 (466)
T PRK10549 384 TLRLTFADSAPGVSDEQLQKLFERFYRTEGSRNRASGGSGLGLAICLNIVEAHNGRIIAAHSPFGGVSITVELPLERD 461 (466)
T ss_pred EEEEEEEecCCCcCHHHHHHhccCcccCCCCcCCCCCCCcHHHHHHHHHHHHcCCEEEEEECCCCeEEEEEEccCCCC
Confidence 8999999999999999999999999643 38999999999999999999999999877 999999999764
No 34
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=99.92 E-value=8.1e-24 Score=246.05 Aligned_cols=208 Identities=16% Similarity=0.211 Sum_probs=169.8
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeH-HHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTL-NEV 969 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L-~~l 969 (1117)
+.++++.++||+||||++|.+.++++..... ++..... ...+++...+++ +++++............+++ .++
T Consensus 137 ~~~~~~~~sHelrtPL~~i~~~~e~l~~~~~-~~~~~~~----~~~~~l~~~i~~ll~~~r~~~~~~~~~~~~~~l~~~~ 211 (356)
T PRK10755 137 ERLFTADVAHELRTPLAGIRLHLELLEKQHH-IDVAPLI----ARLDQMMHTVEQLLQLARAGQSFSSGHYQTVKLLEDV 211 (356)
T ss_pred HHHHHHHhhHhhcChHHHHHHHHHHHHhccc-hhHHHHH----HHHHHHHHHHHHHHHHHHcccccccccchhhhHHHHH
Confidence 3458899999999999999999988865432 2222322 334567777777 47777655555556677888 999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
+..++..+......+++.+.++.++. ...+.+|+..+.+|+.||+.||+||++.++.|.|++...++ .+
T Consensus 212 i~~~~~~~~~~~~~~~~~~~~~~~~~--~~~v~~d~~~l~~il~nLi~NA~k~~~~~~~I~I~~~~~~~---------~~ 280 (356)
T PRK10755 212 ILPSQDELSEMLEQRQQTLLLPESAA--DITVQGDATLLRLLLRNLVENAHRYSPEGSTITIKLSQEDG---------GA 280 (356)
T ss_pred HHHHHHHHHHHHHHhCCeEEeccCCC--ceEEEECHHHHHHHHHHHHHHHHhhCCCCCcEEEEEEEcCC---------EE
Confidence 99998889888888888888753332 23789999999999999999999999878889998877666 79
Q ss_pred EEEEeecCCCCChhhhhhccCCCCC----CCCccccHHHHHHHHHHcCCEEEEEeeCC-e-EEEEEEEeccC
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGD----TSEEGISLLISRKLVKLMNGDVQYLREAG-K-STFIVSVELAA 1115 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~----~~GtGLGL~ivr~iVe~~gG~I~v~s~~g-~-ttF~i~LPl~~ 1115 (1117)
.|.|.|||+|||++..+++|++|+. .+|+||||++|+++++.|||+|+++|.++ + |+|+++||...
T Consensus 281 ~i~V~D~G~Gi~~~~~~~if~~f~~~~~~~~g~GlGL~i~~~i~~~~gg~i~i~s~~~~~Gt~~~i~~p~~~ 352 (356)
T PRK10755 281 VLAVEDEGPGIDESKCGELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQERSGTRAWVWLPKAQ 352 (356)
T ss_pred EEEEEECCCCCCHHHHHHhCCCeEeCCCCCCCcCHHHHHHHHHHHHCCCEEEEEECCCCCeEEEEEEecCCC
Confidence 9999999999999999999999863 35899999999999999999999999986 5 99999999765
No 35
>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=99.92 E-value=1.2e-23 Score=263.39 Aligned_cols=209 Identities=20% Similarity=0.280 Sum_probs=184.8
Q ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHH
Q 001235 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 891 ~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~l 969 (1117)
....+.+.++||+||||+.|.+.++.+......++..++++.+....+++..+++++ .+.+++.+.......++++.++
T Consensus 484 ~l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~~~~~~~~~~~dl~~l 563 (703)
T TIGR03785 484 YLENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQAIQSAEVEDFDLSEV 563 (703)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccceeecHHHH
Confidence 345578889999999999999999999887778888889999999999999999994 8888887777778899999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
++.++..+......+++.+.++.++ ..+.+|+..|.|++.||+.||+||+++++.|.|++...++ .+
T Consensus 564 l~~~i~~~~~~~~~~~i~l~i~~~~----~~i~~d~~~L~~il~NLI~NAik~s~~~~~I~I~~~~~~~---------~v 630 (703)
T TIGR03785 564 LSGCMQGYQMTYPPQRFELNIPETP----LVMRGSPELIAQMLDKLVDNAREFSPEDGLIEVGLSQNKS---------HA 630 (703)
T ss_pred HHHHHHHHHHHhhcCCEEEEecCCC----eEEEECHHHHHHHHHHHHHHHHHHCCCCCeEEEEEEEcCC---------EE
Confidence 9999999998888877777665432 2689999999999999999999999888889998887766 89
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCCC--------CccccHHHHHHHHHHcCCEEEEEeeCC--eEEEEEEEe
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDTS--------EEGISLLISRKLVKLMNGDVQYLREAG--KSTFIVSVE 1112 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~~--------GtGLGL~ivr~iVe~~gG~I~v~s~~g--~ttF~i~LP 1112 (1117)
.|+|+|+|+|||++..+++|+||++++ |+||||+|||+|++.|||+|++.+.++ +++|+|+||
T Consensus 631 ~I~V~D~G~GI~~e~~~~IFe~F~t~~~~~~~~~~g~GLGL~Ivr~Iv~~~gG~I~v~s~~~g~Gt~f~I~LP 703 (703)
T TIGR03785 631 LLTVSNEGPPLPEDMGEQLFDSMVSVRDQGAQDQPHLGLGLYIVRLIADFHQGRIQAENRQQNDGVVFRISLP 703 (703)
T ss_pred EEEEEEcCCCCCHHHHHHHhCCCeecCCCCCCCCCCccHHHHHHHHHHHHcCCEEEEEECCCCCeEEEEEEeC
Confidence 999999999999999999999996322 689999999999999999999999865 499999998
No 36
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.91 E-value=2.3e-23 Score=277.26 Aligned_cols=267 Identities=13% Similarity=0.124 Sum_probs=238.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcC
Q 001235 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1117)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g 683 (1117)
.++..+++++++++++.++++++++++.+|.+|++++||+++++++||+.++++|+++.++++|++.+.....+.....+
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 34556788999999999999999999999999999999999999999999999999999999999998888888887766
Q ss_pred CcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCee
Q 001235 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIF 763 (1117)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~ 763 (1117)
+.. .+..+.+..++||..+|+..+..++++.+|++.+++++++|||++|++|+++++++++++.+++..+. ++|
T Consensus 351 ~~~---~~~~e~~~~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~---~i~ 424 (1092)
T PRK09776 351 EIN---SYSMEKRYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGI---GIW 424 (1092)
T ss_pred Ccc---ceeeeeEEEcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCc---eEE
Confidence 533 33444445588999999999999999999999999999999999999999999999999999999988 899
Q ss_pred eeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCc
Q 001235 764 GSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGK 843 (1117)
Q Consensus 764 ~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~ 843 (1117)
.+|.++++++||+++.+++||+.++..+.. .+....+|++.......+.....++..+..|+++.++||
T Consensus 425 ~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~----------~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG- 493 (1092)
T PRK09776 425 EWDLKPNIISWDKRMFELYEIPPHIKPTWQ----------VWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG- 493 (1092)
T ss_pred EEecCCCeEeeCHHHHHHhCCCcccCCCHH----------HHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-
Confidence 999999999999999999999988843322 234556788888888889999999999999999999999
Q ss_pred EEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHH
Q 001235 844 YAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQ 887 (1117)
Q Consensus 844 ~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~ 887 (1117)
.+|+.....++.|.+|++.+++++.+|||++|+.++++++.+++
T Consensus 494 ~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~ 537 (1092)
T PRK09776 494 VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKER 537 (1092)
T ss_pred eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999887765544
No 37
>PRK09835 sensor kinase CusS; Provisional
Probab=99.91 E-value=6.4e-23 Score=248.41 Aligned_cols=212 Identities=17% Similarity=0.249 Sum_probs=182.0
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGT-ELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLN 967 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~-~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~ 967 (1117)
..+.++++.++|||++||+.|.+..+.+... ....+..+.+..+.....++..++++ +++.+.+.+.......++++.
T Consensus 260 ~~~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~~~~~~~~~~~~l~ 339 (482)
T PRK09835 260 TRQSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADNNQLIPEKKMLDLA 339 (482)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCceeecHH
Confidence 3456789999999999999999888876543 33345566677777778899999999 588988888877888899999
Q ss_pred HHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccccccee
Q 001235 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLA 1047 (1117)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~ 1047 (1117)
++++.++..+......+++.+.++.++ ..+.+|+..|.+++.||+.||++|+++++.|.|++...++
T Consensus 340 ~~i~~~~~~~~~~~~~~~~~~~~~~~~----~~v~~d~~~l~~vl~nll~Na~~~~~~~~~I~i~~~~~~~--------- 406 (482)
T PRK09835 340 DEVGKVFDFFEAWAEERGVELRFVGDP----CQVAGDPLMLRRAISNLLSNALRYTPAGEAITVRCQEVDH--------- 406 (482)
T ss_pred HHHHHHHHHHHHHHhhCCEEEEEeCCC----cEEEECHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEeCC---------
Confidence 999999999998888888888776432 2689999999999999999999999877889999877666
Q ss_pred EEEEEEeecCCCCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEecc
Q 001235 1048 YLELRITHAGGGIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELA 1114 (1117)
Q Consensus 1048 ~l~i~V~D~G~GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl~ 1114 (1117)
.+.|.|.|+|.|||++.++++|+||+. .+|+||||+||+++++.|||+|++.|.+++|+|+|+||..
T Consensus 407 ~~~i~v~d~G~gi~~~~~~~if~~f~~~~~~~~~~~~g~GlGL~i~~~i~~~~~g~i~~~s~~~g~~~~i~lP~~ 481 (482)
T PRK09835 407 QVQLVVENPGTPIAPEHLPRLFDRFYRVDPSRQRKGEGSGIGLAIVKSIVVAHKGTVAVTSDARGTRFVISLPRL 481 (482)
T ss_pred EEEEEEEECCCCcCHHHHHHHhCCcccCCCCCCCCCCCcchHHHHHHHHHHHCCCEEEEEECCCcEEEEEEeeCC
Confidence 789999999999999999999999963 2489999999999999999999999987779999999965
No 38
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.91 E-value=6.3e-23 Score=273.12 Aligned_cols=265 Identities=13% Similarity=0.128 Sum_probs=222.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCc-cccccccCcHHHHHHHHHHHHc
Q 001235 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKH-FLTLVEDSSIDTVKRMLYLALQ 682 (1117)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~-~~dlv~~~~~~~~~~~l~~~l~ 682 (1117)
.++.++++++.+++++.+++.+++++|.+|.+|.+++||+++++++||+.++..+.. +.+.++|++.+.+...+.....
T Consensus 398 rk~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~ 477 (1092)
T PRK09776 398 LKRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQ 477 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHh
Confidence 345667888889999999999999999999999999999999999999998855433 3467899999999888989888
Q ss_pred CCcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCe
Q 001235 683 GQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPI 762 (1117)
Q Consensus 683 g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I 762 (1117)
++.....+++.. ++|| .+|+.....+++|.+|++.+++++.+|||++|++++++++.+++++.+++++++ ++
T Consensus 478 ~~~~~~~e~r~~----~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~---~i 549 (1092)
T PRK09776 478 GRSPFKLEFRIV----VKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGE---AV 549 (1092)
T ss_pred cCCCeeEEEEEE----cCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhcccc---EE
Confidence 877665555554 7789 999999999999999999999999999999999999999999999999999998 89
Q ss_pred eeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCC--ceEeEEEEec
Q 001235 763 FGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP--EKVPFGFFAR 840 (1117)
Q Consensus 763 ~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~--~~~e~~~~~~ 840 (1117)
+..|.+|+++++|+++++++||+.+|++|++....+... +++....... +......... ...+..+.++
T Consensus 550 ~~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~--------~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~ 620 (1092)
T PRK09776 550 VCTDMAMKVTFMNPVAEKMTGWTQEEALGVPLLTVLHIT--------FGDNGPLMEN-IYSCLTSRSAAYLEQDVVLHCR 620 (1092)
T ss_pred EEECCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccc--------cCCcchhhHH-HHHHHhcCCCccccceEEEEeC
Confidence 999999999999999999999999999999864332211 1111111112 3333333333 4567788999
Q ss_pred CCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHH
Q 001235 841 NGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLS 885 (1117)
Q Consensus 841 dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~a 885 (1117)
+|..+|+..+..|+.+.+|++.|++++++|||++|+.++++++.+
T Consensus 621 ~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~L~~~a 665 (1092)
T PRK09776 621 SGGSYDVHYSITPLSTLDGENIGSVLVIQDVTESRKMLRQLSYSA 665 (1092)
T ss_pred CCcEEEEEEEeeeeecCCCCEEEEEEEEEecchHHHHHHHHHhhc
Confidence 999999999999999999999999999999999999887765544
No 39
>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=99.91 E-value=1.1e-22 Score=255.69 Aligned_cols=199 Identities=17% Similarity=0.273 Sum_probs=165.1
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHhcCCCC-HHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHH
Q 001235 893 LKALAYTKRQIRNPLSGIIFSRKMMEGTELG-AEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLV 971 (1117)
Q Consensus 893 ~~~la~isHEIrnPL~~I~~~~~LL~~~~l~-~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~ 971 (1117)
.++.+.++||+|||++.+....+..++...+ +...++++.+.+..++|.++++.+.... ...+..++++.++++
T Consensus 476 ~~~~a~i~HdLrn~l~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l~~~~-----~~~~~~~~~l~~ll~ 550 (679)
T TIGR02916 476 NRMSAFVVHDLKNLVAQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQLRSKG-----LEEEKLCVDLVDLLR 550 (679)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----cccCCccccHHHHHH
Confidence 3457789999999999999888777654444 4456788889999999999998863222 245677899999999
Q ss_pred HHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEE
Q 001235 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1117)
Q Consensus 972 ~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i 1051 (1117)
+++....... .++.++++++. .+.+|+..|.+|+.||+.||+||+++++.|+|++...++ .+.|
T Consensus 551 ~~~~~~~~~~----~~~~l~~~~~~---~v~~d~~~l~~vl~nLl~NAik~~~~~~~I~I~~~~~~~---------~~~i 614 (679)
T TIGR02916 551 RAIASKRAQG----PRPEVSIDTDL---SVRADRERLERVLGHLVQNALEATPGEGRVAIRVERECG---------AARI 614 (679)
T ss_pred HHHHHhhhhc----CCceEEeCCCc---eEEECHHHHHHHHHHHHHHHHHhCCCCCcEEEEEEEcCC---------EEEE
Confidence 9888765432 23334444442 689999999999999999999999888899999887766 8999
Q ss_pred EEeecCCCCChhh-hhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEe
Q 001235 1052 RITHAGGGIPEPL-LDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVE 1112 (1117)
Q Consensus 1052 ~V~D~G~GI~~e~-~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LP 1112 (1117)
+|+|||+|||++. .+++|+||++++ |+|+||++||++++.|||+|+++|.+|+ |+|+++||
T Consensus 615 ~V~D~G~Gi~~~~i~~~lF~pf~~~~~~G~GLGL~i~~~iv~~~gG~i~v~s~~g~Gt~f~i~LP 679 (679)
T TIGR02916 615 EIEDSGCGMSPAFIRERLFKPFDTTKGAGMGIGVYECRQYVEEIGGRIEVESTPGQGTIFTLVLP 679 (679)
T ss_pred EEEEcCCCcChHHHHHhcCCCCCCCCCCCcchhHHHHHHHHHHcCCEEEEEecCCCceEEEEEeC
Confidence 9999999999999 999999997665 7899999999999999999999999987 99999998
No 40
>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=99.91 E-value=1.1e-22 Score=244.44 Aligned_cols=207 Identities=21% Similarity=0.338 Sum_probs=180.0
Q ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHH
Q 001235 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1117)
Q Consensus 891 ~k~~~la~isHEIrnPL~~I~~~~~LL~~~~-l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~ 968 (1117)
....+.+.++||+||||+.+.+..+++.... ..++..+.++.+.....++.+++++ +++.+++.....+...++++.+
T Consensus 240 ~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~~~~~~~~~~~~~ 319 (457)
T TIGR01386 240 RLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADNGQLALERVRLDLAA 319 (457)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccCHHH
Confidence 3445688999999999999998888865433 3445567788877788899999999 6999988888888889999999
Q ss_pred HHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeE
Q 001235 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAY 1048 (1117)
Q Consensus 969 li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~ 1048 (1117)
+++.++..+......+++++.++.+ ..+.+|+..|.+++.|++.||+||++.++.|.|++...++ .
T Consensus 320 ~~~~~~~~~~~~~~~~~i~~~~~~~-----~~~~~~~~~l~~~~~nll~Nai~~~~~~~~I~i~~~~~~~---------~ 385 (457)
T TIGR01386 320 ELAKVAEYFEPLAEERGVRIRVEGE-----GLVRGDPQMFRRAISNLLSNALRHTPDGGTITVRIERRSD---------E 385 (457)
T ss_pred HHHHHHHHHHHHHHhCCeEEEecCC-----ceEEECHHHHHHHHHHHHHHHHHcCCCCceEEEEEEecCC---------E
Confidence 9999999998888888887776543 2689999999999999999999999878899999888766 8
Q ss_pred EEEEEeecCCCCChhhhhhccCCCCC--------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEe
Q 001235 1049 LELRITHAGGGIPEPLLDQMFGSEGD--------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVE 1112 (1117)
Q Consensus 1049 l~i~V~D~G~GI~~e~~~~iFe~f~~--------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LP 1112 (1117)
+.|+|.|+|+|||++...++|++||+ .+|+||||+||+++++.|||++.+.+ +++ |+|+++||
T Consensus 386 ~~i~v~D~G~g~~~~~~~~~~~~~~~~~~~~~~~~~g~GlGL~i~~~~~~~~~G~~~~~~-~~~G~~~~~~~P 457 (457)
T TIGR01386 386 VRVSVSNPGPGIPPEHLSRLFDRFYRVDPARSNSGEGTGLGLAIVRSIMEAHGGRASAES-PDGKTRFILRFP 457 (457)
T ss_pred EEEEEEeCCCCCCHHHHHHhccccccCCcccCCCCCCccccHHHHHHHHHHCCCEEEEEe-CCCceEEEEecC
Confidence 99999999999999999999999974 24899999999999999999999999 666 99999998
No 41
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=99.90 E-value=3e-22 Score=241.72 Aligned_cols=211 Identities=18% Similarity=0.300 Sum_probs=188.7
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVL 970 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li 970 (1117)
..++++.++|+++||++.+.+..+++......+...++++.+....+++..++++ +.+++++..........+++.+++
T Consensus 256 ~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~ 335 (475)
T PRK11100 256 VEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQRQELEVLEPVALAALL 335 (475)
T ss_pred HHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCccceeccHHHHH
Confidence 3457889999999999999999999888666677888999999999999999999 488888877777778999999999
Q ss_pred HHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEE
Q 001235 971 VASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLE 1050 (1117)
Q Consensus 971 ~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~ 1050 (1117)
+.++..+.......++++.++.+ . ..+.+|...|.+++.||+.||++|+.+++.|.|++...++ .+.
T Consensus 336 ~~~~~~~~~~~~~~~i~~~~~~~-~---~~~~~~~~~l~~vl~nli~Na~~~~~~~~~i~i~~~~~~~---------~~~ 402 (475)
T PRK11100 336 EELVEAREAQAAAKGITLRLRPD-D---ARVLGDPFLLRQALGNLLDNAIDFSPEGGTITLSAEVDGE---------QVA 402 (475)
T ss_pred HHHHHHHHHHHHhCCceEEEeCC-C---ceEEECHHHHHHHHHHHHHHHHHhCCCCCEEEEEEEEcCC---------EEE
Confidence 99999999999999999998876 2 2688999999999999999999999878899999887766 899
Q ss_pred EEEeecCCCCChhhhhhccCCCCCC-------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1051 LRITHAGGGIPEPLLDQMFGSEGDT-------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1051 i~V~D~G~GI~~e~~~~iFe~f~~~-------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
|+|+|+|+|||++.++++|++|++. +|+|+||++|+++++.|||++++.|.+++ |+|+|.||.+.
T Consensus 403 i~i~D~G~Gi~~~~~~~i~~~~~~~~~~~~~~~~~GlGL~i~~~~~~~~~G~i~i~s~~~~Gt~v~i~lp~~~ 475 (475)
T PRK11100 403 LSVEDQGPGIPDYALPRIFERFYSLPRPANGRKSTGLGLAFVREVARLHGGEVTLRNRPEGGVLATLTLPRHF 475 (475)
T ss_pred EEEEECCCCCCHHHHHHHHHHHccCCCCCCCCCCcchhHHHHHHHHHHCCCEEEEEEcCCCeEEEEEEeeCCC
Confidence 9999999999999999999998632 48899999999999999999999999866 99999999863
No 42
>PRK10337 sensor protein QseC; Provisional
Probab=99.90 E-value=3.2e-22 Score=240.15 Aligned_cols=205 Identities=15% Similarity=0.215 Sum_probs=175.7
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCH-HHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHH
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTELGA-EQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~-~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~l 969 (1117)
..+|++.++||+|+||+.+.+..+.+.....++ ....+++.+....+++..+++. +.+++++.+.......++++.++
T Consensus 237 ~~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~~~~~~~~~~~~l~~~ 316 (449)
T PRK10337 237 ERRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDSLDNLQDVAEIPLEDL 316 (449)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCcccCHHHH
Confidence 345789999999999999998888776544333 4556888888889999999999 58888877666667789999999
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
++.++..+...+..+++.+.++.++.. ..+.+|+..|.+++.||+.||+||+++++.|.|++.. .
T Consensus 317 ~~~~~~~~~~~~~~~~i~~~~~~~~~~--~~~~~~~~~l~~vl~Nli~NA~k~~~~~~~i~i~~~~-------------~ 381 (449)
T PRK10337 317 LQSAVMDIYHTAQQAGIDVRLTLNAHP--VIRTGQPLLLSLLVRNLLDNAIRYSPQGSVVDVTLNA-------------R 381 (449)
T ss_pred HHHHHHHHHHHHHHcCCEEEEecCCCC--ceeecCHHHHHHHHHHHHHHHHhhCCCCCeEEEEEEe-------------e
Confidence 999999999988999999999887653 2579999999999999999999999888888887543 2
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCC-----CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEE
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDT-----SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSV 1111 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~-----~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~L 1111 (1117)
.++|+|+|+|||++..+++|+||+.. +|+||||+||++++++|||+|++++.+++ ++|+|+|
T Consensus 382 ~i~i~D~G~Gi~~~~~~~if~~f~~~~~~~~~g~GlGL~iv~~i~~~~gg~l~~~s~~~~G~~~~i~~ 449 (449)
T PRK10337 382 NFTVRDNGPGVTPEALARIGERFYRPPGQEATGSGLGLSIVRRIAKLHGMNVSFGNAPEGGFEAKVSW 449 (449)
T ss_pred EEEEEECCCCCCHHHHHHhcccccCCCCCCCCccchHHHHHHHHHHHcCCEEEEEecCCCeEEEEEeC
Confidence 48899999999999999999999643 48999999999999999999999999876 9998874
No 43
>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=6.1e-24 Score=201.69 Aligned_cols=106 Identities=38% Similarity=0.551 Sum_probs=93.3
Q ss_pred hhhhccCCCCCCCceeEEEEecCCceEEEEccChhhhhcCC---cCCCCCCCCCCccCCCCchhhhcChhHHHHHHHHhc
Q 001235 70 YLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMV---NHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALG 146 (1117)
Q Consensus 70 ~~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~l~~~---~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~l~~~~~ 146 (1117)
+-+|||+||+|||||+|||+|+++++|+|+|+|+.++||.+ ++ .++|+++.++|++..++.+++++.
T Consensus 2 ~~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~----------~llG~~l~~ll~~~~~~~l~~~~~ 71 (110)
T PF08446_consen 2 DREPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPELPE----------ELLGRPLSELLGAESAERLREALQ 71 (110)
T ss_dssp GGS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS----HH----------HHTTCBHHHHSCCCCHHHHHHHCT
T ss_pred CcccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccccch----------hhcccCHHHHhCHHHHHHHHHhhh
Confidence 35799999999999999999999999999999999999998 43 379999999999999999999998
Q ss_pred cCCccccCcEEEEecCCCCeEEEEEEeeCCeEEEEeeec
Q 001235 147 FGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPV 185 (1117)
Q Consensus 147 ~~~~~~~~~~~~~~~~~~~~f~~~~hr~~~~~~~e~Ep~ 185 (1117)
.......+|+.+++..+++.|++++||+++++||||||+
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 72 SESLSLSNPIALRLRIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCCCCCEEEEEEEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred ccCccccCCeEEEeccCCeeEEEEEEEECCEEEEEEeeC
Confidence 887777899999877788899999999999999999995
No 44
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=99.90 E-value=8.2e-22 Score=237.26 Aligned_cols=210 Identities=16% Similarity=0.226 Sum_probs=175.1
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNE 968 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~ 968 (1117)
..+.++++.++||++|||+.|.+..+++........ .+..+....+++.+++++ +++++.+.. ..+....+++..
T Consensus 241 ~~~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~~---~~~~i~~~~~~l~~~i~~l~~~~~~~~~-~~~~~~~~~l~~ 316 (461)
T PRK09470 241 TSQQRLLSDISHELRTPLTRLQLATALLRRRQGESK---ELERIETEAQRLDSMINDLLVLSRNQQK-NHLERETFKANS 316 (461)
T ss_pred HHHHHHHHhhhHhhCCHHHHHHHHHHHHhhccCChH---HHHHHHHHHHHHHHHHHHHHHHHHhhcc-cccccceecHHH
Confidence 344567899999999999999999888875443322 345566778899999999 488876543 456778999999
Q ss_pred HHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeE
Q 001235 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAY 1048 (1117)
Q Consensus 969 li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~ 1048 (1117)
+++.++..+.......++.+.++..++. ..+.+|+..|.+++.||+.||++|++ +.|.|++...++ .
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~--~~~~~~~~~l~~~l~nli~NA~~~~~--~~i~i~~~~~~~---------~ 383 (461)
T PRK09470 317 LWSEVLEDAKFEAEQMGKSLTVSAPPGP--WPINGNPNALASALENIVRNALRYSH--TKIEVAFSVDKD---------G 383 (461)
T ss_pred HHHHHHHHHHHHHHHCCCeEEEecCCcc--eEEEECHHHHHHHHHHHHHHHHHhCC--CcEEEEEEEECC---------E
Confidence 9999999888877778888888844442 37899999999999999999999986 567777776665 7
Q ss_pred EEEEEeecCCCCChhhhhhccCCCCCC--------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1049 LELRITHAGGGIPEPLLDQMFGSEGDT--------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1049 l~i~V~D~G~GI~~e~~~~iFe~f~~~--------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
+.|+|.|+|+||+++.++++|+||+++ +|+||||++|+++++.|||++.+.|.+++ |+|+|++|+.++
T Consensus 384 ~~i~V~D~G~Gi~~~~~~~if~~~~~~~~~~~~~~~g~GlGL~iv~~~v~~~~G~l~~~s~~~~Gt~~~i~lp~~~~ 460 (461)
T PRK09470 384 LTITVDDDGPGVPEEEREQIFRPFYRVDEARDRESGGTGLGLAIVENAIQQHRGWVKAEDSPLGGLRLTIWLPLYKR 460 (461)
T ss_pred EEEEEEECCCCCCHHHHHHhcCCCccCCcccCCCCCCcchhHHHHHHHHHHCCCEEEEEECCCCeEEEEEEeeCCCC
Confidence 899999999999999999999999743 48999999999999999999999999877 999999999764
No 45
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=99.89 E-value=1.1e-21 Score=234.35 Aligned_cols=203 Identities=19% Similarity=0.216 Sum_probs=163.9
Q ss_pred HHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeH
Q 001235 888 TALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTL 966 (1117)
Q Consensus 888 ~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L 966 (1117)
....+..+++.++|||||||+.|....+++... .....+.+....++|..+++. +++.+.... ....++++
T Consensus 225 ~~~~~~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~~~---~~~~~~~l 296 (435)
T PRK09467 225 LEDDRTLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTGQE---MPMEMADL 296 (435)
T ss_pred HHHHHHHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhcccCC---CCccccCH
Confidence 344566789999999999999999888776432 223345566677888888888 577664432 34678899
Q ss_pred HHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccce
Q 001235 967 NEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHL 1046 (1117)
Q Consensus 967 ~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~ 1046 (1117)
.+++++++.... ..+..+.++++... ..+.+|+..|.+++.||+.||+||+ .+.|.|++...++
T Consensus 297 ~~~~~~~~~~~~----~~~~~i~~~~~~~~--~~~~~~~~~l~~il~NLl~NA~k~~--~~~i~i~~~~~~~-------- 360 (435)
T PRK09467 297 NALLGEVIAAES----GYEREIETALQPGP--IEVPMNPIAIKRALANLVVNAARYG--NGWIKVSSGTEGK-------- 360 (435)
T ss_pred HHHHHHHHHHhh----hcCCeEEEecCCCC--ceEEECHHHHHHHHHHHHHHHHHhC--CCeEEEEEEecCC--------
Confidence 999999887654 34456666665542 2689999999999999999999998 4788888877665
Q ss_pred eEEEEEEeecCCCCChhhhhhccCCCCC------CCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1047 AYLELRITHAGGGIPEPLLDQMFGSEGD------TSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1047 ~~l~i~V~D~G~GI~~e~~~~iFe~f~~------~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
.+.|+|.|+|+|||++..+++|+||+. .+|+|+||+||+++++.|||++.+.+.+++ ++|+++||+.+
T Consensus 361 -~~~i~V~D~G~Gi~~~~~~~~~~~f~~~~~~~~~~g~GlGL~iv~~i~~~~~g~l~i~~~~~~G~~~~i~lp~~~ 435 (435)
T PRK09467 361 -RAWFQVEDDGPGIPPEQLKHLFQPFTRGDSARGSSGTGLGLAIVKRIVDQHNGKVELGNSEEGGLSARAWLPLTT 435 (435)
T ss_pred -EEEEEEEecCCCcCHHHHHHhcCCcccCCCCCCCCCeehhHHHHHHHHHHCCCEEEEEECCCCcEEEEEEEeCCC
Confidence 799999999999999999999999962 358999999999999999999999998776 99999999863
No 46
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.89 E-value=3e-21 Score=219.48 Aligned_cols=212 Identities=28% Similarity=0.452 Sum_probs=180.8
Q ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCc-ccceeEEeeHHH
Q 001235 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGY-LDLEMVEFTLNE 968 (1117)
Q Consensus 891 ~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~-~~l~~~~~~L~~ 968 (1117)
.+..+++.++||++||++.+.+..+++..... +...+.+..+....+++..+++. +++++..... .......+++..
T Consensus 114 ~~~~~~~~~~hel~~pl~~i~~~~~~~~~~~~-~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~ 192 (336)
T COG0642 114 AKREFLANISHELRTPLTAIRGLLELLLEGLL-DPQRELLEIIEEEAERLLRLVNDLLDLSRLEAGTKLKLLLELVDLAE 192 (336)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHhccCCc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccCCCCcCHHH
Confidence 36678899999999999999998886655422 22677788887788899999999 6888877652 344467788999
Q ss_pred HHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeE
Q 001235 969 VLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAY 1048 (1117)
Q Consensus 969 li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~ 1048 (1117)
++..++..+........+.+....++. ..+.+|+..+.++|.||+.||++|++ ++.|.|.+....+ +
T Consensus 193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~v~~~~~~l~~vl~nLi~NAi~~~~-~~~i~i~~~~~~~---------~ 259 (336)
T COG0642 193 LLEEVVRLLAPLAQEKGIELAVDLPEL---PYVLGDPERLRQVLVNLLSNAIKYTP-GGEITISVRQDDE---------Q 259 (336)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEecCCC---ceEeeCHHHHHHHHHHHHHHHhccCC-CCeEEEEEEecCC---------e
Confidence 999999999988888888888666522 36899999999999999999999999 8999999888766 8
Q ss_pred EEEEEeecCCCCChhhhhhccCCCCCCC----CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1049 LELRITHAGGGIPEPLLDQMFGSEGDTS----EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1049 l~i~V~D~G~GI~~e~~~~iFe~f~~~~----GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
+.++|.|+|+||+++..+++|+||++++ |+|+||++||++++.|||++.+.+.+|. |+|+|++|....
T Consensus 260 i~i~V~D~G~Gi~~~~~~~if~~~~~~~~~~~g~GlGL~i~~~~~~~~~g~i~~~~~~~~Gt~~~i~lP~~~~ 332 (336)
T COG0642 260 VTISVEDTGPGIPEEELERIFEPFFRTDKSRSGTGLGLAIVKRIVELHGGTISVESEPGKGTTFTIRLPLAPA 332 (336)
T ss_pred EEEEEEcCCCCCCHHHHHHhccCeeccCCCCCCCCccHHHHHHHHHHcCCEEEEEecCCCceEEEEEEecccc
Confidence 9999999999999999999999998665 8999999999999999999999999855 999999998763
No 47
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=99.87 E-value=4.1e-21 Score=210.37 Aligned_cols=205 Identities=18% Similarity=0.289 Sum_probs=173.9
Q ss_pred HHHHHhhhhhhHHHHHHHH---HHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHHHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSR---KMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLNEVLV 971 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~---~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~~li~ 971 (1117)
+..++|||++||+++..++ .+.-+...++....+++++..-.++|.+|++.| .|++-.++ +-...+++|.++++
T Consensus 455 mTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~--~~~lqpV~L~~~v~ 532 (673)
T COG4192 455 MTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSS--DESLQPVRLNSVVE 532 (673)
T ss_pred HHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC--CCCcccccHHHHHH
Confidence 6788999999999999553 333345567778899999999999999999998 77775433 44477999999999
Q ss_pred HHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCC-CCeEEEEEEecccccccccceeEEE
Q 001235 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN-GGQLMVSSSLTKDQLGQSVHLAYLE 1050 (1117)
Q Consensus 972 ~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~-~g~I~I~v~~~~~~~~~~~~~~~l~ 1050 (1117)
++...+....+.+.+.+.... +. ++|.||...|+|||.|++.||+++... ..+|.|.+..+.. ..++
T Consensus 533 ~AweLl~~khk~rQ~~Li~pt--D~--~~V~gd~v~ieQVlvNl~~NaldA~~h~~p~i~~~~~~~~~--------e~l~ 600 (673)
T COG4192 533 QAWELLQTKHKRRQIKLINPT--DD--LMVMGDAVSIEQVLVNLIVNALDASTHFAPWIKLIALGTEQ--------EMLR 600 (673)
T ss_pred HHHHHHHhhhhhccccccCCc--cc--ceecchhhhHHHHHHHHHHHHHhhhccCCceEEEEeecCcc--------cceE
Confidence 999999999988888776544 33 379999999999999999999998754 4789888766433 2689
Q ss_pred EEEeecCCCCChhhhhhccCCCCCCC--CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1051 LRITHAGGGIPEPLLDQMFGSEGDTS--EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1051 i~V~D~G~GI~~e~~~~iFe~f~~~~--GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
+-|.|||+|.|-+..+++|.||.++| |.||||+||..+++.|.|++.+-|...+ +++.+.|..+
T Consensus 601 i~i~DnGqGwp~~l~dkLl~PFttsK~vgLGlGLSIsqSlmeqmqG~l~lAStLt~nA~ViL~f~v~ 667 (673)
T COG4192 601 IAIIDNGQGWPHELVDKLLTPFTTSKEVGLGLGLSISQSLMEQMQGRLALASTLTKNAMVILEFQVD 667 (673)
T ss_pred EEEecCCCCCchhHHHHhcCCcccccccccccchhHHHHHHHHhcCcchHhhhcccCcEEEEEEeec
Confidence 99999999999999999999998777 8999999999999999999999999888 8888888765
No 48
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.87 E-value=9.9e-21 Score=226.65 Aligned_cols=243 Identities=14% Similarity=0.073 Sum_probs=189.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCccEEEEeC-CCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc
Q 001235 607 GMKELEAVTSEMVRLIETATVPILAVDV-DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE 685 (1117)
Q Consensus 607 ~~~eL~~~~~~l~~lie~a~~gi~~~D~-dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~ 685 (1117)
..++|++.+++|+.+++++++++|++|. +|+|+++|+++++++||+.++++|+++.+++++++.+.+...+.....++.
T Consensus 124 ~~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~ 203 (442)
T TIGR02040 124 DYWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGS 203 (442)
T ss_pred HHHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCC
Confidence 3457888899999999999999999998 899999999999999999999999999999999999988888888876665
Q ss_pred ceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeee
Q 001235 686 EQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGS 765 (1117)
Q Consensus 686 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~ 765 (1117)
....++. .++|+..| .+...+++. +|.. .+++.++|||+++++++++. ++|+.+++++++ +|++.
T Consensus 204 ~~~~~~~------~~~~~~~~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~~~---~~~~~l~e~~~d---~I~v~ 268 (442)
T TIGR02040 204 AAPVRIL------LRRSQKRL-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDELS---ENLARLYHEAPD---AIVFS 268 (442)
T ss_pred CcceEEE------EcCCCeEE-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHHHH---HHHHHHHHhCCc---eEEEE
Confidence 4333222 12344444 345555554 3333 56778899999998887653 379999999999 89999
Q ss_pred CCCCceeechhhHHHhcCCC-hhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcE
Q 001235 766 DEFGWCCEWNPAMVKLTGWK-REEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKY 844 (1117)
Q Consensus 766 D~~g~i~~~N~a~~~l~G~~-~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~ 844 (1117)
|.+|+|+++|+++++++||+ .++++|+++...+.. ...+. ...+.....++....++..+.+++|..
T Consensus 269 D~~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~---------~~~~~---~~~~~~~~~~g~~~~~~~~~~~~~G~~ 336 (442)
T TIGR02040 269 DADGTIRGANEAFLELTDSSSLEAVRGRTLDRWLGR---------GGVDL---RVLLSNVRRTGQVRLYATTLTGEFGAQ 336 (442)
T ss_pred cCCCcEEehhHHHHHHhCCCChHHHcCCCHHHHhCC---------CcccH---HHHHHHHhhcCceEEEEEEEEcCCCCE
Confidence 99999999999999999997 678999986432211 11111 222333344555566788889999999
Q ss_pred EEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHH
Q 001235 845 AECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1117)
Q Consensus 845 ~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (1117)
+|+.+++.|+.+.++ ..++++++|||+|++.+
T Consensus 337 ~~ve~s~~~i~~~~~--~~~~~v~rDITeR~~~~ 368 (442)
T TIGR02040 337 TEVEISAAWVDQGER--PLIVLVIRDISRRLTMR 368 (442)
T ss_pred EEEEEEEEEeccCCc--eEEEEEEecchhhccCC
Confidence 999999999986655 45788999999988774
No 49
>PRK13560 hypothetical protein; Provisional
Probab=99.86 E-value=3.7e-20 Score=238.73 Aligned_cols=260 Identities=15% Similarity=0.107 Sum_probs=202.9
Q ss_pred HHHHHHHHHHHHH-HHHHHhcCccEEEEeCCCc----EEeecHHHHHHcCCCcccccCCc--cccccccCcHHHHH----
Q 001235 606 EGMKELEAVTSEM-VRLIETATVPILAVDVDGL----VNGWNTKIAELTGLSVDKAIGKH--FLTLVEDSSIDTVK---- 674 (1117)
Q Consensus 606 ~~~~eL~~~~~~l-~~lie~a~~gi~~~D~dG~----I~~~N~a~~~l~G~s~eeliG~~--~~dlv~~~~~~~~~---- 674 (1117)
.++.+|+++++++ +.+++++|.++|.++.+|. +.+++++..+++|+...++++.. +..++||++.+.+.
T Consensus 57 ~~~~~l~~~~e~~~r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~ 136 (807)
T PRK13560 57 IAEAEAQDCREQCERNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPF 136 (807)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChh
Confidence 3566777777777 9999999999999887766 33478888888888888876543 45788999887664
Q ss_pred ---HHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHH
Q 001235 675 ---RMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAI 751 (1117)
Q Consensus 675 ---~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i 751 (1117)
+.+..++..+.....++++. ++||. |+.+...|.++.+|.+ ++.++++|||++|++|++|++++++|+.+
T Consensus 137 ~~~~~~~~~~~~~~~~~~e~r~~----~~dg~--~~~~~~~~~~~~~g~~-~~~g~~~DIT~rk~ae~~l~~~~~~l~~l 209 (807)
T PRK13560 137 RSAETIAMALQSDDWQEEEGHFR----CGDGR--FIDCCLRFERHAHADD-QVDGFAEDITERKRAEERIDEALHFLQQL 209 (807)
T ss_pred hHHHHHHHHhccCcccceEEEEE----eCCcc--EEEEEeeeeecCCCce-EEEEEEEccchHHHHHHHHHHHHHHHHHH
Confidence 23333444444444455444 56774 6777788899988886 68999999999999999999999999999
Q ss_pred HhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCc
Q 001235 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPE 831 (1117)
Q Consensus 752 ~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~ 831 (1117)
++++++ ++|..|.+|+++++|+++++++||++++++|+++.... +++....+.......+..+...
