Query 002191
Match_columns 955
No_of_seqs 740 out of 3770
Neff 8.4
Searched_HMMs 46136
Date Thu Mar 28 18:35:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002191.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002191hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4251 Bacteriophytochrome (l 100.0 6E-119 1E-123 985.3 43.5 509 79-617 11-528 (750)
2 PRK13560 hypothetical protein; 100.0 1E-29 2.2E-34 320.1 39.2 329 606-946 192-659 (807)
3 PF00360 PHY: Phytochrome regi 100.0 1.3E-31 2.8E-36 269.7 11.8 157 427-585 19-178 (182)
4 TIGR02938 nifL_nitrog nitrogen 99.9 3E-25 6.5E-30 262.8 23.9 310 618-946 4-333 (494)
5 PRK09776 putative diguanylate 99.9 9.7E-23 2.1E-27 265.2 28.6 265 607-887 272-537 (1092)
6 PF08446 PAS_2: PAS fold; Int 99.9 7.1E-24 1.5E-28 195.6 7.6 105 84-197 3-110 (110)
7 PRK09776 putative diguanylate 99.9 6E-22 1.3E-26 257.8 27.5 264 606-883 398-663 (1092)
8 PRK11091 aerobic respiration c 99.9 2.7E-22 5.8E-27 251.2 23.3 209 732-955 138-347 (779)
9 TIGR02040 PpsR-CrtJ transcript 99.9 1.4E-20 3.1E-25 219.8 25.9 242 610-878 125-368 (442)
10 PRK13560 hypothetical protein; 99.9 2.9E-20 6.4E-25 234.3 29.2 262 606-886 55-332 (807)
11 PRK11359 cyclic-di-GMP phospho 99.8 4.6E-18 9.9E-23 214.2 28.5 242 618-880 12-257 (799)
12 TIGR02040 PpsR-CrtJ transcript 99.8 1E-17 2.2E-22 195.9 22.6 233 624-880 2-249 (442)
13 PRK13559 hypothetical protein; 99.7 1.9E-15 4.1E-20 172.0 20.8 186 746-953 40-229 (361)
14 COG5002 VicK Signal transducti 99.7 1.4E-15 2.9E-20 158.8 16.3 194 732-954 93-290 (459)
15 PRK13557 histidine kinase; Pro 99.7 2.5E-15 5.3E-20 180.5 20.9 198 742-952 23-229 (540)
16 PRK11006 phoR phosphate regulo 99.6 1.4E-14 3E-19 169.0 17.5 190 729-955 78-269 (430)
17 PRK11360 sensory histidine kin 99.6 1.2E-13 2.6E-18 167.9 23.4 198 740-953 253-452 (607)
18 PRK11073 glnL nitrogen regulat 99.6 7.9E-14 1.7E-18 157.8 18.3 184 749-952 7-191 (348)
19 TIGR02966 phoR_proteo phosphat 99.5 7.6E-14 1.6E-18 156.2 16.1 175 745-954 2-179 (333)
20 PRK09959 hybrid sensory histid 99.4 1.9E-12 4E-17 170.3 20.6 215 730-955 557-777 (1197)
21 PF13426 PAS_9: PAS domain; PD 99.4 1.6E-12 3.5E-17 118.7 12.9 104 628-736 1-104 (104)
22 PF08448 PAS_4: PAS fold; Int 99.4 1.8E-12 3.9E-17 119.8 12.6 110 624-739 1-110 (110)
23 PF01590 GAF: GAF domain; Int 99.4 2.1E-12 4.6E-17 127.4 13.3 153 230-396 1-154 (154)
24 PF13426 PAS_9: PAS domain; PD 99.4 1.3E-12 2.8E-17 119.3 10.6 103 763-873 2-104 (104)
25 PRK10841 hybrid sensory kinase 99.4 1.2E-11 2.6E-16 156.0 22.2 181 741-955 326-511 (924)
26 PF00989 PAS: PAS fold; Inter 99.4 6.7E-12 1.5E-16 116.6 13.0 112 618-734 1-113 (113)
27 PRK11091 aerobic respiration c 99.3 2.9E-11 6.4E-16 151.8 19.6 145 602-751 139-283 (779)
28 PF08448 PAS_4: PAS fold; Int 99.3 1.2E-11 2.5E-16 114.3 11.4 110 755-876 1-110 (110)
29 PF00989 PAS: PAS fold; Inter 99.3 2.3E-11 5E-16 112.9 13.2 112 749-871 1-113 (113)
30 PRK10618 phosphotransfer inter 99.3 4.8E-11 1E-15 148.5 19.5 176 740-955 334-514 (894)
31 PF00512 HisKA: His Kinase A ( 99.3 8.8E-12 1.9E-16 105.0 6.7 65 891-955 1-68 (68)
32 COG3852 NtrB Signal transducti 99.2 3.2E-10 6.9E-15 117.7 15.8 176 753-947 11-187 (363)
33 PRK11086 sensory histidine kin 99.2 9.6E-10 2.1E-14 132.3 22.5 202 712-946 146-390 (542)
34 smart00065 GAF Domain present 99.1 2.3E-09 4.9E-14 102.8 16.5 140 230-399 1-142 (149)
35 PRK10060 RNase II stability mo 99.1 2E-09 4.2E-14 132.1 19.9 167 702-884 69-236 (663)
36 PRK13559 hypothetical protein; 99.1 1.7E-09 3.7E-14 123.1 17.1 133 615-752 40-175 (361)
37 COG5000 NtrY Signal transducti 99.1 2.3E-09 5E-14 120.7 16.5 182 743-952 364-553 (712)
38 PRK13558 bacterio-opsin activa 99.0 3.5E-09 7.6E-14 130.7 18.3 136 619-759 149-287 (665)
39 PRK13557 histidine kinase; Pro 99.0 3.5E-09 7.7E-14 127.1 16.8 131 613-748 25-158 (540)
40 COG3829 RocR Transcriptional r 99.0 1.6E-08 3.4E-13 114.1 18.6 224 621-880 4-228 (560)
41 PRK10060 RNase II stability mo 99.0 1.2E-08 2.6E-13 125.3 18.1 162 613-781 106-284 (663)
42 TIGR00229 sensory_box PAS doma 99.0 1.1E-08 2.5E-13 92.2 13.4 120 618-743 3-123 (124)
43 PF08447 PAS_3: PAS fold; Int 98.9 6.1E-09 1.3E-13 92.9 10.1 90 774-868 1-91 (91)
44 PRK11359 cyclic-di-GMP phospho 98.9 3E-08 6.5E-13 125.3 20.3 126 615-745 133-259 (799)
45 PRK13558 bacterio-opsin activa 98.9 3.3E-08 7.2E-13 122.1 18.3 124 751-885 150-276 (665)
46 PRK15053 dpiB sensor histidine 98.8 3.4E-07 7.3E-12 110.4 24.4 199 712-946 147-385 (545)
47 TIGR00229 sensory_box PAS doma 98.8 4.2E-08 9.2E-13 88.4 11.8 119 749-879 3-122 (124)
48 TIGR02938 nifL_nitrog nitrogen 98.8 1.3E-08 2.8E-13 120.6 10.6 125 749-884 4-128 (494)
49 PF08447 PAS_3: PAS fold; Int 98.8 4.3E-08 9.4E-13 87.4 10.3 86 640-731 1-91 (91)
50 KOG3558 Hypoxia-inducible fact 98.8 1.1E-07 2.5E-12 108.1 15.0 225 622-873 123-378 (768)
51 COG3290 CitA Signal transducti 98.8 8.1E-07 1.7E-11 100.5 21.7 199 705-934 133-371 (537)
52 PF13596 PAS_10: PAS domain; P 98.7 5.7E-08 1.2E-12 89.6 9.4 106 620-735 1-106 (106)
53 COG2203 FhlA FOG: GAF domain [ 98.7 6.7E-08 1.4E-12 95.9 10.6 154 215-399 5-165 (175)
54 PF13492 GAF_3: GAF domain; PD 98.7 5.7E-07 1.2E-11 85.5 15.0 128 230-397 1-128 (129)
55 PRK11360 sensory histidine kin 98.6 6.9E-07 1.5E-11 108.6 16.0 131 611-749 255-386 (607)
56 cd00130 PAS PAS domain; PAS mo 98.5 1.5E-06 3.3E-11 74.2 13.1 103 627-734 1-103 (103)
57 PF13185 GAF_2: GAF domain; PD 98.5 1.7E-06 3.8E-11 84.3 14.4 137 230-397 3-148 (148)
58 PF12860 PAS_7: PAS fold 98.5 6.8E-07 1.5E-11 83.7 9.1 104 624-742 1-115 (115)
59 TIGR02966 phoR_proteo phosphat 98.4 1.6E-06 3.5E-11 96.8 13.5 114 614-745 2-115 (333)
60 cd00130 PAS PAS domain; PAS mo 98.4 3E-06 6.4E-11 72.3 12.0 101 763-871 3-103 (103)
61 COG5002 VicK Signal transducti 98.4 1.5E-06 3.2E-11 92.1 11.6 130 606-747 99-228 (459)
62 TIGR01817 nifA Nif-specific re 98.4 2E-05 4.4E-10 94.3 23.1 153 214-398 5-158 (534)
63 COG2202 AtoS FOG: PAS/PAC doma 98.4 3.1E-05 6.6E-10 77.1 20.7 228 632-877 3-231 (232)
64 PF13596 PAS_10: PAS domain; P 98.4 2.2E-06 4.9E-11 78.9 10.0 106 751-872 1-106 (106)
65 COG2205 KdpD Osmosensitive K+ 98.4 1.1E-06 2.3E-11 103.3 9.2 66 890-955 658-727 (890)
66 PRK11388 DNA-binding transcrip 98.4 1.1E-05 2.3E-10 98.9 18.4 220 619-874 63-309 (638)
67 PRK11073 glnL nitrogen regulat 98.3 3.9E-06 8.4E-11 94.9 13.1 116 619-747 8-124 (348)
68 TIGR02956 TMAO_torS TMAO reduc 98.3 8.2E-07 1.8E-11 114.7 8.4 74 882-955 454-528 (968)
69 smart00388 HisKA His Kinase A 98.3 1.1E-06 2.5E-11 72.4 5.6 64 892-955 2-66 (66)
70 PRK15347 two component system 98.3 1.2E-06 2.5E-11 112.7 8.4 74 882-955 388-462 (921)
71 PRK15429 formate hydrogenlyase 98.2 0.00017 3.7E-09 89.0 24.2 147 228-400 197-345 (686)
72 PRK05022 anaerobic nitric oxid 98.2 0.00017 3.6E-09 85.7 23.2 214 217-462 7-221 (509)
73 PRK11107 hybrid sensory histid 98.2 2.8E-06 6E-11 109.2 8.2 74 882-955 283-357 (919)
74 COG3604 FhlA Transcriptional r 98.1 0.00011 2.3E-09 82.6 18.4 205 229-462 47-257 (550)
75 PF14598 PAS_11: PAS domain; P 98.1 3E-05 6.5E-10 71.9 11.7 102 765-874 5-109 (111)
76 PRK11006 phoR phosphate regulo 98.1 1.6E-05 3.5E-10 92.8 12.3 119 608-746 88-206 (430)
77 PRK11466 hybrid sensory histid 98.1 5.6E-06 1.2E-10 106.3 9.0 72 884-955 436-508 (914)
78 PRK11061 fused phosphoenolpyru 98.1 8.7E-05 1.9E-09 91.2 17.8 151 217-398 6-156 (748)
79 PF12860 PAS_7: PAS fold 98.1 1.4E-05 3.1E-10 74.7 8.4 105 763-878 6-114 (115)
80 PRK10820 DNA-binding transcrip 98.1 7.1E-05 1.5E-09 88.9 16.2 112 613-739 75-190 (520)
81 PF14598 PAS_11: PAS domain; P 98.0 4.8E-05 1E-09 70.5 11.5 101 631-736 5-108 (111)
82 COG3829 RocR Transcriptional r 98.0 9.3E-05 2E-09 84.2 14.3 167 613-794 112-326 (560)
83 PRK11086 sensory histidine kin 98.0 8.2E-05 1.8E-09 89.5 15.2 122 611-750 214-339 (542)
84 PRK09303 adaptive-response sen 97.8 2.9E-05 6.4E-10 89.0 7.7 69 887-955 146-222 (380)
85 KOG3559 Transcriptional regula 97.8 6.2E-05 1.3E-09 80.6 8.8 208 622-858 83-313 (598)
86 COG4191 Signal transduction hi 97.7 0.0023 5.1E-08 73.6 20.3 59 893-951 385-447 (603)
87 cd00082 HisKA Histidine Kinase 97.7 8.7E-05 1.9E-09 60.5 6.2 61 891-951 3-65 (65)
88 COG5000 NtrY Signal transducti 97.7 0.00051 1.1E-08 78.6 13.7 132 599-743 351-483 (712)
89 COG2202 AtoS FOG: PAS/PAC doma 97.6 0.00095 2.1E-08 66.1 13.9 126 609-740 103-231 (232)
90 KOG3560 Aryl-hydrocarbon recep 97.6 0.00031 6.6E-09 78.3 10.5 225 621-873 114-385 (712)
91 COG3290 CitA Signal transducti 97.6 0.00056 1.2E-08 78.0 12.5 122 610-748 207-331 (537)
92 PRK15053 dpiB sensor histidine 97.4 0.0025 5.5E-08 76.8 16.1 123 610-750 214-338 (545)
93 PRK10490 sensor protein KdpD; 97.4 0.00033 7.2E-09 88.8 8.5 67 889-955 661-730 (895)
94 COG4251 Bacteriophytochrome (l 97.4 0.00044 9.6E-09 79.2 8.4 72 882-953 514-589 (750)
95 PRK10820 DNA-binding transcrip 97.4 0.00084 1.8E-08 79.9 11.1 110 744-874 75-188 (520)
96 PRK13837 two-component VirA-li 97.3 0.00043 9.4E-09 87.7 8.6 64 891-954 449-514 (828)
97 KOG0501 K+-channel KCNQ [Inorg 97.3 0.00036 7.9E-09 78.3 6.3 100 771-876 39-138 (971)
98 PF13188 PAS_8: PAS domain; PD 97.3 0.00033 7.1E-09 57.8 4.6 43 618-664 1-43 (64)
99 PRK11388 DNA-binding transcrip 97.1 0.02 4.3E-07 70.4 19.8 113 613-739 198-311 (638)
100 PRK09959 hybrid sensory histid 97.1 0.01 2.2E-07 78.8 18.1 136 606-749 564-703 (1197)
101 KOG0501 K+-channel KCNQ [Inorg 97.1 0.0016 3.5E-08 73.2 8.5 116 619-739 15-138 (971)
102 PRK15429 formate hydrogenlyase 96.8 0.051 1.1E-06 67.3 19.9 203 216-450 11-224 (686)
103 PRK10604 sensor protein RstB; 96.7 0.0027 5.9E-08 74.2 6.7 63 888-955 208-271 (433)
104 PRK10815 sensor protein PhoQ; 96.7 0.0034 7.4E-08 74.3 7.5 63 890-954 264-328 (485)
105 PF13188 PAS_8: PAS domain; PD 96.6 0.0026 5.7E-08 52.3 4.1 36 749-788 1-36 (64)
106 COG2461 Uncharacterized conser 96.6 0.0056 1.2E-07 66.8 7.5 115 618-743 290-404 (409)
107 KOG1229 3'5'-cyclic nucleotide 96.6 0.0023 4.9E-08 69.7 4.5 115 741-866 150-264 (775)
108 PRK10364 sensor protein ZraS; 96.5 0.0063 1.4E-07 71.6 8.4 62 891-952 236-299 (457)
109 smart00091 PAS PAS domain. PAS 96.5 0.009 1.9E-07 45.9 6.7 63 619-682 2-64 (67)
110 TIGR02916 PEP_his_kin putative 96.3 0.16 3.5E-06 63.0 19.5 152 217-399 308-460 (679)
111 PF08670 MEKHLA: MEKHLA domain 96.3 0.064 1.4E-06 51.9 12.1 109 619-734 33-145 (148)
112 TIGR03785 marine_sort_HK prote 96.2 0.014 3.1E-07 72.2 9.2 68 887-954 480-548 (703)
113 KOG3558 Hypoxia-inducible fact 96.0 0.013 2.9E-07 67.9 6.7 100 631-735 277-377 (768)
114 TIGR02373 photo_yellow photoac 95.7 0.047 1E-06 50.5 8.1 62 624-685 22-83 (124)
115 PRK10337 sensor protein QseC; 95.7 0.025 5.4E-07 66.3 8.1 64 891-954 236-301 (449)
116 COG4192 Signal transduction hi 95.7 0.023 5.1E-07 63.0 6.9 61 894-954 453-517 (673)
117 TIGR02916 PEP_his_kin putative 95.5 0.087 1.9E-06 65.4 12.3 55 893-947 476-531 (679)
118 PRK09467 envZ osmolarity senso 95.4 0.034 7.4E-07 64.9 7.6 63 886-953 223-286 (435)
119 PRK09835 sensor kinase CusS; P 95.1 0.054 1.2E-06 64.1 8.3 67 888-954 258-326 (482)
120 TIGR01386 cztS_silS_copS heavy 95.0 0.047 1E-06 64.0 7.4 65 890-954 239-305 (457)
121 PRK09470 cpxA two-component se 95.0 0.042 9.2E-07 64.5 6.9 64 887-953 238-302 (461)
122 PRK10755 sensor protein BasS/P 95.0 0.05 1.1E-06 61.7 7.2 58 891-953 136-194 (356)
123 PRK11100 sensory histidine kin 94.9 0.049 1.1E-06 64.2 6.9 64 891-954 255-319 (475)
124 PRK10549 signal transduction h 94.8 0.045 9.8E-07 64.4 6.6 67 888-955 236-303 (466)
125 PF08670 MEKHLA: MEKHLA domain 94.7 0.61 1.3E-05 45.2 12.5 110 749-870 32-144 (148)
126 smart00086 PAC Motif C-termina 94.4 0.22 4.8E-06 33.8 7.0 40 834-873 3-42 (43)
127 COG3852 NtrB Signal transducti 94.3 0.41 9E-06 51.2 11.3 111 621-742 10-121 (363)
128 TIGR02851 spore_V_T stage V sp 94.0 2.3 5E-05 43.0 15.7 126 230-397 53-180 (180)
129 COG2461 Uncharacterized conser 94.0 0.1 2.2E-06 57.3 6.3 114 748-878 289-402 (409)
130 smart00091 PAS PAS domain. PAS 93.8 0.19 4.1E-06 38.1 6.1 45 751-798 3-47 (67)
131 PRK10841 hybrid sensory kinase 93.7 0.96 2.1E-05 58.1 15.4 115 608-750 324-439 (924)
132 PRK11644 sensory histidine kin 93.3 0.28 6E-06 58.3 8.9 59 891-949 301-361 (495)
133 TIGR02373 photo_yellow photoac 93.1 0.48 1E-05 44.0 8.2 46 755-803 22-67 (124)
134 KOG1229 3'5'-cyclic nucleotide 93.1 0.069 1.5E-06 58.6 3.2 104 620-728 159-263 (775)
135 KOG3753 Circadian clock protei 92.5 0.66 1.4E-05 55.6 10.1 199 630-852 194-416 (1114)
136 COG0642 BaeS Signal transducti 92.4 0.18 4E-06 55.3 5.5 63 891-954 114-177 (336)
137 COG3283 TyrR Transcriptional r 92.0 0.66 1.4E-05 50.7 8.7 55 618-673 80-134 (511)
138 PRK13837 two-component VirA-li 90.7 12 0.00026 47.7 19.9 143 221-398 284-427 (828)
139 COG1956 GAF domain-containing 90.7 11 0.00023 36.9 14.4 118 236-395 38-159 (163)
140 smart00086 PAC Motif C-termina 90.2 1.4 3.1E-05 29.5 6.6 36 701-736 7-42 (43)
141 KOG0519 Sensory transduction h 90.2 0.043 9.4E-07 68.4 -2.6 69 885-955 212-283 (786)
142 PRK10618 phosphotransfer inter 89.3 5.4 0.00012 50.9 14.9 46 608-653 333-379 (894)
143 COG3284 AcoR Transcriptional a 88.8 2.6 5.6E-05 49.9 10.5 179 607-797 63-268 (606)
144 KOG3560 Aryl-hydrocarbon recep 88.2 1.6 3.4E-05 49.8 8.0 94 637-736 292-385 (712)
145 PRK10490 sensor protein KdpD; 87.1 30 0.00065 44.4 19.7 49 346-398 595-644 (895)
146 PF07310 PAS_5: PAS domain; I 85.9 6.2 0.00013 38.0 9.9 93 631-731 42-136 (137)
147 KOG3561 Aryl-hydrocarbon recep 85.4 0.43 9.2E-06 58.2 1.8 98 767-872 377-476 (803)
148 PF14689 SPOB_a: Sensor_kinase 85.0 5.8 0.00013 32.4 7.8 48 894-945 14-61 (62)
149 KOG3559 Transcriptional regula 84.2 2.1 4.6E-05 46.9 6.2 88 628-720 225-312 (598)
150 KOG3561 Aryl-hydrocarbon recep 82.9 0.71 1.5E-05 56.3 2.3 45 96-148 105-149 (803)
151 COG3283 TyrR Transcriptional r 80.8 5.1 0.00011 44.1 7.4 47 749-798 80-126 (511)
152 COG3605 PtsP Signal transducti 80.0 12 0.00026 43.8 10.3 147 216-397 5-155 (756)
153 PF07310 PAS_5: PAS domain; I 79.7 12 0.00026 35.9 9.2 85 773-868 52-136 (137)
154 PF04340 DUF484: Protein of un 78.1 32 0.00069 36.2 12.6 137 217-397 81-221 (225)
155 PF08348 PAS_6: YheO-like PAS 76.0 11 0.00024 35.3 7.3 46 829-876 66-111 (118)
156 PRK10600 nitrate/nitrite senso 74.6 1.2E+02 0.0025 36.8 18.0 124 217-399 223-347 (569)
157 PF07568 HisKA_2: Histidine ki 68.1 16 0.00035 31.1 6.0 48 899-946 2-49 (76)
158 COG3887 Predicted signaling pr 67.9 58 0.0013 38.6 12.1 38 616-653 73-110 (655)
159 COG3920 Signal transduction hi 62.6 24 0.00053 37.0 7.4 58 869-933 2-59 (221)
160 PF08348 PAS_6: YheO-like PAS 58.9 36 0.00079 31.8 7.1 42 701-744 75-116 (118)
161 PRK14538 putative bifunctional 58.5 44 0.00095 42.2 9.8 44 618-664 102-146 (838)
162 PF08446 PAS_2: PAS fold; Int 57.6 12 0.00027 34.4 3.7 47 630-677 17-67 (110)
163 PRK13719 conjugal transfer tra 52.4 22 0.00047 36.8 4.8 39 618-656 19-57 (217)
164 PF14827 Cache_3: Sensory doma 46.0 38 0.00083 31.3 5.1 73 763-870 40-112 (116)
165 COG5385 Uncharacterized protei 44.3 40 0.00086 33.0 4.8 41 895-935 18-58 (214)
166 COG4564 Signal transduction hi 43.7 2.3E+02 0.0051 31.2 10.8 68 749-833 80-148 (459)
167 COG3275 LytS Putative regulato 38.9 99 0.0021 35.8 7.6 118 234-397 226-348 (557)
168 PF02743 Cache_1: Cache domain 38.4 56 0.0012 27.8 4.6 56 708-777 12-68 (81)
169 COG3887 Predicted signaling pr 37.4 2.3E+02 0.0049 33.9 10.3 37 747-786 73-109 (655)
170 COG3284 AcoR Transcriptional a 37.3 2.4E+02 0.0051 34.1 10.7 37 744-780 69-105 (606)
171 PF09884 DUF2111: Uncharacteri 37.0 1.2E+02 0.0025 26.3 5.9 32 703-735 52-83 (84)
172 PF09884 DUF2111: Uncharacteri 35.8 1.1E+02 0.0024 26.3 5.6 48 820-872 36-83 (84)
173 KOG3753 Circadian clock protei 34.4 63 0.0014 39.7 5.4 76 635-715 338-416 (1114)
174 PRK04158 transcriptional repre 34.2 4E+02 0.0086 28.5 10.7 49 346-399 110-158 (256)
175 PF03472 Autoind_bind: Autoind 33.5 4.1E+02 0.0089 24.9 10.9 110 238-372 8-122 (149)
176 KOG0387 Transcription-coupled 30.5 26 0.00057 42.6 1.6 16 244-261 614-629 (923)
177 COG1098 VacB Predicted RNA bin 29.8 34 0.00074 31.9 1.8 24 92-115 15-38 (129)