T Consensus 210 ~e~~~~---~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~ 275 (807)
T PRK13560 210 LDNIAD---PAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFA-----------PAQPADDYQEADAAKFDADGSQ 275 (807)
T ss_pred HhhCCC---eEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcC-----------CcchhHHHHHHHHHHhccCCce
Confidence 999999 89999999999999999999999999999999854321 1222222333344455566667
Q ss_pred eEeEEEEecCCcEEEEEEE--EeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHH
Q 001235 832 KVPFGFFARNGKYAECLLC--VNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSE 886 (1117)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~--~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae 886 (1117)
.++.++.++||+.+|+.+. ..+..+.+|.+.|++++++|||++|+++.++++..+
T Consensus 276 ~~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~ 332 (807)
T PRK13560 276 IIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKED 332 (807)
T ss_pred EEEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHH
Confidence 7889999999999976655 566789999999999999999999999988776544
No 50
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=99.83 E-value=3.9e-19 Score=214.41 Aligned_cols=193 Identities=13% Similarity=0.115 Sum_probs=152.3
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEeeHH
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMMEGTEL-GAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEFTLN 967 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l-~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~~L~ 967 (1117)
..+..+.+.++||++|||++|.+..+++++... .++..+..+.+.+...++.+.++++ +..+ .....++++.
T Consensus 300 ~~r~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~lr------~~~l~~~~L~ 373 (495)
T PRK11644 300 SVRRDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGRLR------PRQLDDLTLE 373 (495)
T ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhccC------CcccccCCHH
Confidence 345567788999999999999999998876443 3445677788888888888888883 4333 2235578999
Q ss_pred HHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccccccee
Q 001235 968 EVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLA 1047 (1117)
Q Consensus 968 ~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~ 1047 (1117)
+.+++++..+.......++++..+.++.. ....++..+.|++.|+++||+||++ .+.|.|++...++
T Consensus 374 ~~l~~l~~~l~~~~~~~~v~l~~~~~~~~---l~~~~~~~L~ril~nlL~NAiKha~-~~~I~I~l~~~~~--------- 440 (495)
T PRK11644 374 QAIRSLMREMELEDRGIVSHLDWRIDESA---LSETQRVTLFRVCQEGLNNIVKHAD-ASAVTLQGWQQDE--------- 440 (495)
T ss_pred HHHHHHHHHHHHhhcCceEEEEecCCccc---CChhHHHHHHHHHHHHHHHHHHhCC-CCEEEEEEEEcCC---------
Confidence 99999998887655555555555444331 4567888999999999999999997 5788888877665
Q ss_pred EEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEec
Q 001235 1048 YLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVEL 1113 (1117)
Q Consensus 1048 ~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl 1113 (1117)
.+.++|+|||+|||++. .|+|+||++||++++.|||+++++| .++|+|+|++|.
T Consensus 441 ~i~l~V~DnG~Gi~~~~-----------~~~GLGL~ivr~iv~~~GG~i~v~S-~~Gt~f~I~LP~ 494 (495)
T PRK11644 441 RLMLVIEDDGSGLPPGS-----------GQQGFGLRGMRERVTALGGTLTISC-THGTRLSVSLPQ 494 (495)
T ss_pred EEEEEEEECCCCCCcCC-----------CCCCCcHHHHHHHHHHcCCEEEEEc-CCCEEEEEEEeC
Confidence 79999999999999752 4679999999999999999999999 445999999995
No 51
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.81 E-value=1.4e-18 Score=223.87 Aligned_cols=248 Identities=12% Similarity=0.048 Sum_probs=197.9
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEe
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1117)
..+..+++.++++++++|.+|+|++||+++++++||+.++++|+++.++++++........+.....++......+..+.
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 45567889999999999999999999999999999999999999999999988777666666666655443222222233
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeech
Q 001235 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWN 775 (1117)
Q Consensus 696 ~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N 775 (1117)
...++||..+|+.++..++ +.+|.. +++++.+|||++++.++++ ..+..++++++. +++.+|.+|+++++|
T Consensus 92 ~~~~~dG~~~~v~~~~~~~-~~~g~~-~~~~~~~DiT~~~~~~~~~----~~~~~~~~~~~~---~i~~~d~~g~i~~~N 162 (799)
T PRK11359 92 QLEKKDGSKIWTRFALSKV-SAEGKV-YYLALVRDASVEMAQKEQT----RQLIIAVDHLDR---PVIVLDPERRIVQCN 162 (799)
T ss_pred EEecCCcCEEEEEEEeeee-ccCCce-EEEEEEeeccchhhhHHHH----HHHHHHHhcCCC---cEEEEcCCCcEEEEC
Confidence 4458899999999988776 445554 5678889999988776654 456678888888 899999999999999
Q ss_pred hhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeee
Q 001235 776 PAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKL 855 (1117)
Q Consensus 776 ~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~ 855 (1117)
+++++++||+.++++|+.....+. +++........+...+.++..+..++++.+++|..+|+..+..|+.
T Consensus 163 ~~~~~l~G~~~~e~~g~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~ 232 (799)
T PRK11359 163 RAFTEMFGYCISEASGMQPDTLLN----------IPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVY 232 (799)
T ss_pred hhhHhhhCCCHHHHCCCChHHhcC----------CCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeee
Confidence 999999999999999997543221 1222233344455666677777888899999999999999999999
Q ss_pred CCCCCEEEEEeehhHHHHHHHHHHHHH
Q 001235 856 DREGAVTGVFCFLQLASHELQQALHVQ 882 (1117)
Q Consensus 856 d~~G~v~g~v~i~~DITerk~~e~el~ 882 (1117)
+.+|.+.+++++.+|||++++.++..+
T Consensus 233 d~~g~~~~~~~~~~DITerk~~e~~~~ 259 (799)
T PRK11359 233 DVLAHLQNLVMTFSDITEERQIRQLEG 259 (799)
T ss_pred cCCCceeEEEEEeehhhhHHHHHHHHH
Confidence 999999999999999999988765433
No 52
>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=99.79 E-value=3.1e-18 Score=205.19 Aligned_cols=233 Identities=15% Similarity=0.140 Sum_probs=178.3
Q ss_pred HHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeecccc
Q 001235 621 LIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKI 700 (1117)
Q Consensus 621 lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~ 700 (1117)
+++.++++++++|.+|+|++||..+++++||+.++++|+++.+++++++.+.+...+..+..++.. .+..+.....+
T Consensus 1 ~~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~e~~~~~~ 77 (442)
T TIGR02040 1 LLATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRG---AVRVELNHIDP 77 (442)
T ss_pred CCcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCC---cceEeeccCCC
Confidence 367899999999999999999999999999999999999999999999988888888777765543 23333344466
Q ss_pred CCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhh-----------hh---hHhhHHHHHHHHHhCCCCCCCCeeeeC
Q 001235 701 NDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTV-----------MD---KFTRIEGDYKAIVQNPNPLIPPIFGSD 766 (1117)
Q Consensus 701 dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~a-----------E~---~L~~se~~l~~i~~~~~~li~~I~~~D 766 (1117)
+|..+|+.++..+..+. .+++++++|||+++.. |+ +|++++++|+.+++++++ +||++|
T Consensus 78 ~g~~~~~~~~~~~~~~~----~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l~~~e~r~~~l~e~~~~---~i~~~d 150 (442)
T TIGR02040 78 SSFELPMRFILVRLGAD----RGVLALGRDLRAVAELQQQLVAAQQAMERDYWTLREMETRYRVVLEVSSD---AVLLVD 150 (442)
T ss_pred CCCccCeEEEEEEeCCC----CeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCc---eEEEEE
Confidence 67788888877776552 2678899999875543 33 677888999999999998 899999
Q ss_pred C-CCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEE
Q 001235 767 E-FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYA 845 (1117)
Q Consensus 767 ~-~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~ 845 (1117)
. +|+++++|+++++++||++++++|+.+. .+.++++...+...+.....++.....++. .++|...
T Consensus 151 ~~~g~i~~~N~a~~~l~G~~~~el~g~~~~-----------~~~~~~~~~~~~~~l~~~~~~g~~~~~~~~--~~~~~~~ 217 (442)
T TIGR02040 151 MSTGRIVEANSAAAALLGGVGQSLVGRAFP-----------QEFEGRRREELMLTLRNVRATGSAAPVRIL--LRRSQKR 217 (442)
T ss_pred CCCCEEEEEcHHHHHHhCcCHHHHcCCCHH-----------HhCCHHHHHHHHHHHHHHHhcCCCcceEEE--EcCCCeE
Confidence 7 8999999999999999999999999853 334566777777788877776665544443 4455444
Q ss_pred EEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHH
Q 001235 846 ECLLCVNKKLDREGAVTGVFCFLQLASHELQQAL 879 (1117)
Q Consensus 846 ~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~ 879 (1117)
| .+...++.. +|.. .+++.+.|||++++.+.
T Consensus 218 ~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~ 248 (442)
T TIGR02040 218 L-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGD 248 (442)
T ss_pred E-EEEEEEEEe-CCce-EEEEEEcccchhhhhhH
Confidence 4 445555543 3333 56788899998876653
No 53
>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=99.73 E-value=2.2e-17 Score=158.19 Aligned_cols=103 Identities=27% Similarity=0.494 Sum_probs=95.6
Q ss_pred ecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCC-------C
Q 001235 1003 GDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD-------T 1075 (1117)
Q Consensus 1003 ~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~-------~ 1075 (1117)
||+.+|.++|.||+.||++|+++++.|.|.+....+ ++.|+|.|+|.|||++.++++|++|+. .
T Consensus 1 gd~~~l~~il~~ll~Na~~~~~~~~~I~i~~~~~~~---------~~~i~i~d~G~gi~~~~l~~~~~~~~~~~~~~~~~ 71 (111)
T PF02518_consen 1 GDPDRLRQILSELLDNAIKHSPEGGKIDITIEEDDD---------HLSIEISDNGVGIPPEELEKLFEPFFTSDKSETSI 71 (111)
T ss_dssp ETHHHHHHHHHHHHHHHHHHHHHTSEEEEEEEEETT---------EEEEEEEESSSSTTHHHHHHHCSTTSHSSSSSGGS
T ss_pred CcHHHHHHHHHHHHHHHHHHhcCCCEEEEEEEEecC---------eEEEEEEeccccccccccccchhhccccccccccc
Confidence 799999999999999999999977999999999877 899999999999999999999999852 3
Q ss_pred CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1076 SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1076 ~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
+|.|+||++|+.++++|+|++++.+.+++ |+|+|+||+.
T Consensus 72 ~g~GlGL~~~~~~~~~~~g~l~~~~~~~~gt~v~~~~p~~ 111 (111)
T PF02518_consen 72 SGHGLGLYIVKQIAERHGGELTIESSEGGGTTVTFTLPLE 111 (111)
T ss_dssp SSSSHHHHHHHHHHHHTTEEEEEEEETTTEEEEEEEEEGS
T ss_pred CCCChHHHHHHHHHHHCCCEEEEEEcCCCcEEEEEEEECc
Confidence 47999999999999999999999999766 9999999973
No 54
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=99.69 E-value=7.3e-15 Score=181.84 Aligned_cols=195 Identities=16% Similarity=0.186 Sum_probs=139.7
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHH----HhcC--CCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCcccceeEEe
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKM----MEGT--ELGAEQKRLLHTSAQCQRQLHKILDDS-DLDSIIDGYLDLEMVEF 964 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~L----L~~~--~l~~~~~~~l~~i~~~~~~l~~ii~dL-d~skie~g~~~l~~~~~ 964 (1117)
.......++||+++|++.+..+..+ +... ...++..+.+..+.....++...+.++ ...+ ....++
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 3344566889988888887765543 3321 223445556666555555555555552 3222 345678
Q ss_pred eHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccccccccc
Q 001235 965 TLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSV 1044 (1117)
Q Consensus 965 ~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~ 1044 (1117)
++.+++..++..+..... ..+.+..+.+... ...+++.++.|++.|++.||+||++ .+.|.|.+....+
T Consensus 433 ~l~~~l~~~~~~~~~~~~-~~i~~~~~~~~~~---~~~~~~~~l~qv~~nll~NA~k~~~-~~~i~i~~~~~~~------ 501 (565)
T PRK10935 433 NLGSALEEMLDQLRNQTD-AKITLDCRLPSQA---LDAQQQVHLLQIIREATLNAIKHAN-ASEIAVSCVTNPD------ 501 (565)
T ss_pred CHHHHHHHHHHHHHHhhC-CeEEEEeeCCCCC---CCHHHHHHHHHHHHHHHHHHHhcCC-CCeEEEEEEEcCC------
Confidence 999999999988876532 2234444433321 2344567799999999999999987 6788888776522
Q ss_pred ceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1045 HLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1045 ~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
..+.|+|.|+|+|||++ ..+|+|+||+||+++++.|||+|++.|.+|+ |+|+|+||+.++
T Consensus 502 --~~~~i~V~D~G~Gi~~~----------~~~~~glGL~i~~~iv~~~~G~i~v~s~~~~Gt~~~i~lP~~~~ 562 (565)
T PRK10935 502 --GEHTVSIRDDGIGIGEL----------KEPEGHYGLNIMQERAERLGGTLTISQPPGGGTTVSLTFPSQQE 562 (565)
T ss_pred --CEEEEEEEECCcCcCCC----------CCCCCCcCHHHHHHHHHHcCCEEEEEECCCCcEEEEEEECCCCC
Confidence 17899999999999974 2357899999999999999999999999887 999999999865
No 55
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=99.67 E-value=5.5e-15 Score=182.83 Aligned_cols=190 Identities=16% Similarity=0.211 Sum_probs=140.2
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHH
Q 001235 895 ALAYTKRQIRNPLSGIIFSRKMMEG--TELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLV 971 (1117)
Q Consensus 895 ~la~isHEIrnPL~~I~~~~~LL~~--~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~ 971 (1117)
....+++.+.++|..+...+.++.. ...+++..+.+..+....+.+...+.+ +...+. ...+.++.+.+.
T Consensus 365 iarelhd~i~~~L~~l~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~~~~~lr~ll~~~r~-------~~~~~~l~~~l~ 437 (569)
T PRK10600 365 IARELHDSIAQSLSCMKMQVSCLQMQGDALPESSRELLSQIRNELNASWRQLRELLTTFRL-------QLTEPGLRPALE 437 (569)
T ss_pred HHHHhccHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc-------CcccCCHHHHHH
Confidence 3445556666677777655554432 334567778888888878888777777 454442 345678999999
Q ss_pred HHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEE
Q 001235 972 ASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLEL 1051 (1117)
Q Consensus 972 ~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i 1051 (1117)
.++..+..... ..+.+..+.++.. ....++..|.+++.|++.||+||++ .+.|.|++...++ .+.|
T Consensus 438 ~~~~~~~~~~~-~~i~~~~~~~~~~---~~~~~~~~l~~il~ell~NA~kha~-a~~i~V~~~~~~~---------~~~l 503 (569)
T PRK10600 438 ASCEEFSARFG-FPVKLDYQLPPRL---VPSHQAIHLLQIAREALSNALKHAQ-ASEVVVTVAQNQN---------QVKL 503 (569)
T ss_pred HHHHHHHHHhC-CeEEEEecCCccc---CCHHHHHHHHHHHHHHHHHHHHhCC-CCeEEEEEEEcCC---------EEEE
Confidence 99888776543 2244444333321 1223455699999999999999997 5788888876655 7999
Q ss_pred EEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1052 RITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1052 ~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
+|.|||+|||++. .+++|+||+||+++++.|||+|++.+.+|+ |+|+|+||..+
T Consensus 504 ~V~D~G~Gi~~~~----------~~~~glGL~i~~~~~~~lgG~l~i~s~~~~Gt~v~i~lp~~~ 558 (569)
T PRK10600 504 SVQDNGCGVPENA----------ERSNHYGLIIMRDRAQSLRGDCRVRRRESGGTEVVVTFIPEK 558 (569)
T ss_pred EEEECCCCCCccc----------cCCCCccHHHHHHHHHHcCCEEEEEECCCCCEEEEEEEecCC
Confidence 9999999999863 347899999999999999999999999987 99999999864
No 56
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.62 E-value=1e-13 Score=148.37 Aligned_cols=212 Identities=16% Similarity=0.189 Sum_probs=161.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhcc
Q 001235 869 QLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSD 948 (1117)
Q Consensus 869 ~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd 948 (1117)
.++|++++.+..+... .+..++..|+|.+||.|+.|.+++.+..+...++ ..+++...+.....|..+.+.|.
T Consensus 2 ~~~~~~~~~e~~~~~~------~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~~~Ri~sla~~He~L~ 74 (221)
T COG3920 2 LLTTARKETEERLAES------EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRESQNRIQSLALIHELLY 74 (221)
T ss_pred chHHHHHHHHHHHHHH------HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566666666443332 4555788999999999999999999888776665 66666666666666666666553
Q ss_pred ccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCC---
Q 001235 949 LDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN--- 1025 (1117)
Q Consensus 949 ~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~--- 1025 (1117)
-+ ....++...+++.+...+......+.+.+..+..+.+. .-......|..|+.+|++||+||+-.
T Consensus 75 ~s---------~~~~~~~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~--l~~d~A~~Lgliv~EL~tNa~Khaf~~~~ 143 (221)
T COG3920 75 KS---------GDDTWDFASYLELLASNLFPSYGGKDIRLILDSGPNVF--LDPDTAVPLGLIVHELVTNALKHAFLSRP 143 (221)
T ss_pred cC---------CcceEcHHHHHHHHHHHHHHhcCCCCceEEEecCCceE--ECchhhHHHHHHHHHHHHHHHHhcCCCCC
Confidence 32 14578889999999988888765566788777776532 23344688999999999999999833
Q ss_pred CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHH-HHcCCEEEEEeeCCe
Q 001235 1026 GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLV-KLMNGDVQYLREAGK 1104 (1117)
Q Consensus 1026 ~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iV-e~~gG~I~v~s~~g~ 1104 (1117)
+|.|.|++....+ ++ ...+.|.|||.|+|.+. .. +..|+|+.+++.+| +..||.+...+.. +
T Consensus 144 ~G~I~I~~~~~~~--~~-----~~~l~v~deg~G~~~~~--------~~-~~~g~G~~Lv~~lv~~q~~g~~~~~~~~-G 206 (221)
T COG3920 144 GGEIRITLSREGD--GG-----RFLLTVWDEGGGPPVEA--------PL-SRGGFGLQLVERLVPEQLGGELEDERPD-G 206 (221)
T ss_pred CCEEEEEEEEcCC--CC-----eEEEEEEECCCCCCCCC--------CC-CCCCcHHHHHHHHHHHHcCCeEEEEcCC-C
Confidence 7899999988776 11 47888999999999863 11 56799999999999 8999999888865 6
Q ss_pred EEEEEEEeccC
Q 001235 1105 STFIVSVELAA 1115 (1117)
Q Consensus 1105 ttF~i~LPl~~ 1115 (1117)
|+|+|++|+..
T Consensus 207 t~~~i~~~~~~ 217 (221)
T COG3920 207 TEFRLRFPLSE 217 (221)
T ss_pred EEEEEEEeccc
Confidence 89999999875
No 57
>PRK10547 chemotaxis protein CheA; Provisional
Probab=99.60 E-value=2e-14 Score=175.46 Aligned_cols=139 Identities=17% Similarity=0.240 Sum_probs=115.2
Q ss_pred eeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHH---HHHHHHHHhhcc------------CCCCe
Q 001235 964 FTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQV---LADFLSISINFV------------PNGGQ 1028 (1117)
Q Consensus 964 ~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qV---L~nLl~NAik~~------------~~~g~ 1028 (1117)
+.+..+++..-..++..++..+.++.+.+... .+..|+..+.++ |.||+.||++|+ |..|.
T Consensus 343 ~p~~~~~~~~~rlvrdla~~~gk~v~l~~~g~----~~~lD~~~l~~l~dpL~hLirNAidHgie~p~~R~~~gkp~~G~ 418 (670)
T PRK10547 343 MPMEYVFSRFPRLVRDLAGKLGKQVELTLVGS----STELDKSLIERIIDPLTHLVRNSLDHGIELPEKRLAAGKNSVGN 418 (670)
T ss_pred ccHHHHHHHHHHHHHHHHHHcCCcEEEEEeCC----ceecCHHHHHHHHHHHHHHHHHHHHhhccchhhHHhcCCCCCCc
Confidence 45677777777777777766666666666554 367899999988 679999999996 34678
Q ss_pred EEEEEEecccccccccceeEEEEEEeecCCCCChhhh---------------------hhccCCCCCC-------CCccc
Q 001235 1029 LMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLL---------------------DQMFGSEGDT-------SEEGI 1080 (1117)
Q Consensus 1029 I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~---------------------~~iFe~f~~~-------~GtGL 1080 (1117)
|.|+....++ ++.|.|+|+|.||+++.+ ..||+|||++ +|.|+
T Consensus 419 I~l~a~~~~~---------~v~I~V~DdG~GId~e~i~~~a~~~Gl~~~~~ls~~e~~~lIF~pgfst~~~~~~~sGrGv 489 (670)
T PRK10547 419 LILSAEHQGG---------NICIEVTDDGAGLNRERILAKAASQGLAVSENMSDEEVGMLIFAPGFSTAEQVTDVSGRGV 489 (670)
T ss_pred eEEEEEEcCC---------EEEEEEEeCCCCCCHHHHHHHHHHcCCCccccCCHHHHHHHhhcCCcccccccccCCCCch
Confidence 9999887666 899999999999998754 3699997655 48999
Q ss_pred cHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1081 SLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1081 GL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
||.+||++++.|||+|++.|.+|+ |+|+|+||+.-
T Consensus 490 GL~iVk~~ve~lgG~I~v~S~~g~Gt~f~i~LPltl 525 (670)
T PRK10547 490 GMDVVKRNIQEMGGHVEIQSKQGKGTTIRILLPLTL 525 (670)
T ss_pred hHHHHHHHHHHcCCEEEEEecCCCcEEEEEEEechh
Confidence 999999999999999999999998 99999999864
No 58
>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=99.48 E-value=3e-13 Score=128.21 Aligned_cols=110 Identities=25% Similarity=0.310 Sum_probs=99.5
Q ss_pred HHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccC
Q 001235 622 IETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKIN 701 (1117)
Q Consensus 622 ie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~d 701 (1117)
|+++|++++++|.+|+|++||+++++++|++.++++|+++.+++++...+.+...+.+++.++.....+.... .+
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 6899999999999999999999999999999999999999999999999999999999999887644333332 27
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEEEccchhhh
Q 001235 702 DDPITLIVNACASRDLHDNVVGVCFVAQDITPQKT 736 (1117)
Q Consensus 702 G~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~ 736 (1117)
|+.+|+.++..|++|.+|++.|++++++|||++|+
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 99999999999999999999999999999999986
No 59
>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=99.45 E-value=6.1e-13 Score=124.52 Aligned_cols=104 Identities=20% Similarity=0.256 Sum_probs=91.2
Q ss_pred CccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceE
Q 001235 626 TVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPI 705 (1117)
Q Consensus 626 ~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~ 705 (1117)
|+|++++|.+|+|+++|+++++++|++.++++|+++.+++++.........+.+++.++.....++.+. +++|..+
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 789999999999999999999999999999999999999998888888888888887666655555554 6789999
Q ss_pred EEEEEEEEeecCCCCEEEEEEEEEccch
Q 001235 706 TLIVNACASRDLHDNVVGVCFVAQDITP 733 (1117)
Q Consensus 706 ~v~v~~~pi~d~~G~v~gv~~v~~DITe 733 (1117)
|+.+++.|+++.+|++.+++++++|||+
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 60
>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=99.44 E-value=8.5e-13 Score=125.72 Aligned_cols=112 Identities=23% Similarity=0.353 Sum_probs=94.9
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc-ceeeEEEEE
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-EQNIQFEIK 694 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~-~~~~e~~~~ 694 (1117)
++|+.+++++++|++++|.+|+|++||++++++||++.++++|+++.+++++++.......+...+.... .........
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 4789999999999999999999999999999999999999999999999998877666666666665444 333333333
Q ss_pred eeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEcc
Q 001235 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDI 731 (1117)
Q Consensus 695 ~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DI 731 (1117)
. ++|+.+|+.++..|+++.+|++.|++++++||
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 61
>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]
Probab=99.42 E-value=2.9e-11 Score=130.39 Aligned_cols=191 Identities=14% Similarity=0.161 Sum_probs=144.3
Q ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHH
Q 001235 891 KRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEV 969 (1117)
Q Consensus 891 ~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~l 969 (1117)
-|.....+++.||.+.+++|.--..+.++...++..++....|+.-+.++-+-+.. +.--+ +....+..+.++
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 34456778899999999999999999998777777777666666555555444444 21111 223457778888
Q ss_pred HHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEE
Q 001235 970 LVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYL 1049 (1117)
Q Consensus 970 i~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l 1049 (1117)
+..++..+. +.++++.+.++...+-. ..-.--...|.++.+++++|.+||+. ...|+|.....++ .+
T Consensus 376 i~~l~~Em~--~~ergihcq~~~~~n~~-~ldet~rvTLyRl~QE~LNNI~KHA~-AS~V~i~l~~~~e---------~l 442 (497)
T COG3851 376 IRSLLREME--LEERGIHCQLDWRINET-ALDETQRVTLYRLCQELLNNICKHAD-ASAVTIQLWQQDE---------RL 442 (497)
T ss_pred HHHHHHHhh--hhhcCeEEEeccccCcc-cCCcceeEeHHHHHHHHHHHHHhccc-cceEEEEEeeCCc---------EE
Confidence 988888765 55677777766543311 12222345688999999999999998 8899999998877 89
Q ss_pred EEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEe
Q 001235 1050 ELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVE 1112 (1117)
Q Consensus 1050 ~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LP 1112 (1117)
.++|+|||.|+|+. .+-.|+||.-+++.|...||++.++|.-| |++.|++|
T Consensus 443 ~Lei~DdG~Gl~~~-----------~~v~G~Gl~GmrERVsaLGG~ltlssq~G-TrviVnLP 493 (497)
T COG3851 443 MLEIEDDGSGLPPG-----------SGVQGFGLTGMRERVSALGGTLTLSSQHG-TRVIVNLP 493 (497)
T ss_pred EEEEecCCcCCCCC-----------CCccCcCcchHHHHHHHhCCceEEEeccC-cEEEEecc
Confidence 99999999999974 34569999999999999999999999433 89999999
No 62
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.40 E-value=2.4e-11 Score=141.79 Aligned_cols=190 Identities=16% Similarity=0.200 Sum_probs=129.2
Q ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHh--cCCCCHHH----HHHHHHHHHHHHHHHHHHhhccccccccCcccceeEE
Q 001235 890 LKRLKALAYTKRQIRNPLSGIIFSRKMME--GTELGAEQ----KRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVE 963 (1117)
Q Consensus 890 ~~k~~~la~isHEIrnPL~~I~~~~~LL~--~~~l~~~~----~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~ 963 (1117)
.+|.+....++..+-+-|+++.....+.. .....++. +...+.++++.+.++.++.+|....++ .
T Consensus 169 ~ER~RIARdLHDsv~q~L~~i~m~~~~~~~~~~~~~e~~~~~l~~i~~~~~e~l~evR~~v~~Lrp~~l~---------~ 239 (365)
T COG4585 169 EERNRIARDLHDSVGQSLTAISMLLALLLLLADEDAEKAQEELKEIEKLLREALQEVRALVRDLRPVELE---------G 239 (365)
T ss_pred HHHHHHHHHHhhHHhhHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhh---------c
Confidence 44555566666666777777765222111 12222323 334455566666777777765444322 1
Q ss_pred eeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccc
Q 001235 964 FTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQS 1043 (1117)
Q Consensus 964 ~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~ 1043 (1117)
..+.+-+...+..+. ...++.+..+.....+ ..-..-...|.+++++.++||+||+. ...+.|++...++
T Consensus 240 ~~l~~~l~~~~~~~~---~~~~~~~~~~~~~~~~-~L~~~~e~~l~rivQEaltN~~rHa~-A~~v~V~l~~~~~----- 309 (365)
T COG4585 240 LGLVEALRALLADFE---ERTGITVDLSLGSELE-RLPPEAEDALFRIVQEALTNAIRHAQ-ATEVRVTLERTDD----- 309 (365)
T ss_pred chHHHHHHHHHHHHH---hhcCeEEEEecCcccc-cCChhHHHHHHHHHHHHHHHHHhccC-CceEEEEEEEcCC-----
Confidence 223444444444443 4455566655543110 12335678899999999999999998 7889999999888
Q ss_pred cceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEec
Q 001235 1044 VHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVEL 1113 (1117)
Q Consensus 1044 ~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl 1113 (1117)
++.++|.|||+|++++. .+ .|+||.-+|+.|+.+||++.+.|.||+ |++++++|+
T Consensus 310 ----~l~l~V~DnG~Gf~~~~----------~~-~~~GL~~mreRv~~lgG~l~i~S~~g~Gt~i~i~lPl 365 (365)
T COG4585 310 ----ELRLEVIDNGVGFDPDK----------EG-GGFGLLGMRERVEALGGTLTIDSAPGQGTTVTITLPL 365 (365)
T ss_pred ----EEEEEEEECCcCCCccc----------cC-CCcchhhHHHHHHHcCCEEEEEecCCCceEEEEecCC
Confidence 89999999999999763 11 689999999999999999999999977 999999996
No 63
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=99.39 E-value=9.2e-12 Score=152.80 Aligned_cols=141 Identities=16% Similarity=0.282 Sum_probs=120.4
Q ss_pred eEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHH---HHHHHHHHhhcc------------CC
Q 001235 961 MVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQV---LADFLSISINFV------------PN 1025 (1117)
Q Consensus 961 ~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qV---L~nLl~NAik~~------------~~ 1025 (1117)
...+.+..++...-..++..+++-+-+|.+.+..+ -...|..-|.++ |..|+.||+.|+ |+
T Consensus 387 ~RMvP~~~vf~RfpR~VRdla~~lgK~V~L~ieG~----~telDksIlE~l~dPL~HLvRNAvDHGIE~pE~R~a~GKp~ 462 (716)
T COG0643 387 IRMVPFEQVFSRFPRMVRDLARKLGKQVELVIEGE----DTELDKSILERLGDPLTHLVRNAVDHGIETPEERRAAGKPE 462 (716)
T ss_pred HhceeHHHHHhhccHHHHHHHHHhCCeeEEEEecC----CeeehHHHHHHhcccHHHHHhcchhccCCCHHHHHHcCCCC
Confidence 44667788888888888888877666666666654 467899888887 899999999996 45
Q ss_pred CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh------------------------ccCCCCCCC-----
Q 001235 1026 GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ------------------------MFGSEGDTS----- 1076 (1117)
Q Consensus 1026 ~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~------------------------iFe~f~~~~----- 1076 (1117)
.|.|+++....++ ++.|.|+|+|.||+.+.+.+ ||.|.|+|+
T Consensus 463 ~G~I~L~A~~~gn---------~ivIev~DDG~Gid~ekI~~KAiErGli~~~~a~~lSd~Ei~~LIF~PGFSTa~~Vtd 533 (716)
T COG0643 463 EGTITLSAYHEGN---------NIVIEVSDDGAGIDREKIREKAIERGLITEEEAETLSDEEILNLIFAPGFSTAEQVTD 533 (716)
T ss_pred cceEEEEEEcCCC---------eEEEEEeeCCCCCCHHHHHHHHHHcCCCChHHhccCCHHHHHHHHhcCCCCcchhhhc
Confidence 7899999998877 99999999999998776433 899988776
Q ss_pred --CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1077 --EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1077 --GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
|.|.||=+||.-|+.+||+|.++|++|+ |+|+++|||.
T Consensus 534 vSGRGVGMDVVk~~I~~LgG~I~V~S~~G~GT~Fti~LPLT 574 (716)
T COG0643 534 VSGRGVGMDVVKTNIEQLGGSISVSSEPGKGTTFTIRLPLT 574 (716)
T ss_pred ccCCccCHHHHHHHHHHcCCEEEEEecCCCCeEEEEecCcH
Confidence 9999999999999999999999999999 9999999985
No 64
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.38 E-value=1.9e-10 Score=122.75 Aligned_cols=217 Identities=14% Similarity=0.123 Sum_probs=149.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHH------HHHHHHHHHHHH
Q 001235 868 LQLASHELQQALHVQRLSEQT----ALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAE------QKRLLHTSAQCQ 937 (1117)
Q Consensus 868 ~~DITerk~~e~el~~~ae~~----~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~------~~~~l~~i~~~~ 937 (1117)
.-...+++.+...+++++++. +.+|.++..+++.-|.+.|-+....+++..+...++. ..+..+....+.
T Consensus 223 alNl~ehRlAD~kLkeL~qrvv~tQedEr~rlaRELHDGIsQ~LVs~k~~lela~~ql~~p~~~a~~aieKaa~aL~~Ai 302 (459)
T COG4564 223 ALNLREHRLADKKLKELAQRVVDTQEDERARLARELHDGISQNLVSVKCALELAARQLNPPKGGAHPAIEKAADALNGAI 302 (459)
T ss_pred HhhhHHHHhhhhHHHHHHHHHhhchhHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccCCCCCCCCchhhhhHHHHHHHHH
Confidence 334455555555555544442 3455556677777789999999999999876432222 222223333334
Q ss_pred HHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHH
Q 001235 938 RQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLS 1017 (1117)
Q Consensus 938 ~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~ 1017 (1117)
+...+|..+|..+- ....-|...++..++.+. ...+++++++.... |......-...|.+|.++-++
T Consensus 303 ~EVRRiSH~LRP~~---------LDDLGL~aALe~L~~~f~---~~tg~~itle~~~~-p~~l~~e~~talyRv~QEalt 369 (459)
T COG4564 303 KEVRRISHDLRPRA---------LDDLGLTAALEALLEDFK---ERTGIEITLEFDTQ-PGKLKPEVATALYRVVQEALT 369 (459)
T ss_pred HHHHHhccccChhh---------hhhhhHHHHHHHHHHHhh---hccCeEEEEEecCC-cccCCcHHHHHHHHHHHHHHH
Confidence 44445555443332 224456666666666655 55677777765432 112334557889999999999
Q ss_pred HHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEE
Q 001235 1018 ISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQ 1097 (1117)
Q Consensus 1018 NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~ 1097 (1117)
|.=+|+. ...|+|.+....+ .+.+.|.|||.|++-+.... +-.|+||--+|+.+...||++.
T Consensus 370 NIErHa~-Atrv~ill~~~~d---------~vql~vrDnG~GF~~~~~~~--------~~~GiGLRNMrERma~~GG~~~ 431 (459)
T COG4564 370 NIERHAG-ATRVTILLQQMGD---------MVQLMVRDNGVGFSVKEALQ--------KRHGIGLRNMRERMAHFGGELE 431 (459)
T ss_pred HHHhhcC-CeEEEEEeccCCc---------ceEEEEecCCCCccchhhcc--------CccccccccHHHHHHHhCceEE
Confidence 9999995 7788888877766 89999999999998765332 2369999999999999999999
Q ss_pred EEeeCCeEEEEEEEeccC
Q 001235 1098 YLREAGKSTFIVSVELAA 1115 (1117)
Q Consensus 1098 v~s~~g~ttF~i~LPl~~ 1115 (1117)
++|+|.+|..++.||+..
T Consensus 432 v~s~p~GTel~v~Lp~~~ 449 (459)
T COG4564 432 VESSPQGTELTVLLPLDA 449 (459)
T ss_pred EEecCCCcEEEEEecchh
Confidence 999999999999999864
No 65
>smart00387 HATPase_c Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Probab=99.33 E-value=1.3e-11 Score=116.40 Aligned_cols=103 Identities=34% Similarity=0.591 Sum_probs=91.4
Q ss_pred ecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCC-------C
Q 001235 1003 GDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD-------T 1075 (1117)
Q Consensus 1003 ~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~-------~ 1075 (1117)
+|+..|.+++.|++.||++|....+.|.|++..... .+.|.|.|+|.|++++...++|.+++. .
T Consensus 1 ~~~~~l~~~~~~l~~n~~~~~~~~~~v~i~~~~~~~---------~~~i~i~d~g~g~~~~~~~~~~~~~~~~~~~~~~~ 71 (111)
T smart00387 1 GDPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGD---------HLEITVEDNGPGIPPEDLEKIFEPFFRTDGRSRKI 71 (111)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEEcCC---------EEEEEEEeCCCCCCHHHHHHHhcCeEECCCCCCCC
Confidence 477889999999999999999877899999888766 899999999999999999999998742 2
Q ss_pred CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEecc
Q 001235 1076 SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1076 ~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
.+.|+||++|+.+++.|+|.+++.+.++. ++|+|.+|+.
T Consensus 72 ~~~g~gl~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~~~~ 111 (111)
T smart00387 72 GGTGLGLSIVKKLVELHGGEISVESEPGGGTTFTITLPLE 111 (111)
T ss_pred CcccccHHHHHHHHHHcCCEEEEEecCCCcEEEEEEeeCC
Confidence 36899999999999999999999998555 9999999974
No 66
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.33 E-value=1.8e-11 Score=157.57 Aligned_cols=147 Identities=16% Similarity=0.142 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcC
Q 001235 604 KIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1117)
Q Consensus 604 ~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g 683 (1117)
..+..+++++.+++++.+++++|++++++|.+|+|++||+++++++|++.++++|+++.++++++....+.......+.+
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 34567788899999999999999999999999999999999999999999999999999999988777777777777776
Q ss_pred CcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhC
Q 001235 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQN 754 (1117)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~ 754 (1117)
+.....+..+. +++|..+|+.++..|+++.+|++.|++++++|||++|++++++++.++....++.+
T Consensus 223 ~~~~~~e~~~~----~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~~~~~~~~a~ 289 (779)
T PRK11091 223 NVSLTYEQWLD----YPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKASRDKTTFIST 289 (779)
T ss_pred CCCeEEEEEEE----cCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHHHHHHHHHHH
Confidence 65544444433 67999999999999999999999999999999999999999998776654444443
No 67
>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=99.32 E-value=1.1e-11 Score=125.20 Aligned_cols=153 Identities=20% Similarity=0.168 Sum_probs=114.5
Q ss_pred cHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCcc
Q 001235 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1117)
Q Consensus 218 ~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~ 297 (1117)
|++++++.+++++++++|+||++||.+++++..-...-.....-.+..+..++.. -+ ...+....+..-.|+|+...|
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 6899999999999999999999999999998776444333222222222222221 11 256666777777788886654
Q ss_pred cccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCC-CCCC
Q 001235 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP-RFVP 376 (1117)
Q Consensus 298 v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p-~~~~ 376 (1117)
- ..+.......++..++|+.+|+..+|+++.|++||..+ |++||.|.++++.| |.|+
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 12223334467889999999999999999999999876 99999999999988 9999
Q ss_pred chhHHHHHHHHHHHHHHH
Q 001235 377 FPLRYACEFLAQVFAIHV 394 (1117)
Q Consensus 377 ~~~r~~~~~l~~~~~~~~ 394 (1117)
.+.+.+++.+++.+++.|
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 999999999999888765
No 68
>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=7.5e-12 Score=117.12 Aligned_cols=102 Identities=22% Similarity=0.277 Sum_probs=87.5
Q ss_pred CeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEec
Q 001235 761 PIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFAR 840 (1117)
Q Consensus 761 ~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~ 840 (1117)
|++++|.+|+|++||+++++++||++++++|+++. .++ .++....+...+.+++.++..+..++.+.++
T Consensus 3 ~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~----------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~ 71 (104)
T PF13426_consen 3 GIFILDPDGRILYVNPAFERLFGYSREELIGKSIS-DFF----------PEEDRPEFEEQIERALEEGGSWSGEVRLRRK 71 (104)
T ss_dssp EEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGG-GGC----------STTSCHHHHHHHHHHHHHTSSEEEEEEEEET
T ss_pred EEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcc-ccc----------CcccchhhHHHHHHHHhcCCceeEEEEEEcC
Confidence 89999999999999999999999999999999853 222 2333455666777777777779999999999
Q ss_pred CCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHH
Q 001235 841 NGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1117)
Q Consensus 841 dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (1117)
+|+.+|+.+++.|+.+.+|++.+++++++|||+
T Consensus 72 ~g~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 72 DGETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp TSEEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred CCCEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 999999999999999999999999999999996
No 69
>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]
Probab=99.29 E-value=2.7e-10 Score=130.12 Aligned_cols=183 Identities=19% Similarity=0.304 Sum_probs=128.7
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHH----HHhcC---CCCHHHHHHHHH----HHHHHHHHHHHHhhccccccccCccccee
Q 001235 893 LKALAYTKRQIRNPLSGIIFSRK----MMEGT---ELGAEQKRLLHT----SAQCQRQLHKILDDSDLDSIIDGYLDLEM 961 (1117)
Q Consensus 893 ~~~la~isHEIrnPL~~I~~~~~----LL~~~---~l~~~~~~~l~~----i~~~~~~l~~ii~dLd~skie~g~~~l~~ 961 (1117)
++.-+.|+.|+...|+-...+++ +|+.. ...++..+.+.. ...|-.+++.++.... +..