178 PF06785 UPF0242: Uncharacteri 26.3 1.7E+02 0.0036 32.1 6.4 90 751-852 285-376 (401)
179 PRK14538 putative bifunctional 24.7 5.7E+02 0.012 32.6 11.8 41 752-798 105-146 (838)
180 PRK10963 hypothetical protein; 23.6 8.6E+02 0.019 25.4 13.5 49 344-397 168-217 (223)
181 COG4191 Signal transduction hi 23.4 4.4E+02 0.0095 31.7 9.6 91 749-870 89-179 (603)
182 COG5388 Uncharacterized protei 22.7 1.9E+02 0.0041 29.2 5.6 97 627-731 57-156 (209)
183 PF02070 NMU: Neuromedin U; I 22.5 60 0.0013 21.0 1.4 16 86-101 6-21 (25)
184 PRK10935 nitrate/nitrite senso 21.9 2.2E+02 0.0049 34.1 7.6 56 891-946 359-420 (565)
185 PF13192 Thioredoxin_3: Thiore 21.4 1.1E+02 0.0025 25.7 3.5 24 447-470 52-75 (76)
186 PF11212 DUF2999: Protein of u 20.7 94 0.002 25.8 2.5 47 904-954 27-76 (82)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=6.1e-119 Score=985.25 Aligned_cols=509 Identities=33% Similarity=0.569 Sum_probs=447.0
Q ss_pred hHHHh-hhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCCCcccccccccccCCccccccCCchHHHHHHHHhc
Q 002191 79 QITAY-LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSGASLAKAAAS 157 (955)
Q Consensus 79 ~~~~~-~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~~ 157 (955)
.++.| .+|||+||+||||||||++|+.++.|+++|+||..+||+.| ++++|+++.++|+..+...++.++..
T Consensus 11 ~l~nce~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~-------e~l~~~tl~~vl~~~qv~~l~~~l~~ 83 (750)
T COG4251 11 TLTNCEREPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREP-------EDLLGRTLGAVLTSEQVPPLQSALTV 83 (750)
T ss_pred cccccccCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCCh-------hhhhcCCHHHhcchhhccHHHHhccc
Confidence 33444 55599999999999999999999999999999999999998 68999999999999999999999988
Q ss_pred ccccccCcceeeccCCCCCcceEEEEEeeCCEEEEEeccCCCCCCcchhhhHHHHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 002191 158 REISLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPSKSGDPALSLAGAVQSQKLAVSAISRLQALPGGDIGLLCDT 237 (955)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~hr~~~~~~ie~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 237 (955)
......||..+-. + .+..|++++||+++.+|+||||....+.. ..+.++.++..++.+||+ +.++.++|+.
T Consensus 84 ~~~~~~np~~~w~--~-~~~~fDv~~HR~~~llIlEfEp~~t~e~~----~~l~f~h~~k~a~~~lq~--a~~l~~l~~~ 154 (750)
T COG4251 84 GGLTTLNPTKMWT--R-KGGSFDVSAHRSKELLILEFEPAGTGETA----SFLGFYHLAKLAMNRLQS--AANLRDLLSR 154 (750)
T ss_pred cCcccCCchhhhh--h-cCCceeEEEEecCcEEEEEEecCcccccc----cccchHHHHHHHHHHHhc--CccHHHHHHH
Confidence 8888888854432 2 23389999999999999999997544321 123467788889999999 5599999999
Q ss_pred HHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCCccccc--c
Q 002191 238 VVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQ--S 315 (955)
Q Consensus 238 ~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~~~l~~--~ 315 (955)
++++||++|||||||+|||++||+|+||||++.++++||||+||||||||+|||+||.+|++|+|+|++++|||++| +
T Consensus 155 ~tqeVr~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavN 234 (750)
T COG4251 155 TTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVN 234 (750)
T ss_pred HHHHHHHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998 7
Q ss_pred cccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHHHHHH
Q 002191 316 KELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQ 395 (955)
Q Consensus 316 ~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~~~l~~~~~~~ 395 (955)
|.+++|+|||+|.||||||||+|||+||||.||||||||++| +|||||+|||.+||++|++.|.+||+++|++|.+
T Consensus 235 p~t~~p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~g----~LWGLIACHH~sPk~ip~~vR~acef~gq~~s~~ 310 (750)
T COG4251 235 PETNEPLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVDG----KLWGLIACHHQSPKVIPYEVRKACEFFGQVLSME 310 (750)
T ss_pred cccCCcccchHHHHhccChHHHHHHHhcCcceeeEEEEEECC----eeEEeeeeccCCCccCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHhhcccC-CcccccCCchhhhhccCCeEEEEECCeEEEecCCCCHHHHHHHHHH
Q 002191 396 LYMELQVA--MQLAEKNILRTQVLLCDMLLRDA-PFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWW 472 (955)
Q Consensus 396 l~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~l~~~~g~a~~~~~~~~~~G~~p~~~~~~~l~~w 472 (955)
++...+-+ ..+.+.+ ....+++..|...++ ..++....+++++|++|||++++++|+|.++|.||+..++..|+.|
T Consensus 311 i~~~e~~~~~d~r~~l~-~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~Ll~w 389 (750)
T COG4251 311 ISALEQSEDADYRVQLT-EHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQW 389 (750)
T ss_pred HHHHhhhhhHHHHHHHH-HHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHHHHH
Confidence 97543321 1111111 112234445555554 4778888999999999999999999999999999999999999999
Q ss_pred HHhccCCCceeecccccccCCCCccccccccceEEEEEecC--CCeEEEeecccceEEeccCCCCCCCc-CCCCCcccCC
Q 002191 473 LLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGMATARITS--KDFLFWFRSHTAKEVKWGGAKHHPEH-KDNGGKMHPR 549 (955)
Q Consensus 473 l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~l~~~i~~--~~~l~wfR~e~~~~v~W~G~p~~~~~-~~~~~~l~PR 549 (955)
|.+..+ ..+|.||+|+.. ||.+..|++.+|||||++|+. .+|++|||+|..++|+|+|+|+|++. .+++.|++||
T Consensus 390 l~~~~~-~~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL~PR 467 (750)
T COG4251 390 LAEREE-GDVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRLTPR 467 (750)
T ss_pred HhcCCc-ccEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCcccCCc
Confidence 988744 489999999985 999999999999999999998 79999999999999999999999976 5557899999
Q ss_pred chHHHHHHHhcccccCCccchHHHHHHHHHHHHHHHHHHHHhhccchhcccccccccccchHHHHHHH
Q 002191 550 SSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRDSFQEMEEENDSKVQGNTQQNGSKMQGVDELSSVA 617 (955)
Q Consensus 550 ~SF~~w~e~v~g~s~pW~~~el~~~~~L~~~l~~~l~~~~~~~~~~~~~~~rl~~~l~~~~~eL~~~~ 617 (955)
+||+.|+|+|++++.||...|++++.+++ .++..+.. +++.+++++++++.+.++|++...
T Consensus 468 kSFe~WkE~vRl~s~PWs~~ei~~A~~LR----~aiv~ivl---~~aeela~l~r~lersn~el~~f~ 528 (750)
T COG4251 468 KSFELWKETVRLQSQPWSEVEIEAALELR----KAIVGIVL---RHAEELAQLRRELERSNAELRAFA 528 (750)
T ss_pred ccHHHHHHHHhccCCCCCHHHHHHHHHHH----HHHHHHHH---HHHHHHHHHHHHHhhhhHHHHHHH
Confidence 99999999999999999999999999984 44444443 556667888888888888887664
No 2
>PRK13560 hypothetical protein; Provisional
Probab=99.97 E-value=1e-29 Score=320.14 Aligned_cols=329 Identities=16% Similarity=0.165 Sum_probs=262.4
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc
Q 002191 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (955)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~ 685 (955)
+++++++|++++++|+.+++++|++++++|.+|+++++|+++++++||+.++++|+++. ++.++.............+.
T Consensus 192 rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~-~~~~~~~~~~~~~~~~~~~~ 270 (807)
T PRK13560 192 RKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIH-DFAPAQPADDYQEADAAKFD 270 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcch-hcCCcchhHHHHHHHHHHhc
Confidence 45667889999999999999999999999999999999999999999999999999998 88777665555444444554
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEE--EEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 002191 686 GEEDKNVELKLRKFELQKQHSVVYILV--NACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIP 763 (955)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v--~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id 763 (955)
.+....++..+ .+++|..+|+.+ +..|+.+.+|.+.|++++++|||++|+++++|++++++|+.++++++.
T Consensus 271 ~~~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~--- 343 (807)
T PRK13560 271 ADGSQIIEAEF----QNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPI--- 343 (807)
T ss_pred cCCceEEEEEE----EcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcc---
Confidence 44455555555 688999996655 456778899999999999999999999999999999999999999875
Q ss_pred CeeeecCCCcEeee-cHHHHHHhCCChhhhccCCccchhc----------------------------------------
Q 002191 764 PIFASDENACCSEW-NAAMEKVTGWMRHEVIGKMLPREIF---------------------------------------- 802 (955)
Q Consensus 764 ~I~~~D~~g~i~~~-N~a~~~l~G~~~eeviGk~~~~~~~---------------------------------------- 802 (955)
+++.+|.+|+++++ |+++++++||+.++++|+.+.+...
T Consensus 344 ~i~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 423 (807)
T PRK13560 344 AAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDG 423 (807)
T ss_pred cEEEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccC
Confidence 59999999999987 6778889999999998875321000
Q ss_pred --------------------------------------------------------------------------------
Q 002191 803 -------------------------------------------------------------------------------- 802 (955)
Q Consensus 803 -------------------------------------------------------------------------------- 802 (955)
T Consensus 424 ~e~~~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~ 503 (807)
T PRK13560 424 QEVLIEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKN 503 (807)
T ss_pred ceEEEEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecch
Confidence
Q ss_pred ---------------ccchhccChhhHHHHHHHHHhhhc-CCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEE
Q 002191 803 ---------------GNFCRMKGQDMLTKFMILLYQGIT-GQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFC 866 (955)
Q Consensus 803 ---------------~~~~~l~~~d~~~~~~~~l~~~~~-g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~ 866 (955)
..+..+.||++...+...+..... +...+..++++.+++|..+|+.....|++|.+|.+.++++
T Consensus 504 ~~~~G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g 583 (807)
T PRK13560 504 ITQFGYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEG 583 (807)
T ss_pred hhhcCCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEE
Confidence 000111233333333333333333 2345677889999999999999999999999999999999
Q ss_pred EEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002191 867 FMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG 946 (955)
Q Consensus 867 i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D 946 (955)
+++|||++|++|.++++ +.+.|.+|++.|||||||||++|.|+++|+.....+++.+.++..+......+..+++.
T Consensus 584 ~~~DITerK~aE~~L~~----a~~~~~~~l~~isHelrnpL~~I~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 659 (807)
T PRK13560 584 IVIDISERKHAEEKIKA----ALTEKEVLLKEIHHRVKNNLQIISSLLDLQAEKLHDEEAKCAFAESQDRICAMALAHEK 659 (807)
T ss_pred EEechHHHHHHHHHHHH----HHHHHHHHHHHhHHHHhChHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999877654 34568899999999999999999999999987667777777777776666666655554
No 3
>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []. The protein undergoes reversible photochemical conversion between a biologically-inactive red light-absorbing form and the active far-red light-absorbing form. Phytochrome is a dimer of identical 124 kDa subunits, each of which contains a linear tetrapyrrole chromophore, covalently-attached via a Cys residue. This domain represents a region specific to phytochrome proteins.; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3C2W_G 3NHQ_B 3G6O_B 3IBR_A 2VEA_A 3ZQ5_A.
Probab=99.97 E-value=1.3e-31 Score=269.74 Aligned_cols=157 Identities=34% Similarity=0.694 Sum_probs=134.4
Q ss_pred CcccccCCchhhhhccCCeEEEEECCeEEEecCCCCHHHHHHHHHHHHhccCCCceeecccccccCCCCccccccccceE
Q 002191 427 PFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPTESQLKDIAWWLLNNHGDCTGLSTDSLAEAGYPGAALLGQAVCGM 506 (955)
Q Consensus 427 ~~~~~~~~~~l~~l~~~~g~a~~~~~~~~~~G~~p~~~~~~~l~~wl~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~ 506 (955)
...+..+.+++++|++|||+|++++|+++++|.+|+..++.+|++||.... ...+|+|++|.+. ||++.++.+.+|||
T Consensus 19 ~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~-~~~v~~T~~L~~~-~p~~~~~~~~aaGv 96 (182)
T PF00360_consen 19 LEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQA-DGEVFATDSLSED-YPDAAALAERAAGV 96 (182)
T ss_dssp HHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTT-T-SEEEESBGGGT-SGGGGGGCCCHSEE
T ss_pred hHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhC-CCccchhhhHhHh-ChhhhhhcccCCCc
Confidence 467888999999999999999999999999999999999999999999774 4589999999985 99999999999999
Q ss_pred EEEEecC--CCeEEEeecccceEEeccCCCCCCCcC-CCCCcccCCchHHHHHHHhcccccCCccchHHHHHHHHHHHHH
Q 002191 507 ATARITS--KDFLFWFRSHTAKEVKWGGAKHHPEHK-DNGGKMHPRSSFKAFLEVVKNRSFPWEVSEINAIHSLQIVMRD 583 (955)
Q Consensus 507 l~~~i~~--~~~l~wfR~e~~~~v~W~G~p~~~~~~-~~~~~l~PR~SF~~w~e~v~g~s~pW~~~el~~~~~L~~~l~~ 583 (955)
|+++|++ ++||+|||+|+.++|+|||+|+|+... +++.+++||+||+.|+|+|+|+|.||+..++.++..++..+..
T Consensus 97 Lai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~~~d~~~A~~lr~~l~~ 176 (182)
T PF00360_consen 97 LAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWSDADLEAAERLRRALLE 176 (182)
T ss_dssp EEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---HHHHHHHHHHHHHHHH
T ss_pred EEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCCHHHHHHHHHHHHHHHH
Confidence 9999986 689999999999999999999999764 4588999999999999999999999999999999999665554
Q ss_pred HH
Q 002191 584 SF 585 (955)
Q Consensus 584 ~l 585 (955)
.+
T Consensus 177 ~~ 178 (182)
T PF00360_consen 177 VI 178 (182)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 4
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=99.93 E-value=3e-25 Score=262.77 Aligned_cols=310 Identities=12% Similarity=0.005 Sum_probs=223.8
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEE
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLR 697 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~ 697 (955)
+.|+.+++.++++++++|.+|+++++|+++++++|+++++++|+... .+.++.........+...+..+..+..++..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 81 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNES-VLSNHTTPPEVYQALWGSLAEQKPWAGKLLN- 81 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCch-hhcCCCCCHHHHHHHHHHHHhCCcccceeec-
Confidence 46889999999999999999999999999999999999999999865 5554443333333444444444444444443
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeee
Q 002191 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEW 777 (955)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~ 777 (955)
.+++|..+|+.....|+++.+|.+.+++++++|||++|++++++++++..++.++++++. +++++|.+|+++++
T Consensus 82 ---~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~---~i~~~d~~~~i~~~ 155 (494)
T TIGR02938 82 ---RRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPV---AFVLLDPTGRVILD 155 (494)
T ss_pred ---cCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccc---eEEEEcCCCCEEEe
Confidence 578999999999999999999999999999999999999999999999999999999875 59999999999999
Q ss_pred cHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCc-EEEEEEEEeeeeC
Q 002191 778 NAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQ-FVEVALTASRRTD 856 (955)
Q Consensus 778 N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~-~~~v~~~~~pi~d 856 (955)
|+++++++|+...+..+..+.+ ..+++....+...+. .+......+.++...+|. .+|+.....++.+
T Consensus 156 N~~~~~~~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (494)
T TIGR02938 156 NQEYKKLATDLRVKEPAHTVLD--------LLREAWREALAENWP---QQLAFSNREARFDRGGGRPARWLSCTGSVIGM 224 (494)
T ss_pred chhHHHhhchhhhhHHHHHHHH--------HhhHHhhhhhhhcch---hhhccccceeeeccCCCceeeEEEecCceEEe
Confidence 9999999999887776654332 122222222211111 111122234455555555 7899988888877
Q ss_pred CCCCE---------EEEEEEEeccCcccHHHHHHHhHHH-------HHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccC
Q 002191 857 AEGKV---------IGCFCFMQILVPDLQPALEAQGLED-------MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESS 920 (955)
Q Consensus 857 ~~G~v---------~g~v~i~~DITerk~~el~lq~~aE-------~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~ 920 (955)
..|.+ .+++++++|||++|++|.+++..+. +..+...++++.++|||||||+.|.++.++++..
T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~~~al~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~i~~~~~~l~~~ 304 (494)
T TIGR02938 225 ESDCADSFFCAAEQPYLLLTIADISNLREEQERARLSALQALMAEEERLEAIRETLSAAIHRLQGPMNLISAAISVLQRR 304 (494)
T ss_pred ecchhhheeccCCCchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHhc
Confidence 66654 3456688999999998876643322 2223445677888999999999999999999863
Q ss_pred CCC---HHHHHHHHHHHHHHHHHHHhhcc
Q 002191 921 SIS---ENQRQYLETSDACERQIMTIIDG 946 (955)
Q Consensus 921 ~l~---~~~~~~l~~i~~~a~rl~~LI~D 946 (955)
..+ ++....+..+.....++...+.+
T Consensus 305 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 333 (494)
T TIGR02938 305 GDDAGNPASAAMLQQALSAGREHMEALRQ 333 (494)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222 33444444444444444444444
No 5
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.91 E-value=9.7e-23 Score=265.15 Aligned_cols=265 Identities=14% Similarity=0.082 Sum_probs=233.1
Q ss_pred ccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcC
Q 002191 607 MQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLG 686 (955)
Q Consensus 607 ~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~ 686 (955)
++..++|++++++++.++++++++++.+|.+|+++++|+++++++||+.++++|+++. ++.++++.+.....+.....+
T Consensus 272 r~~~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~-~~~~~~d~~~~~~~~~~~~~~ 350 (1092)
T PRK09776 272 RAERKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQ-QLTWPEDLNKDLQQVEKLLSG 350 (1092)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCce-eccCcchhHhHHHHHHHHHcC
Confidence 3446678899999999999999999999999999999999999999999999999998 889998887777777777665
Q ss_pred CC-cceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCe
Q 002191 687 EE-DKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPI 765 (955)
Q Consensus 687 ~~-~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I 765 (955)
+. ....+.++ .++||..+|+..+..++++.+|.+.+++++++|||++|++|+++++++++++.+++..+. ++
T Consensus 351 ~~~~~~~e~~~----~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~---~i 423 (1092)
T PRK09776 351 EINSYSMEKRY----YRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGI---GI 423 (1092)
T ss_pred CccceeeeeEE----EcCCCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCc---eE
Confidence 43 23445554 689999999999999999999999999999999999999999999999999999998864 59
Q ss_pred eeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEE
Q 002191 766 FASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFV 845 (955)
Q Consensus 766 ~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~ 845 (955)
|.+|.++++++||+++.+++||+.++..+.. .+....+|++...+...+.+...++..+..|+++.++|| .+
T Consensus 424 ~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~-------~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~ 495 (1092)
T PRK09776 424 WEWDLKPNIISWDKRMFELYEIPPHIKPTWQ-------VWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VR 495 (1092)
T ss_pred EEEecCCCeEeeCHHHHHHhCCCcccCCCHH-------HHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eE
Confidence 9999999999999999999999988843321 133466789988888888888888889999999999999 99
Q ss_pred EEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHH
Q 002191 846 EVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDM 887 (955)
Q Consensus 846 ~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~ 887 (955)
|+.....++.|.+|++.+++++.+|||++|+.+.++++..++
T Consensus 496 w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~ 537 (1092)
T PRK09776 496 HIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKER 537 (1092)
T ss_pred EEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998887665544
No 6
>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=99.89 E-value=7.1e-24 Score=195.60 Aligned_cols=105 Identities=35% Similarity=0.508 Sum_probs=91.6
Q ss_pred hhhccCCCCCCccceEEEEeCCCceEEEEecChhhhhCCC---CcccccccccccCCccccccCCchHHHHHHHHhcccc
Q 002191 84 LSKIQRGGLIQPFGCMLAVEEPTFRIIGYSENCLEMLDLR---SRSEDFELNGLIGIDARTLFTPPSGASLAKAAASREI 160 (955)
Q Consensus 84 ~~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~---~~~~~~~~~~~~g~~~~~~~~~~~~~~l~~~~~~~~~ 160 (955)
+||||+||+|||||+||++|+++++|++||+|++++||.+ + ..++|+++.++|++...+.+++++.....