T Consensus 370 mEERatIAReLHDSiAQsLS~LkiQvt~L~~~~~~~~~e~s~~~i~~~r~~Ln~~Y~QLRELLtTFR----------ltL 439 (574)
T COG3850 370 MEERATIARELHDSIAQSLSFLKIQVTLLKTAIPEELPEKAREIIAQIRQGLNDAYRQLRELLTTFR----------LTL 439 (574)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------Hhc
Confidence 33455677777777766665544 44432 233444444433 3445556666666422 234
Q ss_pred EEeeHHHHHHHHHHHHHhhhcccCcEEEEe--ecCCCcceeEEec-HHHHHHHHHHHHHHHhhccCCCCeEEEEEEeccc
Q 001235 962 VEFTLNEVLVASISQVMMKSNAKGIRIVNE--TAEQIMSETLYGD-SIRLQQVLADFLSISINFVPNGGQLMVSSSLTKD 1038 (1117)
Q Consensus 962 ~~~~L~~li~~v~~~~~~~~~~~~i~i~~~--~~~~~~~~~v~~D-~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~ 1038 (1117)
.+-+|...+++++..+... .++.++++ .|+. .+..+ +..+-||+.+.++||+||+. +..|.|++....+
T Consensus 440 ~e~~L~~AL~~~~~~f~~q---tg~~~~l~~qlp~~----~lpa~qqvHlLqIvREAlsNa~KHa~-As~i~V~~~~~~g 511 (574)
T COG3850 440 QEAELPPALEQMLAEFSNQ---TGITVTLDYQLPPR----ALPAHQQVHLLQIVREALSNAIKHAQ-ASEIKVTVSQNDG 511 (574)
T ss_pred ccCchHHHHHHHHHHHHhc---cCCeEEEeccCCCC----CCCHHHHHHHHHHHHHHHHHHHHhcc-cCeEEEEEEecCC
Confidence 4567888888888877754 44555554 4443 23333 57788999999999999998 7888888877655
Q ss_pred ccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEe
Q 001235 1039 QLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVE 1112 (1117)
Q Consensus 1039 ~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LP 1112 (1117)
.+.+.|.|||+|||+.. ...| --||.|+++.++.+||.+.+.+.+|+ |.+.|+||
T Consensus 512 ---------~~~~~VeDnG~Gi~~~~---------e~~g-HyGL~IM~ERA~~L~~~L~i~~~~~gGT~V~ltf~ 567 (574)
T COG3850 512 ---------QVTLTVEDNGVGIDEAA---------EPSG-HYGLNIMRERAQRLGGQLRIRRREGGGTEVSLTFP 567 (574)
T ss_pred ---------eEEEEEeeCCcCCCCcc---------CCCC-CcchHHHHHHHHHhcCeEEEeecCCCCeEEEEEec
Confidence 79999999999999862 2223 68999999999999999999999888 99999998
No 70
>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=99.26 E-value=3e-11 Score=114.98 Aligned_cols=112 Identities=28% Similarity=0.341 Sum_probs=90.7
Q ss_pred HHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHh
Q 001235 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAM 825 (1117)
Q Consensus 746 ~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l 825 (1117)
++|+.+++++++ +++++|.+|+|++||+++++++||++++++|+++.+.+. +++.......+...+
T Consensus 1 e~~~~i~~~~~~---~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~-----------~~~~~~~~~~~~~~~ 66 (113)
T PF00989_consen 1 ERYRAILENSPD---GIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIH-----------PEDRRELRERLRQAL 66 (113)
T ss_dssp HHHHHHHHCSSS---EEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCS-----------GGGHHHHHHHHHHHH
T ss_pred CHHHHHHhcCCc---eEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcC-----------chhhHHHHHHHHHHH
Confidence 579999999999 999999999999999999999999999999999754433 333334445555555
Q ss_pred cCCC-CceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHH
Q 001235 826 SGQD-PEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLA 871 (1117)
Q Consensus 826 ~g~~-~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DI 871 (1117)
.... ....+..+..++|+.+|+.+++.|+++.+|++.|++++++||
T Consensus 67 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 67 SQGESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp HHCCHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred HcCCCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 5444 445666666689999999999999999999999999999997
No 71
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=99.25 E-value=2.2e-11 Score=143.76 Aligned_cols=107 Identities=14% Similarity=0.320 Sum_probs=86.5
Q ss_pred EecHHHHHHHHHHHHHHHhhccCCCC---eEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCC----
Q 001235 1002 YGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD---- 1074 (1117)
Q Consensus 1002 ~~D~~~L~qVL~nLl~NAik~~~~~g---~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~---- 1074 (1117)
.++...|.|++.||+.||++|++..| .|.|.+..... + ...+.|.|.|||+|||++.++++|++|+.
T Consensus 31 ~~p~~~L~qVLkNLIeNAIDa~~~~gilp~I~I~I~~~~~--~----~~~~~I~V~DNG~GIp~e~l~~iF~~f~~~SK~ 104 (535)
T PRK04184 31 DNPARALYTTVKELVDNSLDACEEAGILPDIKIEIKRVDE--G----KDHYRVTVEDNGPGIPPEEIPKVFGKLLYGSKF 104 (535)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhhhcCCCceEEEEEEEccC--C----CcEEEEEEEcCCCCCCHHHHHHHhhhhhccccc
Confidence 34567899999999999999997544 57777665311 0 12688999999999999999999999631
Q ss_pred ------CCCccccHHHHHHHHHHcCCE-EEEEeeCCe-E-EEEEEEecc
Q 001235 1075 ------TSEEGISLLISRKLVKLMNGD-VQYLREAGK-S-TFIVSVELA 1114 (1117)
Q Consensus 1075 ------~~GtGLGL~ivr~iVe~~gG~-I~v~s~~g~-t-tF~i~LPl~ 1114 (1117)
.++.|+||++|+.+++.|+|. |++.|.+++ + .|+|+||+.
T Consensus 105 ~~~~~s~G~~GLGLsiv~~isq~~~G~~I~V~S~~~~g~~~~~~~l~id 153 (535)
T PRK04184 105 HNLRQSRGQQGIGISAAVLYAQMTTGKPVRVISSTGGSKKAYYFELKID 153 (535)
T ss_pred cccccCCCCCCcchHHHHHHHHHhcCCcEEEEEecCCCceEEEEEEEec
Confidence 135899999999999999997 999999876 5 899999864
No 72
>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=99.19 E-value=4.8e-11 Score=112.99 Aligned_cols=110 Identities=21% Similarity=0.288 Sum_probs=94.0
Q ss_pred HhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCc
Q 001235 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPE 831 (1117)
Q Consensus 752 ~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~ 831 (1117)
++++|+ +++++|.+|++++||+++.+++|++.++++|+++. +++ .+.....+...+.+++.++...
T Consensus 1 l~~~p~---~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~-~~~----------~~~~~~~~~~~~~~~~~~~~~~ 66 (110)
T PF08448_consen 1 LDSSPD---GIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLF-DLL----------PPEDREEFQAALRRALAGGEPV 66 (110)
T ss_dssp HHHCSS---EEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHH-HHS----------CCGCHHHHHHHHHHHHHHTSEE
T ss_pred CCCCCc---eeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccch-hcc----------ccchhhhhHHHHHHhhccCceE
Confidence 356676 89999999999999999999999999999999965 233 3446777888999999998877
Q ss_pred eEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHH
Q 001235 832 KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQ 876 (1117)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~ 876 (1117)
..+..... +|..+|+.+++.|++|.+|++.|++++++|||++|+
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 999999999999999999999999999999999875
No 73
>PRK13559 hypothetical protein; Provisional
Probab=99.15 E-value=4.8e-10 Score=130.76 Aligned_cols=135 Identities=12% Similarity=0.084 Sum_probs=109.9
Q ss_pred HHHHHHHHHHHhcCccEEEEeC---CCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceee
Q 001235 613 AVTSEMVRLIETATVPILAVDV---DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNI 689 (1117)
Q Consensus 613 ~~~~~l~~lie~a~~gi~~~D~---dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~ 689 (1117)
.+...|+.+++.++++++++|. +|.|++||+++++++||+.++++|+++..+.++.........+..++.++.....
T Consensus 40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (361)
T PRK13559 40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVV 119 (361)
T ss_pred hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEE
Confidence 4467788999999999999997 6689999999999999999999999988777766666666666677766654433
Q ss_pred EEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHH
Q 001235 690 QFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAI 751 (1117)
Q Consensus 690 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i 751 (1117)
++. ..+++|..+|+.++..|+++.+|.+.+++++++|||++|+++++.+..+..++.+
T Consensus 120 e~~----~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~~~~~l~~~l 177 (361)
T PRK13559 120 ELL----NYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEAHERRLAREV 177 (361)
T ss_pred EEE----EEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHHHHHHHHHHH
Confidence 333 3478999999999999999999999999999999999999887665554444443
No 74
>PRK10060 RNase II stability modulator; Provisional
Probab=99.12 E-value=1.3e-09 Score=137.06 Aligned_cols=169 Identities=13% Similarity=0.081 Sum_probs=127.9
Q ss_pred cCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHH
Q 001235 700 INDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMV 779 (1117)
Q Consensus 700 ~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~ 779 (1117)
.+|...|+.....++.+. ...|....+.|+++ ...++......++.+++.+++ +|+++|.+|+|+++|++++
T Consensus 70 ~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~~~~~---gI~i~D~~g~I~~~N~a~~ 141 (663)
T PRK10060 70 LDGEPLSVHLVGRKINKR--EWAGTASAWHDTPS---VARDLSHGLSFAEQVVSEANS---VIVILDSRGNIQRFNRLCE 141 (663)
T ss_pred eCCcEEEEEEeeeccCcc--cccchhhHHHHHHH---HHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEEcHHHH
Confidence 379999999876665432 34444555556565 444456667788899999998 8999999999999999999
Q ss_pred HhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCC
Q 001235 780 KLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREG 859 (1117)
Q Consensus 780 ~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G 859 (1117)
+++||+.++++|+++...+ .++++...+...+...+..+..+..++.+.+++|+..|+.....+ .+.+|
T Consensus 142 ~l~Gy~~~eliG~~~~~l~----------~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~~-~~~~g 210 (663)
T PRK10060 142 EYTGLKEHDVIGQSVFKLF----------MSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKFV-HSGSG 210 (663)
T ss_pred HHHCcCHHHHcCCCHHHHh----------CChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeEE-EcCCC
Confidence 9999999999999864322 234444555566677777778888999999999999988766444 44444
Q ss_pred -CEEEEEeehhHHHHHHHHHHHHHHHHHH
Q 001235 860 -AVTGVFCFLQLASHELQQALHVQRLSEQ 887 (1117)
Q Consensus 860 -~v~g~v~i~~DITerk~~e~el~~~ae~ 887 (1117)
...+++++.+|||++++.++++++++..
T Consensus 211 ~~~~~~i~~~~DITe~k~~e~~l~~~a~~ 239 (663)
T PRK10060 211 KNEIFLICSGTDITEERRAQERLRILANT 239 (663)
T ss_pred CceEEEEEEEEechHHHHHHHHHHHHhhc
Confidence 4567889999999999999887776554
No 75
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=99.11 E-value=3.7e-09 Score=118.90 Aligned_cols=130 Identities=17% Similarity=0.227 Sum_probs=100.4
Q ss_pred eEEeeHHHHHHHHHHHHHhhhc--ccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhcc----CCCCeEEEEEE
Q 001235 961 MVEFTLNEVLVASISQVMMKSN--AKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV----PNGGQLMVSSS 1034 (1117)
Q Consensus 961 ~~~~~L~~li~~v~~~~~~~~~--~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~----~~~g~I~I~v~ 1034 (1117)
...+.|.+=++++-..+...-. .....+.+++++++.+ + .-|. -+++-|+.||+||+ .+.|.|+|++.
T Consensus 414 ~~~v~L~kEl~~v~AYl~IEkARF~~rL~v~i~id~~l~~--~-~iP~---filQPLVENAIKHG~~~~~~~g~V~I~V~ 487 (557)
T COG3275 414 QEIVTLSKELEHVNAYLSIEKARFGDRLDVVIDIDEELRQ--V-QIPS---FILQPLVENAIKHGISQLKDTGRVTISVE 487 (557)
T ss_pred ceEeehHHHHHHHHHHHHHHHHhcCCceEEEEecCHHHhh--c-cCch---hhhhHHHHHHHHhcccchhcCCceEEEEE
Confidence 4577888888877766655222 2336777777776532 1 2233 24566888999997 23789999999
Q ss_pred ecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCC---EEEEEeeCCe-EEEEEE
Q 001235 1035 LTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNG---DVQYLREAGK-STFIVS 1110 (1117)
Q Consensus 1035 ~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG---~I~v~s~~g~-ttF~i~ 1110 (1117)
..+. .+.+.|+|||.|++++ +..|+|+||+.+++.++.+=| -+++.+.+.. |+++++
T Consensus 488 ~~d~---------~l~i~VeDng~li~p~----------~~~g~giGL~nv~~RLk~lyG~~~gl~i~~~~q~gTri~f~ 548 (557)
T COG3275 488 KEDA---------DLRIEVEDNGGLIQPD----------EEDGTGIGLANVHKRLKLLYGDDEGLHIESLEQAGTRIIFR 548 (557)
T ss_pred EeCC---------eEEEEEecCCCCcCCC----------CCCCCChHHHHHHHHHHHhcCccccceEEeccCCCcEEEEE
Confidence 9887 8999999999999985 456899999999999999888 7999999885 999999
Q ss_pred EeccC
Q 001235 1111 VELAA 1115 (1117)
Q Consensus 1111 LPl~~ 1115 (1117)
+|...
T Consensus 549 lp~~~ 553 (557)
T COG3275 549 LPLQR 553 (557)
T ss_pred ecCcc
Confidence 99864
No 76
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=99.10 E-value=4.7e-10 Score=134.73 Aligned_cols=120 Identities=13% Similarity=0.160 Sum_probs=84.2
Q ss_pred cCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCC---eEEEEEEecccccccccceeEEEEEEeecCCCC
Q 001235 984 KGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGI 1060 (1117)
Q Consensus 984 ~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g---~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI 1060 (1117)
+.+.+..-+..+....-...|...|.++|.|||.||++|++.+| .|.|.+..... ++.|.|.|||+||
T Consensus 23 ~~iS~aEfF~kN~~~lgfD~d~r~L~tVLkNLIeNALDAs~~~gilp~I~V~Ie~~g~---------~v~I~VeDNG~GI 93 (795)
T PRK14868 23 REISIAEFFEKNKHMLGFDSGARGLVTAVKEAVDNALDATEEAGILPDIYVEIEEVGD---------YYRLVVEDNGPGI 93 (795)
T ss_pred cccceeeecccCcceeeccCCHHHHHHHHHHHHHHHHHhCcccCCCceEEEEEEECCC---------EEEEEEEEcCCCC
Confidence 44555555555543222234577899999999999999997654 68887766554 7899999999999
Q ss_pred ChhhhhhccCCCC-C---------C--CCccccHHHHHHHHHHcCCEEEEEeeCCe--EEEEEEEec
Q 001235 1061 PEPLLDQMFGSEG-D---------T--SEEGISLLISRKLVKLMNGDVQYLREAGK--STFIVSVEL 1113 (1117)
Q Consensus 1061 ~~e~~~~iFe~f~-~---------~--~GtGLGL~ivr~iVe~~gG~I~v~s~~g~--ttF~i~LPl 1113 (1117)
|++.++++|++|+ + . .|.||||++++..+ .+||.|.+.|..++ ..+.+.|++
T Consensus 94 p~EdLp~IFerf~~tSKf~~~~~srG~rG~GLglai~~sql-t~GgpI~I~S~~~~~~~g~~~~L~I 159 (795)
T PRK14868 94 TKEQIPKVFGKLLYGSRFHAREQSRGQQGIGISAAVLYSQL-TSGKPAKITSRTQGSEEAQYFELII 159 (795)
T ss_pred CHHHHHHHhhhhcccccccccccCCCCCceehHHHHHHHHH-cCCCcEEEEeCCCCCCceeEEEEEE
Confidence 9999999999863 1 1 24555555555555 37899999998654 344344443
No 77
>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=99.10 E-value=7.3e-10 Score=102.73 Aligned_cols=95 Identities=37% Similarity=0.614 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHHhhccCC-CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCC------CCCCCccc
Q 001235 1008 LQQVLADFLSISINFVPN-GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSE------GDTSEEGI 1080 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~~-~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f------~~~~GtGL 1080 (1117)
|.+++.+++.||++|... ++.|.|.+..... .+.|.|.|+|.|+++...+.+|.++ ....+.|+
T Consensus 1 l~~~~~~ll~Na~~~~~~~~~~v~i~~~~~~~---------~~~v~i~d~g~g~~~~~~~~~~~~~~~~~~~~~~~~~g~ 71 (103)
T cd00075 1 LQQVLLNLLSNAIKHTPEGGGRITISVERDGD---------HLEIRVEDNGPGIPEEDLERIFERFSDGSRSRKGGGTGL 71 (103)
T ss_pred CHHHHHHHHHHHHHhCcCCCCeEEEEEEecCC---------EEEEEEEeCCCCCCHHHHHHHhhhhhcCCCCCCCCcccc
Confidence 458999999999999975 6788888877665 7999999999999999999999864 12347899
Q ss_pred cHHHHHHHHHHcCCEEEEEeeC-CeEEEEEEE
Q 001235 1081 SLLISRKLVKLMNGDVQYLREA-GKSTFIVSV 1111 (1117)
Q Consensus 1081 GL~ivr~iVe~~gG~I~v~s~~-g~ttF~i~L 1111 (1117)
||++|+++++.|||.+++.+.. ++++|++++
T Consensus 72 gl~~~~~~~~~~~g~~~~~~~~~~g~~~~~~~ 103 (103)
T cd00075 72 GLSIVKKLVELHGGRIEVESEPGGGTTFTITL 103 (103)
T ss_pred CHHHHHHHHHHcCCEEEEEeCCCCcEEEEEEC
Confidence 9999999999999999999987 448887764
No 78
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=99.08 E-value=3e-11 Score=152.22 Aligned_cols=217 Identities=26% Similarity=0.309 Sum_probs=187.2
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeEEeeHHHHHHHH
Q 001235 895 ALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMVEFTLNEVLVAS 973 (1117)
Q Consensus 895 ~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v 973 (1117)
+.+.++||||.|+++ ++...+-.+..+.+++.++.....+......++++ +|.++++.|..++...+|++..+++.+
T Consensus 224 ~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g~~~l~~~rf~l~~ll~~~ 301 (786)
T KOG0519|consen 224 FLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESGKGELVAKRFDLRTLLNFV 301 (786)
T ss_pred hcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccccceeeeeecchHhhhhhh
Confidence 788999999999998 66666777888999999999999999999999999 699999999999999999999999999
Q ss_pred HHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccc------------
Q 001235 974 ISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLG------------ 1041 (1117)
Q Consensus 974 ~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~------------ 1041 (1117)
++.+...+..++..+....+...| ..+.+|..++.||+.|++.||+|++. .|.|.+++........
T Consensus 302 ~~~~~e~~~~~~~~l~~~~~~~~p-~~v~~de~~~~qv~~n~v~naik~t~-~~~i~~~~~~~~~~~~~~~~l~~~~~e~ 379 (786)
T KOG0519|consen 302 ISLLSELSQAKYAILVLDLSSGVP-RNVRGDEARLRQVIANLVSNAIKFTH-AGHLEESVIAREELSESNDVLLRAKEEA 379 (786)
T ss_pred hhhhHHHhhcCCeEEEEecCCCCc-ceeeccceeeeeeehhhccceecccc-cceEEEEEEeehhcchhhHHHHhhhhhh
Confidence 999999999999999999888865 48999999999999999999999997 6666666655444100
Q ss_pred ---c------------c----cc--------eeEEEEEEeecCCCCChhhhhh-ccCCC--------CCCCCccccHHHH
Q 001235 1042 ---Q------------S----VH--------LAYLELRITHAGGGIPEPLLDQ-MFGSE--------GDTSEEGISLLIS 1085 (1117)
Q Consensus 1042 ---~------------~----~~--------~~~l~i~V~D~G~GI~~e~~~~-iFe~f--------~~~~GtGLGL~iv 1085 (1117)
. + .+ .....+.+.|+|.||+.+.... +|..| +..+|+|+|+.++
T Consensus 380 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~~~~~~~~~gt~~~~~i~ 459 (786)
T KOG0519|consen 380 HMAGKARIDFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPDSGLEIQTVMRSSNVFTSLIQADPDITRLYGGTGLGESIV 459 (786)
T ss_pred hhccchhhhHHHHhccccccccccccccchhhHhheEeccCCceeEehhhhhhhHHHHHhccccccccccCCCcccchhh
Confidence 0 0 00 1345678899999999998887 89886 3456999999999
Q ss_pred HHHHHHcCCEEEEEeeCCe-EEEEEEEeccC
Q 001235 1086 RKLVKLMNGDVQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1086 r~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
+.+++.|+|.+.+.+.+.. ++|++.+++..
T Consensus 460 ~~l~~l~~~~~~~~~~~~~~~t~~~~~~~~~ 490 (786)
T KOG0519|consen 460 FSLVELMSGEISDISCISLGKTFSFTLDLLT 490 (786)
T ss_pred ccHHHHHHHHhhhhhhhccCceeeEEEEecc
Confidence 9999999999999999986 99999998865
No 79
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.07 E-value=1.3e-09 Score=137.66 Aligned_cols=138 Identities=17% Similarity=0.165 Sum_probs=116.3
Q ss_pred HHHHHHHHhcCccEEEEe---CCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEE
Q 001235 616 SEMVRLIETATVPILAVD---VDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFE 692 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D---~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~ 692 (1117)
+.++.+++.++.+++.+| .+|.+++||+++++++||+.++++|+++..+.++.........+...+.++.....+++
T Consensus 148 r~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 227 (665)
T PRK13558 148 RLKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELR 227 (665)
T ss_pred HHHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEE
Confidence 345679999999999998 47999999999999999999999999998888877766666666666665554444443
Q ss_pred EEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCC
Q 001235 693 IKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNP 757 (1117)
Q Consensus 693 ~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~ 757 (1117)
. .+++|..+|+.++..|+++.+|.+.+++++++|||++|++|+++++.+..++.+++..+.
T Consensus 228 ~----~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~~ 288 (665)
T PRK13558 228 N----YRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVEG 288 (665)
T ss_pred E----ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3 478999999999999999999999999999999999999999999988888877765543
No 80
>PRK13557 histidine kinase; Provisional
Probab=99.07 E-value=1.2e-09 Score=134.34 Aligned_cols=131 Identities=13% Similarity=0.131 Sum_probs=108.8
Q ss_pred HHHHHHHHHHHHHhcCccEEEEeC---CCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcce
Q 001235 611 LEAVTSEMVRLIETATVPILAVDV---DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQ 687 (1117)
Q Consensus 611 L~~~~~~l~~lie~a~~gi~~~D~---dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~ 687 (1117)
.......|+.++++++++++++|. +|+|+++|+++++++||+.++++|+++..++++++.......+...+..+...
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 345578899999999999999995 78999999999999999999999999999888776666555565555444433
Q ss_pred eeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHH
Q 001235 688 NIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIE 745 (1117)
Q Consensus 688 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se 745 (1117)
..++. ..+++|..+|+.++..|+++.+|.+.+++++.+|||+++++++++...+
T Consensus 105 ~~~~~----~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~ 158 (540)
T PRK13557 105 ATEIL----NYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQ 158 (540)
T ss_pred eEEEE----EEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHH
Confidence 32322 3368999999999999999999999999999999999999998876544
No 81
>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=99.05 E-value=1.3e-09 Score=108.47 Aligned_cols=94 Identities=14% Similarity=0.219 Sum_probs=77.2
Q ss_pred ecHHHHHHHHHHHHHHHhhccC---CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCC---
Q 001235 1003 GDSIRLQQVLADFLSISINFVP---NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS--- 1076 (1117)
Q Consensus 1003 ~D~~~L~qVL~nLl~NAik~~~---~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~--- 1076 (1117)
.+...|.+++.|++.||++|+- .++.|.|++...++ .+.|+|.|+|.|||+ ..++|+||++.+
T Consensus 35 ~~~~~l~~~l~eli~Nai~h~~~~~~~~~I~v~~~~~~~---------~~~i~I~D~G~gi~~--~~~~~~~~~~~~~~~ 103 (137)
T TIGR01925 35 EELTDIKTAVSEAVTNAIIHGYEENCEGVVYISATIEDH---------EVYITVRDEGIGIEN--LEEAREPLYTSKPEL 103 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEEeCC---------EEEEEEEEcCCCcCc--hhHhhCCCcccCCCC
Confidence 4566789999999999999862 25789998887766 799999999999984 668999986443
Q ss_pred -CccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEE
Q 001235 1077 -EEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSV 1111 (1117)
Q Consensus 1077 -GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~L 1111 (1117)
+.|+||+++++ +.+++++.+.+++ ++|+++.
T Consensus 104 ~~~GlGL~lv~~----~~~~l~~~~~~~~Gt~v~i~~ 136 (137)
T TIGR01925 104 ERSGMGFTVMEN----FMDDVSVDSEKEKGTKIIMKK 136 (137)
T ss_pred CCCcccHHHHHH----hCCcEEEEECCCCCeEEEEEe
Confidence 78999999866 5579999998877 8888863
No 82
>PRK10060 RNase II stability modulator; Provisional
Probab=99.04 E-value=3.4e-09 Score=133.24 Aligned_cols=163 Identities=16% Similarity=0.154 Sum_probs=117.5
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCcccccc-ccCcHHHHHHHHHHHHcCCccee
Q 001235 610 ELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLV-EDSSIDTVKRMLYLALQGQEEQN 688 (1117)
Q Consensus 610 eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv-~~~~~~~~~~~l~~~l~g~~~~~ 688 (1117)
+++.....++.+++.++++|+++|.+|+|+++|+++++++||+.++++|+++.+++ ++.+.......+...+..+..+.
T Consensus 105 ~~~~~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (663)
T PRK10060 105 DLSHGLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYE 184 (663)
T ss_pred HHHHHHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceE
Confidence 34555667888999999999999999999999999999999999999999998765 55556666667777776665544
Q ss_pred eEEEEEeeccccCCceEEEEEEEEEeecCCC-CEEEEEEEEEccchhhhhhhhHhhH---------------HHHHHHHH
Q 001235 689 IQFEIKTHGSKINDDPITLIVNACASRDLHD-NVVGVCFVAQDITPQKTVMDKFTRI---------------EGDYKAIV 752 (1117)
Q Consensus 689 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G-~v~gv~~v~~DITerK~aE~~L~~s---------------e~~l~~i~ 752 (1117)
.+..+ .+++|..+|+..+.. +.+.+| ...+++++++|||++|++++++++. .++++..+
T Consensus 185 ~e~~~----~~~~G~~~~~~~~~~-~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~~l~~~l 259 (663)
T PRK10060 185 VERWI----KTRKGQRLFLFRNKF-VHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAI 259 (663)
T ss_pred EEEEE----EeCCCCEEEEEeeeE-EEcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHHHHHHHH
Confidence 44444 477898888765544 444444 4567888999999999999988763 34555554
Q ss_pred hCCCCCCCCeeeeCCCCceeechhhH
Q 001235 753 QNPNPLIPPIFGSDEFGWCCEWNPAM 778 (1117)
Q Consensus 753 ~~~~~li~~I~~~D~~g~i~~~N~a~ 778 (1117)
........+++.+|.++- ..+|..+
T Consensus 260 ~~~~~~~~~ll~idld~f-k~iNd~~ 284 (663)
T PRK10060 260 NAADNNQVGIVYLDLDNF-KKVNDAY 284 (663)
T ss_pred HhCCCCcEEEEEEECcch-hHHHHhh
Confidence 333222225777777643 3455544
No 83
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=99.03 E-value=2.3e-09 Score=98.90 Aligned_cols=120 Identities=20% Similarity=0.336 Sum_probs=99.7
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc-ceeeEEEEE
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-EQNIQFEIK 694 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~-~~~~e~~~~ 694 (1117)
+.++.+++.++.+++++|.+|.++++|+++++++|++..+++|+++.+++++.+.......+..+..++. .....+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 81 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERRV- 81 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEeee-
Confidence 4567899999999999999999999999999999999999999999998888887777777777766332 22222222
Q ss_pred eeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhh
Q 001235 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1117)
Q Consensus 695 ~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~ 740 (1117)
...+|..+|+..+..|+. .+|...+++++++|||++++++++
T Consensus 82 ---~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 82 ---RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred ---EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhc
Confidence 256789999999999998 889999999999999999998765
No 84
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=99.02 E-value=1.5e-09 Score=127.21 Aligned_cols=99 Identities=18% Similarity=0.359 Sum_probs=81.4
Q ss_pred EEecHHHHHHHHHHHHHHHhhccCCCC---eEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCC---
Q 001235 1001 LYGDSIRLQQVLADFLSISINFVPNGG---QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD--- 1074 (1117)
Q Consensus 1001 v~~D~~~L~qVL~nLl~NAik~~~~~g---~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~--- 1074 (1117)
..++...|.+++.||+.||++|+...| .|.|.+...+. .++.|+|.|||+|||++.++++|++|+.
T Consensus 22 f~~~~~~L~~VlkELVeNAIDA~~~~g~~p~I~V~i~~~g~--------~~~~I~V~DNG~GIp~edl~~iF~rf~~tsK 93 (488)
T TIGR01052 22 YSGKIRSLTTVIHELVTNSLDACEEAGILPDIKVEIEKIGK--------DHYKVTVEDNGPGIPEEYIPKVFGKMLAGSK 93 (488)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhhccCCCceEEEEEEECCC--------ceEEEEEEECCCCCCHHHHHhhhhhccccCc
Confidence 456788999999999999999987544 67777665322 1678999999999999999999999631
Q ss_pred -------CCCccccHHHHHHHHHHcCCE-EEEEeeCCeEEE
Q 001235 1075 -------TSEEGISLLISRKLVKLMNGD-VQYLREAGKSTF 1107 (1117)
Q Consensus 1075 -------~~GtGLGL~ivr~iVe~~gG~-I~v~s~~g~ttF 1107 (1117)
.++.|+||+++..+++.|+|. +++.|..++..|
T Consensus 94 ~~~~~~s~G~~GlGLs~~~~isq~~~G~~i~V~S~~~g~~~ 134 (488)
T TIGR01052 94 FHRIIQSRGQQGIGISGAVLYSQMTTGKPVKVISSTGGEIY 134 (488)
T ss_pred cccccccCCCccEehhHHHHHHHHcCCceEEEEEecCCceE
Confidence 136899999999999999999 999998766444
No 85
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=99.00 E-value=1.1e-08 Score=118.38 Aligned_cols=227 Identities=19% Similarity=0.228 Sum_probs=163.2
Q ss_pred HHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeecc
Q 001235 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGS 698 (1117)
Q Consensus 619 ~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~ 698 (1117)
..+++..+++++++|....+..+|..+..+++-....++|+++.+++++...+.+. +++.. .....+.
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 34889999999999999999999999999999999999999999888776665443 22221 1112221
Q ss_pred ccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhH-hhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhh
Q 001235 699 KINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF-TRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPA 777 (1117)
Q Consensus 699 ~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L-~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a 777 (1117)
.+ . .-..+...++.++.++++|+..++.|+++....-++. ++....|+.+++.+.+ ++++.|.+|.++++|++
T Consensus 72 ~~--~-~~~~~~~~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~---~l~vvD~~G~~i~~N~~ 145 (560)
T COG3829 72 LK--V-KRIVVVGKTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDD---GLLVVDEDGIIIYYNKA 145 (560)
T ss_pred cc--c-eeEEEcCCceeecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhccC---ceEEEcCCCcEEEEcHH
Confidence 11 1 3344555666788999999999999999987776665 7777899999999999 99999999999999999
Q ss_pred HHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCC
Q 001235 778 MVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDR 857 (1117)
Q Consensus 778 ~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~ 857 (1117)
+.+++|++.++++|+++.+.+ ... .+ ..+..++..+.+.... .....|... ..+..|++ .
T Consensus 146 ~~~~~gl~~e~~~gk~~~~v~-~~~--------~~------s~~l~vl~~~kp~~~~--~~~~~~~~~--i~~~~pv~-~ 205 (560)
T COG3829 146 YAKLLGLSPEEVLGKHLLDVV-SAG--------ED------STLLEVLRTGKPIRDV--VQTYNGNKI--IVNVAPVY-A 205 (560)
T ss_pred HHHHhCCCHHHHcCCcHHHHH-hcc--------CC------ceehhhhhcCCcceee--eeeecCCce--eEeeccEe-c
Confidence 999999999999999764333 110 00 0112223333332221 222223322 34455554 6
Q ss_pred CCCEEEEEeehhHHHHHHHHHHHHHH
Q 001235 858 EGAVTGVFCFLQLASHELQQALHVQR 883 (1117)
Q Consensus 858 ~G~v~g~v~i~~DITerk~~e~el~~ 883 (1117)
+|.+.|.+++++|+++-.....+..+
T Consensus 206 ~g~l~G~v~~~~~~~~l~~l~~~~~~ 231 (560)
T COG3829 206 DGQLIGVVGISKDVSELERLTRELEE 231 (560)
T ss_pred CCcEEEEEEeecchHHHHHHHHHHHH
Confidence 77999999999999987776655544
No 86
>PRK03660 anti-sigma F factor; Provisional
Probab=98.98 E-value=4.5e-09 Score=105.93 Aligned_cols=99 Identities=15% Similarity=0.292 Sum_probs=80.1
Q ss_pred ecHHHHHHHHHHHHHHHhhccCC---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCC----
Q 001235 1003 GDSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT---- 1075 (1117)
Q Consensus 1003 ~D~~~L~qVL~nLl~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~---- 1075 (1117)
.|...+.+++.|++.||++|+.. ++.|.|++...++ .+.|.|.|+|.|||+ ..+.|++|+..
T Consensus 35 ~~~~~l~~~l~eli~Nai~h~~~~~~~~~i~i~~~~~~~---------~l~i~I~D~G~g~~~--~~~~~~~~~~~~~~~ 103 (146)
T PRK03660 35 EELTEIKTAVSEAVTNAIIHGYENNPDGVVYIEVEIEEE---------ELEITVRDEGKGIED--IEEAMQPLYTTKPEL 103 (146)
T ss_pred HHHHhHHHHHHHHHHHHHHHhcCCCCCCEEEEEEEECCC---------EEEEEEEEccCCCCh--HHHhhCCCcccCCCC
Confidence 35677899999999999998742 3678888776655 799999999999986 55788887543
Q ss_pred CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEeccCC
Q 001235 1076 SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus 1076 ~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
.+.|+||+++++ +.+.+++.+.+++ ++|+|++++...
T Consensus 104 ~~~GlGL~i~~~----~~~~i~~~~~~~~Gt~~~i~~~~~~~ 141 (146)
T PRK03660 104 ERSGMGFTVMES----FMDEVEVESEPGKGTTVRMKKYLKKS 141 (146)
T ss_pred CCccccHHHHHH----hCCeEEEEecCCCcEEEEEEEEeccc
Confidence 368999999864 5678999998877 999999998764
No 87
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=98.97 E-value=3e-09 Score=128.14 Aligned_cols=105 Identities=12% Similarity=0.260 Sum_probs=84.1
Q ss_pred EecHHH---HHHHHHHHHHHHhhccCCCC---eEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCC
Q 001235 1002 YGDSIR---LQQVLADFLSISINFVPNGG---QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDT 1075 (1117)
Q Consensus 1002 ~~D~~~---L~qVL~nLl~NAik~~~~~g---~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~ 1075 (1117)
.|+... |.+++.||+.||+++....+ .|.|.+...+. ..+.|+|.|||+|||++.++++|++|+.+
T Consensus 28 lGf~~~~r~L~~VVkELVeNAIDA~~~~g~~p~I~V~I~~~g~--------~~~~I~V~DNG~GIp~e~l~~iFerF~at 99 (659)
T PRK14867 28 LGYSGKLRSMTTIIHELVTNSLDACEEAEILPDIKVEIEKLGS--------DHYKVAVEDNGPGIPPEFVPKVFGKMLAG 99 (659)
T ss_pred eechhHHHHHHHHHHHHHHHHHHHhhccCCCceEEEEEEECCC--------cEEEEEEEeeCeeCCHHHHhhhhcccccc
Confidence 344444 45999999999999987533 78887765432 26899999999999999999999997431
Q ss_pred ----------CCccccHHHHHHHHHHc-CCEEEEEeeCCe-EEEEEEEecc
Q 001235 1076 ----------SEEGISLLISRKLVKLM-NGDVQYLREAGK-STFIVSVELA 1114 (1117)
Q Consensus 1076 ----------~GtGLGL~ivr~iVe~~-gG~I~v~s~~g~-ttF~i~LPl~ 1114 (1117)
++.|+||+++..+.+.+ ||.+.+.|.++. ++|++.+|+.
T Consensus 100 SK~~~~~qS~G~rG~GLa~a~~vsql~~G~pI~I~S~~g~G~~f~i~L~i~ 150 (659)
T PRK14867 100 SKMHRLIQSRGQQGIGAAGVLLFSQITTGKPLKITTSTGDGKIHEMEIKMS 150 (659)
T ss_pred CcccceeccCCCCcccHHHHHHHHHHhcCCcEEEEEEcCCCEEEEEEEEEE
Confidence 26899999999999875 666999998776 8899998883
No 88
>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=98.97 E-value=1.5e-08 Score=99.36 Aligned_cols=139 Identities=29% Similarity=0.371 Sum_probs=110.6
Q ss_pred cHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCcc
Q 001235 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1117)
Q Consensus 218 ~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~ 297 (1117)
|++++++.+++.+.+++++||+.||.++++..+............+..+..+|..+ ...+.++..+....+.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999888888887776555556677788766 4567777778777787765443
Q ss_pred cccccCCCCCCcccccCCcccCCChhHHHHHHhc-CceeEEEEEEEEcCCccccCCCcccccccceeeEEeecc-CCCCC
Q 001235 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENM-NSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNT-TPRFV 375 (1117)
Q Consensus 298 v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~-~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~-~p~~~ 375 (1117)
.+ . ..+...+ |+++.+++||..+ +++||+|.+.++ .++.|
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 1122233 3899999999977 999999999998 79999
Q ss_pred CchhHHHHHHHHHHHHHHHHH
Q 001235 376 PFPLRYACEFLAQVFAIHVNK 396 (1117)
Q Consensus 376 ~~~~r~~~~~l~~~~~~~~~~ 396 (1117)
+...+..++.+++.++..|..
T Consensus 121 ~~~~~~~l~~~~~~i~~~l~~ 141 (149)
T smart00065 121 TEEDEELLQALANQLAIALAN 141 (149)
T ss_pred CHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999888754
No 89
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.91 E-value=5.2e-08 Score=126.02 Aligned_cols=124 Identities=15% Similarity=0.179 Sum_probs=100.8
Q ss_pred HHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccc-cCcHHHHHHHHHHHHcCCcceeeEEE
Q 001235 614 VTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVE-DSSIDTVKRMLYLALQGQEEQNIQFE 692 (1117)
Q Consensus 614 ~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~-~~~~~~~~~~l~~~l~g~~~~~~e~~ 692 (1117)
.++.+..+++.++++++.+|.+|+++++|+++++++||+.++++|+++.++++ +.+.......+.....++.....++.
T Consensus 134 ~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 213 (799)
T PRK11359 134 QTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFL 213 (799)
T ss_pred HHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeE
Confidence 34556678999999999999999999999999999999999999999987764 44444455555556555444333443
Q ss_pred EEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhH
Q 001235 693 IKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1117)
Q Consensus 693 ~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L 741 (1117)
. .+++|..+|+.++..|+.+.+|.+.+++++.+|||++|++++..
T Consensus 214 ~----~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~ 258 (799)
T PRK11359 214 L----LTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLE 258 (799)
T ss_pred E----eCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHH
Confidence 3 36789999999999999999999999999999999999887544
No 90
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.86 E-value=1.6e-08 Score=95.83 Aligned_cols=106 Identities=23% Similarity=0.312 Sum_probs=83.0
Q ss_pred HHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeec
Q 001235 618 MVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHG 697 (1117)
Q Consensus 618 l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~ 697 (1117)
+..++++++.++.++|.+++|.++|+++.++|++...+ +|+++.++.++...+.+...+..+..|+.. ..+....
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 46789999999999999999999999999999987655 799999999998888899999888888763 2222222
Q ss_pred cccCCceEEEEEEEEEeecCCCCEEEEEEEEEccc
Q 001235 698 SKINDDPITLIVNACASRDLHDNVVGVCFVAQDIT 732 (1117)
Q Consensus 698 ~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DIT 732 (1117)
.+.+|+.++..|++|.+|+..|++.++.|||
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 4467889999999999999999999999998
No 91
>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]
Probab=98.83 E-value=2.1e-07 Score=111.72 Aligned_cols=184 Identities=17% Similarity=0.233 Sum_probs=114.8
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeH-HHHHHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTL-NEVLVASI 974 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L-~~li~~v~ 974 (1117)
....-|.+.|-|++|..++..-. .....+. ...+.++.+ .++.+.. +..+... ..+++..+
T Consensus 263 sqi~pHfL~NtL~~I~~~~~~~~-------~~~~~~~----v~~l~~llR-~~l~~~~------~~~~l~~E~~~~~kyl 324 (456)
T COG2972 263 SQINPHFLYNTLETIRMLAEEDD-------PEEAAKV----VKALSKLLR-YSLSNLD------NIVTLEIELLLIEKYL 324 (456)
T ss_pred hhcchHHHHhHHHHHHHHHHhcC-------HHHHHHH----HHHHHHHHH-HHhhCCC------CeeeHHHHHHHHHHHH
Confidence 34457999999999987765321 1222222 223333333 1112111 1111111 12222322
Q ss_pred HHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhcc----CCCCeEEEEEEecccccccccceeEEE
Q 001235 975 SQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFV----PNGGQLMVSSSLTKDQLGQSVHLAYLE 1050 (1117)
Q Consensus 975 ~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~----~~~g~I~I~v~~~~~~~~~~~~~~~l~ 1050 (1117)
..-..... ..+++..++++... -..||. .+++.|+.||++|+ +++|+|.|.....++ .+.
T Consensus 325 ~iq~~r~~-~~le~~~~i~~~~~---~l~~p~---l~lqpLvENAi~hgi~~~~~~~~I~i~~~~~~~---------~i~ 388 (456)
T COG2972 325 EIQKLRIG-DRLEVPLPIDEELE---PLIDPK---LVLQPLVENAIEHGIEPKRPGGSIAISAKKQDD---------VIQ 388 (456)
T ss_pred HHHHhccC-cceEEEeccCcccc---cccCch---HHHhHHHHHHHHHhcccCCCCCEEEEEEEEcCC---------EEE
Confidence 22222222 22455555555432 135544 67788999999998 347799998888766 899
Q ss_pred EEEeecCCCCChhhhhhccCCCCCCCCccccHHHHHHHHHHcCCE--EEEEeeCCe-EEEEEEEeccC
Q 001235 1051 LRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGD--VQYLREAGK-STFIVSVELAA 1115 (1117)
Q Consensus 1051 i~V~D~G~GI~~e~~~~iFe~f~~~~GtGLGL~ivr~iVe~~gG~--I~v~s~~g~-ttF~i~LPl~~ 1115 (1117)
++|+|||+||+++....+...-... .|+||.-++++++.+-|. +.++|.+++ |+..+.+|...
T Consensus 389 i~i~Dng~g~~~~~~~~~~~~~~~r--~giGL~Nv~~rl~~~~g~~~~~i~s~~~~gt~v~~~~~~~~ 454 (456)
T COG2972 389 ISISDNGPGIDEEKLEGLSTKGENR--SGIGLSNVKERLKLYFGEPGLSIDSQPGKGTFVQIIIPKRE 454 (456)
T ss_pred EEEeeCCCCCChhHHHHHHhhccCc--ccccHHHHHHHHHHeeCCcceeEeecCCCcEEEEEEeehhh
Confidence 9999999999998766544332111 499999999999999888 689999998 99999999764
No 92
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=98.82 E-value=3.5e-08 Score=101.08 Aligned_cols=98 Identities=14% Similarity=0.218 Sum_probs=78.3
Q ss_pred ecHHHHHHHHHHHHHHHhhccCC---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCC-----
Q 001235 1003 GDSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGD----- 1074 (1117)
Q Consensus 1003 ~D~~~L~qVL~nLl~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~----- 1074 (1117)
.+...+..++.+++.||++|+.. ++.|.|++....+ .+.|.|+|+|+||+++.....|.||+.
T Consensus 38 ~~~~~l~lav~Ea~~Nai~Hg~~~~~~~~I~I~~~~~~~---------~l~i~V~D~G~g~d~~~~~~~~~p~~~~~~~~ 108 (161)
T PRK04069 38 DDIEDMKIAVSEACTNAVQHAYKEDEVGEIHIRFEIYED---------RLEIVVADNGVSFDYETLKSKLGPYDISKPIE 108 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCCeEEEEEEEECC---------EEEEEEEECCcCCChHHhccccCCCCCCCccc
Confidence 34566888999999999999853 4688888887766 899999999999999988888888742
Q ss_pred -CCCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEecc
Q 001235 1075 -TSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELA 1114 (1117)
Q Consensus 1075 -~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl~ 1114 (1117)
..+.|+||++++.+++. +++.+. ++++|.+.-.+.
T Consensus 109 ~~~~~G~GL~li~~l~d~----v~~~~~-~G~~v~~~k~~~ 144 (161)
T PRK04069 109 DLREGGLGLFLIETLMDD----VTVYKD-SGVTVSMTKYIN 144 (161)
T ss_pred ccCCCceeHHHHHHHHHh----EEEEcC-CCcEEEEEEEcC
Confidence 23679999999999986 777764 446777766554
No 93
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.81 E-value=6.1e-08 Score=122.67 Aligned_cols=124 Identities=18% Similarity=0.154 Sum_probs=102.0
Q ss_pred HHHHHHhCCCCCCCCeeeeC---CCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHH
Q 001235 747 DYKAIVQNPNPLIPPIFGSD---EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNK 823 (1117)
Q Consensus 747 ~l~~i~~~~~~li~~I~~~D---~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~ 823 (1117)
.++.+++..+. +++..| .+|.+++||+++++++||++++++|+.+.. +.+++........+..
T Consensus 149 ~~~~~~~~~~~---gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~-----------l~~~~~~~~~~~~~~~ 214 (665)
T PRK13558 149 LKERALDEAPV---GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRF-----------LQGEDTNEERVAELRE 214 (665)
T ss_pred HHHHHHhcCCc---cEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHH-----------hcCCCccHHHHHHHHH
Confidence 34678888887 889987 479999999999999999999999997531 1222333334445666
Q ss_pred HhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHH
Q 001235 824 AMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRL 884 (1117)
Q Consensus 824 ~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ 884 (1117)
.+.++.....++++++++|..+|+.++..|+.+.+|.+.+++++++|||++|+.++++++.
T Consensus 215 ~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~ 275 (665)
T PRK13558 215 AIDEERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRE 275 (665)
T ss_pred HHhcCCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHH
Confidence 6777778889999999999999999999999999999999999999999999998876653
No 94
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=98.80 E-value=1.9e-08 Score=121.80 Aligned_cols=127 Identities=18% Similarity=0.100 Sum_probs=101.8
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHH
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1117)
.+.|+.++++++. +++..|.+|++++||+++++++||++++++|+..... . ++.........+.+.
T Consensus 3 ~~~~~~i~~~~~~---~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~-~----------~~~~~~~~~~~~~~~ 68 (494)
T TIGR02938 3 PEAYRQTVDQAPL---AISITDLKANILYANDAFTRITGYTKEEIIGKNESVL-S----------NHTTPPEVYQALWGS 68 (494)
T ss_pred hHHHHHHHHhCCc---eEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhh-c----------CCCCCHHHHHHHHHH
Confidence 3578999999998 8999999999999999999999999999999863211 1 111112223334445
Q ss_pred hcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHH
Q 001235 825 MSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLS 885 (1117)
Q Consensus 825 l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~a 885 (1117)
+..+.++..++...+++|+.+|+..+..|+++.+|.+.+++++++|||++++.+.++++..
T Consensus 69 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~ 129 (494)
T TIGR02938 69 LAEQKPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQK 129 (494)
T ss_pred HHhCCcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHH
Confidence 5556677777888899999999999999999999999999999999999999887766543
No 95
>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=98.78 E-value=3.2e-08 Score=90.65 Aligned_cols=90 Identities=12% Similarity=0.234 Sum_probs=74.8
Q ss_pred eeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHH-HhcCCCCceEeEEEEecCCcEEEEEE
Q 001235 771 CCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNK-AMSGQDPEKVPFGFFARNGKYAECLL 849 (1117)
Q Consensus 771 i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~-~l~g~~~~~~e~~~~~~dG~~~~v~~ 849 (1117)
|++||+.+.+++||+++++ +..-. ..+....||++...+...+.. ...++..+..++++++++|+++|+..
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 5799999999999999999 54422 335678899999999999999 78888899999999999999999999
Q ss_pred EEeeeeCCCCCEEEEEeeh
Q 001235 850 CVNKKLDREGAVTGVFCFL 868 (1117)
Q Consensus 850 ~~~pi~d~~G~v~g~v~i~ 868 (1117)
++.+++|.+|++++++|++
T Consensus 73 ~~~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 73 RGRPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEEEETTTS-EEEEEEEE
T ss_pred EEEEEECCCCCEEEEEEEC
Confidence 9999999999999999874
No 96
>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=7.1e-08 Score=88.74 Aligned_cols=120 Identities=20% Similarity=0.233 Sum_probs=94.2
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHH
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1117)
+..++.++++++. +++..|.+|.++++|+++.+++|++.++++|+.+.. + .+++....+...+...
T Consensus 2 ~~~~~~~~~~~~~---~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~-~----------~~~~~~~~~~~~~~~~ 67 (124)
T TIGR00229 2 EERYRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLE-L----------IPEEDREEVRERIERL 67 (124)
T ss_pred chHHHHHHhhCCc---eEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhh-h----------cChhhhHHHHHHHHHH
Confidence 3467788999988 899999999999999999999999999999887543 1 2233334444455555
Q ss_pred hcCC-CCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHH
Q 001235 825 MSGQ-DPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQAL 879 (1117)
Q Consensus 825 l~g~-~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~ 879 (1117)
..+. .....++.+..++|..+|+..+..|+. .+|...++++++.|||++++.+.
T Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 68 LEGEREPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred HcCCCCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 5543 334556666789999999999999998 88999999999999999887764
No 97
>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=98.75 E-value=4.9e-08 Score=89.43 Aligned_cols=86 Identities=20% Similarity=0.293 Sum_probs=70.8
Q ss_pred EEeecHHHHHHcCCCcccccCCc----cccccccCcHHHHHHHHHH-HHcCCcceeeEEEEEeeccccCCceEEEEEEEE
Q 001235 638 VNGWNTKIAELTGLSVDKAIGKH----FLTLVEDSSIDTVKRMLYL-ALQGQEEQNIQFEIKTHGSKINDDPITLIVNAC 712 (1117)
Q Consensus 638 I~~~N~a~~~l~G~s~eeliG~~----~~dlv~~~~~~~~~~~l~~-~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~ 712 (1117)
|++||+.+++++||+++++ +.. +..++||+|++.+...+.. +..++.....++++. +++|+.+|+.+++.
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 6899999999999999999 777 7789999999999999999 677666656566555 78999999999999
Q ss_pred EeecCCCCEEEEEEEE
Q 001235 713 ASRDLHDNVVGVCFVA 728 (1117)
Q Consensus 713 pi~d~~G~v~gv~~v~ 728 (1117)
+++|.+|++..++|+.
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 98
>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=98.70 E-value=4.5e-08 Score=84.69 Aligned_cols=64 Identities=27% Similarity=0.437 Sum_probs=58.7
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhc-CCCCHHH-HHHHHHHHHHHHHHHHHHhh-ccccccccC
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEG-TELGAEQ-KRLLHTSAQCQRQLHKILDD-SDLDSIIDG 955 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~-~~l~~~~-~~~l~~i~~~~~~l~~ii~d-Ld~skie~g 955 (1117)
|.+|++.++|||||||++|.++++++.. ...+++. +++++.+..+.+++..++++ ++++++++|
T Consensus 2 ~~~~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G 68 (68)
T PF00512_consen 2 KGEFLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 6679999999999999999999999999 8888887 99999999999999999999 699998765
No 99
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.69 E-value=2.8e-07 Score=114.60 Aligned_cols=134 Identities=19% Similarity=0.268 Sum_probs=105.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcC-C
Q 001235 606 EGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG-Q 684 (1117)
Q Consensus 606 ~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g-~ 684 (1117)
.....++..+..++.++++++++++++|.+|+++++|+++++++|++.++++|+++.+++++... +...+...+.. .
T Consensus 252 ~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~ 329 (607)
T PRK11360 252 NLAQALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP--FASPLLDTLEHGT 329 (607)
T ss_pred HHHHHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh--HHHHHHHHHhcCC
Confidence 34456777778889999999999999999999999999999999999999999999988875432 22333344433 3
Q ss_pred cceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHH
Q 001235 685 EEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEG 746 (1117)
Q Consensus 685 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~ 746 (1117)
.....++.+. +++|... +.++..|+.+.+|++.|++++++|||++|++|+++++.++
T Consensus 330 ~~~~~~~~~~----~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~ 386 (607)
T PRK11360 330 EHVDLEISFP----GRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQER 386 (607)
T ss_pred CccceEEEEE----cCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHH
Confidence 3333333333 4456655 8899999999999999999999999999999999887653
No 100
>PF14501 HATPase_c_5: GHKL domain
Probab=98.68 E-value=2.5e-07 Score=86.72 Aligned_cols=96 Identities=19% Similarity=0.289 Sum_probs=76.8
Q ss_pred cHHHHHHHHHHHHHHHhhccCC---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCCCccc
Q 001235 1004 DSIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGI 1080 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~GtGL 1080 (1117)
+..-|..+|.||+.||+++... ...|.|.+....+ .+.|.|+..-.+ + .+.++......++.|+
T Consensus 2 ~~~dl~~il~nlldNAiea~~~~~~~~~I~i~~~~~~~---------~~~i~i~N~~~~---~-~~~~~~~~~~~~~~G~ 68 (100)
T PF14501_consen 2 DDLDLCRILGNLLDNAIEACKKYEDKRFISISIREENG---------FLVIIIENSCEK---E-IEKLESSSSKKKGHGI 68 (100)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCcEEEEEEEecCC---------EEEEEEEECCCC---c-cccccccccCCCCCCc
Confidence 4556889999999999998743 5689999888877 899999998544 2 2444433234568999
Q ss_pred cHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEe
Q 001235 1081 SLLISRKLVKLMNGDVQYLREAGKSTFIVSVE 1112 (1117)
Q Consensus 1081 GL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LP 1112 (1117)
||..+++++++++|++.++.+.+.-+++|.||
T Consensus 69 GL~~v~~i~~~y~g~~~~~~~~~~f~~~i~ip 100 (100)
T PF14501_consen 69 GLKNVKKILEKYNGSLSIESEDGIFTVKIVIP 100 (100)
T ss_pred CHHHHHHHHHHCCCEEEEEEECCEEEEEEEEC
Confidence 99999999999999999999887788888887
No 101
>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=98.66 E-value=2.2e-07 Score=94.83 Aligned_cols=95 Identities=19% Similarity=0.332 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHHHHHhhccCC---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC------CC
Q 001235 1005 SIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG------DT 1075 (1117)
Q Consensus 1005 ~~~L~qVL~nLl~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~------~~ 1075 (1117)
...+..++.+++.||++|+-. ++.|.|.+....+ .+.+.|+|+|.|++++.....|.++. ..
T Consensus 40 ~~~l~lav~Ea~~Nai~ha~~~~~~~~I~I~~~~~~~---------~l~i~V~D~G~gfd~~~~~~~~~~~~~~~~~~~~ 110 (159)
T TIGR01924 40 IEDLKIAVSEACTNAVKHAYKEGENGEIGISFHIYED---------RLEIIVSDQGDSFDMDTFKQSLGPYDGSEPIDDL 110 (159)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCCCeEEEEEEEeCC---------EEEEEEEEcccccCchhhccccCCCCCCCCcccC
Confidence 345788999999999999842 5689998887766 89999999999999998888887653 22
Q ss_pred CCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEec
Q 001235 1076 SEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVEL 1113 (1117)
Q Consensus 1076 ~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LPl 1113 (1117)
.+.|+||++++++++ ++.|.+..| +++++...+
T Consensus 111 ~~~G~GL~Li~~L~D----~v~~~~~~G-~~l~l~k~~ 143 (159)
T TIGR01924 111 REGGLGLFLIETLMD----EVEVYEDSG-VTVAMTKYL 143 (159)
T ss_pred CCCccCHHHHHHhcc----EEEEEeCCC-EEEEEEEEE
Confidence 367999999999988 788888655 455555433
No 102
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.60 E-value=3.2e-07 Score=99.64 Aligned_cols=133 Identities=17% Similarity=0.200 Sum_probs=108.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHH
Q 001235 601 CDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLA 680 (1117)
Q Consensus 601 ~~~~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~ 680 (1117)
.+..+.++.-++...+++..++-.+.+|++..|..|+|+.+|..+.+++|.+.++++|+++.+++.-++.-.+...+..
T Consensus 96 t~~~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL~e~- 174 (459)
T COG5002 96 TKRVQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDLVEK- 174 (459)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHHHhc-
Confidence 3344556677778888999999999999999999999999999999999999999999999999877766655444322
Q ss_pred HcCCcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhH
Q 001235 681 LQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRI 744 (1117)
Q Consensus 681 l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~s 744 (1117)
.. ++.+... ..++...+.++.+.++-+.|-+.|++.+..|+||+.+.|++.++.
T Consensus 175 ---~~----s~lld~~---~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRef 228 (459)
T COG5002 175 ---ND----SLLLDSS---DEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERREF 228 (459)
T ss_pred ---CC----cEEEeec---CCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHHHH
Confidence 11 3333322 268888899999999999999999999999999999999887643
No 103
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.59 E-value=7e-07 Score=104.52 Aligned_cols=224 Identities=12% Similarity=0.116 Sum_probs=150.9
Q ss_pred HHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc---------ceeeEE
Q 001235 621 LIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE---------EQNIQF 691 (1117)
Q Consensus 621 lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~---------~~~~e~ 691 (1117)
++++....|++++.||.++|+++.....+|++.-|+.|.+++|++||.|.+.+.+.+.-...... +..+-+
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 55566666788999999999999999999999999999999999999999998888765443111 123333
Q ss_pred EEEeeccccCCce--------EEEEEEEEE-eecCCCC----------EEEEEEEEEccchhhhhhhhHhhHHHHHHHHH
Q 001235 692 EIKTHGSKINDDP--------ITLIVNACA-SRDLHDN----------VVGVCFVAQDITPQKTVMDKFTRIEGDYKAIV 752 (1117)
Q Consensus 692 ~~~~~~~~~dG~~--------~~v~v~~~p-i~d~~G~----------v~gv~~v~~DITerK~aE~~L~~se~~l~~i~ 752 (1117)
+.+... .+-|.. .-+.++... +++..+. ..|.+.++.=|-.-+-.|-.|.
T Consensus 204 RMKsTL-T~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL~---------- 272 (768)
T KOG3558|consen 204 RMKSTL-TKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPLD---------- 272 (768)
T ss_pred Eeeeee-ccCCceeeeeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCcccccccC----------
Confidence 433221 222322 222222211 1111111 1122222111111111111110
Q ss_pred hCCCCCCCCe--eeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCC
Q 001235 753 QNPNPLIPPI--FGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP 830 (1117)
Q Consensus 753 ~~~~~li~~I--~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~ 830 (1117)
-.. .-...|-+|++|.+.+.++.||.++|++|+.+ ..+.|+.|...+.......+..+..
T Consensus 273 -------~~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~-----------Ye~~Ha~Ds~~v~KSh~dL~~KGQv 334 (768)
T KOG3558|consen 273 -------CHMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSC-----------YEFVHALDSDRVRKSHHDLLTKGQV 334 (768)
T ss_pred -------CceeEEeeecceeEEEEchhHHHHhcCCHHHhhchhH-----------HHhhhHhhhhHHHHHHHHHHhcCcc
Confidence 012 23457889999999999999999999999984 4677888999999999999999999
Q ss_pred ceEeEEEEecCCcEEEEEEEEeeeeCCCC-CEEEEEeehhHHHH
Q 001235 831 EKVPFGFFARNGKYAECLLCVNKKLDREG-AVTGVFCFLQLASH 873 (1117)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~~~pi~d~~G-~v~g~v~i~~DITe 873 (1117)
....+|+..++|.|+|+...++.+.+..+ +...++|+-.-++.
T Consensus 335 ~TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~ 378 (768)
T KOG3558|consen 335 VTGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSN 378 (768)
T ss_pred chhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeecc
Confidence 99999999999999999999998887543 34555665555543
No 104
>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=98.59 E-value=7.3e-07 Score=77.82 Aligned_cols=103 Identities=24% Similarity=0.367 Sum_probs=86.3
Q ss_pred cCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCce
Q 001235 625 ATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDP 704 (1117)
Q Consensus 625 a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~ 704 (1117)
++.+++++|.+|.+.++|+++++++|++..+++|+.+.+++++.+...+...+.....+......++.+. ..+|..
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ 76 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLR----RKDGSV 76 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEE----ccCCCE
Confidence 3678999999999999999999999999999999999999988888777777777766544433344433 457889
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEEcc
Q 001235 705 ITLIVNACASRDLHDNVVGVCFVAQDI 731 (1117)
Q Consensus 705 ~~v~v~~~pi~d~~G~v~gv~~v~~DI 731 (1117)
+|+.+...++.+.+|...+++++.+||
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 77 IWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 999999999999999999999998886
No 105
>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=98.52 E-value=5.7e-07 Score=102.89 Aligned_cols=113 Identities=15% Similarity=0.194 Sum_probs=87.2
Q ss_pred HHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEE
Q 001235 612 EAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQF 691 (1117)
Q Consensus 612 ~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~ 691 (1117)
++..++|+.+++.+++|++++|.+|+|++||++++++||++.++.+|+++.++.++++ +...+..... .. .+
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 4566789999999999999999999999999999999999999999999998876532 2222222211 11 22
Q ss_pred EEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhH
Q 001235 692 EIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1117)
Q Consensus 692 ~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L 741 (1117)
... .++|..+|+.++..|+.+.+ ++++++|||++++.++..
T Consensus 74 ~~~----~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~ 114 (333)
T TIGR02966 74 ELP----SPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMR 114 (333)
T ss_pred Eee----cCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHH
Confidence 222 35788999999999988753 677889999999887654
No 106
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.52 E-value=4.1e-07 Score=92.32 Aligned_cols=152 Identities=20% Similarity=0.284 Sum_probs=106.3
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCC--ceEEEEeccCC----CCCccCCcCCCCCchH-
Q 001235 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDH--GEVVSEITKSG----LEPYLGLHYPATDIPQ- 276 (1117)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~--g~vvaE~~~~~----~~~~lg~~~p~~dip~- 276 (1117)
+......+.. +.+.+++++.+++.+.+.++.||..||++++++. +.++++..... ..+..+.. ..|.
T Consensus 6 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ 79 (175)
T COG2203 6 LNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLV----ILPAC 79 (175)
T ss_pred HHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhccc----Ccchh
Confidence 3445555666 5699999999999999999999999999999995 77766665443 11111111 0000
Q ss_pred HHHHHHHhCCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCccc
Q 001235 277 AARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQ 356 (1117)
Q Consensus 277 ~~r~l~~~~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~ 356 (1117)
.........+..++.|+...+. ...+|..++... ++|.+++||+.+
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~-i~~~l~vPl~~~------------ 125 (175)
T COG2203 80 LIGIALREGRPVVVEDILQDPR---------------------FRDNPLVLLEPP-IRSYLGVPLIAQ------------ 125 (175)
T ss_pred hhhhhhcCCceEEeeccccCcc---------------------cccCHHHHHHHH-HHHheeeeeeEC------------
Confidence 0111122333344444443331 122777777766 899999999987
Q ss_pred ccccceeeEEeeccCCC-CCCchhHHHHHHHHHHHHHHHHHH
Q 001235 357 KRKRLWGLVVCHNTTPR-FVPFPLRYACEFLAQVFAIHVNKE 397 (1117)
Q Consensus 357 ~~~~lWGl~~~hh~~p~-~~~~~~r~~~~~l~~~~~~~~~~~ 397 (1117)
+++||.+..||+.++ .|+.+.....+.+++.++..|...
T Consensus 126 --~~~~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ai~~~ 165 (175)
T COG2203 126 --GELLGLLCVHDSEPRRQWSEEELELLEELAEQVAIAIERA 165 (175)
T ss_pred --CEeeEEeeeeccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999877 599999999999999999888643
No 107
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.48 E-value=8.9e-06 Score=102.11 Aligned_cols=222 Identities=14% Similarity=0.169 Sum_probs=130.2
Q ss_pred HHHHHHHhcCccEEEEeCCCcEEeecHHHHHH-----cCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEE
Q 001235 617 EMVRLIETATVPILAVDVDGLVNGWNTKIAEL-----TGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQF 691 (1117)
Q Consensus 617 ~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l-----~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~ 691 (1117)
.+..++...+..+++.|.+|.|+.++....-+ .|+. .|..|.+-.-.. ..+-.++..+.+..+.
T Consensus 63 ~l~~~l~~~~~~~~l~D~~G~vL~~~g~~~~~~~~~~~~~~----~G~~w~E~~~GT------naig~al~~~~pv~v~- 131 (638)
T PRK11388 63 DAWEYMADRECALLILDETGCILSRNGDPQTLQQLSALGFN----DGTYCAEGIIGT------NALSLAAISGQPVKTM- 131 (638)
T ss_pred HHHHHhcCCCcEEEEEcCCceEEEEeCCHHHHHHHHHcCCc----cCCccchhccCc------CHHHHHHhcCCceEEe-
Confidence 34556667788999999999999875433221 1221 233333111100 1223334333321111
Q ss_pred EEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccch------------------hhhhhh---hHhhHHHHHHH
Q 001235 692 EIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITP------------------QKTVMD---KFTRIEGDYKA 750 (1117)
Q Consensus 692 ~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITe------------------rK~aE~---~L~~se~~l~~ 750 (1117)
.. -+-......+.+.+.|++|++|+++|++.+..+... +..... ++......+..
T Consensus 132 -g~---EH~~~~~~~~~c~aaPI~d~~G~liGvl~l~~~~~~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~~~~~~~~ 207 (638)
T PRK11388 132 -GD---QHFKQALHNWAFCATPVFDSKGRLTGTIALACPVEQTSAADLPLTLSIAREVGNLLLTDSLLAESNRHLNQLNA 207 (638)
T ss_pred -cH---HHHHHhccCceEEeeEEEcCCCCEEEEEEEEecccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 011122334677899999999999999987764432 221211 12223334455
Q ss_pred HHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCC
Q 001235 751 IVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDP 830 (1117)
Q Consensus 751 i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~ 830 (1117)
+++..++ ||+++|.+|+|+++|+++++++|++.++++|+.+. ++++. +. .+..++..+..
T Consensus 208 il~~~~~---gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~-~l~~~---------~~-------~l~~vl~~~~~ 267 (638)
T PRK11388 208 LLESMDD---GVIAWDEQGNLQFLNAQAARLLRLDATASQGRAIT-ELLTL---------PA-------VLQQAIKQAHP 267 (638)
T ss_pred HHhccCC---cEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHH-HHhcc---------ch-------HHHHHHhcCCc
Confidence 8888877 99999999999999999999999999999999853 33221 11 12223333332
Q ss_pred c-eEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHH
Q 001235 831 E-KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQ 876 (1117)
Q Consensus 831 ~-~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~ 876 (1117)
. ..+..+ ..+|..+++.++..|+.+..|. +++.+++|++..++
T Consensus 268 ~~~~~~~l-~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 268 LKHVEVTF-ESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred eeeEEEEE-ecCCceEEEEEEEEeecccCce--EEEEEehhhHHHHH
Confidence 2 233333 3467777889999999755553 35666778876543
No 108
>PF12860 PAS_7: PAS fold
Probab=98.45 E-value=6.7e-07 Score=86.09 Aligned_cols=104 Identities=23% Similarity=0.325 Sum_probs=73.8
Q ss_pred HHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccc-cCCcccccc---------ccCc-HHHHHHHHHHHHcCCcceeeE
Q 001235 622 IETATVPILAVDVDGLVNGWNTKIAELTGLSVDKA-IGKHFLTLV---------EDSS-IDTVKRMLYLALQGQEEQNIQ 690 (1117)
Q Consensus 622 ie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eel-iG~~~~dlv---------~~~~-~~~~~~~l~~~l~g~~~~~~e 690 (1117)
+++++.||.++|.+|++++||+++.+++|++.+.+ .|.++.+++ .+.+ ...+.+.+..... .... .
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 46889999999999999999999999999999988 798887665 1222 2223333333332 2222 2
Q ss_pred EEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhh
Q 001235 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMD 739 (1117)
Q Consensus 691 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~ 739 (1117)
+... ....+|+.++..|..+ | |++.++.|||++|++|+
T Consensus 78 ~~~~------~~dgr~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 78 FELR------LPDGRWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred eEEE------CCCCEEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 2222 2445677888888754 4 78889999999999875
No 109
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.39 E-value=6.3e-06 Score=80.29 Aligned_cols=128 Identities=21% Similarity=0.240 Sum_probs=89.5
Q ss_pred cHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCcc
Q 001235 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1117)
Q Consensus 218 ~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~ 297 (1117)
|++++++.+++.+++++|+|++.||.++++..--.++.+. .+ .+-+.-.+| .+-|. ....+.+++...++|....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~~-~~~~~~~l~-~~~~~-~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW-GG-DPRLSESLP-EDDPL-IGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE-SS--GCGHHCEE-TTSHH-HHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe-CC-CccccccCC-CCccH-HHHHHhhCCeEEeccccccc
Confidence 6899999999999999999999999999874433333333 21 222222555 33333 33667777665555532221
Q ss_pred cccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCCCc
Q 001235 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPF 377 (1117)
Q Consensus 298 v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~~~ 377 (1117)
. .+.++.|++||..+ ++++|+|..++..++.++.
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 55588899999987 8999999998888889999
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 001235 378 PLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 378 ~~r~~~~~l~~~~~~~~~ 395 (1117)
..+...+.++..+|..|.
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 999999999999888774
No 110
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.39 E-value=2.7e-05 Score=79.08 Aligned_cols=229 Identities=22% Similarity=0.276 Sum_probs=149.7
Q ss_pred EEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEE
Q 001235 629 ILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLI 708 (1117)
Q Consensus 629 i~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~ 708 (1117)
.+..+..+.+.+.|......+++......+ ......................... ...........++...++.
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~ 75 (232)
T COG2202 2 ILVLDRDGRIIYANEAAEELLGYSAEELLG--LLLALHPEDRDRLRELLRRLLAGEE----LLSEELRLVRKDGEERWVE 75 (232)
T ss_pred eEEEcccccEEEecccchhhcCCChHHhhh--hhhccCccchhhhHHHHHHHhccCC----cchhhHHhhhcCCcEEEEE
Confidence 345677888899999999999888776655 1111111111111111222221111 1111111123345555555
Q ss_pred EEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhh
Q 001235 709 VNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREE 788 (1117)
Q Consensus 709 v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eE 788 (1117)
..........+........ .|++..+..++.++..+.+++.++++.+. +++..|.+|.+.++|+++.+++|++..+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~d~~~~~~~~n~~~~~~~g~~~~~ 151 (232)
T COG2202 76 LSAAPLRDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASPD---GIWVLDEDGRILYANPAAEELLGYSPEE 151 (232)
T ss_pred ecceEEEcCCCCEEEEEee-eecchHHHHHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEeCHHHHHHhCCChHH
Confidence 4444445555666666666 89999999999999999999999999998 8999999999999999999999999888
Q ss_pred HhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcE-EEEEEEEeeeeCCCCCEEEEEee
Q 001235 789 VIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKY-AECLLCVNKKLDREGAVTGVFCF 867 (1117)
Q Consensus 789 liGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~-~~v~~~~~pi~d~~G~v~g~v~i 867 (1117)
..++.......... .+.. ..................++....++|.. .+......+... +|.+.++.+.
T Consensus 152 ~~~~~~~~~~~~~~--------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~ 221 (232)
T COG2202 152 ELGRGLSDLIHPED--------EERR-ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGI 221 (232)
T ss_pred hcCCChhheEecCC--------Cchh-hHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEE
Confidence 77665432222110 1000 11112222223344578899999999996 888888877765 7999999999
Q ss_pred hhHHHHHHHH
Q 001235 868 LQLASHELQQ 877 (1117)
Q Consensus 868 ~~DITerk~~ 877 (1117)
..|++++++.
T Consensus 222 ~~d~~~~~~~ 231 (232)
T COG2202 222 ARDITERKQA 231 (232)
T ss_pred EechHHHhhc
Confidence 9999987754
No 111
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.33 E-value=2.8e-06 Score=98.50 Aligned_cols=118 Identities=14% Similarity=0.139 Sum_probs=88.5
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcc-eeeEEEEE
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQFEIK 694 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~-~~~e~~~~ 694 (1117)
..++.+++++++|++++|.+|+|+++|+++++++||+.++++|+++.++++..... ...+...+..+.. ...++.+
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 35688999999999999999999999999999999999999999999887654322 1223333433322 1112222
Q ss_pred eeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHH
Q 001235 695 THGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIE 745 (1117)
Q Consensus 695 ~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se 745 (1117)
.++|..+|+.++..|+.. .+++..++|||++++.++++.+..
T Consensus 84 ----~~~g~~~~~~~~~~~~~~-----~~~~~~~~dit~~~~~~~~~~~~~ 125 (348)
T PRK11073 84 ----VIDGRSHILSLTAQRLPE-----GMILLEMAPMDNQRRLSQEQLQHA 125 (348)
T ss_pred ----EECCceEEEEEEEEEccC-----ceeEEEEechhHHHHHHHHHHHHH
Confidence 347999999999999882 356777899999999887765443
No 112
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=98.31 E-value=5.2e-06 Score=81.17 Aligned_cols=92 Identities=22% Similarity=0.281 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHHHhhccCC---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCC-CCCCCCccc
Q 001235 1005 SIRLQQVLADFLSISINFVPN---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGS-EGDTSEEGI 1080 (1117)
Q Consensus 1005 ~~~L~qVL~nLl~NAik~~~~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~-f~~~~GtGL 1080 (1117)
...+..++.+++.||++|+.. ++.|.|.+....+ .+.|.|.|+|.|+|+.....-... .......|+
T Consensus 29 ~~~~~lav~E~~~Nav~H~~~~~~~~~v~v~~~~~~~---------~l~i~v~D~G~~~d~~~~~~~~~~~~~~~~~~G~ 99 (125)
T PF13581_consen 29 RDDLELAVSEALTNAVEHGYPGDPDGPVDVRLEVDPD---------RLRISVRDNGPGFDPEQLPQPDPWEPDSLREGGR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCCCcEEEEEEEEcCC---------EEEEEEEECCCCCChhhccCcccccCCCCCCCCc
Confidence 457888999999999999864 3678888888777 899999999999998865443221 134457799
Q ss_pred cHHHHHHHHHHcCCEEEEEeeCCeEEEEEE
Q 001235 1081 SLLISRKLVKLMNGDVQYLREAGKSTFIVS 1110 (1117)
Q Consensus 1081 GL~ivr~iVe~~gG~I~v~s~~g~ttF~i~ 1110 (1117)
||+|++++++.. .| +..++++++++
T Consensus 100 Gl~li~~l~D~~----~~-~~~~gn~v~l~ 124 (125)
T PF13581_consen 100 GLFLIRSLMDEV----DY-REDGGNTVTLR 124 (125)
T ss_pred CHHHHHHHHcEE----EE-ECCCeEEEEEE
Confidence 999999999876 55 55566777764
No 113
>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]
Probab=98.27 E-value=2.6e-05 Score=86.18 Aligned_cols=174 Identities=16% Similarity=0.226 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh-c-cccccccCccc------ceeEEeeHHHHHHHHHHHHHhhhcccC---cEEEEeec
Q 001235 925 EQKRLLHTSAQCQRQLHKILDD-S-DLDSIIDGYLD------LEMVEFTLNEVLVASISQVMMKSNAKG---IRIVNETA 993 (1117)
Q Consensus 925 ~~~~~l~~i~~~~~~l~~ii~d-L-d~skie~g~~~------l~~~~~~L~~li~~v~~~~~~~~~~~~---i~i~~~~~ 993 (1117)
....+|+.--.+--.++-|++. + -++ +|+-+ .-...+++.++|.++.+..+-.+..+- -++.++..
T Consensus 172 ~iqyFLdr~y~sRIsiRMLv~qh~~l~~---~~kp~~~~~iG~I~~~c~v~~vi~~a~e~ar~lCd~yy~~sPel~i~~~ 248 (414)
T KOG0787|consen 172 NIQYFLDRFYMSRISIRMLVNQHLLLFA---SGKPDHPRHIGIIDPRCSVKKVIKDASENARFLCDQYYLNSPELIIEGH 248 (414)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhheec---CCCCCCcceeeeeCCCCCHHHHHHHHHHHHHHHHHHhccCCCeeEecCc
Confidence 3455666654444456666776 4 333 12221 223567899999999888776555432 34555544
Q ss_pred CCCcceeEEecHHHHHHHHHHHHHHHhhcc----CCCC----eEEEEEEecccccccccceeEEEEEEeecCCCCChhhh
Q 001235 994 EQIMSETLYGDSIRLQQVLADFLSISINFV----PNGG----QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLL 1065 (1117)
Q Consensus 994 ~~~~~~~v~~D~~~L~qVL~nLl~NAik~~----~~~g----~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~ 1065 (1117)
..+.. . ..-|..|.-++-+|+.||.+++ ...+ .|.|.|...++ -+.|.|+|-|.||+.+..
T Consensus 249 ~a~~~-~-vyvPshL~ymlfElfKNamrATve~h~~~~~~~ppI~V~V~~gde---------Dl~ikISDrGGGV~~~~~ 317 (414)
T KOG0787|consen 249 NALSF-T-VYVPSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDE---------DLLIKISDRGGGVPHRDI 317 (414)
T ss_pred ccccC-c-cccchHHHHHHHHHHHHHHHHHHHHhccCCCCCCCeEEEEecCCc---------ceEEEEecCCCCcChhHH
Confidence 44321 1 2357789999999999999876 1233 38887777665 688999999999999999
Q ss_pred hhccCCCCCC--------------CCccccHHHHHHHHHHcCCEEEEEeeCCe-EEEEEEEe
Q 001235 1066 DQMFGSEGDT--------------SEEGISLLISRKLVKLMNGDVQYLREAGK-STFIVSVE 1112 (1117)
Q Consensus 1066 ~~iFe~f~~~--------------~GtGLGL~ivr~iVe~~gG~I~v~s~~g~-ttF~i~LP 1112 (1117)
+++|.-.++| .|-|.||.|||.-.+..||.+.+.|=.|- |-..|.|-
T Consensus 318 drlf~Y~ySTa~~~~~d~~~~~plaGfG~GLPisrlYa~yf~Gdl~L~SleG~GTD~yI~Lk 379 (414)
T KOG0787|consen 318 DRLFSYMYSTAPAPSSDNNRTAPLAGFGFGLPISRLYARYFGGDLKLQSLEGIGTDVYIYLK 379 (414)
T ss_pred HHHHhhhcccCCCCCCCCCCcCcccccccCCcHHHHHHHHhCCCeeEEeeeccccceEEEec
Confidence 9999743211 28899999999999999999999998887 77777764
No 114
>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=98.26 E-value=9.6e-06 Score=70.53 Aligned_cols=100 Identities=25% Similarity=0.295 Sum_probs=81.6
Q ss_pred CeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEec
Q 001235 761 PIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFAR 840 (1117)
Q Consensus 761 ~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~ 840 (1117)
+++..|.+|.++++|+++.+++|++.++++|+.+...+ ++++...+...+.....+......++.+...
T Consensus 4 ~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (103)
T cd00130 4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLI-----------HPEDREELRERLENLLSGGEPVTLEVRLRRK 72 (103)
T ss_pred eEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhc-----------CCccchHHHHHHHHHHhcCcCeEEEEEEEcc
Confidence 78999999999999999999999999999998754322 2333334555566666666667788888999
Q ss_pred CCcEEEEEEEEeeeeCCCCCEEEEEeehhHH
Q 001235 841 NGKYAECLLCVNKKLDREGAVTGVFCFLQLA 871 (1117)
Q Consensus 841 dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DI 871 (1117)
+|...|+.....+..+.+|...+++++++||
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred CCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999999999999999999999988875
No 115
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.22 E-value=8.4e-06 Score=97.59 Aligned_cols=119 Identities=14% Similarity=0.143 Sum_probs=84.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCC
Q 001235 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQ 684 (1117)
Q Consensus 605 ~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~ 684 (1117)
++..+++++.+++|+.+++++|++++++|.+|+|+++|+++++++||+.++.+|+++.+++.+.+.. ..+.. ..
T Consensus 87 ~~~~~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~~---~~~~~---~~ 160 (430)
T PRK11006 87 RKRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEFT---QYLKT---RD 160 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHHH---HHHHh---cc
Confidence 4456778888899999999999999999999999999999999999999999999998877543322 11211 11
Q ss_pred cceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHh
Q 001235 685 EEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFT 742 (1117)
Q Consensus 685 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~ 742 (1117)
... ..... ..++ .++.++..|..+ + +++.+.+|||++++.+++.+
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 11121 1223 356666666543 2 35667899999998876544
No 116
>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=98.15 E-value=3.4e-05 Score=77.09 Aligned_cols=137 Identities=17% Similarity=0.165 Sum_probs=87.7
Q ss_pred CcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCC--CC-Cc-hHHHH-----HHHHhCCe
Q 001235 217 GSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYP--AT-DI-PQAAR-----FLFMKNKV 287 (1117)
Q Consensus 217 ~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p--~~-di-p~~~r-----~l~~~~~~ 287 (1117)
.+++++++.+++.+.+++++|...||-++++. +-......... ...++..++ .. +. |...+ .++..++-
T Consensus 2 ~~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (148)
T PF13185_consen 2 EDLEELLQQILDALLELTGADAGAIYLYDPDG-QLLPVAASGDP-SEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEP 79 (148)
T ss_dssp HHHHHHHHHHHHHHHHHHS-SEEEEEEEETTS-EEEEEEEESSS-CTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-
T ss_pred cCHHHHHHHHHHHHHHHhCCCEEEEEEEECCC-cEEEEEEeCCc-hhhhhhhcccCcccccccchhhhhHHHHHHhcCce
Confidence 37899999999999999999999999997777 32222222222 223222221 11 11 11110 01445555
Q ss_pred EEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEe
Q 001235 288 RMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVC 367 (1117)
Q Consensus 288 r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~ 367 (1117)
.++. .+... ..+ .......|+++-+++||+.+ +++||.|..
T Consensus 80 ~~~~-~~~~~----------------------~~~--~~~~~~~~~~s~l~vPl~~~--------------~~~~Gvl~l 120 (148)
T PF13185_consen 80 IIIN-DDDSS----------------------FPP--WELARHPGIRSILCVPLRSG--------------GEVIGVLSL 120 (148)
T ss_dssp EEES-CCCGG----------------------GST--THHHCCTT-SEEEEEEEEET--------------TEEEEEEEE
T ss_pred EEEe-Ccccc----------------------ccc--hhhhccccCCEEEEEEEeEC--------------CEEEEEEEE
Confidence 4554 10000 111 36689999999999999987 899999998
Q ss_pred eccCCCCCCchhHHHHHHHHHHHHHHH
Q 001235 368 HNTTPRFVPFPLRYACEFLAQVFAIHV 394 (1117)
Q Consensus 368 hh~~p~~~~~~~r~~~~~l~~~~~~~~ 394 (1117)
-+..++.++...+..++.+++.+|..|
T Consensus 121 ~~~~~~~f~~~~~~~l~~la~~~a~ai 147 (148)
T PF13185_consen 121 YSKEPNAFSEEDLELLEALADQIAIAI 147 (148)
T ss_dssp EESSTT---HHHHHHHHHHHHHHHHHH
T ss_pred eeCCCCCcCHHHHHHHHHHHHHHHHHh
Confidence 888888999999999999999888776
No 117
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.13 E-value=7.5e-06 Score=77.54 Aligned_cols=106 Identities=19% Similarity=0.208 Sum_probs=74.8
Q ss_pred HHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcC
Q 001235 748 YKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSG 827 (1117)
Q Consensus 748 l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g 827 (1117)
++.++++++. ++.++|.+++|.++|+++.++|+..+ ..+|+++. .+..+.....+...+.....|
T Consensus 1 L~~il~s~~~---~i~~vD~~~~I~~~n~~a~~~f~~~~-~~iGr~l~-----------~~~~~~~~~~l~~~i~~~~~~ 65 (106)
T PF13596_consen 1 LNNILDSMPI---GIIFVDRNLRIRYFNPAAARLFNLSP-SDIGRPLF-----------DIHPPLSYPNLKKIIEQVRSG 65 (106)
T ss_dssp HHHHHHHSSS---EEEEEETTSBEEEE-SCGC-SS---G-GGTTSBCC-----------CSS-HHHHHHHHHHHHHHHTT
T ss_pred ChHHHhcCCC---CEEEEcCCCeEEEeChhHhhhcCCCh-HHCCCCHH-----------HcCCccchHHHHHHHHHHHcC
Confidence 4678888888 89999999999999999999999775 44798853 333455666777778888877
Q ss_pred CCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHH
Q 001235 828 QDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLAS 872 (1117)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DIT 872 (1117)
+... .++.+ ..+| +|+.++..|+++.+|+..|++.++.|||
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 6632 22222 2444 5677899999999999999999999998
No 118
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.08 E-value=2.8e-05 Score=95.78 Aligned_cols=126 Identities=19% Similarity=0.221 Sum_probs=92.0
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCC---cccccCCccccccccCcHHHHHHHHHHHHcCCc
Q 001235 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLS---VDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE 685 (1117)
Q Consensus 609 ~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s---~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~ 685 (1117)
.++....++++.+++++++||+++|.+|+|++||+++++++|++ .++.+|+.+.++.++.. +...+..+.