T Consensus 3 ~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~-------~~llG~~l~~ll~~~~~~~l~~~~~~~~~ 75 (110)
T PF08446_consen 3 REPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPELP-------EELLGRPLSELLGAESAERLREALQSESL 75 (110)
T ss_dssp GS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS----H-------HHHTTCBHHHHSCCCCHHHHHHHCTCCCC
T ss_pred cccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccccc-------hhhcccCHHHHhCHHHHHHHHHhhhccCc
Confidence 6779999999999999999999999999999999999999 5 57999999999999999999999887776
Q ss_pred cccCcceeeccCCCCCcceEEEEEeeCCEEEEEeccC
Q 002191 161 SLLNPILVHSNSRSIEKPFYAILHRIDVGIVIDLEPS 197 (955)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~hr~~~~~~ie~Ep~ 197 (955)
...+|+.++. ..+++.|++++||+++++||||||+
T Consensus 76 ~~~~~~~~~~--~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 76 SLSNPIALRL--RIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCEEEEE--EEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred cccCCeEEEe--ccCCeeEEEEEEEECCEEEEEEeeC
Confidence 6678888875 4478899999999999999999995
No 7
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.89 E-value=6e-22 Score=257.78 Aligned_cols=264 Identities=17% Similarity=0.193 Sum_probs=220.6
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc
Q 002191 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (955)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~ 685 (955)
+++.++++++.+++++.+++..++++|.+|.++++++||+++.+++|++.++..+...+...++|++.+.....+.....
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 34567788888999999999999999999999999999999999999999885543322267888888888888888888
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCe
Q 002191 686 GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPI 765 (955)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I 765 (955)
++.....++++ .++|| .+|+.....+++|.+|++.+++++.+|||++|++++++++++++++.++++++. ++
T Consensus 478 ~~~~~~~e~r~----~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~---~i 549 (1092)
T PRK09776 478 GRSPFKLEFRI----VVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGE---AV 549 (1092)
T ss_pred cCCCeeEEEEE----EcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhcccc---EE
Confidence 88877777777 78899 999999999999999999999999999999999999999999999999999875 59
Q ss_pred eeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCc--ceeeEEEEcCCCc
Q 002191 766 FASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT--ENFPFGFFNRQGQ 843 (955)
Q Consensus 766 ~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~--~~~e~~~~~~dG~ 843 (955)
+.+|.+|+++++|+++++++||+.++++|++..+ ++. ..++++...... +......... ...++.+.+++|+
T Consensus 550 ~~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~-~~~----~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~G~ 623 (1092)
T PRK09776 550 VCTDMAMKVTFMNPVAEKMTGWTQEEALGVPLLT-VLH----ITFGDNGPLMEN-IYSCLTSRSAAYLEQDVVLHCRSGG 623 (1092)
T ss_pred EEECCCCeEEEEcHHHHHHhCCCHHHHcCCCHHH-Hcc----cccCCcchhhHH-HHHHHhcCCCccccceEEEEeCCCc
Confidence 9999999999999999999999999999997653 222 112222222222 3333333222 4567778999999
Q ss_pred EEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHh
Q 002191 844 FVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQG 883 (955)
Q Consensus 844 ~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~ 883 (955)
.+|+..+..|+.+.+|++.|++++.+|||++|+.+.+++.
T Consensus 624 ~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~L~~ 663 (1092)
T PRK09776 624 SYDVHYSITPLSTLDGENIGSVLVIQDVTESRKMLRQLSY 663 (1092)
T ss_pred EEEEEEEeeeeecCCCCEEEEEEEEEecchHHHHHHHHHh
Confidence 9999999999999999999999999999999988866543
No 8
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.89 E-value=2.7e-22 Score=251.15 Aligned_cols=209 Identities=17% Similarity=0.181 Sum_probs=187.2
Q ss_pred ecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccCh
Q 002191 732 QDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQ 811 (955)
Q Consensus 732 ~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~ 811 (955)
++|+++++++++++++++.++.++++++. +|++.|.+|+++++|+++++++||+.++++|+.+.+ +.++
T Consensus 138 ~~i~~r~~~~~~l~~~~~~l~~il~~~~~---~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~--------l~~~ 206 (779)
T PRK11091 138 NEIKEREETQIELEQQSSLLRSFLDASPD---LVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKD--------VYSP 206 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcc---eEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHH--------hCCH
Confidence 48999999999999999999999999985 599999999999999999999999999999998653 3335
Q ss_pred hhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHH
Q 002191 812 DMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYA 891 (955)
Q Consensus 812 d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~a 891 (955)
+....+.........++....++..+..++|+.+|+.++..|+.+.+|.+.|++++++|||++|+++.+++ ++++.
T Consensus 207 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~----~a~~~ 282 (779)
T PRK11091 207 EAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALE----KASRD 282 (779)
T ss_pred HHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHH----HHHHH
Confidence 55556666666777777788889999999999999999999999999999999999999999998876543 44557
Q ss_pred HHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 892 KIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 892 k~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
|.+|+++|||||||||++|.|+.+++....++++++++++.|..+++++..+|+| ||++|+++|
T Consensus 283 ~~~~~a~isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~ 347 (779)
T PRK11091 283 KTTFISTISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERR 347 (779)
T ss_pred HHHHHHHhhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCC
Confidence 8899999999999999999999999988888999999999999999999999999 999999875
No 9
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.87 E-value=1.4e-20 Score=219.84 Aligned_cols=242 Identities=15% Similarity=0.116 Sum_probs=185.4
Q ss_pred hHHHHHHHHHHHHHHHhcCccEEEEcC-CCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCC
Q 002191 610 VDELSSVACEMVRLIETATAPIFGVDS-SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEE 688 (955)
Q Consensus 610 ~~eL~~~~~~l~~lie~~~~~I~~~D~-dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~ 688 (955)
..+|++++++|+.+++++++++|++|. +|+|+++|+++++++||+.++++|+++. +++++++...+...+.....++.
T Consensus 125 ~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~-~~~~~~~~~~~~~~l~~~~~~g~ 203 (442)
T TIGR02040 125 YWTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFP-QEFEGRRREELMLTLRNVRATGS 203 (442)
T ss_pred HHHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHH-HhCCHHHHHHHHHHHHHHHhcCC
Confidence 457888889999999999999999998 8999999999999999999999999988 88888888888888877776655
Q ss_pred cceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeee
Q 002191 689 DKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFAS 768 (955)
Q Consensus 689 ~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~ 768 (955)
....++.. ++|+..| .+...++.. ++.. .+++.+.|||+++++++++. .+|+.++++++. +|+++
T Consensus 204 ~~~~~~~~------~~~~~~~-~~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~~~---~~~~~l~e~~~d---~I~v~ 268 (442)
T TIGR02040 204 AAPVRILL------RRSQKRL-LVVVSVFRQ-DGES-LFLCQLSPAGATQPVGDELS---ENLARLYHEAPD---AIVFS 268 (442)
T ss_pred CcceEEEE------cCCCeEE-EEEEEEEEe-CCce-EEEEEEcccchhhhhhHHHH---HHHHHHHHhCCc---eEEEE
Confidence 44433332 3343344 345555553 3333 45677889999998877653 379999999975 59999
Q ss_pred cCCCcEeeecHHHHHHhCCC-hhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEE
Q 002191 769 DENACCSEWNAAMEKVTGWM-RHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEV 847 (955)
Q Consensus 769 D~~g~i~~~N~a~~~l~G~~-~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v 847 (955)
|.+|+|+++|+++++++||+ .++++|+++...+ . ....+...+ +.....++....++..+.+++|..+|+
T Consensus 269 D~~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~-~-----~~~~~~~~~---~~~~~~~g~~~~~~~~~~~~~G~~~~v 339 (442)
T TIGR02040 269 DADGTIRGANEAFLELTDSSSLEAVRGRTLDRWL-G-----RGGVDLRVL---LSNVRRTGQVRLYATTLTGEFGAQTEV 339 (442)
T ss_pred cCCCcEEehhHHHHHHhCCCChHHHcCCCHHHHh-C-----CCcccHHHH---HHHHhhcCceEEEEEEEEcCCCCEEEE
Confidence 99999999999999999997 5789999865321 1 112222222 333344555566788889999999999
Q ss_pred EEEEeeeeCCCCCEEEEEEEEeccCcccHHH
Q 002191 848 ALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (955)
Q Consensus 848 ~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (955)
.+++.|+.+.++. .++++++|||+||+.+
T Consensus 340 e~s~~~i~~~~~~--~~~~v~rDITeR~~~~ 368 (442)
T TIGR02040 340 EISAAWVDQGERP--LIVLVIRDISRRLTMR 368 (442)
T ss_pred EEEEEEeccCCce--EEEEEEecchhhccCC
Confidence 9999999876553 4778899999988774
No 10
>PRK13560 hypothetical protein; Provisional
Probab=99.86 E-value=2.9e-20 Score=234.26 Aligned_cols=262 Identities=16% Similarity=0.131 Sum_probs=203.0
Q ss_pred cccchHHHHHHHHHH-HHHHHhcCccEEEEcCCCc----EeeecHHHHHHhCCCchhhcCCC--ccccccccccHHHHH-
Q 002191 606 KMQGVDELSSVACEM-VRLIETATAPIFGVDSSGT----INGWNAKVAELTGLPASEAMGKS--LIDEVVHEESQGAVE- 677 (955)
Q Consensus 606 l~~~~~eL~~~~~~l-~~lie~~~~~I~~~D~dg~----i~~~N~~~~~l~G~~~eeliG~~--~~~~l~~~~~~~~~~- 677 (955)
++.++.+|+++++++ +.+++++|+++|.++.+|. +.+++.+...++|+...++++.. +. .++||++.+.+.
T Consensus 55 r~~~~~~l~~~~e~~~r~l~~~~p~~i~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~p~d~~~~~~ 133 (807)
T PRK13560 55 RAIAEAEAQDCREQCERNLKANIPGGMFLFALDGDGTFSFPSLLDANGELAAIAKHDLMADKGLLA-MLIGGDDGDFFFA 133 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCceEEEEEEcCccccccceeeccchhHHHhcCcccCCccchhh-hhcCCCcchhhhh
Confidence 445677888888888 9999999999999877665 33477777888888888766532 33 678888776543
Q ss_pred ------HHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHH
Q 002191 678 ------NLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDY 751 (955)
Q Consensus 678 ------~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~l 751 (955)
+.+..++..+....+++++ .++||+ |+.+...|.++.+|.. ++.+++.|||++|+++++|++++.+|
T Consensus 134 ~~~~~~~~~~~~~~~~~~~~~e~r~----~~~dg~--~~~~~~~~~~~~~g~~-~~~g~~~DIT~rk~ae~~l~~~~~~l 206 (807)
T PRK13560 134 NPFRSAETIAMALQSDDWQEEEGHF----RCGDGR--FIDCCLRFERHAHADD-QVDGFAEDITERKRAEERIDEALHFL 206 (807)
T ss_pred ChhhHHHHHHHHhccCcccceEEEE----EeCCcc--EEEEEeeeeecCCCce-EEEEEEEccchHHHHHHHHHHHHHHH
Confidence 3334444555556667766 677885 6667778888888875 68899999999999999999999999
Q ss_pred HHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcc
Q 002191 752 EAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE 831 (955)
Q Consensus 752 r~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~ 831 (955)
+.++++++. +++..|.+|+++++|+++++++||+.++++|+++.+ +++ ++....+.......+..+...