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~ 286 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVSR-------LKEVLRTGT 286 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCchh-------HHHHHhcCC
Confidence 45666677889999999999999999999999999999999865 34667777776655322 233443333
Q ss_pred ceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHH
Q 001235 686 EQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKA 750 (1117)
Q Consensus 686 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~ 750 (1117)
.... .... .+| .++.++..|+.+ +|.+.|++.+++|+|+.++.++++.......+.
T Consensus 287 ~~~~-~~~~-----~~g--~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~~~~~~ 342 (542)
T PRK11086 287 PRRD-EEIN-----ING--RLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMVNYADA 342 (542)
T ss_pred Cccc-eEEE-----ECC--EEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHHHHHHH
Confidence 2111 1111 123 456677889998 899999999999999999998888766544443
No 119
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.05 E-value=4.8e-05 Score=92.67 Aligned_cols=113 Identities=19% Similarity=0.239 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceee
Q 001235 610 ELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNI 689 (1117)
Q Consensus 610 eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~ 689 (1117)
-+++...++..+++++++||+++|.+|+|+++|++++++||++.++++|+++.++++.... ...+..+.....
T Consensus 74 ~~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~l-------~~~le~~~~~~~ 146 (520)
T PRK10820 74 PSEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFNF-------LRWLESEPQDSH 146 (520)
T ss_pred hHHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcchH-------HHHHHcCCCccc
Confidence 3555667789999999999999999999999999999999999999999999999876442 223333322111
Q ss_pred EEEEEeeccccCCceEEEEEEEEEee--cCCCCE--EEEEEEEEccchhhh
Q 001235 690 QFEIKTHGSKINDDPITLIVNACASR--DLHDNV--VGVCFVAQDITPQKT 736 (1117)
Q Consensus 690 e~~~~~~~~~~dG~~~~v~v~~~pi~--d~~G~v--~gv~~v~~DITerK~ 736 (1117)
...+. .+|.. +.++..|+. |++|.. .|++.+++|+|+..+
T Consensus 147 ~~~v~-----~~g~~--~~v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 NEHVV-----INGQD--FLMEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred eEEEE-----ECCEE--EEEEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 12221 23543 446677876 666664 899999999998643
No 120
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.01 E-value=7e-05 Score=71.54 Aligned_cols=101 Identities=11% Similarity=0.152 Sum_probs=81.0
Q ss_pred EEEEeCCCcEEeecHH-HHHHcCCCcccccCCccccccccCcHHH-HHHHHHHHHcCCcceeeEEEEEeeccccCCceEE
Q 001235 629 ILAVDVDGLVNGWNTK-IAELTGLSVDKAIGKHFLTLVEDSSIDT-VKRMLYLALQGQEEQNIQFEIKTHGSKINDDPIT 706 (1117)
Q Consensus 629 i~~~D~dG~I~~~N~a-~~~l~G~s~eeliG~~~~dlv~~~~~~~-~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~ 706 (1117)
+.-.+.||+|+++-++ ...++||.++|++|+++.+++||+|... +.+....+++.+......+++. .++|+.+|
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 3457899999999999 6999999999999999999999999996 8888888887776544455555 67899999
Q ss_pred EEEEEEEeecC-CCCEEEEEEEEEccch
Q 001235 707 LIVNACASRDL-HDNVVGVCFVAQDITP 733 (1117)
Q Consensus 707 v~v~~~pi~d~-~G~v~gv~~v~~DITe 733 (1117)
+...+.++.++ .+++..++++-+=|++
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 99999999874 4566667776555554
No 121
>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=98.00 E-value=0.00021 Score=87.78 Aligned_cols=151 Identities=9% Similarity=0.042 Sum_probs=105.6
Q ss_pred HHHHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHH
Q 001235 203 LAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLF 282 (1117)
Q Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~ 282 (1117)
.+.++...+.+ +.+++++++.+++.+.+++|+||..||-+++++.-. +..+....-+..-...||... --....+
T Consensus 6 ~L~~is~~l~~--~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l-~~aa~g~~~~~~~~~~~~~~~--gi~g~v~ 80 (534)
T TIGR01817 6 ALYEISKILSA--PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPL-LVAAIGWSEEGFAPIRYRVGE--GAIGQIV 80 (534)
T ss_pred HHHHHHHHHhc--cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEE-EEEEeCCChhhcccccccCCc--cHHHHHH
Confidence 34445555666 669999999999999999999999999998886543 333332221111113343221 2355677
Q ss_pred HhCCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccce
Q 001235 283 MKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLW 362 (1117)
Q Consensus 283 ~~~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lW 362 (1117)
..+..-+|.|+...|-.. .+.. +...|++|-|++||..+ |+++
T Consensus 81 ~~~~pvii~Dv~~d~~~~---------------------~~~~--~~~~~~~S~l~VPL~~~--------------g~vi 123 (534)
T TIGR01817 81 ATGNSLVVPDVAAEPLFL---------------------DRLS--LYDPGPVPFIGVPIKAD--------------SETI 123 (534)
T ss_pred hcCCeEEecccccCchhh---------------------hccc--cccCCcceEEEEEEcCC--------------CEEE
Confidence 888888899987654211 0000 23467899999999876 9999
Q ss_pred eeEEeeccC-CCCCCchhHHHHHHHHHHHHHHHH
Q 001235 363 GLVVCHNTT-PRFVPFPLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 363 Gl~~~hh~~-p~~~~~~~r~~~~~l~~~~~~~~~ 395 (1117)
|.|..+... +++...+....++.++..++..|.
T Consensus 124 GvL~v~s~~~~~~ft~~d~~lL~~lA~~ia~aI~ 157 (534)
T TIGR01817 124 GVLAADRDFRSRERLEEEVRFLEMVANLIGQTVR 157 (534)
T ss_pred EEEEEEeccccccccHHHHHHHHHHHHHHHHHHH
Confidence 999988875 566688888899999999998875
No 122
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=97.99 E-value=2.2e-05 Score=88.55 Aligned_cols=100 Identities=16% Similarity=0.348 Sum_probs=78.4
Q ss_pred HHHHHHHHHHHHHHHhhccCCCC---eEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCC---------
Q 001235 1005 SIRLQQVLADFLSISINFVPNGG---QLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSE--------- 1072 (1117)
Q Consensus 1005 ~~~L~qVL~nLl~NAik~~~~~g---~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f--------- 1072 (1117)
...|.|++.+|+.|+++++...| .|.|.+...+. .+..+.|.|||+|||++.++++|..+
T Consensus 34 ~RsL~~tv~ElV~NSLDA~eeaGILPdI~v~I~~~~~--------d~y~v~veDNGpGIP~e~IPkvFGk~LygSKfh~~ 105 (538)
T COG1389 34 IRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGK--------DHYKVIVEDNGPGIPEEQIPKVFGKMLYGSKFHRN 105 (538)
T ss_pred hhHHHHHHHHHHhcchhhHHhcCCCCceEEEEEecCC--------ceEEEEEecCCCCCChhHhHHHHHHHhccchhhhh
Confidence 45688999999999999997655 78888877643 39999999999999999999999873
Q ss_pred -CCCCCccccHHHHHHHHHHcCCE-EEEEeeCCe--EEEEEEEe
Q 001235 1073 -GDTSEEGISLLISRKLVKLMNGD-VQYLREAGK--STFIVSVE 1112 (1117)
Q Consensus 1073 -~~~~GtGLGL~ivr~iVe~~gG~-I~v~s~~g~--ttF~i~LP 1112 (1117)
++.+.-|||++-|--.....-|+ +.+.|..+. +...+.|-
T Consensus 106 ~QsRGqqGiGis~avLysQmTtGkPv~V~s~T~~s~~~~~~~l~ 149 (538)
T COG1389 106 IQSRGQQGIGISAAVLYSQMTTGKPVRVISSTGDSGTAYEYELK 149 (538)
T ss_pred hhccccccccHHHHHHHHHhcCCCceEEEecCCCCcceEEEEEE
Confidence 13335699999998888887776 888877553 44444443
No 123
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.98 E-value=6.8e-05 Score=87.58 Aligned_cols=126 Identities=24% Similarity=0.390 Sum_probs=91.4
Q ss_pred HHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeE
Q 001235 611 LEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQ 690 (1117)
Q Consensus 611 L~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e 690 (1117)
|....+.|+.+++.+.++++++|.+|.++++|.++..++|++.++++|+++.+++..... .....++..+.+. .
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 566778899999999999999999999999999999999999999999999888611110 1122233333321 1
Q ss_pred EEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHH
Q 001235 691 FEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYK 749 (1117)
Q Consensus 691 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~ 749 (1117)
....+. .|... ..+..|++. +|.+.|++++++|+|+-+.+..++.+++...+
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 122211 12222 455556554 56999999999999999999988887776655
No 124
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=97.84 E-value=0.00047 Score=79.63 Aligned_cols=219 Identities=19% Similarity=0.138 Sum_probs=130.7
Q ss_pred CcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHH-HHHhCC-eEEE-ecc
Q 001235 217 GSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARF-LFMKNK-VRMI-VDC 293 (1117)
Q Consensus 217 ~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~-l~~~~~-~r~i-~d~ 293 (1117)
.+++.++..+++++..+.|||+++++++|.+. .+..+...-..+++|.+-+....|.+.-+ .+..+. ++++ .|+
T Consensus 47 ~~~e~ll~~v~~~l~~~~~~~~~~ll~~d~~~---l~~~~~~gl~~~~~~~~~~~~~~~~~~l~~i~~~~~p~~~~~~d~ 123 (550)
T COG3604 47 LRLERLLAEVAKELHSLFGCDASALLRLDSKN---LIPLATDGLSKDHLGREQRFVVEGHPLLEQILKAGRPLVFHPADS 123 (550)
T ss_pred hhHHHHHHHHHHHHHHHhcCCeeEEEEecccc---cchhhhhcccccccccccccccCcchHHHHHHhCCCcEEEecCCc
Confidence 58999999999999999999999999999988 55555554455666664444445544433 344444 4441 222
Q ss_pred CCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCC
Q 001235 294 RARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR 373 (1117)
Q Consensus 294 ~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~ 373 (1117)
. .|++..+- +--.+|+++.|.|.+||.++ +++||.|.--|+.|.
T Consensus 124 ~------~~~~~~~l----------------~~~~~~~~~~a~i~~PL~~~--------------~~~~G~Ltld~~~~~ 167 (550)
T COG3604 124 L------FPDPYDGL----------------LPDTEGNKKHACIGVPLKSG--------------DKLIGALTLDHTEPD 167 (550)
T ss_pred c------cCCccccc----------------ccCccCCcceeEEeeeeeeC--------------CeeeeeEEeeeeccc
Confidence 2 12221110 01145678899999999988 999999998888887
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHhhhc--CCCcccccCCcchhhhccCCEEEEEECC
Q 001235 374 FVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRT-QTLLCDMLMR--DAPLGIVTQSPNIMDLVKCDGAALLYKN 450 (1117)
Q Consensus 374 ~~~~~~r~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~--~~~~~~~~~~~~~~~l~~~~g~a~~~~~ 450 (1117)
...+..-....+|+...+..+......+.-...++.+.. +..+..-+.. -...+|+.++|.++++++.=-.+--.+-
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 776766677788888777766432111110011110000 0111111111 1245788888888877665444444455
Q ss_pred eEEEecCCCCHHHH-HHHHHHHHhc
Q 001235 451 KIWRLGVTPNDFQL-HDIVSWLSEY 474 (1117)
Q Consensus 451 ~~~~~G~~p~~~~~-~~l~~~l~~~ 474 (1117)
.+...|+|=+=.++ ...+..++.+
T Consensus 248 tVLi~GETGtGKElvAraIH~~S~R 272 (550)
T COG3604 248 TVLIRGETGTGKELVARAIHQLSPR 272 (550)
T ss_pred eEEEecCCCccHHHHHHHHHhhCcc
Confidence 56666777666554 2334444443
No 125
>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]
Probab=97.84 E-value=0.00016 Score=72.31 Aligned_cols=88 Identities=25% Similarity=0.473 Sum_probs=67.9
Q ss_pred EecHHHHHHHHHHHHHHHhhccC----CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCC-
Q 001235 1002 YGDSIRLQQVLADFLSISINFVP----NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS- 1076 (1117)
Q Consensus 1002 ~~D~~~L~qVL~nLl~NAik~~~----~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~- 1076 (1117)
+.+..++.-++.+++.||++|+- +.|.|.|.+....+ .+.++|.|.|+|+++ .+.-+.|.+.+.
T Consensus 35 ~~~~~~l~~av~E~~~N~v~Ha~~~~~~~g~I~i~~~~~~~---------~~~i~i~D~G~~~~~--~~~~~~~~~~~~~ 103 (146)
T COG2172 35 YVDIADLAIAVSEALTNAVKHAYKLDPSEGEIRIEVSLDDG---------KLEIRIWDQGPGIED--LEESLGPGDTTAE 103 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCceEEEEEEEcCC---------eEEEEEEeCCCCCCC--HHHhcCCCCCCCc
Confidence 35778899999999999999983 25899999998888 899999999977654 445566643333
Q ss_pred Cc---cccHHHHHHHHHHcCCEEEEEeeCCe
Q 001235 1077 EE---GISLLISRKLVKLMNGDVQYLREAGK 1104 (1117)
Q Consensus 1077 Gt---GLGL~ivr~iVe~~gG~I~v~s~~g~ 1104 (1117)
+. |+||.++++++. ++.+.+++++
T Consensus 104 ~~~~~G~Gl~l~~~~~D----~~~~~~~~~~ 130 (146)
T COG2172 104 GLQEGGLGLFLAKRLMD----EFSYERSEDG 130 (146)
T ss_pred ccccccccHHHHhhhhe----eEEEEeccCC
Confidence 34 999999977654 7888865544
No 126
>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=97.78 E-value=9.3e-05 Score=70.69 Aligned_cols=99 Identities=12% Similarity=0.110 Sum_probs=80.6
Q ss_pred eeeCCCCceeechhh-HHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHH-HHHHHHHHhcCCCCceEeEEEEec
Q 001235 763 FGSDEFGWCCEWNPA-MVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVN-LGIVLNKAMSGQDPEKVPFGFFAR 840 (1117)
Q Consensus 763 ~~~D~~g~i~~~N~a-~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~-~~~~l~~~l~g~~~~~~e~~~~~~ 840 (1117)
.-.+.+|+|+++-+. ...++||.++|++|+.+ ..+.||+|... +.......+..+......+|+..+
T Consensus 6 trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~-----------y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k 74 (111)
T PF14598_consen 6 TRHSLDGKITYVDSRAVSSLLGYLPEELVGRSI-----------YDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTK 74 (111)
T ss_dssp EEEETTSBEEEEETTHHHHHHSS-HHHHTTSBG-----------GGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-T
T ss_pred EEECCCcEEEEEcCccChhhcCCCcHHHcCCch-----------HHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEec
Confidence 456789999999999 69999999999999994 46778889987 778888888877777778999999
Q ss_pred CCcEEEEEEEEeeeeC-CCCCEEEEEeehhHHH
Q 001235 841 NGKYAECLLCVNKKLD-REGAVTGVFCFLQLAS 872 (1117)
Q Consensus 841 dG~~~~v~~~~~pi~d-~~G~v~g~v~i~~DIT 872 (1117)
+|.++|+...+....+ ..+++..++|+-.-++
T Consensus 75 ~g~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vls 107 (111)
T PF14598_consen 75 NGGYVWVQTKATLFYNPWTSKPEFIVCTNTVLS 107 (111)
T ss_dssp TSSEEEEEEEEEEEEETTTTCEEEEEEEEEEES
T ss_pred CCcEEEEEEEEEEEECCCCCCccEEEEEEEEec
Confidence 9999999999999986 4456676777655444
No 127
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=97.76 E-value=0.0022 Score=78.33 Aligned_cols=152 Identities=11% Similarity=0.057 Sum_probs=104.6
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhC
Q 001235 206 KAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKN 285 (1117)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~ 285 (1117)
++...|-+ +.+++++++.+++.+++.+++|.+-|+-++.+ .+...+..+.-....+..|+..+=|--...+ ..+
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 34455555 78999999999999999999999999999753 4333344333344566678777655433333 335
Q ss_pred CeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeE
Q 001235 286 KVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLV 365 (1117)
Q Consensus 286 ~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~ 365 (1117)
++-.|+|...-|.++ + |-.. ....++|++|.|+|||.++ ++.+|.|
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 444555443222111 0 0000 0134579999999999988 9999999
Q ss_pred EeeccCCCCCCchhHHHHHHHHHHHHHHHHHH
Q 001235 366 VCHNTTPRFVPFPLRYACEFLAQVFAIHVNKE 397 (1117)
Q Consensus 366 ~~hh~~p~~~~~~~r~~~~~l~~~~~~~~~~~ 397 (1117)
.+....|..........++.++.+++..|...
T Consensus 128 ~l~~~~~~~f~~~~~~~l~~~a~~~a~Al~~a 159 (509)
T PRK05022 128 TLDALDPGQFDAFSDEELRALAALAAATLRNA 159 (509)
T ss_pred EEeeCCCCcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 99988888777777888888999998888644
No 128
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.75 E-value=0.00056 Score=69.24 Aligned_cols=126 Identities=20% Similarity=0.294 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHH-HHHHHHHHH-cCC
Q 001235 607 GMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDT-VKRMLYLAL-QGQ 684 (1117)
Q Consensus 607 ~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~-~~~~l~~~l-~g~ 684 (1117)
...++.....+++.+++..+.+++.+|.+|.+.++|+++++++|++..+..++...++........ ......... ...
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (232)
T COG2202 103 AEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRG 182 (232)
T ss_pred HHHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCC
Confidence 445556666669999999999999999999999999999999999988877887776654433321 122222222 222
Q ss_pred cceeeEEEEEeeccccCCce-EEEEEEEEEeecCCCCEEEEEEEEEccchhhhh
Q 001235 685 EEQNIQFEIKTHGSKINDDP-ITLIVNACASRDLHDNVVGVCFVAQDITPQKTV 737 (1117)
Q Consensus 685 ~~~~~e~~~~~~~~~~dG~~-~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~a 737 (1117)
.....++... .++|.. .+......+... .|.+.++.....|+|++++.
T Consensus 183 ~~~~~~~~~~----~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 183 GPLEIEYRVR----RKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred CCcceEEEEE----ecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 2223333333 557885 777776666655 78999999999999998875
No 129
>PF12860 PAS_7: PAS fold
Probab=97.74 E-value=6.6e-05 Score=72.17 Aligned_cols=112 Identities=10% Similarity=0.052 Sum_probs=69.0
Q ss_pred hCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhH-hhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCc
Q 001235 753 QNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEV-IDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPE 831 (1117)
Q Consensus 753 ~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEl-iGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~ 831 (1117)
++++. ||+++|.+|++++||+++.+++|++.+.+ .|.++ ..++.......... +.+................
T Consensus 2 d~l~~---Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~-~~l~~~~~~~g~~~-~~~~~~~~~~~~~~~~~~~-- 74 (115)
T PF12860_consen 2 DSLPQ---GVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASF-RDLLRRLAERGEFP-PGDPEAWVRQRLARLRRRQ-- 74 (115)
T ss_pred CCcCc---eEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCH-HHHHHHHHHcCCCC-CCCHHHHHHHHHHHHhcCC--
Confidence 45666 99999999999999999999999999998 67664 33332211111111 2222222222222222222
Q ss_pred eEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHH
Q 001235 832 KVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1117)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (1117)
...+.+...||++ +.++..|.- +| |++.++.|||+++++|
T Consensus 75 ~~~~~~~~~dgr~--l~~~~~~~~--~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 75 PRSFELRLPDGRW--LEVRAQPLP--DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred CceeEEECCCCEE--EEEEeEECC--CC---CEEEEEEeCCHHHHhc
Confidence 2234456678865 455666663 34 5678999999999876
No 130
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.70 E-value=0.0034 Score=79.55 Aligned_cols=147 Identities=8% Similarity=0.029 Sum_probs=100.3
Q ss_pred CCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEec--cCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEecc
Q 001235 216 SGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEIT--KSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDC 293 (1117)
Q Consensus 216 ~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~--~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~ 293 (1117)
+.++++++..+++++++++++|++.|+-++++...-++.-+. ..+.....+...|... --+...+..++..++.|.
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 679999999999999999999999999998876443332222 1122223333333221 234567777887777766
Q ss_pred CCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCC
Q 001235 294 RARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR 373 (1117)
Q Consensus 294 ~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~ 373 (1117)
...+-... .....+ +..-++++.|++|++.+ ++.=|.|..-++.+.
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 22345789999999987 999999998888888
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHH
Q 001235 374 FVPFPLRYACEFLAQVFAIHVNKEL 398 (1117)
Q Consensus 374 ~~~~~~r~~~~~l~~~~~~~~~~~~ 398 (1117)
.++......+.+++..+|+.|....
T Consensus 321 ~F~~~dl~lL~~iA~~~A~Aie~a~ 345 (686)
T PRK15429 321 VFTTTNLKLLRQIAERVAIAVDNAL 345 (686)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888889999999999999886443
No 131
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.64 E-value=0.00035 Score=81.81 Aligned_cols=127 Identities=20% Similarity=0.318 Sum_probs=97.1
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcc--cccCCccccccccCcHHHHHHHHHHHHcCCc-
Q 001235 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVD--KAIGKHFLTLVEDSSIDTVKRMLYLALQGQE- 685 (1117)
Q Consensus 609 ~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~e--eliG~~~~dlv~~~~~~~~~~~l~~~l~g~~- 685 (1117)
.|+.+.-++..++++++..|++.+|..|.|..+|.++++++|+... +.+|+++.++++|+.. +...++.+.
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 5677777788899999999999999999999999999999998765 7899999999987221 122232222
Q ss_pred ceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHH
Q 001235 686 EQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAI 751 (1117)
Q Consensus 686 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i 751 (1117)
..+-++++ ...++.++..|++- +|+++|++.++||=||-++..++|........++
T Consensus 282 ~~~~e~~~---------ng~~~i~nr~pI~~-~~~~~GaI~tFRdktei~~L~eqLt~vr~ya~aL 337 (537)
T COG3290 282 QHDEEIRI---------NGRLLVANRVPIRS-GGQIVGAIITFRDKTEIKKLTEQLTGVRQYAEAL 337 (537)
T ss_pred ccchhhhc---------CCeEEEEEeccEEE-CCEEeEEEEEEecHHHHHHHHHHHHHHHHHHHHH
Confidence 22222222 23467788888886 7899999999999999999999987766554444
No 132
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.57 E-value=0.00075 Score=83.43 Aligned_cols=125 Identities=20% Similarity=0.303 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCc--ccccCCccccccccCcHHHHHHHHHHHHcCCcc
Q 001235 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSV--DKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE 686 (1117)
Q Consensus 609 ~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~--eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~ 686 (1117)
.++....++++.+++++++|++++|.+|+|+++|+++++++|++. ++++|+++.+++++.... ..... ...
T Consensus 215 ~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~~------~~~~~-~~~ 287 (545)
T PRK15053 215 KQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADFF------TEQID-EKR 287 (545)
T ss_pred HHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchhh------hhhcC-Ccc
Confidence 345555567888999999999999999999999999999999875 468999998887654211 11111 111
Q ss_pred eeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHH
Q 001235 687 QNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKA 750 (1117)
Q Consensus 687 ~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~ 750 (1117)
....... +| ..+.++..|+.+ +|++.|++.+++|+|+.++.+.++...+...+.
T Consensus 288 ~~~~~~~-------~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~~~e~ 341 (545)
T PRK15053 288 QDVVANF-------NG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQYVES 341 (545)
T ss_pred cceEEEE-------CC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHHHHHH
Confidence 1111111 23 345577788776 567889999999999999998888776655443
No 133
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.56 E-value=0.00055 Score=83.51 Aligned_cols=112 Identities=15% Similarity=0.149 Sum_probs=77.8
Q ss_pred HhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHH
Q 001235 741 FTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIV 820 (1117)
Q Consensus 741 L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~ 820 (1117)
+++.+..++++++++++ ||+.+|.+|+|+++|+++++++|++.++++|+++...+... .
T Consensus 75 ~e~e~~~L~aIL~sm~e---GVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~-----------~------- 133 (520)
T PRK10820 75 SEREHRALSALLEALPE---PVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGF-----------N------- 133 (520)
T ss_pred HHHHHHHHHHHHHhCCC---cEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcc-----------h-------
Confidence 44556678999999999 99999999999999999999999999999999864322211 1
Q ss_pred HHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeee--CCCCCE--EEEEeehhHHHHHHH
Q 001235 821 LNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKL--DREGAV--TGVFCFLQLASHELQ 876 (1117)
Q Consensus 821 l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~--d~~G~v--~g~v~i~~DITerk~ 876 (1117)
+...+..+...... .....+|+.++ +...|+. +.+|.. .|++.+++|+++..+
T Consensus 134 l~~~le~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 134 FLRWLESEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred HHHHHHcCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 11222332221111 12344576554 5556666 666664 899999999997543
No 134
>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=97.54 E-value=0.00042 Score=79.07 Aligned_cols=78 Identities=13% Similarity=0.156 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCCCCC----------
Q 001235 1007 RLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS---------- 1076 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~~~~---------- 1076 (1117)
.+.+++.||+.||+++.. ..|.|.+... . ...|.|.|||.||+++.++++|++|++.+
T Consensus 22 ~~~~~l~eLi~Na~dA~a--~~I~i~~~~~-~---------~~~i~V~DnG~Gi~~~~l~~~~~~~~tsk~~~~~~~~~~ 89 (312)
T TIGR00585 22 RPASVVKELVENSLDAGA--TRIDVEIEEG-G---------LKLIEVSDNGSGIDKEDLPLACERHATSKIQSFEDLERI 89 (312)
T ss_pred hHHHHHHHHHHHHHHCCC--CEEEEEEEeC-C---------EEEEEEEecCCCCCHHHHHHHhhCCCcCCCCChhHhhcc
Confidence 467999999999999864 6777776542 2 35699999999999999999999986443
Q ss_pred ---C-ccccHHHHHHHHHHcCCEEEEEee
Q 001235 1077 ---E-EGISLLISRKLVKLMNGDVQYLRE 1101 (1117)
Q Consensus 1077 ---G-tGLGL~ivr~iVe~~gG~I~v~s~ 1101 (1117)
| .|.||+-...+ +.+.+.|.
T Consensus 90 ~~~G~rG~al~si~~~-----s~~~i~S~ 113 (312)
T TIGR00585 90 ETLGFRGEALASISSV-----SRLTITTK 113 (312)
T ss_pred cccCccchHHHHHHhh-----CcEEEEEe
Confidence 2 36777666333 25777665
No 135
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.51 E-value=0.00013 Score=62.05 Aligned_cols=47 Identities=26% Similarity=0.282 Sum_probs=38.5
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccc
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVE 666 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~ 666 (1117)
++|+.+++++|.||+++| +++|+++|+++++++||+ ..|+.+..+++
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~~~~~ 47 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIGQLFP 47 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHHCTST
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHHHhCc
Confidence 478999999999999999 889999999999999998 55666654443
No 136
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=97.51 E-value=0.0017 Score=82.26 Aligned_cols=149 Identities=10% Similarity=0.034 Sum_probs=104.9
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhC
Q 001235 206 KAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKN 285 (1117)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~ 285 (1117)
+....+.+ +.+++++++.+++.+++++|+|+..||-+++|+..-+++-+...+-+..-..+||-.. --....+..+
T Consensus 7 eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~ge--Gi~G~Va~tg 82 (748)
T PRK11061 7 EIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDE--GIVGLVGRLA 82 (748)
T ss_pred HHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCc--chHHHHhccC
Confidence 34444555 6699999999999999999999999999999876655554443222222223444211 1234556666
Q ss_pred CeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeE
Q 001235 286 KVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLV 365 (1117)
Q Consensus 286 ~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~ 365 (1117)
..-.|.|+...|--. +...+...+++|.|++||+.+ +++=|.|
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 666778887654110 000122468899999999876 8999999
Q ss_pred EeeccCCCCCCchhHHHHHHHHHHHHHHHH
Q 001235 366 VCHNTTPRFVPFPLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 366 ~~hh~~p~~~~~~~r~~~~~l~~~~~~~~~ 395 (1117)
.+++..|+.++......++.|+.+++..|.
T Consensus 126 ~v~~~~~~~Fs~~d~~lL~~LA~~aAiAL~ 155 (748)
T PRK11061 126 VVQQRELRQFDESEESFLVTLATQLAAILS 155 (748)
T ss_pred EEeeCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 999999999998888888888888887774
No 137
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=97.48 E-value=0.00028 Score=59.42 Aligned_cols=61 Identities=31% Similarity=0.437 Sum_probs=51.8
Q ss_pred HHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccc
Q 001235 893 LKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSII 953 (1117)
Q Consensus 893 ~~~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie 953 (1117)
.++++.++||+||||++|.++++.+.....+++...+++.+..+.+++..++++ +++++.+
T Consensus 3 ~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~ 64 (66)
T smart00388 3 REFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIE 64 (66)
T ss_pred HHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 457889999999999999999998887666666688999999999999999999 4777643
No 138
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.45 E-value=0.001 Score=78.14 Aligned_cols=132 Identities=14% Similarity=0.182 Sum_probs=97.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHH
Q 001235 602 DLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLAL 681 (1117)
Q Consensus 602 ~~~~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l 681 (1117)
+.++++.+++++..+.++.+++..+.|++.+|.+|+|.-+|+++++++|.+.++++|.++..+.+. +...+..+-
T Consensus 356 ~~l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap~-----~~~vf~~~~ 430 (712)
T COG5000 356 EALERAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSAIAPE-----LEEVFAEAG 430 (712)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhhhhhH-----HHHHHHHhh
Confidence 345567788888999999999999999999999999999999999999999999999997765432 222222221
Q ss_pred -cCCcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHH
Q 001235 682 -QGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIE 745 (1117)
Q Consensus 682 -~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se 745 (1117)
.++..+.++..+. ..|+.+.+.+..+....+ +-.|++.++.|||+...++..-...+
T Consensus 431 a~~~~~~~~ev~~~-----r~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~AQRs~AW~d 488 (712)
T COG5000 431 AAARTDKRVEVKLA-----REGEERTLNVQATREPED--NGNGYVVTFDDITDLVIAQRSAAWGD 488 (712)
T ss_pred hhcCCCccceeecc-----cCCCceeeeeeeeecccc--cCCceEEEecchHHHHHHHHHHHHHH
Confidence 2233444455544 237788888777654433 33478999999999999887655444
No 139
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.35 E-value=0.0014 Score=72.43 Aligned_cols=208 Identities=17% Similarity=0.178 Sum_probs=127.6
Q ss_pred HHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHH--cC-CcceeeEEEEE--
Q 001235 620 RLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLAL--QG-QEEQNIQFEIK-- 694 (1117)
Q Consensus 620 ~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l--~g-~~~~~~e~~~~-- 694 (1117)
.+++.....|++++++|.|.|+++.+.--+|++.-|+.|..+.+.+|+.|.+.+...+...- +. +-++.+.++..
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 45667777899999999999999999999999999999999999999999988776654332 10 01111111111
Q ss_pred ----eeccccCCceE-----EEEEEEEEeec-CCC---CEEEEEEEEEc-----cchhhhhhhhHhhHHHHHHHHHhCCC
Q 001235 695 ----THGSKINDDPI-----TLIVNACASRD-LHD---NVVGVCFVAQD-----ITPQKTVMDKFTRIEGDYKAIVQNPN 756 (1117)
Q Consensus 695 ----~~~~~~dG~~~-----~v~v~~~pi~d-~~G---~v~gv~~v~~D-----ITerK~aE~~L~~se~~l~~i~~~~~ 756 (1117)
..+....|..+ ++.+...++.- ..+ +-+|++.++.- ||+.|-- .+
T Consensus 163 lakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteikl~-----------------sN 225 (598)
T KOG3559|consen 163 LAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIKLH-----------------SN 225 (598)
T ss_pred heeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEEec-----------------cc
Confidence 11111111111 01122222211 111 34566666442 3332221 11
Q ss_pred CCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEE
Q 001235 757 PLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFG 836 (1117)
Q Consensus 757 ~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~ 836 (1117)
. =+|....|-.+++......+++||.+.+++++++...+.+.+ ...+...-...+..+....--+|
T Consensus 226 m---FmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D-----------~~~lr~~H~~ll~kGqvtTkYYR 291 (598)
T KOG3559|consen 226 M---FMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCD-----------SFHLRCAHHLLLVKGQVTTKYYR 291 (598)
T ss_pred e---EEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhh-----------HHHHHHHHHHHHhccccccHHHH
Confidence 1 256777899999999999999999999999999876555432 22222222222223333344467
Q ss_pred EEecCCcEEEEEEEEeeeeCCC
Q 001235 837 FFARNGKYAECLLCVNKKLDRE 858 (1117)
Q Consensus 837 ~~~~dG~~~~v~~~~~pi~d~~ 858 (1117)
+..+.|.++|+.-...-+.+.-
T Consensus 292 ~l~k~ggwvwvqsyat~vHnSr 313 (598)
T KOG3559|consen 292 FLLKQGGWVWVQSYATFVHNSR 313 (598)
T ss_pred HHHcCCceEEEEEeeEEEeccc
Confidence 8889999999887776665543
No 140
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.27 E-value=0.0007 Score=77.97 Aligned_cols=122 Identities=13% Similarity=0.139 Sum_probs=88.6
Q ss_pred HHHHHHHhCCCCCCCCeeeeCC---CCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHH
Q 001235 746 GDYKAIVQNPNPLIPPIFGSDE---FGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLN 822 (1117)
Q Consensus 746 ~~l~~i~~~~~~li~~I~~~D~---~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~ 822 (1117)
..++.++.-.+..-...++.+. |.-|+|+|..|+++.||.+.|++.|+..-.+.- ..+.+.+..+ .++
T Consensus 14 TFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMy-----GEltdk~ti~----k~~ 84 (971)
T KOG0501|consen 14 TFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMY-----GELTDKGTIE----KVR 84 (971)
T ss_pred hHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeee-----ccccchhhHH----HHH
Confidence 4556666655521112333332 456999999999999999999999975211110 1222233333 455
Q ss_pred HHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHH
Q 001235 823 KAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQ 876 (1117)
Q Consensus 823 ~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~ 876 (1117)
..++..+...+|+-++.++...+|+.+.+.|++++...++-++|.+.|||.-||
T Consensus 85 ~t~eN~~~~qfEillyKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 85 QTLENYETNQFEILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred HHHHhhhhcceeeEeeecCCCceEEEEEeecccCCCceEEEEEeecccchhhcC
Confidence 566666777899999999999999999999999999999999999999997665
No 141
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.13 E-value=0.0056 Score=83.21 Aligned_cols=139 Identities=12% Similarity=-0.055 Sum_probs=80.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHc-C
Q 001235 605 IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQ-G 683 (1117)
Q Consensus 605 ~~~~~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~-g 683 (1117)
+..+.+++..++.++.+++++|+|++++|.+|+|+++|++++++||++.....+.+.....+ ...+.+......... .
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 44567788888899999999999999999999999999999999997754433332221111 111111111111111 1
Q ss_pred CcceeeEEEEEeeccccCCceEEEE-EEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHH
Q 001235 684 QEEQNIQFEIKTHGSKINDDPITLI-VNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDY 748 (1117)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dG~~~~v~-v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l 748 (1117)
........... ..+|...++. ....+.....+...++++..+|||++++.+++++....+.
T Consensus 644 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~~~ 705 (1197)
T PRK09959 644 ENRTIYTQVFE----IDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERNKA 705 (1197)
T ss_pred hccccceeeEe----eecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHHHH
Confidence 11101111111 1223322222 2222223334555677888899999999988887655443
No 142
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=97.02 E-value=0.0038 Score=71.71 Aligned_cols=229 Identities=13% Similarity=0.086 Sum_probs=148.2
Q ss_pred HHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcc-eeeEEEEEee-
Q 001235 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEE-QNIQFEIKTH- 696 (1117)
Q Consensus 619 ~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~-~~~e~~~~~~- 696 (1117)
+.++++....++++..+|.|-|++...+..+|+-..+++-+++.|++|.+|++.+.+.+.-++.-... .......++.
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 45778888888999999999999999999999999999999999999999999998887655421100 0000100100
Q ss_pred -----------ccccCCc---eEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHh--------------------
Q 001235 697 -----------GSKINDD---PITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFT-------------------- 742 (1117)
Q Consensus 697 -----------~~~~dG~---~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~-------------------- 742 (1117)
....+.. ++-+.++...+.|..- |++. .|+-.+-+.---.+
T Consensus 194 ~~~~~~~~~~d~~ppens~yleRcficR~RCLLDnTs---GFLa--mdfqGklk~LhGqkkk~~~g~~lpP~LaLf~iat 268 (712)
T KOG3560|consen 194 DAILRAQEWGDGTPPENSAYLERCFICRFRCLLDNTS---GFLA--MDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIAT 268 (712)
T ss_pred ccceeeeccCccCCcccchHHhhhheeeEEEeecCCc---ceee--eecccceeeecCCcccCCCCccCCCceeEEEEec
Confidence 0001111 1334455555555433 3332 35444322110000
Q ss_pred ------hHHHHH-HHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHH
Q 001235 743 ------RIEGDY-KAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFV 815 (1117)
Q Consensus 743 ------~se~~l-~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~ 815 (1117)
.+|-+. ..|+..-. -.|+..+.+......++||...|+.|.. ...+.|-+|..
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---------KLDFALVSMDAKVKATLGYCEAELHGMP-----------GYNLVHVEDKV 328 (712)
T ss_pred CCCCchhhhhhhhhhhhhccc---------ccccceeccchhhhhhhccchhhccCCC-----------ccceeehhhhh
Confidence 000000 01111111 1355666677788889999999999865 33666777777
Q ss_pred HHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHH
Q 001235 816 NLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1117)
Q Consensus 816 ~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (1117)
-..+.-.+.++.++.--.-+|...++|++.||..++.-++ .+|++-.+++.-+-.++
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 6777778888888888899999999999999988876665 67887777777666665
No 143
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.01 E-value=0.01 Score=74.80 Aligned_cols=114 Identities=13% Similarity=0.181 Sum_probs=79.7
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc-cee
Q 001235 610 ELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-EQN 688 (1117)
Q Consensus 610 eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~-~~~ 688 (1117)
++......+..++++.++|++++|.+|+|+++|+++++++|++.++++|+++.++++... .+..++..+. ...
T Consensus 197 ~~~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~~------~l~~vl~~~~~~~~ 270 (638)
T PRK11388 197 ESNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLTLPA------VLQQAIKQAHPLKH 270 (638)
T ss_pred HHHHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhccch------HHHHHHhcCCceee
Confidence 334444556679999999999999999999999999999999999999999998875321 1223333332 212
Q ss_pred eEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhh
Q 001235 689 IQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKT 736 (1117)
Q Consensus 689 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~ 736 (1117)
.+..+ ..+|..+++.++..|+.+..| .+++.+.+|++..++
T Consensus 271 ~~~~l-----~~~g~~~~~~v~~~Pi~~~~g--~~~v~~l~~~~~~~~ 311 (638)
T PRK11388 271 VEVTF-----ESQGQFIDAVITLKPIIEGQG--TSFILLLHPVEQMRQ 311 (638)
T ss_pred EEEEE-----ecCCceEEEEEEEEeecccCc--eEEEEEehhhHHHHH
Confidence 22222 124666788899999875444 345666788887654
No 144
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.01 E-value=0.002 Score=74.33 Aligned_cols=99 Identities=21% Similarity=0.225 Sum_probs=74.0
Q ss_pred CCcEEeecHHHHHHcCCCcccccCCccc-cccccCcHHH-HHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEEE
Q 001235 635 DGLVNGWNTKIAELTGLSVDKAIGKHFL-TLVEDSSIDT-VKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNAC 712 (1117)
Q Consensus 635 dG~I~~~N~a~~~l~G~s~eeliG~~~~-dlv~~~~~~~-~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~ 712 (1117)
|.-|+|+|+.||.+-||.+.|++.++.. .+++.+..+. -.+.++..+..-+...+|+-+. +|+..++|+.+...
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEilly----KKN~TPvW~~vqiA 114 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLY----KKNRTPVWLLVQIA 114 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEee----ecCCCceEEEEEee
Confidence 6779999999999999999999999876 4444432211 1122333443333333344433 67899999999999
Q ss_pred EeecCCCCEEEEEEEEEccchhhhh
Q 001235 713 ASRDLHDNVVGVCFVAQDITPQKTV 737 (1117)
Q Consensus 713 pi~d~~G~v~gv~~v~~DITerK~a 737 (1117)
|++++.+.++-+++.+.|||..|+-
T Consensus 115 PIrNe~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 115 PIRNEKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred cccCCCceEEEEEeecccchhhcCC
Confidence 9999999999999999999999884
No 145
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.01 E-value=0.21 Score=63.54 Aligned_cols=201 Identities=11% Similarity=0.064 Sum_probs=113.4
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHh
Q 001235 205 AKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMK 284 (1117)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~ 284 (1117)
..+-..+.+ ..|++++++.+-..++++..+|||-|.-+|+.. +.+..=....+-+++ .| + ....+..
T Consensus 12 ~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~---~~----~---~~~~~~~ 78 (686)
T PRK15429 12 FDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV---KY----E---DETVLAH 78 (686)
T ss_pred HHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch---hc----c---chhhhcc
Confidence 334344445 459999999999999999999999999999976 555421111111110 00 0 0111222
Q ss_pred CCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhH--HHHHHhcCceeEEEEEEEEcCCccccCCCcccccccce
Q 001235 285 NKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCH--LQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLW 362 (1117)
Q Consensus 285 ~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h--~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lW 362 (1117)
+.+..+- .+++|+-+++..++-..|-- ..+...| .+-+.|||.+. ++..
T Consensus 79 g~~g~vl-------------~~~~~l~~~~~~~~~~~~~l~~~~~~~~~--~~~lgvPl~~~--------------~~v~ 129 (686)
T PRK15429 79 GPVRRIL-------------SRPDTLHCSYEEFCETWPQLAAGGLYPKF--GHYCLMPLAAE--------------GHIF 129 (686)
T ss_pred CcceEEe-------------ecCceEEEchHHhhhccHHHhhcccccCc--cceEEeceeeC--------------CeeE
Confidence 2222211 12444444333333322211 1122355 45888999988 9999
Q ss_pred eeEEeeccCCCCCCchhHHHHHHHHHHHHHHHHHHHH-HHHHHH----HHHHHHHHHHHHHh----hhcCCCcccccC-C
Q 001235 363 GLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELE-LEYQIL----EKNILRTQTLLCDM----LMRDAPLGIVTQ-S 432 (1117)
Q Consensus 363 Gl~~~hh~~p~~~~~~~r~~~~~l~~~~~~~~~~~~~-~~~~~~----~~~~~~~~~~~~~~----~~~~~~~~~~~~-~ 432 (1117)
|-|.--.+.+...+.+......+|+++.+..|..... .+.+.+ +++... +..+.++ +....+..+... .
T Consensus 130 G~l~l~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~-~~~L~eIs~~l~s~~dl~ell~~I~ 208 (686)
T PRK15429 130 GGCEFIRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDN-FRILVAITNAVLSRLDMDELVSEVA 208 (686)
T ss_pred EEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH-HHHHHHHHHHHccCCCHHHHHHHHH
Confidence 9999877778888999999999999999998864321 111111 111111 1222222 111222222222 3
Q ss_pred cchhhhccCCEEEEEE
Q 001235 433 PNIMDLVKCDGAALLY 448 (1117)
Q Consensus 433 ~~~~~l~~~~g~a~~~ 448 (1117)
..+..+++|+.+.|+.
T Consensus 209 ~~i~~~~~a~~~~I~L 224 (686)
T PRK15429 209 KEIHYYFDIDAISIVL 224 (686)
T ss_pred HHHHHHhCCCEEEEEE
Confidence 4677789999988765
No 146
>PF13589 HATPase_c_3: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; PDB: 3IED_A 2XCM_B 2JKI_B 3OPD_A 2O1V_B 2GQP_A 2O1W_C 1YT2_A 1TC6_A 2H8M_B ....
Probab=96.87 E-value=0.00084 Score=66.80 Aligned_cols=89 Identities=19% Similarity=0.286 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC----------CCCCc
Q 001235 1009 QQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG----------DTSEE 1078 (1117)
Q Consensus 1009 ~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~----------~~~Gt 1078 (1117)
.++|.+|+.||+++.. ..|.|.+..... + ...|.|.|||.||+.+.+...|.... ..+.-
T Consensus 4 ~~al~ElI~Ns~DA~a--~~I~I~i~~~~~--~------~~~i~I~DnG~Gm~~~~l~~~~~~g~s~k~~~~~~~~~G~~ 73 (137)
T PF13589_consen 4 EDALRELIDNSIDAGA--TNIKISIDEDKK--G------ERYIVIEDNGEGMSREDLESFFRIGRSSKKSEKDRQSIGRF 73 (137)
T ss_dssp THHHHHHHHHHHHHHH--HHEEEEEEEETT--T------TTEEEEEESSS---HHHHHHHTTCHHTHHHHHHHGGGGGGG
T ss_pred HHHHHHHHHHHHHccC--CEEEEEEEcCCC--C------CcEEEEEECCcCCCHHHHHHhccccCCCCCchhhhhcCCCc
Confidence 3789999999999764 457777776532 1 24678889999999999999776532 11134
Q ss_pred ccc--HHHHHHHHHHcCCEEEEEeeCCe--EEEEEEEe
Q 001235 1079 GIS--LLISRKLVKLMNGDVQYLREAGK--STFIVSVE 1112 (1117)
Q Consensus 1079 GLG--L~ivr~iVe~~gG~I~v~s~~g~--ttF~i~LP 1112 (1117)
|+| +++. .++.++.+.|...+ .++++..+
T Consensus 74 G~G~k~A~~-----~~~~~~~v~S~~~~~~~~~~~~~~ 106 (137)
T PF13589_consen 74 GIGLKLAIF-----SLGDRVEVISKTNGESFTYTIDYD 106 (137)
T ss_dssp TSGCGGGGG-----GTEEEEEEEEESTTSSSEEEEEEE
T ss_pred ceEHHHHHH-----HhcCEEEEEEEECCCCcEEEEEEe
Confidence 777 4444 57899999997443 66666665
No 147
>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=96.83 E-value=0.0031 Score=49.90 Aligned_cols=64 Identities=27% Similarity=0.372 Sum_probs=55.3
Q ss_pred HHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHH
Q 001235 617 EMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLA 680 (1117)
Q Consensus 617 ~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~ 680 (1117)
+++.+++.++++++.+|.++.+.++|+.+.+++|++..++.|+.+.+++++.+...+...+..+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
T smart00091 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQRL 65 (67)
T ss_pred hHHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHHH
Confidence 4567889999999999999999999999999999999999999888888888877666655543
No 148
>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=96.78 E-value=0.0046 Score=51.41 Aligned_cols=59 Identities=24% Similarity=0.342 Sum_probs=48.1
Q ss_pred HHHHHHHHHhhhhhhHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHHHHHHhhc-ccc
Q 001235 892 RLKALAYTKRQIRNPLSGIIFSRKMMEGTE-LGAEQKRLLHTSAQCQRQLHKILDDS-DLD 950 (1117)
Q Consensus 892 k~~~la~isHEIrnPL~~I~~~~~LL~~~~-l~~~~~~~l~~i~~~~~~l~~ii~dL-d~s 950 (1117)
+.++.+.++||+||||+++.++++.+.... ..+.....++.+..+..++..+++++ +++
T Consensus 4 ~~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~ 64 (65)
T cd00082 4 KGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLS 64 (65)
T ss_pred HHHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445788899999999999999988887543 35677888899999999999999984 544
No 149
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=96.66 E-value=0.0018 Score=54.99 Aligned_cols=42 Identities=24% Similarity=0.307 Sum_probs=35.2
Q ss_pred HHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcch
Q 001235 746 GDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLL 794 (1117)
Q Consensus 746 ~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l 794 (1117)
++|+.++++++. ||++.| +++|+++|+++++++||+ ..|+.+
T Consensus 1 e~~~~l~~~~~~---~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPD---GILIID-GGRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSS---EEEEEE-TSBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCcc---ceEEEE-CCChHHhhHHHHHHhCCC---CCCCCH
Confidence 478999999999 999999 889999999999999998 555543
No 150
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.53 E-value=0.0052 Score=68.90 Aligned_cols=115 Identities=20% Similarity=0.214 Sum_probs=95.1
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEe
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKT 695 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~ 695 (1117)
+++.+++++.|.-+-.+|.++++.+.|+. .++|..++.. +|++....-+|.....+...+.....|..... ++-+.
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 56788999999989999999999999998 8888877655 69999988889999999998888887765432 22222
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhh
Q 001235 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1117)
Q Consensus 696 ~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~ 740 (1117)
....++.++..+++|.+|...|++-+.+|||.-|..+-+
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 344567788899999999999999999999999987654
No 151
>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=96.23 E-value=0.054 Score=53.99 Aligned_cols=110 Identities=15% Similarity=0.078 Sum_probs=86.0
Q ss_pred HHHHHHHHhcCccEEEEeC--CCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeE-EE
Q 001235 616 SEMVRLIETATVPILAVDV--DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQ-FE 692 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~--dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e-~~ 692 (1117)
..++.+++ +|.+|+..|. |=.++|.|.++.++|+++-+++++.+..--..+..++.-...+.++.+.+-..+.. ++
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 44566666 9999999875 45899999999999999999999999987778888888888998888766432221 22
Q ss_pred EEeeccccCCceEEEE-EEEEEeecCCCCEEEEEEEEEcc
Q 001235 693 IKTHGSKINDDPITLI-VNACASRDLHDNVVGVCFVAQDI 731 (1117)
Q Consensus 693 ~~~~~~~~dG~~~~v~-v~~~pi~d~~G~v~gv~~v~~DI 731 (1117)
+ .+.|..+++. ..+-.+.|++|+..|..+++.+-
T Consensus 111 i-----ss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~W 145 (148)
T PF08670_consen 111 I-----SSTGRRFRIERATVWNLIDEDGNYCGQAAMFSNW 145 (148)
T ss_pred E-----cCCCCeEEEeceEEEEEEcCCCCEEEEEEEEeee
Confidence 2 3457777776 66777899999999998887653
No 152
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=96.23 E-value=0.016 Score=72.06 Aligned_cols=55 Identities=13% Similarity=0.200 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC
Q 001235 1007 RLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG 1073 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~ 1073 (1117)
++..++.+|+.||+++. ...|.|.+... + ...|+|.|||.||+++.+..+|.++.
T Consensus 22 ~~~svvkElveNsiDAg--at~I~v~i~~~-g---------~~~i~V~DnG~Gi~~~~~~~~~~~~~ 76 (617)
T PRK00095 22 RPASVVKELVENALDAG--ATRIDIEIEEG-G---------LKLIRVRDNGCGISKEDLALALARHA 76 (617)
T ss_pred CHHHHHHHHHHHHHhCC--CCEEEEEEEeC-C---------eEEEEEEEcCCCCCHHHHHHHhhccC
Confidence 45689999999999976 56788887432 2 57899999999999999999998863
No 153
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.16 E-value=0.46 Score=47.15 Aligned_cols=191 Identities=15% Similarity=0.173 Sum_probs=113.9
Q ss_pred HHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHH
Q 001235 896 LAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASIS 975 (1117)
Q Consensus 896 la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~ 975 (1117)
.+.++|++-.|..+|..-++||++...+++...++....+... .. |.|.++--|-..-.-..+|-.+.=.....
T Consensus 19 csRvCHDiISPvgAInnGLeLLdeg~addDAm~LIrsSArnas---~r---LqFaR~AFGAsgSag~~iDtgeaek~A~~ 92 (214)
T COG5385 19 CSRVCHDIISPVGAINNGLELLDEGGADDDAMDLIRSSARNAS---VR---LQFARLAFGASGSAGASIDTGEAEKAAQD 92 (214)
T ss_pred HHHHHhhccCcHHHhhchhhhhccCCccHHHHHHHHHHhhhHH---HH---HHHHHHHhcccccccccccchhHHHHHHH
Confidence 5678999999999999999999998888877777666544332 22 33444433322222234444443332222
Q ss_pred HHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEee
Q 001235 976 QVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITH 1055 (1117)
Q Consensus 976 ~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D 1055 (1117)
.+. .+| -++..+.+..+ +.-... ..+.||+.-|--..|.+|.+.+++..-.. .-+|+|.-
T Consensus 93 ~~a---~ek-pe~~W~g~r~~----~~Kn~v---kllLNl~lia~~aiPrGG~~~vtle~~e~---------d~rfsi~a 152 (214)
T COG5385 93 FFA---NEK-PELTWNGPRAI----LPKNRV---KLLLNLFLIAYGAIPRGGSLVVTLENPET---------DARFSIIA 152 (214)
T ss_pred HHh---ccC-CcccccCChhh----cCcchH---HHHHHHHHHHcccCCCCCeeEEEeecCCc---------CceEEEEe
Confidence 221 223 56777766653 233333 45688888888888889988887765433 22344444
Q ss_pred cCC--CCChhhhhhccCC-C-CCCCCccccHHHHHHHHHHcCCEEEEEeeCCeEEEEEEEe
Q 001235 1056 AGG--GIPEPLLDQMFGS-E-GDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVE 1112 (1117)
Q Consensus 1056 ~G~--GI~~e~~~~iFe~-f-~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF~i~LP 1112 (1117)
.|. -+|++.++-.=.. - ....+...-=|-.--+++.-|++|.+....+...|+-++|
T Consensus 153 kG~m~Rvppk~lel~~G~~~eE~vdahsVQpyYt~lLa~eAgm~I~v~~~~e~iv~~A~v~ 213 (214)
T COG5385 153 KGRMMRVPPKFLELHSGEPPEEAVDAHSVQPYYTLLLAEEAGMTISVHATAERIVFTAWVV 213 (214)
T ss_pred cCccccCCHHHHhhhcCCCccccCCCccccHHHHHHHHHHcCCeEEEEeccceEEEEEecc
Confidence 454 3466544421110 0 0111223344555567899999999999888877776654
No 154
>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=95.53 E-value=0.078 Score=46.84 Aligned_cols=74 Identities=12% Similarity=0.114 Sum_probs=61.4
Q ss_pred HHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHH
Q 001235 898 YTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQV 977 (1117)
Q Consensus 898 ~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~ 977 (1117)
++.|.+||.|+.|.+++.+..+...+++.+..+..+......|..+-+.|.-+. ....+++.++++.++..+
T Consensus 1 E~~HRVkNnLq~i~sll~lq~~~~~~~e~~~~L~~~~~RI~aia~vh~~L~~~~--------~~~~v~l~~yl~~L~~~l 72 (76)
T PF07568_consen 1 ELHHRVKNNLQIISSLLRLQARRSEDPEAREALEDAQNRIQAIALVHEQLYQSE--------DLSEVDLREYLEELCEDL 72 (76)
T ss_pred ChHHhHHhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCC--------CCCeecHHHHHHHHHHHH
Confidence 378999999999999999998888888889999888887877777777764333 356899999999999877
Q ss_pred Hh
Q 001235 978 MM 979 (1117)
Q Consensus 978 ~~ 979 (1117)
..
T Consensus 73 ~~ 74 (76)
T PF07568_consen 73 RQ 74 (76)
T ss_pred HH
Confidence 54
No 155
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=95.36 E-value=0.011 Score=66.34 Aligned_cols=96 Identities=15% Similarity=0.091 Sum_probs=80.7
Q ss_pred CeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEec
Q 001235 761 PIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFAR 840 (1117)
Q Consensus 761 ~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~ 840 (1117)
+|-+.|.+..|.|+|++++.++|+-+.|++|+...+ +. +....+..+...++..+..+..+..+..-+++
T Consensus 169 AiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~ad-lp---------kkdknradlldtintcikkgke~qG~~~aRRk 238 (775)
T KOG1229|consen 169 AIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEAD-LP---------KKDKNRADLLDTINTCIKKGKEAQGEEEARRK 238 (775)
T ss_pred hheeccchhHHHHhcHHHHhhhcchhhhhcCCchhh-cc---------ccccchhhhhhhhhHhhhcCccccchHHHhhc
Confidence 788999999999999999999999999999998431 11 11234566778899999999999888888999
Q ss_pred CCcEEEEEEEEeeeeCCCCCEEEEEe
Q 001235 841 NGKYAECLLCVNKKLDREGAVTGVFC 866 (1117)
Q Consensus 841 dG~~~~v~~~~~pi~d~~G~v~g~v~ 866 (1117)
.|......+...|+.+..|++..++.
T Consensus 239 sgdS~dqh~~itP~~gqggkirhfvs 264 (775)
T KOG1229|consen 239 SGDSCDQHFIITPFAGQGGKIRHFVS 264 (775)
T ss_pred cCCcccceEEEeeecCCCCceeeehh
Confidence 99998889999999999999987764
No 156
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=95.30 E-value=0.034 Score=69.12 Aligned_cols=73 Identities=15% Similarity=0.301 Sum_probs=53.6
Q ss_pred cHHHHHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh--------ccCCCC
Q 001235 1004 DSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ--------MFGSEG 1073 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~--------iFe~f~ 1073 (1117)
+...|..++.+++.||++.... ...|.|.+.... .|+|.|||.|||.+..+. +|....
T Consensus 34 ~~~gl~~lv~EivdNaiDe~~ag~a~~I~V~i~~dg------------~I~V~DnGrGIP~~~~~~~~~~~~E~v~t~lh 101 (631)
T PRK05559 34 DTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADG------------SVSVRDNGRGIPVGIHPEEGKSGVEVILTKLH 101 (631)
T ss_pred CCchhhhhhhhhhccccchhhcCCCCEEEEEEeCCC------------cEEEEEcCCCCCcccccccCCcchheeeeecc
Confidence 4567889999999999997543 347777766432 488999999999998887 776521
Q ss_pred ----------CC-CC-ccccHHHHHHH
Q 001235 1074 ----------DT-SE-EGISLLISRKL 1088 (1117)
Q Consensus 1074 ----------~~-~G-tGLGL~ivr~i 1088 (1117)
.. .| .|.|++.+--+
T Consensus 102 agsKf~~~~yk~SgGl~GvGls~vNal 128 (631)
T PRK05559 102 AGGKFSNKAYKFSGGLHGVGVSVVNAL 128 (631)
T ss_pred ccCccCCccccccCcccccchhhhhhh
Confidence 11 23 58999988554
No 157
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=95.30 E-value=0.028 Score=67.12 Aligned_cols=99 Identities=12% Similarity=0.102 Sum_probs=78.8
Q ss_pred EeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEE
Q 001235 632 VDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNA 711 (1117)
Q Consensus 632 ~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~ 711 (1117)
...|-+|.|+.+++.+++||++++++|+++.+++|..|.+.+.+-....+..+....-.+++ ..++|+++|+...+
T Consensus 280 hs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~----lak~GGyvWlQTqA 355 (768)
T KOG3558|consen 280 HSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRL----LAKNGGYVWLQTQA 355 (768)
T ss_pred eecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHH----HHhcCCeEEEEeee
Confidence 56789999999999999999999999999999999999999999999998777654434443 47789999999999
Q ss_pred EEeecCC-CCEEEEEEEEEccchh
Q 001235 712 CASRDLH-DNVVGVCFVAQDITPQ 734 (1117)
Q Consensus 712 ~pi~d~~-G~v~gv~~v~~DITer 734 (1117)
+.+.+.. ++.--+++|-.=|+.+
T Consensus 356 TVi~~tkn~q~q~IicVnYVlS~~ 379 (768)
T KOG3558|consen 356 TVIYNTKNPQEQNIICVNYVLSNI 379 (768)
T ss_pred EEEecCCCCCcceEEEEEeeeccc
Confidence 8887543 3334455554444444
No 158
>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=95.05 E-value=0.16 Score=48.59 Aligned_cols=62 Identities=15% Similarity=0.317 Sum_probs=51.1
Q ss_pred HHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccc-cccccCcHHHHHHHHHHHHc
Q 001235 621 LIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFL-TLVEDSSIDTVKRMLYLALQ 682 (1117)
Q Consensus 621 lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~-dlv~~~~~~~~~~~l~~~l~ 682 (1117)
-++..|-|++-+|.+|+|+..|.+-.++.|++++.++|+++. ++.|-.....+...+.+..+
T Consensus 21 elD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~ 83 (124)
T TIGR02373 21 QFDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVA 83 (124)
T ss_pred HhhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhh
Confidence 378999999999999999999999999999999999999998 55554455556655555443
No 159
>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=94.97 E-value=0.71 Score=58.80 Aligned_cols=152 Identities=14% Similarity=0.085 Sum_probs=89.6
Q ss_pred HHHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHH
Q 001235 204 AAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFM 283 (1117)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~ 283 (1117)
..+..++|.+ +.+.+++++.+++.+.+++++++..+|-.+++ .+........ +++. .+...|. +.|-. +.+-.
T Consensus 307 ~l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~-~~~~~~~~~~-~~~~-~~~~~~~-~~~~~-~~~~~ 379 (679)
T TIGR02916 307 WLRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGN-DGLYRPAARW-NQPL-AQAFEPS-DSAFC-QFLQE 379 (679)
T ss_pred HHHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCC-CCEEeeehhc-CCCC-cccCCCC-CCHHH-HHHHh
Confidence 3567778877 55899999999999999999999999965544 3544443321 1111 1112222 22211 12222
Q ss_pred hCCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCccccccccee
Q 001235 284 KNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWG 363 (1117)
Q Consensus 284 ~~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWG 363 (1117)
.+++--+.+....| +. .++.+..+..+..-++.+.+||..+ +++.|
T Consensus 380 ~~~v~~~~~~~~~~-----~~---------------~~~~~~~~~~~~~~~~~l~vPL~~~--------------~~~~G 425 (679)
T TIGR02916 380 SGWIINLEEARSEP-----DH---------------YSGLVLPEWLREIPNAWLIVPLISG--------------EELVG 425 (679)
T ss_pred CCCcccchhhcCCc-----cc---------------ccccccchhhhcCCCceEEEEeccC--------------CEEEE
Confidence 33321111111111 00 0000111122223356899999877 89999
Q ss_pred eEEeecc-CCCCCCchhHHHHHHHHHHHHHHHHH
Q 001235 364 LVVCHNT-TPRFVPFPLRYACEFLAQVFAIHVNK 396 (1117)
Q Consensus 364 l~~~hh~-~p~~~~~~~r~~~~~l~~~~~~~~~~ 396 (1117)
.+++-+. .++.++.+.+...+.++..++..+..
T Consensus 426 ~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~~ 459 (679)
T TIGR02916 426 FVVLARPRTAGEFNWEVRDLLKTAGRQAASYLAQ 459 (679)
T ss_pred EEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9987665 56678889999999999988887754
No 160
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=94.60 E-value=0.21 Score=54.79 Aligned_cols=112 Identities=13% Similarity=0.114 Sum_probs=81.0
Q ss_pred HHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCc-ceeeEEEEEeec
Q 001235 619 VRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQE-EQNIQFEIKTHG 697 (1117)
Q Consensus 619 ~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~-~~~~e~~~~~~~ 697 (1117)
..++++.+.+++.+|.+|.|.|+|++++.+||.|...+.|.++.++++....- ...+......+. ....+..+.
T Consensus 10 ~~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs~l--l~ll~q~~~~~~~~~~~~v~l~--- 84 (363)
T COG3852 10 GAILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPFGSLL--LSLLDQVLERGQPVTEYEVTLV--- 84 (363)
T ss_pred HhHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCcHH--HHHHHHHHHhcCCcccceeeee---
Confidence 36789999999999999999999999999999999999999999988654432 334555543332 222233333
Q ss_pred cccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhh
Q 001235 698 SKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDK 740 (1117)
Q Consensus 698 ~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~ 740 (1117)
.+|....+.....|+-...|-+ +..++-+....+...+
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 4689999999999998766644 3445555555544444
No 161
>PF10090 DUF2328: Uncharacterized protein conserved in bacteria (DUF2328); InterPro: IPR018762 Members of this family of hypothetical bacterial proteins have no known function.
Probab=94.41 E-value=2.7 Score=43.87 Aligned_cols=175 Identities=12% Similarity=0.098 Sum_probs=106.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcE
Q 001235 908 SGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIR 987 (1117)
Q Consensus 908 ~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~ 987 (1117)
.+|...++||......+... .++-|..+++....-+.- .|+--|.... -..++..++-.- + ........++
T Consensus 2 GAI~NGLELL~~~~~~~~~~-~~~LI~~Sa~~A~aRl~F---~RlAFGaag~-~~~i~~~e~~~~-~---~~~~~~~r~~ 72 (182)
T PF10090_consen 2 GAINNGLELLDDEGDPEMRP-AMELIRESARNASARLRF---FRLAFGAAGS-GQQIDLGEARSV-L---RGYFAGGRIT 72 (182)
T ss_pred cchhhhHHHHcCCCCccchH-HHHHHHHHHHHHHHHHHH---HHHHcCCCCC-CCCCCHHHHHHH-H---HHHHhCCceE
Confidence 46778889998766533322 667776666666555554 3333333322 346666664332 2 2233334567
Q ss_pred EEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCC--CCChhhh
Q 001235 988 IVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGG--GIPEPLL 1065 (1117)
Q Consensus 988 i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~--GI~~e~~ 1065 (1117)
+....+... + +....+++.|++.-+....|-+|.|+|.+....+ ...++|.=+|. -+|++..
T Consensus 73 l~W~~~~~~----~---~k~~vklllnl~l~a~~alprGG~i~V~~~~~~~---------~~~~~v~a~G~~~~~~~~~~ 136 (182)
T PF10090_consen 73 LDWQVERDL----L---PKPEVKLLLNLLLCAEDALPRGGEITVSIEGSEG---------DGGWRVRAEGPRARLDPDLW 136 (182)
T ss_pred EEccCcccc----C---CHHHHHHHHHHHHHHHhhcCCCCEEEEEEeccCC---------CceEEEEEeccccCCCHHHH
Confidence 777766652 1 2233488899999999999999999998666555 23455555555 4566554
Q ss_pred hhccCCC--CCCCCccccHHHHHHHHHHcCCEEEEEeeCCeEEE
Q 001235 1066 DQMFGSE--GDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTF 1107 (1117)
Q Consensus 1066 ~~iFe~f--~~~~GtGLGL~ivr~iVe~~gG~I~v~s~~g~ttF 1107 (1117)
.-+=..- ........--+....+++..|++|.++...+..+|
T Consensus 137 ~~L~g~~~~~~l~~~~VQ~~~~~~la~~~G~~l~~~~~~~~i~l 180 (182)
T PF10090_consen 137 AALAGEDPEEDLDPRNVQFYLLPLLAREAGRRLSVEATEDAIVL 180 (182)
T ss_pred HHhcCCCCCCCCCHHhHHHHHHHHHHHHcCCeEEEEecCCEEEE
Confidence 4332221 12234456677888999999999999987665444
No 162
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=94.28 E-value=0.65 Score=61.14 Aligned_cols=119 Identities=13% Similarity=0.102 Sum_probs=73.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCccEEEEe-CCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcC
Q 001235 605 IEGMKELEAVTSEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQG 683 (1117)
Q Consensus 605 ~~~~~eL~~~~~~l~~lie~a~~gi~~~D-~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g 683 (1117)
.+..++|++.++.++.+++.+|+|+++++ .+|.++.+|+.+..++|+...+ +.... ......
T Consensus 323 ~~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~-------------~~~~~----~~~~~~ 385 (924)
T PRK10841 323 ESNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHE-------------DRQRL----TQIICG 385 (924)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChh-------------HHHHH----HHHHhc
Confidence 34556788889999999999999999997 6999999999999999864322 11111 111111
Q ss_pred CcceeeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHH
Q 001235 684 QEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKA 750 (1117)
Q Consensus 684 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~ 750 (1117)
..... .... ..++.. +.+.....+.. +.. ..++++.|||+++++|+++++..+..+.
T Consensus 386 ~~~~~--~~~~----~~~~~~--~~i~~~~~~~~-~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~ 442 (924)
T PRK10841 386 QQVNF--VDVL----TSNNTN--LQISFVHSRYR-NEN-VAICVLVDVSARVKMEESLQEMAQAAEQ 442 (924)
T ss_pred cccce--eeEE----cCCCcE--EEEEEEeeeec-Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHHH
Confidence 11111 1111 112333 33333333322 222 3567889999999999998876655543
No 163
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=94.18 E-value=0.15 Score=56.98 Aligned_cols=56 Identities=25% Similarity=0.334 Sum_probs=50.8
Q ss_pred HHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHH
Q 001235 616 SEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSID 671 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~ 671 (1117)
-.+.+++++.|++++.+|..|.+..+|++++++||.+.+++.|..+..++....-.
T Consensus 80 l~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~ 135 (511)
T COG3283 80 LALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL 135 (511)
T ss_pred HHHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHH
Confidence 45778999999999999999999999999999999999999999999888766543
No 164
>TIGR01059 gyrB DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.
Probab=94.03 E-value=0.14 Score=64.31 Aligned_cols=75 Identities=13% Similarity=0.223 Sum_probs=50.1
Q ss_pred cHHHHHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh--------ccCC--
Q 001235 1004 DSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ--------MFGS-- 1071 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~--------iFe~-- 1071 (1117)
++.-|.+++.+|+.||++-... ...|.|.+... + .|+|.|||.|||.+.... +|.-
T Consensus 27 ~~~gl~~vv~Elv~NaiDe~~ag~a~~I~V~i~~~-g-----------~I~V~DnG~GIp~~~h~~~ki~~~e~i~~~l~ 94 (654)
T TIGR01059 27 GETGLHHLVYEVVDNSIDEAMAGYCDTINVTINDD-G-----------SVTVEDNGRGIPVDIHPEEGISAVEVVLTVLH 94 (654)
T ss_pred CcchHHhhhHHhhhccccccccCCCCEEEEEEeCC-C-----------cEEEEEeCCCcCccccCcCCCCchHHheeeec
Confidence 3456889999999999984322 45787776642 2 289999999999875432 3332
Q ss_pred ----CC-----CCCC-ccccHHHHHHHHH
Q 001235 1072 ----EG-----DTSE-EGISLLISRKLVK 1090 (1117)
Q Consensus 1072 ----f~-----~~~G-tGLGL~ivr~iVe 1090 (1117)
|. .+.| .|.||+.+-.+-+
T Consensus 95 ag~kf~~~~~k~s~G~~G~gl~~inalS~ 123 (654)
T TIGR01059 95 AGGKFDKDSYKVSGGLHGVGVSVVNALSE 123 (654)
T ss_pred ccCccCCCcceecCCccchhHHHHHHhcC
Confidence 11 1223 5999988855544
No 165
>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=93.89 E-value=0.73 Score=46.08 Aligned_cols=111 Identities=14% Similarity=-0.001 Sum_probs=81.7
Q ss_pred HHHHHHHHhCCCCCCCCeeeeC--CCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHH
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSD--EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLN 822 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D--~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~ 822 (1117)
+..++.+++ .|. +|+-.| .+-.++|.|.++.++++++-+|+++.+. ..-..+..+......+.
T Consensus 31 ~~~~~~L~~-ap~---ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPs-----------r~sae~~~r~er~~lL~ 95 (148)
T PF08670_consen 31 EELAKALWH-APF---AILSHGTKADPIFIYANQAALDLFETTWDELVGLPS-----------RLSAEEPERKERQSLLA 95 (148)
T ss_pred HHHHHHHHc-CCC---EEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcH-----------hhccChhhHHHHHHHHH
Confidence 456677777 555 566665 4568999999999999999999999873 12223555666677788
Q ss_pred HHhcCCCCceEeEEEEecCCcEEEEE-EEEeeeeCCCCCEEEEEeehhH
Q 001235 823 KAMSGQDPEKVPFGFFARNGKYAECL-LCVNKKLDREGAVTGVFCFLQL 870 (1117)
Q Consensus 823 ~~l~g~~~~~~e~~~~~~dG~~~~v~-~~~~pi~d~~G~v~g~v~i~~D 870 (1117)
++...+-.....-.-..+.|+.++++ .++=.+.|++|...|.-..+.+
T Consensus 96 ~v~~qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 96 QVMQQGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSN 144 (148)
T ss_pred HHHHhCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEee
Confidence 88887776666666678888876664 4578899999999887766543
No 166
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=93.80 E-value=0.15 Score=63.56 Aligned_cols=75 Identities=15% Similarity=0.233 Sum_probs=50.9
Q ss_pred cHHHHHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh--------ccCC--
Q 001235 1004 DSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ--------MFGS-- 1071 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~--------iFe~-- 1071 (1117)
++.-|..++.+|+.||++-... ...|.|.+...+ .|+|.|||.|||.+.... +|.-
T Consensus 34 ~~~gl~~~v~ElvdNaiDe~~ag~a~~I~V~i~~~g------------~I~V~DnG~GIp~~~h~~~ki~~~e~i~~~lh 101 (638)
T PRK05644 34 GERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDG------------SITVTDNGRGIPVDIHPKTGKPAVEVVLTVLH 101 (638)
T ss_pred ChhhHHhhhHHhhhcccccccCCCCCEEEEEEeCCC------------cEEEEEeCccccCCccCCCCCCchHHheeeec
Confidence 4567889999999999984321 457887766432 488999999999975442 4432
Q ss_pred ----C----CC-CCC-ccccHHHHHHHHH
Q 001235 1072 ----E----GD-TSE-EGISLLISRKLVK 1090 (1117)
Q Consensus 1072 ----f----~~-~~G-tGLGL~ivr~iVe 1090 (1117)
| +. +.| .|.||+.+-.+-+
T Consensus 102 ag~kfd~~~yk~s~G~~G~Gls~vnalS~ 130 (638)
T PRK05644 102 AGGKFGGGGYKVSGGLHGVGVSVVNALST 130 (638)
T ss_pred ccCccCCCcccccCCccccchhhhhheec
Confidence 1 11 223 5999998855544
No 167
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer.
Probab=93.75 E-value=0.095 Score=65.08 Aligned_cols=75 Identities=15% Similarity=0.288 Sum_probs=51.6
Q ss_pred cHHHHHHHHHHHHHHHhhccC--CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhh--------hhhcc-CC-
Q 001235 1004 DSIRLQQVLADFLSISINFVP--NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPL--------LDQMF-GS- 1071 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~--~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~--------~~~iF-e~- 1071 (1117)
....+..++.+|+.||++-.- ....|.|.+.... .|+|.|||.|||.+. .+-+| ..
T Consensus 27 gs~~~~~lv~ElvdNsiDE~~ag~a~~I~V~i~~d~------------~I~V~DnGrGIp~~~h~~~g~~~~e~v~t~lh 94 (625)
T TIGR01055 27 DTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQDQ------------SIEVFDNGRGMPVDIHPKEGVSAVEVILTTLH 94 (625)
T ss_pred CCCCcceeehhhhhcccchhhcCCCCEEEEEEeCCC------------eEEEEecCCccCcccccccCCcHHHHhhhccc
Confidence 334457899999999998221 1567888775442 388889999999988 66666 22
Q ss_pred ----C----CC-CCC-ccccHHHHHHHHH
Q 001235 1072 ----E----GD-TSE-EGISLLISRKLVK 1090 (1117)
Q Consensus 1072 ----f----~~-~~G-tGLGL~ivr~iVe 1090 (1117)
| +. +.| .|.||+.+-.+-+
T Consensus 95 agsK~~~~~~~~SgG~~GvGls~vnalS~ 123 (625)
T TIGR01055 95 AGGKFSNKNYHFSGGLHGVGISVVNALSK 123 (625)
T ss_pred ccCCCCCCcceecCCCcchhHHHHHHhcC
Confidence 2 11 123 5999999966655
No 168
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=93.67 E-value=0.059 Score=60.62 Aligned_cols=112 Identities=10% Similarity=0.083 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccC-cHHHHHHHHHHHHcCCcce
Q 001235 609 KELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDS-SIDTVKRMLYLALQGQEEQ 687 (1117)
Q Consensus 609 ~eL~~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~-~~~~~~~~l~~~l~g~~~~ 687 (1117)
-.++.....| ..++....+|-+.|.+..|.|+|+++++++|+-..|++|+...++-..+ .+..+...+...++.+.
T Consensus 151 fkiRAcnalF-aaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgk-- 227 (775)
T KOG1229|consen 151 FKIRACNALF-AALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGK-- 227 (775)
T ss_pred HHHhhhHHHH-HHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCc--
Confidence 3344443333 4567778899999999999999999999999999999999999885433 34445555566665443
Q ss_pred eeEEEEEeeccccCCceEEEEEEEEEeecCCCCEEEEE
Q 001235 688 NIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVC 725 (1117)
Q Consensus 688 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~ 725 (1117)
+++-+...+++.|...-..+...|+....|++..++
T Consensus 228 --e~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfv 263 (775)
T KOG1229|consen 228 --EAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFV 263 (775)
T ss_pred --cccchHHHhhccCCcccceEEEeeecCCCCceeeeh
Confidence 344444456788888888889999999999887664
No 169
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=93.64 E-value=0.31 Score=46.65 Aligned_cols=46 Identities=24% Similarity=0.204 Sum_probs=41.0
Q ss_pred HhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcC
Q 001235 752 VQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFG 800 (1117)
Q Consensus 752 ~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~ 800 (1117)
++..|- |++-+|.+|.|+.+|.+-.++.|++++.++|+.++.++.|
T Consensus 22 lD~lpF---GvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAP 67 (124)
T TIGR02373 22 FDALPF---GAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAP 67 (124)
T ss_pred hhcCCc---ceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhccc
Confidence 455554 9999999999999999999999999999999998877765
No 170
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=93.53 E-value=0.21 Score=38.81 Aligned_cols=45 Identities=36% Similarity=0.372 Sum_probs=38.9
Q ss_pred HHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcch
Q 001235 747 DYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLL 794 (1117)
Q Consensus 747 ~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l 794 (1117)
+++.+++..+. +++..|.++.+..+|+.+.+++|+...++.++..
T Consensus 2 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (67)
T smart00091 2 RLRAILESLPD---GIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46 (67)
T ss_pred hHHHHHhhCCc---eEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcH
Confidence 35667788777 7999999999999999999999999988887754
No 171
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=93.53 E-value=0.2 Score=61.26 Aligned_cols=199 Identities=18% Similarity=0.170 Sum_probs=114.1
Q ss_pred cEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHc-CC--------------cceeeEEE
Q 001235 628 PILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQ-GQ--------------EEQNIQFE 692 (1117)
Q Consensus 628 gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~-g~--------------~~~~~e~~ 692 (1117)
.+++-+.+|+|+|+.+.+..++|+.++-+.|..+.|++++.|...+...+.+..- .+ ..+.+..+
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 4566678999999999999999999999999999999999999887665544310 00 01111111
Q ss_pred EEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhH------hhHHHHHHHHHhCCCCCCCCeeeeC
Q 001235 693 IKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF------TRIEGDYKAIVQNPNPLIPPIFGSD 766 (1117)
Q Consensus 693 ~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L------~~se~~l~~i~~~~~~li~~I~~~D 766 (1117)
+..+. ......++ .+..++-.+..+-++..++.+. .+...-|++= +..++- -||..-
T Consensus 274 isgr~-~~~~~~~y-------------~PFRl~pyl~ev~~~~~~~s~~ccLllaerihSgYeAP-rIps~K--riFtT~ 336 (1114)
T KOG3753|consen 274 ISGRK-DRENEIRY-------------HPFRLTPYLVEVRDQQGAESQPCCLLLAERIHSGYEAP-RIPSNK--RIFTTT 336 (1114)
T ss_pred eeccc-CCcCcccc-------------CcccccceeEEeccccccCcCcceeehhhhhhcccccC-cCCccc--ceeEec
Confidence 11110 00111111 1111122222222222232221 1111112211 111111 255554
Q ss_pred --CCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhc-CCCC--ceEeEEEEecC
Q 001235 767 --EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMS-GQDP--EKVPFGFFARN 841 (1117)
Q Consensus 767 --~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~-g~~~--~~~e~~~~~~d 841 (1117)
..+.+..+..++..++||-+.+++|+.++..+ |++|+.-+...-...+. ++.+ ..-.+||...+
T Consensus 337 HTptClf~hVDeaAVp~LGyLPqDLIG~sil~f~-----------H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqN 405 (1114)
T KOG3753|consen 337 HTPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFV-----------HPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQN 405 (1114)
T ss_pred cCCcceeeecchhhhhhhccCchhhhccchhhhh-----------cCCchHHHHHHHHHHHHhCCCCcccccceeeeecC
Confidence 45667789999999999999999999976444 45565544444444443 3333 46778999999
Q ss_pred CcEEEEEEEEeee
Q 001235 842 GKYAECLLCVNKK 854 (1117)
Q Consensus 842 G~~~~v~~~~~pi 854 (1117)
|.|+.+.......
T Consensus 406 G~yv~ldTeWSsF 418 (1114)
T KOG3753|consen 406 GSYVRLDTEWSSF 418 (1114)
T ss_pred CcEEEEechhhhc
Confidence 9998877654333
No 172
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=93.05 E-value=0.26 Score=55.77 Aligned_cols=114 Identities=12% Similarity=0.020 Sum_probs=80.2
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHH
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1117)
-+.+.+++...|. -|-..|.++++.++|+. .++|-+++. ++|+.+. .+..|.... ....+.+.
T Consensus 289 ~~e~naif~~lP~---Ditfvdk~diV~ffs~~-~rif~rt~s-viGr~v~-----------~chpPksv~-iv~ki~~~ 351 (409)
T COG2461 289 LEELNAIFKHLPV---DITFVDKNDIVRFFSGG-ERIFPRTPS-VIGRRVQ-----------LCHPPKSVH-IVEKILKD 351 (409)
T ss_pred HHHHHHHHhhCCC---ceEEecccceEEecCCc-ceecccChH-hhCCccc-----------CCCCCchHH-HHHHHHHH
Confidence 3578899999984 47889999999999999 889888865 5666642 122233333 33344444
Q ss_pred hcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHH
Q 001235 825 MSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1117)
Q Consensus 825 l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (1117)
+..+.....+|. .+..++ .+.++..++.|.+|+..|++-+++|||+-++.+
T Consensus 352 fksG~kd~~efw-~~~~~~--~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 352 FKSGEKDFAEFW-INMGDK--FIHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred hhcCCcchHHHh-ccCCCc--eEEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 455555566666 333333 356778889999999999999999999876654
No 173
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=92.63 E-value=0.14 Score=63.86 Aligned_cols=54 Identities=13% Similarity=0.143 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC
Q 001235 1008 LQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG 1073 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~ 1073 (1117)
..-|+.+|+.||++++. .+|.|.+...+ .-.|+|+|||+||++++++-.+.+..