T Consensus 207 ~~l~e~~~~---~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~-~~~-------~~~~~~~~~~~~~~~~~~~~~ 275 (807)
T PRK13560 207 QQLLDNIAD---PAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHD-FAP-------AQPADDYQEADAAKFDADGSQ 275 (807)
T ss_pred HHHHhhCCC---eEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchh-cCC-------cchhHHHHHHHHHHhccCCce
Confidence 999999985 599999999999999999999999999999998654 222 222222323334444455567
Q ss_pred eeeEEEEcCCCcEEEEEEE--EeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHH
Q 002191 832 NFPFGFFNRQGQFVEVALT--ASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLED 886 (955)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~--~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE 886 (955)
.++.++.+++|..+|+.+. ..|+.+.+|.+.|++++++|||++|++|.++++..+
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 456789999999999999999999999988765443
No 11
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.80 E-value=4.6e-18 Score=214.17 Aligned_cols=242 Identities=14% Similarity=0.105 Sum_probs=189.4
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCc----ceEE
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED----KNVE 693 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~----~~~e 693 (955)
..+..+++.++++++++|.+|++++||+++++++||+.++++|+++. .+++++........+.....++.. ...+
T Consensus 12 ~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 90 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNID-MLIPRDLRPAHPEYIRHNREGGKARVEGMSRE 90 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHH-HhcCccccccchHHHhhhhccCCcccccccee
Confidence 34567889999999999999999999999999999999999999988 888876655544555544443322 1224
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCc
Q 002191 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENAC 773 (955)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~ 773 (955)
+++ .++||..+|+.+...++. .+|.. +++++.+|||++++.+++. ..+..++++++. +++.+|.+|+
T Consensus 91 ~~~----~~~dG~~~~v~~~~~~~~-~~g~~-~~~~~~~DiT~~~~~~~~~----~~~~~~~~~~~~---~i~~~d~~g~ 157 (799)
T PRK11359 91 LQL----EKKDGSKIWTRFALSKVS-AEGKV-YYLALVRDASVEMAQKEQT----RQLIIAVDHLDR---PVIVLDPERR 157 (799)
T ss_pred eEE----ecCCcCEEEEEEEeeeec-cCCce-EEEEEEeeccchhhhHHHH----HHHHHHHhcCCC---cEEEEcCCCc
Confidence 444 678999999999988874 44554 5678889999988776654 445567888764 5999999999
Q ss_pred EeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEee
Q 002191 774 CSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASR 853 (955)
Q Consensus 774 i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~p 853 (955)
++++|+++++++||+.++++|+.+.+.+.. ++........+...+.++..+..++++.+++|..+|+..+..|
T Consensus 158 i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~ 230 (799)
T PRK11359 158 IVQCNRAFTEMFGYCISEASGMQPDTLLNI-------PEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISP 230 (799)
T ss_pred EEEEChhhHhhhCCCHHHHCCCChHHhcCC-------CCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeee
Confidence 999999999999999999999976532211 2222223344555566666777888999999999999999999
Q ss_pred eeCCCCCEEEEEEEEeccCcccHHHHH
Q 002191 854 RTDAEGKVIGCFCFMQILVPDLQPALE 880 (955)
Q Consensus 854 i~d~~G~v~g~v~i~~DITerk~~el~ 880 (955)
+.+.+|.+.+++++.+|||++|+.+..
T Consensus 231 v~d~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 231 VYDVLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred eecCCCceeEEEEEeehhhhHHHHHHH
Confidence 999999999999999999999877644
No 12
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.78 E-value=1e-17 Score=195.90 Aligned_cols=233 Identities=16% Similarity=0.152 Sum_probs=174.0
Q ss_pred HHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeecc
Q 002191 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQK 703 (955)
Q Consensus 624 ie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~ 703 (955)
++.++++++++|.+|+|++||..+++++||+.++++|+++. +++++++.+.+...+.....++.. .++... .+..+
T Consensus 2 ~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~e~--~~~~~ 77 (442)
T TIGR02040 2 LATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWE-EIVTAESVEKFELRLSEALRTGRG-AVRVEL--NHIDP 77 (442)
T ss_pred CcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHh-HhhCcchHHHHHHHHHHHhccCCC-cceEee--ccCCC
Confidence 57889999999999999999999999999999999999998 999998877777777666655432 122222 11455
Q ss_pred CCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHH-----------HH---HHHHHHHHHHHHHHhcCCCCCCeeeec
Q 002191 704 QHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVL-----------MD---KFIRLQGDYEAIIQSVNPLIPPIFASD 769 (955)
Q Consensus 704 dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~a-----------e~---~L~~se~~lr~i~e~~~~~id~I~~~D 769 (955)
+|..+|+.++..++.+. .+++++.+|||+++.. |+ ++++++++|+.++++++. ++|++|
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 66677888877776542 2567889999875543 33 677788899999999875 599999
Q ss_pred C-CCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEE
Q 002191 770 E-NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVA 848 (955)
Q Consensus 770 ~-~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~ 848 (955)
. +|+++++|+++++++||+.++++|+++.+ +.++++...+...+.....++.....++ ..++|...| .
T Consensus 151 ~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~--------~~~~~~~~~~~~~l~~~~~~g~~~~~~~--~~~~~~~~~-~ 219 (442)
T TIGR02040 151 MSTGRIVEANSAAAALLGGVGQSLVGRAFPQ--------EFEGRRREELMLTLRNVRATGSAAPVRI--LLRRSQKRL-L 219 (442)
T ss_pred CCCCEEEEEcHHHHHHhCcCHHHHcCCCHHH--------hCCHHHHHHHHHHHHHHHhcCCCcceEE--EEcCCCeEE-E
Confidence 7 89999999999999999999999998553 4457777777777877776665544444 345555444 4
Q ss_pred EEEeeeeCCCCCEEEEEEEEeccCcccHHHHH
Q 002191 849 LTASRRTDAEGKVIGCFCFMQILVPDLQPALE 880 (955)
Q Consensus 849 ~~~~pi~d~~G~v~g~v~i~~DITerk~~el~ 880 (955)
+..+++.. +|.. .+++.++|||++++.+.+
T Consensus 220 ~~~~~~~~-~~~~-~~l~~~~dit~~~~~e~~ 249 (442)
T TIGR02040 220 VVVSVFRQ-DGES-LFLCQLSPAGATQPVGDE 249 (442)
T ss_pred EEEEEEEe-CCce-EEEEEEcccchhhhhhHH
Confidence 45555553 3333 467788999998776644
No 13
>PRK13559 hypothetical protein; Provisional
Probab=99.67 E-value=1.9e-15 Score=172.01 Aligned_cols=186 Identities=12% Similarity=0.089 Sum_probs=148.0
Q ss_pred HHHHHHHHHHHhcCCCCCCeeeecC---CCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHH
Q 002191 746 RLQGDYEAIIQSVNPLIPPIFASDE---NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLY 822 (955)
Q Consensus 746 ~se~~lr~i~e~~~~~id~I~~~D~---~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~ 822 (955)
.+...|+.++++.+. +++++|. +|+++++|+++++++||+.++++|+.+.. + .++.........+.
T Consensus 40 ~~~~~~~~~~e~~~~---~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~-l-------~~~~~~~~~~~~~~ 108 (361)
T PRK13559 40 ASGRLFEQAMEQTRM---AMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRF-L-------QGAATDPIAVAKIR 108 (361)
T ss_pred hhhhHHHHHHHhCCC---cEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhh-h-------cCCCCCHHHHHHHH
Confidence 346678889999874 5999996 56899999999999999999999998542 1 11222223344455
Q ss_pred hhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 002191 823 QGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQE 902 (955)
Q Consensus 823 ~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHE 902 (955)
..+.++..+..++...+++|..+|+..+..|+++.+|.+.+++++.+|||++|+.+.+. +.+.+|++.++|+
T Consensus 109 ~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~--------~~~~~l~~~l~H~ 180 (361)
T PRK13559 109 AAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE--------AHERRLAREVDHR 180 (361)
T ss_pred HHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH--------HHHHHHHHHHHHh
Confidence 66667767788888899999999999999999999999999999999999998765332 2334688899999
Q ss_pred hhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 903 VKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 903 LRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
+||||+.|.++..++.. ..+..++++.+...+.+|.+++++ |+.++.+
T Consensus 181 ~~n~L~~i~~~~~l~~~---~~~~~~~~~~i~~~~~~l~~~~~~ll~~~~~~ 229 (361)
T PRK13559 181 SKNVFAVVDSIVRLTGR---ADDPSLYAAAIQERVQALARAHETLLDERGWE 229 (361)
T ss_pred hhhHHHHHHHHHHhhcc---CCCHHHHHHHHHHHHHHHHHHHHHHhccCCcC
Confidence 99999999999998873 234556888888999999999988 7776643
No 14
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.66 E-value=1.4e-15 Score=158.78 Aligned_cols=194 Identities=11% Similarity=0.175 Sum_probs=150.8
Q ss_pred ecchHhHH-HHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccC
Q 002191 732 QDITHEKV-LMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKG 810 (955)
Q Consensus 732 ~DITerk~-ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~ 810 (955)
.|.|++.+ +++.++....++..++..+. ||++.+|..|+|+.+|..+.+++|.+.++++|+...+.+-.
T Consensus 93 n~Lt~~~~~aq~n~e~Er~kL~SvlayMt---DGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i------- 162 (459)
T COG5002 93 NDLTKRVQEAQANTEQERRKLDSVLAYMT---DGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKI------- 162 (459)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHc---CceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCC-------
Confidence 46666544 44445555668899998886 57999999999999999999999999999999986642211
Q ss_pred hhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHH
Q 002191 811 QDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIY 890 (955)
Q Consensus 811 ~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ 890 (955)
.+.+. +...+........+ ..+ .++..-..++.+.+.-+.|-+.|++.++.|+||+.+.|.+
T Consensus 163 ~d~y~-----~~dL~e~~~s~lld--~~~-~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~E---------- 224 (459)
T COG5002 163 EDTYT-----FEDLVEKNDSLLLD--SSD-EEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERE---------- 224 (459)
T ss_pred cccee-----HHHHHhcCCcEEEe--ecC-CCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHH----------
Confidence 22221 22222323222222 222 7778888899999999999999999999999986655543
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHH--HHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN--QRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~--~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
+.+|.|++||||||||+++.++++.|+.....++ ..+++.......+||.+|++| |.+||++.