T Consensus 24 PaSVVKELVENSlDAGA--t~I~I~ve~gG----------~~~I~V~DNG~Gi~~~Dl~la~~rHa 77 (638)
T COG0323 24 PASVVKELVENSLDAGA--TRIDIEVEGGG----------LKLIRVRDNGSGIDKEDLPLALLRHA 77 (638)
T ss_pred HHHHHHHHHhcccccCC--CEEEEEEccCC----------ccEEEEEECCCCCCHHHHHHHHhhhc
Confidence 34789999999999985 67777655432 23488999999999999999998853
No 174
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=91.96 E-value=2.1 Score=52.04 Aligned_cols=229 Identities=15% Similarity=0.121 Sum_probs=114.5
Q ss_pred hhhhhhhhccccCCCchHHHHHHHHHHHHHHHHHhhhcc---cccccc-chhhhhhhHHHHHHHHHHHHHHHHHHHHHhc
Q 001235 550 FKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGT---LDLDTK-SIHSKLCDLKIEGMKELEAVTSEMVRLIETA 625 (1117)
Q Consensus 550 F~~w~e~v~~~s~pW~~~El~aa~sL~liL~~~l~~l~~---~~~~~~-~~~~~l~~~~~~~~~eL~~~~~~l~~lie~a 625 (1117)
-+.|...+++...+|. ..--.+.+. +.....-.. ...... .-+.++.+...+...-|......|..++..+
T Consensus 9 ~~~v~~~~~~g~~~~~-l~p~I~~SW----~RC~~~h~ldP~~~~~p~~Ls~~el~~~rE~~~~LL~iA~~~L~~L~~~v 83 (606)
T COG3284 9 ADRVLRFAQTGAAAPS-LRPLIAESW----RRCLKLHVLDPELAKGPRVLSETELREARERAEALLTIAQPELDRLFQAV 83 (606)
T ss_pred HHHHHHHhccCCCCcc-cccHHHHHH----HHHHHhcCCCccccCCCeecCHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Confidence 3567777777777775 111123333 222211111 011111 2233444444455555666667777776664
Q ss_pred ---CccEEEEeCCCcEEeecHHHHHHcCCCccc-ccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccC
Q 001235 626 ---TVPILAVDVDGLVNGWNTKIAELTGLSVDK-AIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKIN 701 (1117)
Q Consensus 626 ---~~gi~~~D~dG~I~~~N~a~~~l~G~s~ee-liG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~d 701 (1117)
+..+++.|.+|.++..+-.-......+.-- ..|-.|.+-... ...+-.++..+++- .+.-. .|=.
T Consensus 84 ~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WSE~~~G------TNgIGTcLve~~aV--tI~~~---qHF~ 152 (606)
T COG3284 84 AGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWSEPREG------TNGIGTCLVEGEAV--TIHGD---QHFI 152 (606)
T ss_pred cCCCeEEEEEcCceeEEEeecChhhhhhhhhhcccccccccccccc------ccchhhhhccCcce--EEehh---hhHh
Confidence 456889999999987644422222211100 012222221110 11223333333221 11110 1112
Q ss_pred CceEEEEEEEEEeecCCCCEEEEEEEE---Eccchhhh-------------hhhh--HhhHHHHHHHHHhCCCC----CC
Q 001235 702 DDPITLIVNACASRDLHDNVVGVCFVA---QDITPQKT-------------VMDK--FTRIEGDYKAIVQNPNP----LI 759 (1117)
Q Consensus 702 G~~~~v~v~~~pi~d~~G~v~gv~~v~---~DITerK~-------------aE~~--L~~se~~l~~i~~~~~~----li 759 (1117)
.....+.+++.|++|++|++.|++-+. .|+|+.-. .|.+ ++..+..+...+...|+ .-
T Consensus 153 ~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~~~~~~s~~~~~~iV~~~ar~IE~~~~~~~~~~~~~lr~~~~p~~~d~~~ 232 (606)
T COG3284 153 QAHHGLSCSAAPIFDEQGELVGVLDISSCRSDLSEASQPLTLAIVTDAARRIEAELFLAAFEGHWLLRIALAPDYLDSQS 232 (606)
T ss_pred hcccCceeeeeccccCCCcEEEEEEeccCCcchhhhhhHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHhcCccccCccc
Confidence 344568899999999999999987554 23333222 1111 11111111122222221 12
Q ss_pred CCeeeeCCCCceeechhhHHHhcCCC-hhhHhhcch
Q 001235 760 PPIFGSDEFGWCCEWNPAMVKLTGWK-REEVIDKLL 794 (1117)
Q Consensus 760 ~~I~~~D~~g~i~~~N~a~~~l~G~~-~eEliGk~l 794 (1117)
.+.+..|.+|+++..|.++..+++.+ ..-++|.+.
T Consensus 233 ~~~lavd~~grvl~at~aA~~~La~~~~~~l~g~p~ 268 (606)
T COG3284 233 EALLAVDQDGRVLGATRAARQLLALTDRQRLIGQPV 268 (606)
T ss_pred ceeeeecCcchhhhccHHHHHhhccchhhHhhcCCc
Confidence 26889999999999999999999988 444555543
No 175
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=91.57 E-value=0.57 Score=60.17 Aligned_cols=215 Identities=16% Similarity=0.185 Sum_probs=155.6
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHH-HHhcCCCCHHHHHHHHHHHHHHHHHHHHHhh-ccccccccCcccceeE
Q 001235 885 SEQTALKRLKALAYTKRQIRNPLSGIIFSRK-MMEGTELGAEQKRLLHTSAQCQRQLHKILDD-SDLDSIIDGYLDLEMV 962 (1117)
Q Consensus 885 ae~~~~~k~~~la~isHEIrnPL~~I~~~~~-LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~d-Ld~skie~g~~~l~~~ 962 (1117)
+......+..++..+.|..+.|.+.+.+... ++....+.++..-.++...+....+..++.. .+..+...|.......
T Consensus 379 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~~~q~~~~~~~~~~gt~~~~~i 458 (786)
T KOG0519|consen 379 AHMAGKARIDFLQKMSHAMRAPRHNIISLLSLLLQDIVLSPDSGLEIQTVMRSSNVFTSLIQADPDITRLYGGTGLGESI 458 (786)
T ss_pred hhhccchhhhHHHHhccccccccccccccchhhHhheEeccCCceeEehhhhhhhHHHHHhccccccccccCCCcccchh
Confidence 3333344445566667999999999987777 4455556666667777777777788888888 7888888887788889
Q ss_pred EeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhh--ccCCCCeEEEEEEeccccc
Q 001235 963 EFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISIN--FVPNGGQLMVSSSLTKDQL 1040 (1117)
Q Consensus 963 ~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik--~~~~~g~I~I~v~~~~~~~ 1040 (1117)
.+.|..++...+.........+...+..++....+. .+.+|..++.|++.++..++.+ ++..++...+.+......+
T Consensus 459 ~~~l~~l~~~~~~~~~~~~~~~t~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ 537 (786)
T KOG0519|consen 459 VFSLVELMSGEISDISCISLGKTFSFTLDLLTNLPK-SVVGDEKRLFQIILDFNGMLALLIDTKLGREQIFQVLAELLGI 537 (786)
T ss_pred hccHHHHHHHHhhhhhhhccCceeeEEEEeccCCCc-cchhhhhhhhhhhhhhcchhhhhhccccCcceeEEEEecccCc
Confidence 999999999999999988888888888888777764 7888888889999999999988 5554432222222221100
Q ss_pred c--------------cccce-eEEEEEEeecCCCCChhhhhhccCCC---C---C--CCCccccHHHHHHHHHHcCCEEE
Q 001235 1041 G--------------QSVHL-AYLELRITHAGGGIPEPLLDQMFGSE---G---D--TSEEGISLLISRKLVKLMNGDVQ 1097 (1117)
Q Consensus 1041 ~--------------~~~~~-~~l~i~V~D~G~GI~~e~~~~iFe~f---~---~--~~GtGLGL~ivr~iVe~~gG~I~ 1097 (1117)
. +.... ..+.+.+.+++.|........+|.-| + . ..+.++++..|.+..+.+.|..+
T Consensus 538 ~vd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 617 (786)
T KOG0519|consen 538 SVDVSLSLSLAFWFLDLSLSDLEVCKQIEDNEEGSNNGDISSSNPLHKSLRDLTSKLSSGSGLSLALCPENSQLMEGNIG 617 (786)
T ss_pred cccccccchhhhhhcccccccchheEEeeeccccccCCCcchhhhhhhccccchhhcccccccccccchhhHHhhhcccc
Confidence 0 00001 26778888999988887777665544 1 1 23578999999999999999988
Q ss_pred EEe
Q 001235 1098 YLR 1100 (1117)
Q Consensus 1098 v~s 1100 (1117)
+..
T Consensus 618 ~~~ 620 (786)
T KOG0519|consen 618 LVP 620 (786)
T ss_pred ccc
Confidence 873
No 176
>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=91.50 E-value=0.44 Score=33.12 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=35.4
Q ss_pred eEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHH
Q 001235 834 PFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASH 873 (1117)
Q Consensus 834 e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (1117)
++.+...+|...|+.....++.+.+|.+.+++++..|+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 4567788999999999999999989999999999999885
No 177
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=91.28 E-value=0.18 Score=62.57 Aligned_cols=47 Identities=13% Similarity=0.263 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1008 LQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
|.+++.+|+.||++..-. ...|.|.+.... .|+|.|||.|||.+..+
T Consensus 2 L~~~v~ElvdNAiD~~~~g~at~I~V~i~~~g------------~I~V~DnG~GIp~~~h~ 50 (594)
T smart00433 2 LHHLVDEIVDNAADEALAGYMDTIKVTIDKDN------------SISVEDNGRGIPVEIHP 50 (594)
T ss_pred ceEEEeeehhcccchhccCCCCEEEEEEeCCC------------eEEEEEeCCceeCCccC
Confidence 346778999999998632 457777765432 48899999999986654
No 178
>PRK14939 gyrB DNA gyrase subunit B; Provisional
Probab=91.22 E-value=0.35 Score=60.86 Aligned_cols=49 Identities=14% Similarity=0.279 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1006 IRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1006 ~~L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
.-|..++.+++.||++-.-. ...|.|.+.... .|+|.|||.|||.+..+
T Consensus 36 ~GLhhlv~EivdNaiDE~~AG~a~~I~V~i~~dg------------sIsV~DnGrGIPvd~h~ 86 (756)
T PRK14939 36 TGLHHMVYEVVDNAIDEALAGHCDDITVTIHADG------------SVSVSDNGRGIPTDIHP 86 (756)
T ss_pred cchhhhhhHhhcccccccccCCCCEEEEEEcCCC------------eEEEEEcCCcccCCccc
Confidence 45889999999999983322 467877765432 48899999999998443
No 179
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=91.09 E-value=1.8 Score=56.56 Aligned_cols=46 Identities=13% Similarity=0.021 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccEEEEe-CCCcEEeecHHHHHHcCC
Q 001235 606 EGMKELEAVTSEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGL 651 (1117)
Q Consensus 606 ~~~~eL~~~~~~l~~lie~a~~gi~~~D-~dG~I~~~N~a~~~l~G~ 651 (1117)
+..+++++.+..++.+++.+|+|++++| .+|+|+.+|+++++++|.
T Consensus 333 ~l~~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 333 SMSHELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHHHHhCc
Confidence 3446788889999999999999999999 688999999999999984
No 180
>PRK05218 heat shock protein 90; Provisional
Probab=91.04 E-value=0.36 Score=60.07 Aligned_cols=57 Identities=21% Similarity=0.332 Sum_probs=37.4
Q ss_pred EEecHHHHHHHHHHHHHHHhhccC--------------CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1001 LYGDSIRLQQVLADFLSISINFVP--------------NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1001 v~~D~~~L~qVL~nLl~NAik~~~--------------~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
+|.|+. -.|.+|+.||.++.. +.....|.+....+ .-.|+|.|||+||+.+.+.
T Consensus 23 LYs~~~---v~lRELiqNA~DA~~k~r~~~~~~~~~~~~~~~~~I~I~~d~~---------~~~i~I~DnG~GMt~eel~ 90 (613)
T PRK05218 23 LYSNKE---IFLRELISNASDAIDKLRFEALTDPALYEGDGDLKIRISFDKE---------ARTLTISDNGIGMTREEVI 90 (613)
T ss_pred hcCCch---HHHHHHHhCHHHHHHHHHHHhccCccccCCCCCcEEEEEEcCC---------CCeEEEEECCCCCCHHHHH
Confidence 455553 368999999998731 12233444434333 1248899999999999988
Q ss_pred hcc
Q 001235 1067 QMF 1069 (1117)
Q Consensus 1067 ~iF 1069 (1117)
.-|
T Consensus 91 ~~l 93 (613)
T PRK05218 91 ENL 93 (613)
T ss_pred HHH
Confidence 765
No 181
>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=89.81 E-value=1.3 Score=30.53 Aligned_cols=36 Identities=31% Similarity=0.375 Sum_probs=31.5
Q ss_pred ccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchh
Q 001235 699 KINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQ 734 (1117)
Q Consensus 699 ~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITer 734 (1117)
..+|...|+.....++.+.+|.+.+++++..|||++
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 8 RKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 (43)
T ss_pred ecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence 457888999999999999899999999999999963
No 182
>PRK14083 HSP90 family protein; Provisional
Probab=89.11 E-value=0.39 Score=59.32 Aligned_cols=56 Identities=14% Similarity=0.287 Sum_probs=39.6
Q ss_pred EEecHHHHHHHHHHHHHHHhhccCC--------CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhcc
Q 001235 1001 LYGDSIRLQQVLADFLSISINFVPN--------GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMF 1069 (1117)
Q Consensus 1001 v~~D~~~L~qVL~nLl~NAik~~~~--------~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iF 1069 (1117)
++.|+. -.+.||+.||.++... .+.|.|.+. ..+ .-.|.|.|||+||+.+.+.+.|
T Consensus 20 LYs~~~---iflrELiqNA~DA~~~~~~~~~~~~~~I~I~~~-d~~---------~~~l~I~DnGiGmt~eel~~~l 83 (601)
T PRK14083 20 LYSSPR---VYVRELLQNAVDAITARRALDPTAPGRIRIELT-DAG---------GGTLIVEDNGIGLTEEEVHEFL 83 (601)
T ss_pred hcCCcH---HHHHHHHHhHHHHHHhhhccCCCCCceEEEEEc-cCC---------CcEEEEEeCCCCCCHHHHHHHH
Confidence 445543 5779999999987531 346777653 222 3467888999999999988865
No 183
>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=88.07 E-value=21 Score=37.13 Aligned_cols=125 Identities=12% Similarity=0.187 Sum_probs=86.1
Q ss_pred cHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCcc
Q 001235 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARH 297 (1117)
Q Consensus 218 ~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~ 297 (1117)
++...++.+++-+.+.||+ -|+|- +.-.|+|=+-.. -.-|+ |.+ +.+..++.+..+++.+..+.+...
T Consensus 53 ~~~~~A~~~aeII~~~t~~-aVaIT-----Dr~~ILA~~G~g-~d~~~----~~~-is~~t~~~i~~gk~~~~~~~~~~~ 120 (180)
T TIGR02851 53 ELGDFAKEYAESLYQSLGH-IVLIT-----DRDTVIAVAGVS-KKEYL----NKP-ISDELEDTMEERKTVILSDTKDGP 120 (180)
T ss_pred chHHHHHHHHHHHHHHhCC-EEEEE-----CCCcEEEEECCC-hhhcC----CCc-cCHHHHHHHHcCCEEEecCCccce
Confidence 4556666677778888999 88885 344566544222 23333 344 999999999999999888753221
Q ss_pred cccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCC--CC
Q 001235 298 VKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR--FV 375 (1117)
Q Consensus 298 v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~--~~ 375 (1117)
++.... +.|. ..+.+++||+.+ |+.=|.|.-- ...+ .+
T Consensus 121 i~c~~~-----------------~~~~--------l~s~ii~Pl~~~--------------g~viGtLkly-~k~~~~~~ 160 (180)
T TIGR02851 121 IEIIDG-----------------QEFE--------YTSQVIAPIIAE--------------GDPIGAVIIF-SKEPGEKL 160 (180)
T ss_pred eccccC-----------------CCCC--------cceEEEEEEEEC--------------CeEEEEEEEE-ECCccCCC
Confidence 222100 1111 278999999987 8888955544 6666 78
Q ss_pred CchhHHHHHHHHHHHHHHH
Q 001235 376 PFPLRYACEFLAQVFAIHV 394 (1117)
Q Consensus 376 ~~~~r~~~~~l~~~~~~~~ 394 (1117)
+...+.+.+-|+++||.||
T Consensus 161 ~~~e~~la~glA~lLS~QL 179 (180)
T TIGR02851 161 GEVEQKAAETAAAFLGKQM 179 (180)
T ss_pred CHHHHHHHHHHHHHHHHhh
Confidence 8889999999999999997
No 184
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=87.48 E-value=4.9 Score=39.83 Aligned_cols=86 Identities=13% Similarity=0.017 Sum_probs=70.1
Q ss_pred CcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEEEEee
Q 001235 636 GLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASR 715 (1117)
Q Consensus 636 G~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~ 715 (1117)
-++..+-...++++|+ |+.|+++.+++.+.....+...+..+.....+.-...... ..+|....++.-..|+.
T Consensus 51 ~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~----~~~g~~~~~e~l~LPL~ 123 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAE----DADGRYLEYERLLLPLR 123 (137)
T ss_pred eEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEe----cCCCCeeEEEEEEcccC
Confidence 3566889999999996 4669999999999999999999999997776544343333 45788888999999999
Q ss_pred cCCCCEEEEEEEE
Q 001235 716 DLHDNVVGVCFVA 728 (1117)
Q Consensus 716 d~~G~v~gv~~v~ 728 (1117)
+++|.+..++|++
T Consensus 124 ~~~~~v~rilG~~ 136 (137)
T PF07310_consen 124 SDGGTVDRILGAL 136 (137)
T ss_pred CCCCCccEEEEec
Confidence 9999998888864
No 185
>PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional
Probab=85.70 E-value=0.93 Score=56.82 Aligned_cols=50 Identities=16% Similarity=0.211 Sum_probs=35.4
Q ss_pred HHHHHHHHHhhccC--------------CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhcc
Q 001235 1011 VLADFLSISINFVP--------------NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMF 1069 (1117)
Q Consensus 1011 VL~nLl~NAik~~~--------------~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iF 1069 (1117)
.|.+|++||.++.. .++.+.|++....+ ...+.|.|||+||+.+.+.+-|
T Consensus 29 flRELIsNA~DA~~k~r~~~l~~~~~~~~~~~~~I~i~~d~~---------~~~L~I~DnGiGMt~edl~~~L 92 (701)
T PTZ00272 29 FLRELISNASDACDKIRYQSLTDPSVLGESPRLCIRVVPDKE---------NKTLTVEDNGIGMTKADLVNNL 92 (701)
T ss_pred hHHHHHhhHHHHHHHHHHHhcCCchhcCCCCceEEEEEEcCC---------CCEEEEEECCCCCCHHHHHHHh
Confidence 46899999987631 13456777766544 3467899999999998866544
No 186
>COG0326 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]
Probab=84.75 E-value=0.97 Score=54.91 Aligned_cols=48 Identities=23% Similarity=0.367 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhcc----------CC----CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh
Q 001235 1011 VLADFLSISINFV----------PN----GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ 1067 (1117)
Q Consensus 1011 VL~nLl~NAik~~----------~~----~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~ 1067 (1117)
-|.+||+||.++. |. ++.+.|++....+ .=.++|+|||+||..+.+..
T Consensus 31 FLRELISNAsDAidKlr~~al~~~~~~~~~~~~~I~i~~Dk~---------~kTLtI~DNGIGMT~~Ev~~ 92 (623)
T COG0326 31 FLRELISNASDAIDKLRFEALSDPELGEGDSDLRIRISFDKD---------NKTLTISDNGIGMTKDEVIE 92 (623)
T ss_pred HHHHHHhhhHHHHHHHHHHhccCccccCCCCCceEEEEEccc---------CCEEEEEeCCCCCCHHHHHH
Confidence 4688999997642 11 2246666666555 34688889999999988654
No 187
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=83.30 E-value=0.76 Score=57.54 Aligned_cols=97 Identities=11% Similarity=0.091 Sum_probs=67.1
Q ss_pred eCCCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCC-CceEeEEEEecCCc
Q 001235 765 SDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQD-PEKVPFGFFARNGK 843 (1117)
Q Consensus 765 ~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~-~~~~e~~~~~~dG~ 843 (1117)
.+.+|.++++-..+..+.||...++.|+..+ ...|+++.......+........ ....-++++.++|.
T Consensus 378 ~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~-----------~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~ 446 (803)
T KOG3561|consen 378 SSSDGSFTFVDQRASAILGYQPQELLGRSSY-----------ESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGS 446 (803)
T ss_pred cCcCCceeccccccccccccCchhhcCcccc-----------cccCccccchhhchHHHHHHhcccccccccccccCCCC
Confidence 4568889999999999999999999999853 23344454444444544444333 33667788999999
Q ss_pred EEEEEEEEeeeeCC-CCCEEEEEeehhHHH
Q 001235 844 YAECLLCVNKKLDR-EGAVTGVFCFLQLAS 872 (1117)
Q Consensus 844 ~~~v~~~~~pi~d~-~G~v~g~v~i~~DIT 872 (1117)
+.|.........+. ..++.+++|.-..+.
T Consensus 447 ~~~~~~~~~~~~n~~s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 447 SIPNKSSAYLFSNPGSDEVEYIVCTNSNVP 476 (803)
T ss_pred ccccccccccccCCCccccceeeecccccc
Confidence 99988877666643 345667777766655
No 188
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=81.42 E-value=2.3 Score=53.02 Aligned_cols=51 Identities=20% Similarity=0.345 Sum_probs=37.2
Q ss_pred cHHHHHHHHHHHHHHHhhccCC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1004 DSIRLQQVLADFLSISINFVPN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1004 D~~~L~qVL~nLl~NAik~~~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
++.-|..++.+++.||++-.-. ...|.|.+.... .|+|.|||.|||-+..+
T Consensus 31 ~~~GL~hlv~EIvdNavDE~~ag~~~~I~V~i~~dg------------sitV~DnGrGIPv~~h~ 83 (637)
T TIGR01058 31 DSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDN------------SITVQDDGRGIPTGIHQ 83 (637)
T ss_pred CcchhheehhhhhcchhhhhhcCCCcEEEEEEcCCC------------eEEEEECCCcccCcccC
Confidence 3566889999999999985432 457777766432 38899999999976543
No 189
>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.25 E-value=2.6 Score=41.06 Aligned_cols=42 Identities=10% Similarity=0.277 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCC
Q 001235 1008 LQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGG 1059 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~G 1059 (1117)
+.=+..+|+.||+||.. .|.|.|....... .+.+.|++.-.+
T Consensus 64 vgYl~NELiENAVKfra-~geIvieasl~s~---------~f~~kvsN~vd~ 105 (184)
T COG5381 64 VGYLANELIENAVKFRA-TGEIVIEASLYSH---------KFIFKVSNIVDL 105 (184)
T ss_pred HHHHHHHHHHhhhcccC-CCcEEEEEEeccc---------eEEEEecccCCC
Confidence 44567899999999987 6788888887766 788888765443
No 190
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=80.44 E-value=4.5 Score=47.52 Aligned_cols=94 Identities=10% Similarity=-0.066 Sum_probs=75.2
Q ss_pred CCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEEEEe
Q 001235 635 DGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACAS 714 (1117)
Q Consensus 635 dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi 714 (1117)
|+..+.+..+...++||...|+.|.+-.+++|-+|.-.....-.+.++.++..-+.++.. .|+|.+.|+..++..+
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 566677778888999999999999999999999999777777788888887766666655 6789999998777655
Q ss_pred ecCCCCEEEEEEEEEccch
Q 001235 715 RDLHDNVVGVCFVAQDITP 733 (1117)
Q Consensus 715 ~d~~G~v~gv~~v~~DITe 733 (1117)
+ .+|++-.++.+-+-.++
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 47888878777666665
No 191
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=79.77 E-value=3.9 Score=46.20 Aligned_cols=88 Identities=10% Similarity=0.023 Sum_probs=67.6
Q ss_pred ccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEE
Q 001235 627 VPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPIT 706 (1117)
Q Consensus 627 ~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~ 706 (1117)
..+|....|-.+++...++.+++||++.+++++.+...++..|...+..+-...+-.+....--+ +...+.|+++|
T Consensus 226 mFmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYY----R~l~k~ggwvw 301 (598)
T KOG3559|consen 226 MFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYY----RFLLKQGGWVW 301 (598)
T ss_pred eEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHH----HHHHcCCceEE
Confidence 45666778899999999999999999999999999999999998888777766665444322222 23356799999
Q ss_pred EEEEEEEeecCC
Q 001235 707 LIVNACASRDLH 718 (1117)
Q Consensus 707 v~v~~~pi~d~~ 718 (1117)
+...+.-+.+..
T Consensus 302 vqsyat~vHnSr 313 (598)
T KOG3559|consen 302 VQSYATFVHNSR 313 (598)
T ss_pred EEEeeEEEeccc
Confidence 988777665543
No 192
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=78.30 E-value=2.9 Score=47.13 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=43.6
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCChhhHhhcchh
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLL 795 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~~eEliGk~l~ 795 (1117)
.-.+.++++++++ +++.+|..|.+..+|+|++++||.+.+++.|+++.
T Consensus 79 hl~L~aLL~al~~---pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~ 126 (511)
T COG3283 79 HLALSALLEALPE---PVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA 126 (511)
T ss_pred hHHHHHHHHhCCC---ceEEecccCceeecCHHHHHHhCCChhhhcCccHH
Confidence 3457889999998 99999999999999999999999999999999853
No 193
>PTZ00108 DNA topoisomerase 2-like protein; Provisional
Probab=76.24 E-value=5.7 Score=53.31 Aligned_cols=49 Identities=16% Similarity=0.261 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhhccC------CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1007 RLQQVLADFLSISINFVP------NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~~------~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
-|..+|-++|.||++..- ....|.|.+....+ .|+|.|||.|||-+..+
T Consensus 57 GL~ki~dEIldNAvDe~~r~~~~g~~~~I~V~i~~d~g-----------~IsV~dnGrGIPv~~h~ 111 (1388)
T PTZ00108 57 GLYKIFDEILVNAADNKARDKGGHRMTYIKVTIDEENG-----------EISVYNDGEGIPVQIHK 111 (1388)
T ss_pred hhhhhHHHHhhhhhhhhcccCCCCCccEEEEEEeccCC-----------eEEEEecCCcccCCCCC
Confidence 466788888888887532 24577777766533 48889999999987654
No 194
>PTZ00130 heat shock protein 90; Provisional
Probab=74.29 E-value=2.6 Score=53.26 Aligned_cols=47 Identities=23% Similarity=0.251 Sum_probs=30.4
Q ss_pred HHHHHHHHhhccC--------------CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh
Q 001235 1012 LADFLSISINFVP--------------NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ 1067 (1117)
Q Consensus 1012 L~nLl~NAik~~~--------------~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~ 1067 (1117)
|.+|++||.++.. .+..+.|++....+ .-.|.|.|||+||..+.+..
T Consensus 93 LRELISNAsDAldKlr~~~lt~~~~~~~~~~~~I~I~~D~~---------~~tLtI~DnGIGMT~eEl~~ 153 (814)
T PTZ00130 93 LRELISNAADALEKIRFLSLSDESVLGEEKKLEIRISANKE---------KNILSITDTGIGMTKEDLIN 153 (814)
T ss_pred eehHhhhHHHHHHHHHHHHcCCchhcCCCCCceEEEEECCC---------CCEEEEEECCCCCCHHHHHH
Confidence 4688888876541 12245555554433 12577889999999998664
No 195
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=72.90 E-value=17 Score=44.00 Aligned_cols=102 Identities=15% Similarity=0.182 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEE
Q 001235 613 AVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFE 692 (1117)
Q Consensus 613 ~~~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~ 692 (1117)
+.+..+..++.++|.||+.+|.++.+.|+|+-+..+|+-. .+|+...++ ..+.+.....+.+...+.+.
T Consensus 72 ~~~~~~~~al~nmPiGii~~~e~~~veW~Npf~~~if~~~---~~~~~~~~~--------~~~il~~~~~~~~~~~~~i~ 140 (655)
T COG3887 72 QAEKSLEEALTNMPIGIILFNETNKVEWVNPFASKIFNKN---EIGESLSEL--------IPEILKQLARNDEKQYIKIN 140 (655)
T ss_pred HHHHHHHHHHHhCCceEEEEcCCCceEEecHHHHHhcChh---hhhhhHHHH--------hHHHHHHHhcCCcceEEEEc
Confidence 3445677899999999999999999999999999999722 233333322 23344444433332222221
Q ss_pred EEeeccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhH
Q 001235 693 IKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRI 744 (1117)
Q Consensus 693 ~~~~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~s 744 (1117)
-. . +.+ ..+.+.+ +..+-|+|++.+.+++++.+
T Consensus 141 e~----------~-y~~----~~~~~~~----liYf~DvT~~~~~~~~~~~~ 173 (655)
T COG3887 141 EK----------K-YDV----YFDSDKR----LIYFFDVTEEEAIEEEYENS 173 (655)
T ss_pred ce----------E-EEE----EEecCCC----EEEEEeccHHHHHHHHHhcc
Confidence 11 1 111 1333443 34567999998888776544
No 196
>PLN03237 DNA topoisomerase 2; Provisional
Probab=72.55 E-value=4.2 Score=54.41 Aligned_cols=49 Identities=16% Similarity=0.331 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHhhcc---CCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1007 RLQQVLADFLSISINFV---PNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~---~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
-|..+|-++|.||++.. +....|.|.+...++ .|+|.|||.|||-+..+
T Consensus 77 GL~kifdEIldNAvDe~~r~g~~~~I~V~I~~~~g-----------sIsV~DnGRGIPV~iH~ 128 (1465)
T PLN03237 77 GLYKIFDEILVNAADNKQRDPKMDSLRVVIDVEQN-----------LISVYNNGDGVPVEIHQ 128 (1465)
T ss_pred hhhhhHHHHhhhhHhHHhhcCCCCEEEEEEEcCCC-----------EEEEEecCccccCCCCC
Confidence 36678888888888765 224578877775544 48888999999987654
No 197
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=71.85 E-value=69 Score=34.63 Aligned_cols=137 Identities=15% Similarity=0.069 Sum_probs=72.2
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHh
Q 001235 205 AKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMK 284 (1117)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~ 284 (1117)
.++.-+|=+ +.++.++++++...+++..+.|-|-+--|++++.- +++.. .++..+ .........
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 55999999999999999999999999999877662 11111 111111 111111111
Q ss_pred CCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHh---cCceeEEEEEEEEcCCccccCCCcccccccc
Q 001235 285 NKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMEN---MNSIASLVMAVVVNDEEEEGDNTLPQKRKRL 361 (1117)
Q Consensus 285 ~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n---~~v~asl~~~i~~~~~~~~~~~~~~~~~~~l 361 (1117)
..+ . .+.|. +--++..-...|=. -+++|...+|+. . ++.
T Consensus 145 ~~l-------~----------~~~p~------~G~~~~~~~~~lF~~~~~~v~S~AlipL~-~--------------~~~ 186 (225)
T PF04340_consen 145 DLL-------G----------LQQPY------CGRLSEEEAALLFGDEAAQVGSVALIPLG-S--------------GRP 186 (225)
T ss_dssp CCH-------T----------T---C------CCS--HHHHHHHHHHCHCC-SEEEEEEEE-S--------------SSE
T ss_pred HHh-------C----------CCCce------eCCCCcchhHHhcCCCCccccchheeecc-C--------------CCc
Confidence 100 0 00111 11122222222222 457888899996 5 899
Q ss_pred eeeEEe-eccCCCCCCchhHHHHHHHHHHHHHHHH
Q 001235 362 WGLVVC-HNTTPRFVPFPLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 362 WGl~~~-hh~~p~~~~~~~r~~~~~l~~~~~~~~~ 395 (1117)
+|+|+- .+..-||-|----...++|+.+++..|.
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 999984 4445566666667788888988877653
No 198
>PLN03128 DNA topoisomerase 2; Provisional
Probab=71.79 E-value=5 Score=53.15 Aligned_cols=49 Identities=18% Similarity=0.358 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHhhcc---CCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1007 RLQQVLADFLSISINFV---PNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~---~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
-|..+|-++|.||++-. +....|.|.+...++ .|+|.|||.|||-+..+
T Consensus 52 GL~ki~dEIldNAvDe~~~~g~~~~I~V~i~~~dg-----------sIsV~DnGrGIPv~ih~ 103 (1135)
T PLN03128 52 GLYKIFDEILVNAADNKQRDPSMDSLKVDIDVEQN-----------TISVYNNGKGIPVEIHK 103 (1135)
T ss_pred hHHHHHHHHHHHHHHHhhhcCCCcEEEEEEEcCCC-----------eEEEEecCccccCCCCC
Confidence 46788899999998765 224577777776433 48888999999987554
No 199
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=70.55 E-value=1.5 Score=53.16 Aligned_cols=80 Identities=14% Similarity=0.191 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHHhhccC--CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhh--------ccCC----
Q 001235 1006 IRLQQVLADFLSISINFVP--NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQ--------MFGS---- 1071 (1117)
Q Consensus 1006 ~~L~qVL~nLl~NAik~~~--~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~--------iFe~---- 1071 (1117)
..|..++.+.+.||++=+- -...|.|.+..+.. ++|.|||.|||-+..++ ||..
T Consensus 35 ~GLhHlv~EVvDNsiDEalaG~~~~I~V~l~~d~s------------isV~DnGRGIPvdiH~~~~~~~vEvI~T~LHAG 102 (635)
T COG0187 35 RGLHHLVWEVVDNSIDEALAGYADRIDVTLHEDGS------------ISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAG 102 (635)
T ss_pred CcceeeEeEeeechHhHHhhCcCcEEEEEEcCCCe------------EEEEECCCCCccccCCCCCCCceEEEEEeeccC
Confidence 5577778888888886542 25578877764443 88889999999988554 3332
Q ss_pred --C----CCCC-C-ccccHHHHHHHHHHcCCEEEEEee
Q 001235 1072 --E----GDTS-E-EGISLLISRKLVKLMNGDVQYLRE 1101 (1117)
Q Consensus 1072 --f----~~~~-G-tGLGL~ivr~iVe~~gG~I~v~s~ 1101 (1117)
| |..+ | .|.|.+.| +.+.=.+.++..
T Consensus 103 GKFd~~~YkvSGGLHGVG~SVV----NALS~~l~v~v~ 136 (635)
T COG0187 103 GKFDNDSYKVSGGLHGVGVSVV----NALSTWLEVEVK 136 (635)
T ss_pred cccCCCccEeecCCCccceEEE----ecccceEEEEEE
Confidence 2 2222 3 48888887 445445554443
No 200
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=70.11 E-value=23 Score=35.09 Aligned_cols=85 Identities=15% Similarity=0.086 Sum_probs=68.9
Q ss_pred ceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEE
Q 001235 770 WCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLL 849 (1117)
Q Consensus 770 ~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~ 849 (1117)
++..+=...++++|++ +.|+.+. .+..++....+...+..+.....+..........+|....++.
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 4555778888888874 5566643 3334666777888999999999998888899999999999999
Q ss_pred EEeeeeCCCCCEEEEEeeh
Q 001235 850 CVNKKLDREGAVTGVFCFL 868 (1117)
Q Consensus 850 ~~~pi~d~~G~v~g~v~i~ 868 (1117)
..-|+.+.+|.+..++|.+
T Consensus 118 l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 118 LLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred EEcccCCCCCCccEEEEec
Confidence 9999999999998888865
No 201
>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=69.86 E-value=3.9 Score=38.92 Aligned_cols=47 Identities=26% Similarity=0.411 Sum_probs=38.9
Q ss_pred EEEEeC-CCcEEeecHHHHHHcCCC---cccccCCccccccccCcHHHHHH
Q 001235 629 ILAVDV-DGLVNGWNTKIAELTGLS---VDKAIGKHFLTLVEDSSIDTVKR 675 (1117)
Q Consensus 629 i~~~D~-dG~I~~~N~a~~~l~G~s---~eeliG~~~~dlv~~~~~~~~~~ 675 (1117)
++++|. +++|+.++..+.+++|.+ .++++|+++.+++.+.....+..
T Consensus 18 LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~ 68 (110)
T PF08446_consen 18 LLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLRE 68 (110)
T ss_dssp EEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHH
T ss_pred EEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHH
Confidence 566776 689999999999999999 99999999999998877664433
No 202
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=68.45 E-value=1.8e+02 Score=38.07 Aligned_cols=130 Identities=12% Similarity=0.033 Sum_probs=77.4
Q ss_pred cHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHh---CCeEEEeccC
Q 001235 218 SMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMK---NKVRMIVDCR 294 (1117)
Q Consensus 218 ~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~---~~~r~i~d~~ 294 (1117)
.++..++.+.+.+.++++.+++.++-|+.++...+... -|.. |..+++...+.+-.. ..-..+..
T Consensus 293 ~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---------~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-- 360 (828)
T PRK13837 293 ELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---------PGLT-PDPVWPDRLRALASTVKAAERDVVFV-- 360 (828)
T ss_pred hhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---------CccC-CCCCchHHHHHHHHHHhccCCceEEe--
Confidence 45689999999999999999999999987765433221 1111 233444433333211 00000000
Q ss_pred CcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCC-
Q 001235 295 ARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPR- 373 (1117)
Q Consensus 295 ~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~- 373 (1117)
.+..++....++...+....+++|+... ++++|++.+....+.
T Consensus 361 ----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~g~l~~~~~~~~~ 404 (828)
T PRK13837 361 ----------------------DRNGPVRKRSCLTRRGPALWACLAFKSG--------------DRIVALLGLGRQRYGL 404 (828)
T ss_pred ----------------------ecccchhhhcccccCCcceEEEEEeccC--------------CceEEEEEecccccCC
Confidence 0112233334455667888999999876 999999998766433
Q ss_pred CCCchhHHHHHHHHHHHHHHHH
Q 001235 374 FVPFPLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 374 ~~~~~~r~~~~~l~~~~~~~~~ 395 (1117)
.+...+...++.++..++..+.
T Consensus 405 ~~~~~~~~~l~~~~~~~~~~~~ 426 (828)
T PRK13837 405 RPPAGELQLLELALDCLAHAIE 426 (828)
T ss_pred CCChhHHHHHHHHHHHHHHHHH
Confidence 2334556666766666666554
No 203
>KOG1978 consensus DNA mismatch repair protein - MLH2/PMS1/Pms2 family [Replication, recombination and repair]
Probab=68.18 E-value=4.9 Score=49.07 Aligned_cols=52 Identities=12% Similarity=0.153 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCC
Q 001235 1008 LQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGS 1071 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~ 1071 (1117)
+.-++.+|+.|+++++. .+|.|.+...+- =.|+|+|||.||++...+-|-..
T Consensus 21 l~sAVKELvENSiDAGA--T~I~I~~kdyG~----------d~IEV~DNG~GI~~~n~~~l~lk 72 (672)
T KOG1978|consen 21 LVSAVKELVENSIDAGA--TAIDIKVKDYGS----------DSIEVSDNGSGISATDFEGLALK 72 (672)
T ss_pred HHHHHHHHHhcCcccCC--ceeeEecCCCCc----------ceEEEecCCCCCCccchhhhhhh
Confidence 44788999999999884 788887665422 24788899999999887655444
No 204
>PHA02569 39 DNA topoisomerase II large subunit; Provisional
Probab=67.25 E-value=3.1 Score=51.61 Aligned_cols=45 Identities=18% Similarity=0.486 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhhccC--C---CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhh
Q 001235 1008 LQQVLADFLSISINFVP--N---GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLL 1065 (1117)
Q Consensus 1008 L~qVL~nLl~NAik~~~--~---~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~ 1065 (1117)
|..+|.++|.||++-.- + ...|.|.+. ++ .|+|.|||.|||-+..