T Consensus 225 -rRefvanvSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~ 290 (459)
T COG5002 225 -RREFVANVSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDN 290 (459)
T ss_pred -HHHHHHhcchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcc
Confidence 4589999999999999999999999998666555 788999999999999999999 89999875
No 15
>PRK13557 histidine kinase; Provisional
Probab=99.66 E-value=2.5e-15 Score=180.46 Aligned_cols=198 Identities=13% Similarity=0.085 Sum_probs=157.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCeeeecC---CCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHH
Q 002191 742 DKFIRLQGDYEAIIQSVNPLIPPIFASDE---NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFM 818 (955)
Q Consensus 742 ~~L~~se~~lr~i~e~~~~~id~I~~~D~---~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~ 818 (955)
+.....+..|+.++++++. +|+++|. +|+|+|+|+++++++||+.++++|+++.. +.++++.....
T Consensus 23 ~~~~~~~~~~~~~~~~~~~---~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~--------l~~~~~~~~~~ 91 (540)
T PRK13557 23 DVSDHRSDIFFAAVETTRM---PMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRF--------LQGPETDRATV 91 (540)
T ss_pred hhhhhhhHHHHHHHHhCcC---cEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHh--------hcCCCCCHHHH
Confidence 3344557789999999874 5999985 78999999999999999999999998653 22233333344
Q ss_pred HHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHH
Q 002191 819 ILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAY 898 (955)
Q Consensus 819 ~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~ 898 (955)
..+...+..+..+..+++..+++|+.+|+.....|+.+.+|.+++++++.+|||++++++.+++...+ ......+++.
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~~--~~~l~~~~~~ 169 (540)
T PRK13557 92 AEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQK--MEALGQLTGG 169 (540)
T ss_pred HHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHHH--HHHhhhhhhh
Confidence 45555566666677788888999999999999999999999999999999999999888766544332 2345578899
Q ss_pred HHHHhhhHhHhHHHHHHHhccC-----CCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccc
Q 002191 899 IRQEVKNPLNGIRFVHKLLESS-----SISENQRQYLETSDACERQIMTIIDG-MDLRCI 952 (955)
Q Consensus 899 iSHELRnPL~~I~g~~~LL~~~-----~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrI 952 (955)
++||+||||+.|.++.+++... ...+...+.++.+...++++..++++ +++++.
T Consensus 170 i~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~ 229 (540)
T PRK13557 170 IAHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARK 229 (540)
T ss_pred hhHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 9999999999999999988531 23355778899999999999999999 777764
No 16
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=99.60 E-value=1.4e-14 Score=168.97 Aligned_cols=190 Identities=13% Similarity=0.122 Sum_probs=142.8
Q ss_pred EEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhc
Q 002191 729 FVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRM 808 (955)
Q Consensus 729 ~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l 808 (955)
++.+++++.++.++++++.+++|+.++++++. +++++|.+|+|+++|+++++++||+.+++.|+++... +
T Consensus 78 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~-~------ 147 (430)
T PRK11006 78 GLYQMQLRNRKRRRELGNLIKRFRSGAESLPD---AVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNL-L------ 147 (430)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---eEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHH-h------
Confidence 44568888999999999999999999999985 5999999999999999999999999999999975531 1
Q ss_pred cChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHH
Q 002191 809 KGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMD 888 (955)
Q Consensus 809 ~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~ 888 (955)
.+++. ...+... .......+...+|. ++.+...|..+ +. ++.+.+|||++++.+.
T Consensus 148 -~~~~~---~~~~~~~-----~~~~~~~~~~~~~~--~~~~~~~~~~~--~~---~~~~~~dit~~~~~e~--------- 202 (430)
T PRK11006 148 -RYPEF---TQYLKTR-----DFSRPLTLVLNNGR--HLEIRVMPYTE--GQ---LLMVARDVTQMHQLEG--------- 202 (430)
T ss_pred -cCHHH---HHHHHhc-----ccCCCeEEEcCCCC--EEEEEEEEcCC--Cc---EEEEEehhhHHHHHHH---------
Confidence 12221 1112111 11122334455565 44555556543 32 4567799998765542
Q ss_pred HHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCC-CHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 889 IYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSI-SENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 889 ~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l-~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
++.+|++.+||||||||++|.++.+++..... ++...++++.+.+++++|..++++ ++++|++++
T Consensus 203 --~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~~~~ 269 (430)
T PRK11006 203 --ARRNFFANVSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKIEAA 269 (430)
T ss_pred --HHHHHHHHhHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 34579999999999999999999999986443 455778999999999999999999 899998764
No 17
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.57 E-value=1.2e-13 Score=167.87 Aligned_cols=198 Identities=20% Similarity=0.301 Sum_probs=159.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHH
Q 002191 740 LMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMI 819 (955)
Q Consensus 740 ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~ 819 (955)
+.+.++..+..++.++++++. +++++|.+|+++++|+++++++|++.++++|+.+.. +++ ++. .+..
T Consensus 253 ~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~-~~~-------~~~--~~~~ 319 (607)
T PRK11360 253 LAQALRETRSLNELILESIAD---GVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSE-LFP-------PNT--PFAS 319 (607)
T ss_pred HHHHHHHHHHHHHHHHHhccC---eEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHH-HcC-------Cch--hHHH
Confidence 445677777888999999875 599999999999999999999999999999987553 232 111 1112
Q ss_pred HHHhhh-cCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHH
Q 002191 820 LLYQGI-TGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAY 898 (955)
Q Consensus 820 ~l~~~~-~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~ 898 (955)
.+.+.+ .+......++.+..++|... +.++..|+.+.+|++.|++++++|||++++.+.++++..+.+ +..++++.
T Consensus 320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~~~--~l~~~~~~ 396 (607)
T PRK11360 320 PLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQERLA--ALGELVAG 396 (607)
T ss_pred HHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHHHH--HHHHHHHH
Confidence 222223 34444556778888888877 899999999999999999999999999999988876654433 45688999
Q ss_pred HHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 899 IRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 899 iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
++||+||||+.|.++.+++.....+++..++++.+...++++..++++ +++++.+
T Consensus 397 ~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~~ 452 (607)
T PRK11360 397 VAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRPR 452 (607)
T ss_pred HHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 999999999999999999887666777889999999999999999999 7887754
No 18
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=99.56 E-value=7.9e-14 Score=157.78 Aligned_cols=184 Identities=17% Similarity=0.140 Sum_probs=136.7
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~ 828 (955)
..++.++++++. +++++|.+|+|+++|+++++++||+.++++|+++.+ +++.. ..+... +...+..+
T Consensus 7 ~~~~~il~~~~~---gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~-~~~~~-----~~~~~~----~~~~~~~~ 73 (348)
T PRK11073 7 PDAGQILNSLIN---SILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPE-LLSYF-----SLNIEL----MRESLQAG 73 (348)
T ss_pred chHHHHHhcCcC---eEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHH-HcCcc-----hhhHHH----HHHHHHcC
Confidence 356789999875 599999999999999999999999999999998654 22211 111111 22233332
Q ss_pred CcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhH
Q 002191 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLN 908 (955)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~ 908 (955)
..+..+......+|+.+|+.++..|+. . .+++..++|+|++++.+.++.+.++. ....+|++.++||+||||+
T Consensus 74 ~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~~~~--~~~~~~~~~iaHelr~pL~ 146 (348)
T PRK11073 74 QGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQHAQQ--VAARDLVRGLAHEIKNPLG 146 (348)
T ss_pred CcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHHHHH--HHHHHHHHhhhHhhcChHH
Confidence 222222233456999999999999987 2 23566789999988776655433332 3456789999999999999
Q ss_pred hHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccc
Q 002191 909 GIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCI 952 (955)
Q Consensus 909 ~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrI 952 (955)
+|.++.+++.....+++..++++.+...++++..++++ +++.+.
T Consensus 147 ~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~~ 191 (348)
T PRK11073 147 GLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQRP 191 (348)
T ss_pred HHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 99999999987556677889999999999999999999 776654
No 19
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=99.54 E-value=7.6e-14 Score=156.21 Aligned_cols=175 Identities=15% Similarity=0.160 Sum_probs=136.5
Q ss_pred HHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhh
Q 002191 745 IRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQG 824 (955)
Q Consensus 745 ~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (955)
++..++|+.++++++. +++++|.+|++++||+++++++|++.++++|+.+.+.. ++++ +...+...
T Consensus 2 ~~~~~~l~~~~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~--------~~~~---~~~~l~~~ 67 (333)
T TIGR02966 2 SALLSRFRAAAQALPD---AVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLI--------RHPE---FVEYLAAG 67 (333)
T ss_pred hhHHHHHHHHHHhCcC---cEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHc--------cCHH---HHHHHHhc
Confidence 4567789999999975 59999999999999999999999999999998765422 2222 22222222
Q ss_pred hcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhh
Q 002191 825 ITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVK 904 (955)
Q Consensus 825 ~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELR 904 (955)
.. .....+..++|..+|+.....|+.+.+ ++++.+|||++++.+. .+.+|++.++||+|
T Consensus 68 ~~-----~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~-----------~~~~~~~~l~h~l~ 126 (333)
T TIGR02966 68 RF-----SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQ-----------MRRDFVANVSHELR 126 (333)
T ss_pred cc-----CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHH-----------HHHHHHHhhhhhhc
Confidence 11 223556668899999999999987653 6677899998665542 23468999999999
Q ss_pred hHhHhHHHHHHHhccC--CCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 905 NPLNGIRFVHKLLESS--SISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 905 nPL~~I~g~~~LL~~~--~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
|||++|.++.+++... ..+++..++++.+..+++++..++++ +++++++.
T Consensus 127 ~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~~~ 179 (333)
T TIGR02966 127 TPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRLES 179 (333)
T ss_pred ccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999988743 45566888999999999999999999 88888765
No 20
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.44 E-value=1.9e-12 Score=170.28 Aligned_cols=215 Identities=15% Similarity=0.089 Sum_probs=144.7
Q ss_pred EEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhcc
Q 002191 730 VGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMK 809 (955)
Q Consensus 730 v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~ 809 (955)
..++++.+++++.+++..+..++.++++++. +|+++|.+|+|+++|+++++++|.+.....+..... ...++.
T Consensus 557 l~~~i~~r~~~~~~l~~~~~~~~~i~~~~~~---~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~~-~~~~~~--- 629 (1197)
T PRK09959 557 LLRSVRRRKVIQGDLENQISFRKALSDSLPN---PTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLEN-SDSPFK--- 629 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---cEEEEcCCCcEEEehHHHHHHhCccccccccccccc-ccCchh---
Confidence 3468899999999999999999999999985 599999999999999999999998754333222110 000000
Q ss_pred ChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEE-EeeeeCCCCCEEEEEEEEeccCcccHHHHHHHh---HH
Q 002191 810 GQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALT-ASRRTDAEGKVIGCFCFMQILVPDLQPALEAQG---LE 885 (955)
Q Consensus 810 ~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~-~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~---~a 885 (955)
+................ ..+...+...+|....+... ..+.....+...++++..+|||++++.+.+++. .+
T Consensus 630 --~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~~~ 705 (1197)
T PRK09959 630 --DVFSNAHEVTAETKENR--TIYTQVFEIDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERNKA 705 (1197)
T ss_pred --hhHhHHHHHHHHHhhcc--ccceeeEeeecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHHHH
Confidence 10000001011111111 11222233344433322222 222222334455678888999998877766543 34
Q ss_pred HHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 886 DMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 886 E~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~-~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+++..++.+|++.|||||||||++|.|+.++|.....+++ ..++++.+..+++++..+|++ |+++|+++|
T Consensus 706 ~~~~~~~~~~~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~ 777 (1197)
T PRK09959 706 INATVAKSQFLATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESG 777 (1197)
T ss_pred HHHHHHHHHHHHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4556688999999999999999999999999986555544 557899999999999999999 999999875
No 21
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.43 E-value=1.6e-12 Score=118.65 Aligned_cols=104 Identities=29% Similarity=0.345 Sum_probs=90.7
Q ss_pred CccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcE
Q 002191 628 TAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSV 707 (955)
Q Consensus 628 ~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~ 707 (955)
|+|++++|.+|+|+++|+++++++|++.++++|+++. ++++++........+.+.+.++.....++.+ .+++|..