T Consensus 46 L~hi~~EIldNavDe~~~~~~g~~~~I~V~i~--dg-----------sisV~dnGrGIPv~~h 95 (602)
T PHA02569 46 LVKIIDEIIDNSVDEAIRTNFKFANKIDVTIK--NN-----------QVTVSDNGRGIPQAMV 95 (602)
T ss_pred ceeeeehhhhhhhhhhhccCCCCCcEEEEEEc--CC-----------EEEEEECCCcccCCcc
Confidence 55677777778876531 1 346777765 33 3888899999998765
No 205
>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=66.41 E-value=15 Score=35.40 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=36.1
Q ss_pred eccccCCceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhH
Q 001235 696 HGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKF 741 (1117)
Q Consensus 696 ~~~~~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L 741 (1117)
....++| +.+..+...++|++|+++|++++=.|+|...++.+-|
T Consensus 73 ~~~~~~G--k~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~~~L 116 (118)
T PF08348_consen 73 KTKTKDG--KILRSSTFFIRDENGKLIGALCINFDISALEQAQNFL 116 (118)
T ss_pred cccCCCC--CEEEEEEEEEECCCCCEEEEEEEEeccHHHHHHHHHH
Confidence 3335566 6677888899999999999999999999988876654
No 206
>KOG1977 consensus DNA mismatch repair protein - MLH3 family [Replication, recombination and repair]
Probab=65.72 E-value=9.1 Score=46.60 Aligned_cols=54 Identities=15% Similarity=0.183 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC
Q 001235 1007 RLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG 1073 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~ 1073 (1117)
-|.|++.+|+-|++++.. ..|.|.+.. . .+.+.|.|+|.|+..+.+..+-++++
T Consensus 21 sla~~VeElv~NSiDA~A--t~V~v~V~~--~---------t~sv~ViDdG~G~~rdDl~~lg~ry~ 74 (1142)
T KOG1977|consen 21 SLAQCVEELVLNSIDAEA--TCVAVRVNM--E---------TFSVQVIDDGFGMGRDDLEKLGNRYF 74 (1142)
T ss_pred HHHHHHHHHHhhccccCc--eEEEEEecC--c---------eeEEEEEecCCCccHHHHHHHHhhhh
Confidence 478999999999999874 445544333 3 68899999999999999998877753
No 207
>PRK10490 sensor protein KdpD; Provisional
Probab=64.25 E-value=2.5e+02 Score=37.16 Aligned_cols=48 Identities=8% Similarity=0.147 Sum_probs=36.0
Q ss_pred eEEEEEEEEcCCccccCCCcccccccceeeEEeeccCC-CCCCchhHHHHHHHHHHHHHHHHH
Q 001235 335 ASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP-RFVPFPLRYACEFLAQVFAIHVNK 396 (1117)
Q Consensus 335 asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p-~~~~~~~r~~~~~l~~~~~~~~~~ 396 (1117)
+.+.+|+... ++++|.+......+ +.++.+.+...+.++..++..+..
T Consensus 596 ~~~~lPl~~~--------------~~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler 644 (895)
T PRK10490 596 PYQILPLKSA--------------QKTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALER 644 (895)
T ss_pred ceEEEEEEEC--------------CEEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 4568999876 89999998876654 446667777888888777777653
No 208
>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=64.03 E-value=20 Score=34.66 Aligned_cols=48 Identities=17% Similarity=0.116 Sum_probs=38.3
Q ss_pred CCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHH
Q 001235 829 DPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQA 878 (1117)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (1117)
..+...+.-..++|+ .+..+...++|++|+++|++|+-.|+|.-.+..
T Consensus 66 ~~~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~ 113 (118)
T PF08348_consen 66 EDYIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQAQ 113 (118)
T ss_pred CCccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHHH
Confidence 445566777888995 456778889999999999999999999766554
No 209
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=63.84 E-value=4.2 Score=51.23 Aligned_cols=98 Identities=11% Similarity=0.070 Sum_probs=72.5
Q ss_pred EeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEEEEEEE
Q 001235 632 VDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNA 711 (1117)
Q Consensus 632 ~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~v~v~~ 711 (1117)
...+|.++++-..+-.+.||...++.|++...+.|+++.......++.+....+. ....-.+.+.++|..+|.....
T Consensus 378 ~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~s~h~~d~~~~~~s~~~~~~~s~~---~~~~~yr~~~~n~~~~~~~~~~ 454 (803)
T KOG3561|consen 378 SSSDGSFTFVDQRASAILGYQPQELLGRSSYESSHPADSSPLSESLKQVQALSEQ---RSTLLYRFRSKNGSSIPNKSSA 454 (803)
T ss_pred cCcCCceeccccccccccccCchhhcCcccccccCccccchhhchHHHHHHhccc---ccccccccccCCCCcccccccc
Confidence 3467888888899999999999999999999999999998888887776654443 2333344557789998888776
Q ss_pred EEeec-CCCCEEEEEEEEEccc
Q 001235 712 CASRD-LHDNVVGVCFVAQDIT 732 (1117)
Q Consensus 712 ~pi~d-~~G~v~gv~~v~~DIT 732 (1117)
....+ ....+.+++++-..+.
T Consensus 455 ~~~~n~~s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 455 YLFSNPGSDEVEYIVCTNSNVP 476 (803)
T ss_pred ccccCCCccccceeeecccccc
Confidence 65553 3455666666655554
No 210
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=63.75 E-value=46 Score=28.09 Aligned_cols=46 Identities=17% Similarity=0.093 Sum_probs=33.6
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 001235 895 ALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKIL 944 (1117)
Q Consensus 895 ~la~isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii 944 (1117)
.+....||+.|-|+.|.|++++= ..++..++++.+....+....++
T Consensus 15 ~lR~~RHD~~NhLqvI~gllqlg----~~~~a~eYi~~~~~~~~~~s~l~ 60 (62)
T PF14689_consen 15 SLRAQRHDFLNHLQVIYGLLQLG----KYEEAKEYIKELSKDLQQESELL 60 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHhHHHHHHHHHHHHHHHCC----CHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667899999999999998853 23567777777766666665553
No 211
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=63.31 E-value=1e+02 Score=37.43 Aligned_cols=145 Identities=16% Similarity=0.174 Sum_probs=94.5
Q ss_pred HHHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCc-eEEEEeccCCCCCccCCcCCCCCchHHHHHHHH
Q 001235 205 AKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHG-EVVSEITKSGLEPYLGLHYPATDIPQAARFLFM 283 (1117)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g-~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~ 283 (1117)
.+....+.+ .+++.+-++.+|++|..-....=.-||=-+.|.+- |..| .+++.+.-|.
T Consensus 6 r~i~E~va~--~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~A---TeGLnk~av~---------------- 64 (756)
T COG3605 6 RRIVEKVAS--ALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELMA---TEGLNKPAVH---------------- 64 (756)
T ss_pred HHHHHHHhc--ccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEe---ccccCccccc----------------
Confidence 345555666 56889999999999998888888889988888742 2222 2222211110
Q ss_pred hCCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcC---ceeEEEEEEEEcCCccccCCCccccccc
Q 001235 284 KNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMN---SIASLVMAVVVNDEEEEGDNTLPQKRKR 360 (1117)
Q Consensus 284 ~~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~---v~asl~~~i~~~~~~~~~~~~~~~~~~~ 360 (1117)
.+++-.| .-=|.++ ....+||+|+++. -||-. .|+..-| -.|-|-+||+.. ++
T Consensus 65 --~~~l~~~--eGLVG~v--~~~aePlNLsdAq---sHPsF-~Y~petgEE~Y~sFLGvPIi~~--------------~r 120 (756)
T COG3605 65 --LVQLAFG--EGLVGLV--GRSAEPLNLADAQ---SHPSF-KYLPETGEERYHSFLGVPIIRR--------------GR 120 (756)
T ss_pred --eEEecCC--Cchhhhh--hhccCCCChhhhh---hCCcc-ccccccchHHHHHhhccceeec--------------Cc
Confidence 1111111 1111111 2346788888764 34443 3666665 367889999977 99
Q ss_pred ceeeEEeeccCCCCCCchhHHHHHHHHHHHHHHH
Q 001235 361 LWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHV 394 (1117)
Q Consensus 361 lWGl~~~hh~~p~~~~~~~r~~~~~l~~~~~~~~ 394 (1117)
+-|.+|.++.++|.....+-.+.+.++.+++--+
T Consensus 121 ~lGVLVVQqk~~R~y~E~Eve~L~T~A~~lA~iv 154 (756)
T COG3605 121 LLGVLVVQQRELRQYDEDEVEFLVTLAMQLAEIV 154 (756)
T ss_pred eeEEEEEecccccccchHHHHHHHHHHHHHHHHH
Confidence 9999999999999999998888887776665544
No 212
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=62.87 E-value=1.8e+02 Score=29.55 Aligned_cols=122 Identities=19% Similarity=0.180 Sum_probs=81.7
Q ss_pred HHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHH---HHHHHHhCCeEEEeccCC
Q 001235 219 MERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQA---ARFLFMKNKVRMIVDCRA 295 (1117)
Q Consensus 219 ~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~---~r~l~~~~~~r~i~d~~~ 295 (1117)
+..+.++.+--=..+..+|=|=.|.++ +++-| +.||-|. -+-.+||-- -..-..+|++-.|.|+++
T Consensus 34 ianlan~sall~~~l~~~nW~GFYl~~---~~~Lv-------LgPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~ 102 (163)
T COG1956 34 IANLANASALLKERLPDVNWVGFYLLE---GDELV-------LGPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHA 102 (163)
T ss_pred HHHHHHHHHHHHhhccCCceEEEEEec---CCeEE-------EecccCC-cceEEeccCcchhHHHHhcCCeEEeccccc
Confidence 333333333333344458888888888 66666 5677776 445567642 223456899999999987
Q ss_pred cccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCC
Q 001235 296 RHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFV 375 (1117)
Q Consensus 296 ~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~ 375 (1117)
-|=-|--++ -++|-+++||+.+ |++-|.|=.-..+|-+.
T Consensus 103 ~~ghiaCD~---------------------------as~SEIVvPi~~~--------------g~~iGvlDiDS~~~~~F 141 (163)
T COG1956 103 FPGHIACDA---------------------------ASNSEIVVPIFKD--------------GKLIGVLDIDSPTPGRF 141 (163)
T ss_pred CCCcccccc---------------------------ccCceEEEEEEEC--------------CEEEEEEecCCCCcccC
Confidence 763221111 2478899999987 99999998877778778
Q ss_pred CchhHHHHHHHHHHHHH
Q 001235 376 PFPLRYACEFLAQVFAI 392 (1117)
Q Consensus 376 ~~~~r~~~~~l~~~~~~ 392 (1117)
+.+.+...+.++..++.
T Consensus 142 d~~D~~~Le~~~~~l~~ 158 (163)
T COG1956 142 DEEDEAGLEKLAALLEK 158 (163)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 88777777776665543
No 213
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=62.38 E-value=62 Score=42.01 Aligned_cols=46 Identities=9% Similarity=0.051 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCccEEEEe-CCCcEEeecHHHHHHcCCCcccccCCccccc
Q 001235 616 SEMVRLIETATVPILAVD-VDGLVNGWNTKIAELTGLSVDKAIGKHFLTL 664 (1117)
Q Consensus 616 ~~l~~lie~a~~gi~~~D-~dG~I~~~N~a~~~l~G~s~eeliG~~~~dl 664 (1117)
.--+.++...|.|+.++| .+|.|.++|+.+.+++| .+ ++|+++.++
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 445678999999999999 69999999999999988 33 889998874
No 214
>KOG1979 consensus DNA mismatch repair protein - MLH1 family [Replication, recombination and repair]
Probab=61.75 E-value=8.6 Score=46.01 Aligned_cols=52 Identities=19% Similarity=0.198 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC
Q 001235 1010 QVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG 1073 (1117)
Q Consensus 1010 qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~ 1073 (1117)
-++.+|+.|++++.. ..|.|.+.. + | -=.+.|+|||-||-.+..+-+-++|.
T Consensus 30 NAlKEliENSLDA~S--T~I~V~vk~--G--G------LKLlQisDnG~GI~reDl~ilCeRft 81 (694)
T KOG1979|consen 30 NALKELIENSLDANS--TSIDVLVKD--G--G------LKLLQISDNGSGIRREDLPILCERFT 81 (694)
T ss_pred HHHHHHHhccccCCC--ceEEEEEec--C--C------eEEEEEecCCCccchhhhHHHHHHhh
Confidence 477899999998874 556655443 3 1 34567889999999999998888873
No 215
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=55.34 E-value=40 Score=32.22 Aligned_cols=74 Identities=22% Similarity=0.230 Sum_probs=44.1
Q ss_pred ccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCceEE
Q 001235 627 VPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPIT 706 (1117)
Q Consensus 627 ~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~~~ 706 (1117)
+-+++.|.+|++++-+ ..+.+|+++.+ - + ...+++|+.. .... .|..-+
T Consensus 40 ~~i~v~D~~g~~l~~s----------~~~~iG~~~~~-~---~-------~~~aL~G~~~-----~~~~-----~~~~~~ 88 (116)
T PF14827_consen 40 DYIVVTDRDGIVLAHS----------DPERIGDRYSD-E---D-------VRKALQGKSY-----TSVS-----QGTGGP 88 (116)
T ss_dssp SEEEEECTTSBECE-S----------SCCCTTSB-SS-C---C-------HCHHCCT--E-----EEEE-----ECTTCE
T ss_pred eEEEEEcCCCCEEEcC----------ChHHcCCcccC-C---C-------hhhhhcCCce-----EEee-----ecCCce
Confidence 4588899999988764 33556777664 1 1 2245655322 1111 133355
Q ss_pred EEEEEEEeecCCCCEEEEEEEEEcc
Q 001235 707 LIVNACASRDLHDNVVGVCFVAQDI 731 (1117)
Q Consensus 707 v~v~~~pi~d~~G~v~gv~~v~~DI 731 (1117)
......|++|.+|+++|++.+...+
T Consensus 89 ~~~~~~PV~d~~g~viG~V~VG~~~ 113 (116)
T PF14827_consen 89 SLRAFAPVYDSDGKVIGVVSVGVSL 113 (116)
T ss_dssp EEEEEEEEE-TTS-EEEEEEEEEEH
T ss_pred EEEEEEeeECCCCcEEEEEEEEEEc
Confidence 6677889999999999999987654
No 216
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=54.24 E-value=5.1e+02 Score=32.02 Aligned_cols=39 Identities=18% Similarity=-0.008 Sum_probs=34.3
Q ss_pred hHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCC
Q 001235 743 RIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGW 784 (1117)
Q Consensus 743 ~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~ 784 (1117)
+.+.-++.++.++|. ||+..|.++.+.++||-+..+|+-
T Consensus 72 ~~~~~~~~al~nmPi---Gii~~~e~~~veW~Npf~~~if~~ 110 (655)
T COG3887 72 QAEKSLEEALTNMPI---GIILFNETNKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHhCCc---eEEEEcCCCceEEecHHHHHhcCh
Confidence 455667889999998 999999999999999999999963
No 217
>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=53.72 E-value=80 Score=28.36 Aligned_cols=81 Identities=11% Similarity=0.106 Sum_probs=45.3
Q ss_pred HHhhhhhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhccccccccCcccceeEEeeHHHHHHHHHHHHH
Q 001235 899 TKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVM 978 (1117)
Q Consensus 899 isHEIrnPL~~I~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dLd~skie~g~~~l~~~~~~L~~li~~v~~~~~ 978 (1117)
+.|.+||-|+.|.+....-.+...+. .++.+.+......|...-+-+. .-.+..++|.++++..+.-+.
T Consensus 2 L~HRvKN~lavv~ai~~~t~r~~~s~--~~~~~~~~~Rl~ALa~a~~ll~---------~~~~~~~~L~~lv~~~l~p~~ 70 (83)
T PF07536_consen 2 LNHRVKNLLAVVQAIARQTARSAASV--EEFAEAFSGRLQALARAHDLLS---------RSDWEGVSLRDLVEAELAPYG 70 (83)
T ss_pred chhHHHHHHHHHHHHHHHHcccCCCH--HHHHHHHHHHHHHHHHHHHHHh---------cCCCCCccHHHHHHHHHHhcc
Confidence 68999999999999888776543332 2222222221222222221111 113668899999998776544
Q ss_pred hhhcccCcEEEEeec
Q 001235 979 MKSNAKGIRIVNETA 993 (1117)
Q Consensus 979 ~~~~~~~i~i~~~~~ 993 (1117)
. ..+-+|.++.|
T Consensus 71 ~---~~~~ri~~~Gp 82 (83)
T PF07536_consen 71 S---EDGERITLSGP 82 (83)
T ss_pred C---CCCCeEEeeCc
Confidence 3 23345555443
No 218
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=53.35 E-value=3.1 Score=52.96 Aligned_cols=49 Identities=22% Similarity=0.303 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHhhccC--CCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1006 IRLQQVLADFLSISINFVP--NGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1006 ~~L~qVL~nLl~NAik~~~--~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
.-|.+++.++|.||++-.- ....|.|.+..+. .|+|.|||.|||-+..+
T Consensus 128 ~GLhhLv~EIlDNSVDE~laG~~~~I~V~i~~Dg------------sItV~DnGRGIPvd~h~ 178 (903)
T PTZ00109 128 KGLHQLLFEILDNSVDEYLAGECNKITVVLHKDG------------SVEISDNGRGIPCDVSE 178 (903)
T ss_pred CcceEEEEEEeeccchhhccCCCcEEEEEEcCCC------------eEEEEeCCccccccccc
Confidence 3466788888888887442 2457777765432 38888999999987654
No 219
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=49.77 E-value=26 Score=43.95 Aligned_cols=90 Identities=13% Similarity=0.067 Sum_probs=64.4
Q ss_pred eCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCC-cc--eeeEEEEEeeccccCCceEEEEE
Q 001235 633 DVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQ-EE--QNIQFEIKTHGSKINDDPITLIV 709 (1117)
Q Consensus 633 D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~-~~--~~~e~~~~~~~~~~dG~~~~v~v 709 (1117)
-+.+.+..+..++..++||-+.++||+++..++|++|+..+.+.-..+++.+ .. ..-.+++. ..+|.++.+..
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~----aqNG~yv~ldT 413 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFC----AQNGSYVRLDT 413 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeee----ecCCcEEEEec
Confidence 3566788899999999999999999999999999999998888888777543 22 11123333 34788888877
Q ss_pred EEEEeecCCC-CEEEEEE
Q 001235 710 NACASRDLHD-NVVGVCF 726 (1117)
Q Consensus 710 ~~~pi~d~~G-~v~gv~~ 726 (1117)
....+.+.-- ++..|++
T Consensus 414 eWSsFVNPWSRKieFVvG 431 (1114)
T KOG3753|consen 414 EWSSFVNPWSRKIEFVVG 431 (1114)
T ss_pred hhhhccChhhhheeeeee
Confidence 6665555433 3333433
No 220
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=48.57 E-value=6.2e+02 Score=31.35 Aligned_cols=122 Identities=12% Similarity=0.110 Sum_probs=73.4
Q ss_pred HHHHHHhcCCCCcHHHHHHHHHHHHHhhhCCCEEEEEeecCCCCceE-EEEeccCCCCCccCCcCCCCCchHHHHHHHHh
Q 001235 206 KAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEV-VSEITKSGLEPYLGLHYPATDIPQAARFLFMK 284 (1117)
Q Consensus 206 ~~~~~~~~~~~~~~~~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~v-vaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~ 284 (1117)
.+-.+|.+ +..+...|+.+.+++.++++.+.+.+.-+++++.... ...+.. +. +.|
T Consensus 224 ~~~~~l~~--~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---~~----~~~-------------- 280 (569)
T PRK10600 224 QANRRLHS--RAPLCERLSPVLNGLQNLTLLRDIELRVYETDDEENHQEFTCQS---DM----TCD-------------- 280 (569)
T ss_pred HHHHHHhc--CcchHHHHHHHHHHHHHhcCCCceEEEEeccccccceeeccCCC---cc----Ccc--------------
Confidence 34455666 4578888999999999999999999988775554322 111110 00 000
Q ss_pred CCeEEEeccCCcccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceee
Q 001235 285 NKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGL 364 (1117)
Q Consensus 285 ~~~r~i~d~~~~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl 364 (1117)
...|...+....|. . .+ ...+.+||..+ ++.-|.
T Consensus 281 -----~~~~~~~~~~~~~~-------~---------~~-----------~~~~~~~l~~~--------------~~~~G~ 314 (569)
T PRK10600 281 -----DKGCQLCPRGVLPV-------G---------DR-----------GTTLKWRLSDK--------------HGQYGI 314 (569)
T ss_pred -----ccccccccccCCCc-------C---------CC-----------CceEEEEeecC--------------CcceEE
Confidence 00011111100000 0 00 25667899755 778898
Q ss_pred EEeeccCCCCCCchhHHHHHHHHHHHHHHHHH
Q 001235 365 VVCHNTTPRFVPFPLRYACEFLAQVFAIHVNK 396 (1117)
Q Consensus 365 ~~~hh~~p~~~~~~~r~~~~~l~~~~~~~~~~ 396 (1117)
+...-..++.++.+.+..++.++..++..+..
T Consensus 315 ~~~~~~~~~~l~~~~~~ll~~l~~~l~~~l~~ 346 (569)
T PRK10600 315 LLATLPQGRHLSHDQQQLVDTLVEQLTATLAL 346 (569)
T ss_pred EEEEcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 87654446678888899999998888876643
No 221
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=45.28 E-value=2.4e+02 Score=33.93 Aligned_cols=89 Identities=13% Similarity=0.137 Sum_probs=54.0
Q ss_pred HHHHHHHHHHhhcc---CCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccC--CCCCC---------
Q 001235 1010 QVLADFLSISINFV---PNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFG--SEGDT--------- 1075 (1117)
Q Consensus 1010 qVL~nLl~NAik~~---~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe--~f~~~--------- 1075 (1117)
.++.+++.||+-|. ..++.|.|.+..+ ++.|+.+|.=.+.-..+.++. ++...
T Consensus 273 ~alREai~NAv~HRDYs~~~~~v~I~iydD-------------RieI~NPGgl~~gi~~~~l~~~~s~~RNp~LA~~l~~ 339 (467)
T COG2865 273 EALREAIINAVIHRDYSIRGRNVHIEIYDD-------------RIEITNPGGLPPGITPEDLLKGRSKSRNPVLAKVLRD 339 (467)
T ss_pred HHHHHHHHHHHHhhccccCCCceEEEEECC-------------eEEEECCCCCCCCCChhHcccCCCcccCHHHHHHHHH
Confidence 68899999999765 4345888876653 355668884333333333333 22111
Q ss_pred ----CCccccHHHHHHHHHHcCCE-EEEEeeCCeEEEEEEEec
Q 001235 1076 ----SEEGISLLISRKLVKLMNGD-VQYLREAGKSTFIVSVEL 1113 (1117)
Q Consensus 1076 ----~GtGLGL~ivr~iVe~~gG~-I~v~s~~g~ttF~i~LPl 1113 (1117)
..-|-|+--++++++.||.. ..+.... ..|++.++.
T Consensus 340 ~~liE~~GSGi~rm~~~~~~~gl~~p~f~~~~--~~~~~~~~~ 380 (467)
T COG2865 340 MGLIEERGSGIRRMFDLMEENGLPKPEFEEDN--DYVTVILHG 380 (467)
T ss_pred hhhHHHhCccHHHHHHHHHHcCCCCceeeccC--CeEEEEEec
Confidence 14588999999999988875 3444333 344554443
No 222
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=44.41 E-value=8.3e+02 Score=32.01 Aligned_cols=216 Identities=14% Similarity=0.099 Sum_probs=110.6
Q ss_pred HHHHHHHhCCCCCCCCeeeeC-CCCceeechhhHHHhcCCChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHH
Q 001235 746 GDYKAIVQNPNPLIPPIFGSD-EFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKA 824 (1117)
Q Consensus 746 ~~l~~i~~~~~~li~~I~~~D-~~g~i~~~N~a~~~l~G~~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (1117)
...+.++...|. |+.+.| .+|.|.++|+.|.+++| .+ ++|+++.. +. ++ +...
T Consensus 102 ~~~~~~l~~~p~---gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~~-~~-----------~~--------~~~~ 155 (838)
T PRK14538 102 QIGEEVLNELPI---GIVLIDISSKEIQWLNPYANFILK--NP-EINTPLAQ-IN-----------ES--------MAQL 155 (838)
T ss_pred HHHHHHHHhCCc---eEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHHH-hc-----------hH--------hhhc
Confidence 344566777777 899999 79999999999999987 22 78887532 11 10 1111
Q ss_pred hcCCCC-ceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEEEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 001235 825 MSGQDP-EKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQI 903 (1117)
Q Consensus 825 l~g~~~-~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEI 903 (1117)
..+... .... ..-+++++.+..... ..++ .+.|+|+..+...+....
T Consensus 156 ~~~~~~~~~~~---~~~~~~~y~~~~~~~---------~~~l-y~~D~T~~~~~~~~~~~~------------------- 203 (838)
T PRK14538 156 LLTSDKIPKTI---ITLKNQKFECFYKKD---------LNVF-YLFNATEKEQIKHLFLQK------------------- 203 (838)
T ss_pred ccccccccceE---EEECCEEEEEEEecc---------ceEE-EEEeccHHHHHHHHHHhc-------------------
Confidence 110000 0111 222444433333321 2233 348999876655432221
Q ss_pred hhhHHHH---HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhhc--cccccccCcccceeEEeeHHHHHHH---HHH
Q 001235 904 RNPLSGI---IFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDS--DLDSIIDGYLDLEMVEFTLNEVLVA---SIS 975 (1117)
Q Consensus 904 rnPL~~I---~~~~~LL~~~~l~~~~~~~l~~i~~~~~~l~~ii~dL--d~skie~g~~~l~~~~~~L~~li~~---v~~ 975 (1117)
.|.-++ ..+-+.+..... .+.......+. +.+.+..... -+.+++++++-+-...-.|..+.++ ++.
T Consensus 204 -~~v~g~i~iDNyde~~~~~~~-~~~s~l~~~i~---~~l~~~~~~~~~~~r~~~~dry~~~~~~~~l~~~~~~kF~iLd 278 (838)
T PRK14538 204 -TLALAMITFDNLEESLIRYDL-SEQSQIQGEYL---SALSDFIEPYEGYLKQLIDDRFLLLINRQNLDKMIENKFSILD 278 (838)
T ss_pred -CcEEEEEEeeCHHHHhcccch-HHHHHHHHHHH---HHHHHHHHhCCEEEEEecCCcEEEEEEHHHHHHHHHhCCcHHH
Confidence 111111 123333333221 11222222232 2355555553 4566777887777777777777776 666
Q ss_pred HHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHhhccCC--CCeEEEE
Q 001235 976 QVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPN--GGQLMVS 1032 (1117)
Q Consensus 976 ~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAik~~~~--~g~I~I~ 1032 (1117)
.++......++.+++.+.-... ..+...+ .++..+|++-+-. |.++.|.
T Consensus 279 ~ir~~~~~~~~~vTLSiGig~g----~~~~~e~----~~~A~~aldlAlgRGGDQvvvk 329 (838)
T PRK14538 279 TIRNISHKYQLKVTLSMGIACW----NLSYDKL----ATYSQNAIELAQKRGGDQAVVN 329 (838)
T ss_pred HHHHhhcCCCCceEEEEEEeCC----CCCHHHH----HHHHHHHHHHHhccCCCEEEEE
Confidence 6666665655666666543221 1123333 4455556655422 4477665
No 223
>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=44.00 E-value=26 Score=30.88 Aligned_cols=58 Identities=16% Similarity=0.074 Sum_probs=37.9
Q ss_pred ceEEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCC-CeeeeCCCCceeec
Q 001235 703 DPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIP-PIFGSDEFGWCCEW 774 (1117)
Q Consensus 703 ~~~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~-~I~~~D~~g~i~~~ 774 (1117)
...++..-+.|+++.+|++.|++++-.++.. +..++......-. -+|++|.+|.++.-
T Consensus 10 ~~~~vi~~s~pi~~~~g~~~Gvv~~di~l~~--------------l~~~i~~~~~~~~g~~~ivd~~G~ii~h 68 (81)
T PF02743_consen 10 TGQPVITISVPIYDDDGKIIGVVGIDISLDQ--------------LSEIISNIKFGNNGYAFIVDKNGTIIAH 68 (81)
T ss_dssp TTEEEEEEEEEEEETTTEEEEEEEEEEEHHH--------------HHHHHTTSBBTTTBEEEEEETTSBBCE-
T ss_pred CCcEEEEEEEEEECCCCCEEEEEEEEeccce--------------eeeEEEeeEECCCEEEEEEECCCCEEEe
Confidence 4456777889999999999999997555433 2233333222111 27889999998753
No 224
>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=39.66 E-value=34 Score=29.92 Aligned_cols=25 Identities=24% Similarity=0.461 Sum_probs=19.6
Q ss_pred EEEECCeEEEecCCCCHHHHHHHHH
Q 001235 445 ALLYKNKIWRLGVTPNDFQLHDIVS 469 (1117)
Q Consensus 445 a~~~~~~~~~~G~~p~~~~~~~l~~ 469 (1117)
+++.||++...|..|+.++++.+++
T Consensus 52 alvIng~~~~~G~~p~~~el~~~l~ 76 (76)
T PF13192_consen 52 ALVINGKVVFVGRVPSKEELKELLE 76 (76)
T ss_dssp EEEETTEEEEESS--HHHHHHHHHH
T ss_pred EEEECCEEEEEecCCCHHHHHHHhC
Confidence 4788999999999999999887753
No 225
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=39.01 E-value=1.5e+02 Score=36.64 Aligned_cols=37 Identities=14% Similarity=-0.024 Sum_probs=28.3
Q ss_pred HhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhh
Q 001235 741 FTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPA 777 (1117)
Q Consensus 741 L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a 777 (1117)
|+..+..+..+++........+++.|.+|.++..+-.
T Consensus 69 L~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~ 105 (606)
T COG3284 69 LTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGD 105 (606)
T ss_pred HHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecC
Confidence 5556666777777776666689999999999987654
No 226
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=37.97 E-value=4.2e+02 Score=28.52 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=35.4
Q ss_pred HHHHHHHHHhcCccEEEEeCCCcEEeecHHHHHHcCCCcc
Q 001235 615 TSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVD 654 (1117)
Q Consensus 615 ~~~l~~lie~a~~gi~~~D~dG~I~~~N~a~~~l~G~s~e 654 (1117)
.+.+..+++..+.|+.+-+.+|.+++.|.+|.++|.-+..
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~~ 57 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQ 57 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcCC
Confidence 3478889999999999999999999999999999985543
No 227
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=37.81 E-value=2.6e+02 Score=33.47 Aligned_cols=119 Identities=18% Similarity=0.276 Sum_probs=81.1
Q ss_pred HHHHHHHHHHHhhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCC----cCCCCCchHH-HHHHHHhCCeEEEeccCC
Q 001235 221 RLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGL----HYPATDIPQA-ARFLFMKNKVRMIVDCRA 295 (1117)
Q Consensus 221 ~~~~~~~~~vr~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~----~~p~~dip~~-~r~l~~~~~~r~i~d~~~ 295 (1117)
+=|..+++-|++.+|.|=|. +.-+..+-.+.|. |-|.++|--. .|.--..+.+ +..|-..
T Consensus 225 es~~~va~Ii~~~~~~~AVa--------------iTd~e~ilA~vg~g~dhhi~g~~i~s~~t~~ai~~g~v-v~~~~~e 289 (557)
T COG3275 225 ESLMKVAEIIYEELGAGAVA--------------ITDREKLLAFVGIGDDHHIPGKPIISSLTRKAIKTGEV-VYADGNE 289 (557)
T ss_pred hhHHHHHHHHHHHhCCCeEE--------------ecCHHHHHHhhcccccccCCCCeeccHHHHHHHhhCCE-EEEccch
Confidence 34566777788999998764 4444555555544 6787777443 4445555554 3444332
Q ss_pred cccccccCCCCCCcccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCC
Q 001235 296 RHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFV 375 (1117)
Q Consensus 296 ~~v~~~~~~~~~~~l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~ 375 (1117)
. +. | +-.-||+ .|.+++|+--+ |+.=|-|--.-+.|+.+
T Consensus 290 ~----~~------------c---sh~~c~l--------~s~lViPL~~~--------------g~ViGTiK~y~~~~~li 328 (557)
T COG3275 290 V----YE------------C---SHPTCKL--------GSALVIPLRGK--------------GRVIGTIKLYEAKARLI 328 (557)
T ss_pred h----hc------------c---CCCCCCc--------CCceEeecccC--------------CceeeeEEEEeccHhHh
Confidence 2 10 0 0123544 88899999533 88888888888899999
Q ss_pred CchhHHHHHHHHHHHHHHHH
Q 001235 376 PFPLRYACEFLAQVFAIHVN 395 (1117)
Q Consensus 376 ~~~~r~~~~~l~~~~~~~~~ 395 (1117)
+.-.|.+.+-+++.+|.|+.
T Consensus 329 s~~~r~la~Gia~l~SaQie 348 (557)
T COG3275 329 SSINRELAEGIAQLLSAQIE 348 (557)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999996
No 228
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.77 E-value=1.2e+02 Score=31.50 Aligned_cols=95 Identities=13% Similarity=0.065 Sum_probs=68.6
Q ss_pred CccEEE-EeCCCcEE--eecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCC
Q 001235 626 TVPILA-VDVDGLVN--GWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKIND 702 (1117)
Q Consensus 626 ~~gi~~-~D~dG~I~--~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG 702 (1117)
++-++. .|.+|.+. .+-...|.+|| .|+-|+++..+..+.++.........+.+...+.-+..... ...|
T Consensus 58 ~d~FiL~~~~~G~~~FRLAGTriC~LfG---RELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~----s~~G 130 (209)
T COG5388 58 PDVFILERDGRGKLPFRLAGTRICDLFG---RELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGR----SHGG 130 (209)
T ss_pred CceEEEeccCCCCceEEecccchhhhhc---hhhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchh----hccC
Confidence 444333 44556544 56777888888 67889999999999999999999988887766544443333 4457
Q ss_pred ceEEEEEEEEEeecCCCCEEEEEEE
Q 001235 703 DPITLIVNACASRDLHDNVVGVCFV 727 (1117)
Q Consensus 703 ~~~~v~v~~~pi~d~~G~v~gv~~v 727 (1117)
...-+++-..|.....|+...+.|+
T Consensus 131 ~sl~fEmLl~PL~~~~g~~~R~LGa 155 (209)
T COG5388 131 RSLGFEMLLAPLQGASGETDRFLGA 155 (209)
T ss_pred cccceeeeeecccCCCCCccchhhh
Confidence 7778888899999988886655555
No 229
>KOG0020 consensus Endoplasmic reticulum glucose-regulated protein (GRP94/endoplasmin), HSP90 family [Posttranslational modification, protein turnover, chaperones]
Probab=29.90 E-value=62 Score=38.11 Aligned_cols=46 Identities=22% Similarity=0.255 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhcc--------------CCCCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhh
Q 001235 1011 VLADFLSISINFV--------------PNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLL 1065 (1117)
Q Consensus 1011 VL~nLl~NAik~~--------------~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~ 1065 (1117)
.|.+||+||-++- .....++|++..... .-.+.|.|+|+||..+.+
T Consensus 99 FLRELISNASDAlDKIRllaLtd~~~L~~~~el~ikIK~Dke---------~klLhi~DtGiGMT~edL 158 (785)
T KOG0020|consen 99 FLRELISNASDALDKIRLLALTDKDVLGETEELEIKIKADKE---------KKLLHITDTGIGMTREDL 158 (785)
T ss_pred HHHHHHhhhhhhhhheeeeeccChhHhCcCcceEEEEeechh---------hCeeeEecccCCccHHHH
Confidence 3566777775542 112345555555544 335677899999987764
No 230
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=28.82 E-value=75 Score=34.01 Aligned_cols=38 Identities=16% Similarity=0.061 Sum_probs=33.0
Q ss_pred HHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCCC
Q 001235 745 EGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWK 785 (1117)
Q Consensus 745 e~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~~ 785 (1117)
.+.+.++++..+- |+++.|.+|.++++|.+|.++|.-.
T Consensus 18 ~~~~~~~i~~~~~---P~CiR~~~g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 18 PESLTAFIDDYSY---PACIRNESGKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHHHcCCC---CeEEECCCCCeeecchHHHHHHHhc
Confidence 3467788888887 9999999999999999999998654
No 231
>PRK04158 transcriptional repressor CodY; Validated
Probab=28.53 E-value=8.3e+02 Score=26.96 Aligned_cols=50 Identities=12% Similarity=0.154 Sum_probs=36.1
Q ss_pred eeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCCCchhHHHHHHHHHHHHHHHHHHH
Q 001235 334 IASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEL 398 (1117)
Q Consensus 334 ~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~~~~~r~~~~~l~~~~~~~~~~~~ 398 (1117)
+=.+++||..+ |..-|-|+.-.+...+ ..+.-.++|..+.+.+++|..+.
T Consensus 110 ~~~tIvPI~gg--------------GeRLGTLvl~r~~~~f-~~dDliL~EyaATVVgLEIlR~~ 159 (256)
T PRK04158 110 KLTTIVPIIGG--------------GERLGTLILARFDKEF-TDDDLILAEYAATVVGMEILREK 159 (256)
T ss_pred ceEEEEEEecC--------------CeEEEEEEEEecCCCC-CHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678999876 7777877776665333 33457799999999999986543
No 232
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=27.77 E-value=33 Score=42.94 Aligned_cols=16 Identities=44% Similarity=0.655 Sum_probs=14.2
Q ss_pred hhhCCCEEEEEeecCCCC
Q 001235 232 ELTGYDRVMAYKFHEDDH 249 (1117)
Q Consensus 232 ~~~~~dRv~iy~f~~d~~ 249 (1117)
.|||++||+| ||||||
T Consensus 614 NLTgAnRVII--fDPdWN 629 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN 629 (923)
T ss_pred ccccCceEEE--ECCCCC
Confidence 5899999999 589987
No 233
>KOG0355 consensus DNA topoisomerase type II [Chromatin structure and dynamics]
Probab=25.90 E-value=67 Score=40.58 Aligned_cols=54 Identities=17% Similarity=0.309 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhh-ccCC-CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh--hccCC
Q 001235 1007 RLQQVLADFLSISIN-FVPN-GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD--QMFGS 1071 (1117)
Q Consensus 1007 ~L~qVL~nLl~NAik-~~~~-~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~--~iFe~ 1071 (1117)
-|.+|+-+++.||.. -..+ -..|.+.+..+.. +++|.+||.|||-+..+ +++-|
T Consensus 53 Gl~ki~dEilvNaadk~rd~~m~~i~v~i~~e~~-----------~isv~nnGkGIPv~~H~~ek~yvp 110 (842)
T KOG0355|consen 53 GLYKIFDEILVNAADKQRDPKMNTIKVTIDKEKN-----------EISVYNNGKGIPVTIHKVEKVYVP 110 (842)
T ss_pred cHHHHHHHHhhcccccccCCCcceeEEEEccCCC-----------EEEEEeCCCcceeeecccccccch
Confidence 367999999999999 2221 2356666555544 68899999999988764 45544
No 234
>KOG0019 consensus Molecular chaperone (HSP90 family) [Posttranslational modification, protein turnover, chaperones]
Probab=24.90 E-value=66 Score=39.21 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhcc----------CC--CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhh
Q 001235 1011 VLADFLSISINFV----------PN--GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLD 1066 (1117)
Q Consensus 1011 VL~nLl~NAik~~----------~~--~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~ 1066 (1117)
-+.+|++||-++. |. +....|++.+..+ .-.++|.|+|+||..+.+-
T Consensus 61 FlRELISNaSDAldKiRy~~lt~~~~~~~~l~I~i~~nk~---------~~tlti~DtGIGMTk~dLv 119 (656)
T KOG0019|consen 61 FLRELISNASDALEKLRYLELKGDEKALPELEIRIITNKD---------KRTITIQDTGIGMTKEDLV 119 (656)
T ss_pred HHHhhhccccchHHHHHHHhhcCccccccceeEEeccCCC---------cceEEEEecCCCcCHHHHH
Confidence 4567777775432 21 4567777777666 4568888999999987754
No 235
>COG0813 DeoD Purine-nucleoside phosphorylase [Nucleotide transport and metabolism]
Probab=23.52 E-value=75 Score=33.88 Aligned_cols=52 Identities=21% Similarity=0.355 Sum_probs=37.2
Q ss_pred eEEecHHHHHHHHHHHHHHHhhccCCCCeEEEEEEecccccccccceeEEEEEEeecCCCCCh
Q 001235 1000 TLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPE 1062 (1117)
Q Consensus 1000 ~v~~D~~~L~qVL~nLl~NAik~~~~~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~ 1062 (1117)
++.|||.|-.=|-.+++.|++.+....+-.-.+-...+ -.++|.-.|.|||.
T Consensus 18 LmPGDPlRAK~iAetfLe~~~~vnevR~mlgfTGtYKG-----------k~iSvmg~GmGipS 69 (236)
T COG0813 18 LMPGDPLRAKYIAETFLENAVCVNEVRGMLGFTGTYKG-----------KKISVMGHGMGIPS 69 (236)
T ss_pred ecCCCCchHHHHHHHHHhhhhhhhhhcchhcccceecC-----------cEEEEEEecCCCcc
Confidence 67899999999999999999999854443333322222 24666677999986
No 236
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=23.13 E-value=53 Score=31.67 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=21.0
Q ss_pred CCCceeEEEEecCCceEEEEccChhhh
Q 001235 80 IQPFGCLLALDEKTFKVIAYSENAPEL 106 (1117)
Q Consensus 80 iQp~G~ll~~~~~~~~i~~~S~N~~~~ 106 (1117)
|||||+.+.|+..+-=.+++||=+..+
T Consensus 16 I~~yGAFV~l~~g~tGLVHISEIa~~f 42 (129)
T COG1098 16 ITPYGAFVELEGGKTGLVHISEIADGF 42 (129)
T ss_pred eEecceEEEecCCCcceEEehHhhhhh
Confidence 999999999998655588899744333
No 237
>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=23.08 E-value=2.3e+02 Score=25.37 Aligned_cols=32 Identities=22% Similarity=0.165 Sum_probs=25.7
Q ss_pred cCCceEEEEEEEEEeecCCCCEEEEEEEEEccc
Q 001235 700 INDDPITLIVNACASRDLHDNVVGVCFVAQDIT 732 (1117)
Q Consensus 700 ~dG~~~~v~v~~~pi~d~~G~v~gv~~v~~DIT 732 (1117)
..|.+.=+-+...|+++.+|++++.+++ -|+|
T Consensus 52 ~~G~Y~G~PViV~PI~~~~g~viaAiGv-VD~t 83 (84)
T PF09884_consen 52 IEGPYKGVPVIVAPIKDEDGEVIAAIGV-VDLT 83 (84)
T ss_pred CCcccCCeeEEEEEEEcCCCCEEEEEEE-EEcc
Confidence 3466655667788999999999999998 5776
Done!