T Consensus 1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~----~~~~g~~ 75 (104)
T PF13426_consen 1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSIS-DFFPEEDRPEFEEQIERALEEGGSWSGEVRL----RRKDGET 75 (104)
T ss_dssp -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGG-GGCSTTSCHHHHHHHHHHHHHTSSEEEEEEE----EETTSEE
T ss_pred CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcc-cccCcccchhhHHHHHHHHhcCCceeEEEEE----EcCCCCE
Confidence 6899999999999999999999999999999999998 8888777677777777777766666667776 6789999
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEecchH
Q 002191 708 VYILVNACTSRDYKNNVKGVCFVGQDITH 736 (955)
Q Consensus 708 ~~v~v~~~pi~d~~g~v~gvv~v~~DITe 736 (955)
+|+.++..|+.+.+|++.+++++++|||+
T Consensus 76 ~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 76 FWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 99999999999999999999999999996
No 22
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=99.42 E-value=1.8e-12 Score=119.82 Aligned_cols=110 Identities=27% Similarity=0.356 Sum_probs=99.5
Q ss_pred HHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeecc
Q 002191 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQK 703 (955)
Q Consensus 624 ie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~ 703 (955)
++++|++++++|.+|+|+++|+++.+++|++.++++|+++. +++++...+.+...+.+++.++.....+... ..
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ 74 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLF-DLLPPEDREEFQAALRRALAGGEPVFFEEIL-----LR 74 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHH-HHSCCGCHHHHHHHHHHHHHHTSEEEEEEEE-----CT
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccch-hccccchhhhhHHHHHHhhccCceEEEEEEE-----ee
Confidence 58899999999999999999999999999999999999999 8899888999999999999988765555444 33
Q ss_pred CCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHH
Q 002191 704 QHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKV 739 (955)
Q Consensus 704 dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 739 (955)
+|+.+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 75 ~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 75 DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 899999999999999999999999999999999985
No 23
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=99.41 E-value=2.1e-12 Score=127.39 Aligned_cols=153 Identities=18% Similarity=0.222 Sum_probs=115.5
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCC
Q 002191 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (955)
Q Consensus 230 ~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~ 309 (955)
|++++++.+++.+++++|+||++||.+++++..-...-.....-.+..+..++.. .....+....+..-.|+|+...|
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~d~~~~~ 78 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMD--ESICGQVLQSREPIVISDVAADP 78 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETT--SSHHHHHHHHTSCEEESSSGGST
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccccccccccc--ccHHHHHHhCCCeEeeccccccc
Confidence 6899999999999999999999999999999876444333222222222222221 11255667778888899987654
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCC-CCCChhHHHHHHHH
Q 002191 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSP-RYIPFPLRYACEFL 388 (955)
Q Consensus 310 ~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~p-r~~~~~~r~~~~~l 388 (955)
- ..+.......+++.++++.+|+..+|++|.|++||..+| ++||+|+++++.+ |.|+..++.+++.+
T Consensus 79 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g----~~~G~l~l~~~~~~~~~~~~d~~ll~~~ 146 (154)
T PF01590_consen 79 R--------FAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGG----RLIGVLSLYRTRPGRPFTEEDLALLESF 146 (154)
T ss_dssp T--------SSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETT----EEEEEEEEEEESSSSS--HHHHHHHHHH
T ss_pred c--------ccccccccccccccccccccccccccCceeeEeeeeccc----CcEEEEEEEECCCCCCcCHHHHHHHHHH
Confidence 3 122233344667889999999999999999999999888 9999999999997 99999999999999
Q ss_pred HHHHHHHH
Q 002191 389 VQAFSLQL 396 (955)
Q Consensus 389 ~~~~~~~l 396 (955)
++++++.|
T Consensus 147 a~~~a~ai 154 (154)
T PF01590_consen 147 AQQLAIAI 154 (154)
T ss_dssp HHHHHHHH
T ss_pred HHHHHhhC
Confidence 99988765
No 24
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.40 E-value=1.3e-12 Score=119.32 Aligned_cols=103 Identities=21% Similarity=0.315 Sum_probs=87.2
Q ss_pred CCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCC
Q 002191 763 PPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQG 842 (955)
Q Consensus 763 d~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG 842 (955)
+|++++|.+|+|+++|+++++++||+.++++|+++.. ++ .++....+...+.+++.++..+..+..+.+++|
T Consensus 2 ~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~-~~-------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g 73 (104)
T PF13426_consen 2 DGIFILDPDGRILYVNPAFERLFGYSREELIGKSISD-FF-------PEEDRPEFEEQIERALEEGGSWSGEVRLRRKDG 73 (104)
T ss_dssp SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGG-GC-------STTSCHHHHHHHHHHHHHTSSEEEEEEEEETTS
T ss_pred EEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCccc-cc-------CcccchhhHHHHHHHHhcCCceeEEEEEEcCCC
Confidence 4799999999999999999999999999999998653 22 233344556667777776667899999999999
Q ss_pred cEEEEEEEEeeeeCCCCCEEEEEEEEeccCc
Q 002191 843 QFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (955)
Q Consensus 843 ~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (955)
+.+|+.+++.|+.+.+|++.+++++++||||
T Consensus 74 ~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 74 ETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred CEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 9999999999999999999999999999996
No 25
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=99.39 E-value=1.2e-11 Score=156.01 Aligned_cols=181 Identities=16% Similarity=0.197 Sum_probs=131.9
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCeeeec-CCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHH
Q 002191 741 MDKFIRLQGDYEAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMI 819 (955)
Q Consensus 741 e~~L~~se~~lr~i~e~~~~~id~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~ 819 (955)
..+++++++.++.+++++|.. +++++ .+|.++..|+.+..++|+...+. ...+..
T Consensus 326 ~~~L~e~e~~~r~iv~~~p~g---i~i~~~~~g~~~~~N~~a~~~~~l~~~~~---------------------~~~~~~ 381 (924)
T PRK10841 326 ALRLEEHEQFNRKIVASAPVG---ICILRTSDGTNILSNELAHNYLNMLTHED---------------------RQRLTQ 381 (924)
T ss_pred HHHHHHHHHHHHHHHHhCCcc---EEEEEcCCCcEEEehHHHHHHhccCChhH---------------------HHHHHH
Confidence 346788888999999999864 77775 79999999999999887643221 111111
Q ss_pred HHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHh---HHHHHHHHHHHHH
Q 002191 820 LLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQG---LEDMDIYAKIKEL 896 (955)
Q Consensus 820 ~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~---~aE~~~~ak~~fl 896 (955)
.+ ..... .. ......++....+........ +.. ..++++.|||++++.+.++++ ++++++++|.+|+
T Consensus 382 ~~----~~~~~-~~-~~~~~~~~~~~~i~~~~~~~~---~~~-~~i~~~~Dit~r~~~e~~L~~~~~~~e~a~~~k~~fl 451 (924)
T PRK10841 382 II----CGQQV-NF-VDVLTSNNTNLQISFVHSRYR---NEN-VAICVLVDVSARVKMEESLQEMAQAAEQASQSKSMFL 451 (924)
T ss_pred HH----hcccc-ce-eeEEcCCCcEEEEEEEeeeec---Cce-EEEEEEEEhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 11101 11 122334454443333322222 222 367888999999998877754 4566677899999
Q ss_pred HHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 897 AYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 897 a~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+.|||||||||++|.|+.++|....++++++++++.|..++++|.++|+| ||++|+|+|
T Consensus 452 a~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~ 511 (924)
T PRK10841 452 ATVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESE 511 (924)
T ss_pred HHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 99999999999999999999998888899999999999999999999999 999999875
No 26
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=99.36 E-value=6.7e-12 Score=116.56 Aligned_cols=112 Identities=24% Similarity=0.371 Sum_probs=93.3
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCC-CcceEEEEE
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE-EDKNVELKL 696 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~-~~~~~e~~~ 696 (955)
++|+.+++++++|++++|.+|+|+++|++++++||++.++++|+++. +++++++.......+...+... .....+..+
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLF-DLIHPEDRRELRERLRQALSQGESGESFEVRF 79 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGG-GGCSGGGHHHHHHHHHHHHHHCCHECEEEEEE
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHH-HhcCchhhHHHHHHHHHHHHcCCCceeEEEEE
Confidence 47899999999999999999999999999999999999999999999 8888876655555555555433 344444444
Q ss_pred EeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecc
Q 002191 697 RKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDI 734 (955)
Q Consensus 697 ~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DI 734 (955)
..++|+.+|+.++..|+++.+|++.|++++++||
T Consensus 80 ----~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 80 ----RLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp ----EETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred ----EecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 3368999999999999999999999999999997
No 27
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.33 E-value=2.9e-11 Score=151.82 Aligned_cols=145 Identities=16% Similarity=0.143 Sum_probs=125.2
Q ss_pred cccccccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHH
Q 002191 602 QNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLIC 681 (955)
Q Consensus 602 l~~~l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~ 681 (955)
...+++++++++++.+++++.+++++|++++++|.+|+|++||+++++++|++.++++|+++. ++++++....+.....
T Consensus 139 ~i~~r~~~~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~-~l~~~~~~~~~~~~~~ 217 (779)
T PRK11091 139 EIKEREETQIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPK-DVYSPEAAEKVIETDE 217 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChH-HhCCHHHHHHHHHHHH
Confidence 334456678889999999999999999999999999999999999999999999999999998 8888876666666666
Q ss_pred HHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHH
Q 002191 682 RALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDY 751 (955)
Q Consensus 682 ~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~l 751 (955)
.....+....++..+ ..++|..+|+.++..|+++.+|.+.|++++++|||++|++++++++..+..
T Consensus 218 ~~~~~~~~~~~e~~~----~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~a~~~~ 283 (779)
T PRK11091 218 KVFRHNVSLTYEQWL----DYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEKASRDK 283 (779)
T ss_pred HHHhcCCCeEEEEEE----EcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHHHHHHH
Confidence 677666666666655 678999999999999999999999999999999999999999887765543
No 28
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=99.32 E-value=1.2e-11 Score=114.31 Aligned_cols=110 Identities=19% Similarity=0.242 Sum_probs=93.4
Q ss_pred HHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceee
Q 002191 755 IQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFP 834 (955)
Q Consensus 755 ~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e 834 (955)
+++++. +++++|.+|+++++|+++.+++|++.++++|+++.+ ++ ++.....+...+.+++.++.....+
T Consensus 1 l~~~p~---~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~-~~-------~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (110)
T PF08448_consen 1 LDSSPD---GIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFD-LL-------PPEDREEFQAALRRALAGGEPVFFE 69 (110)
T ss_dssp HHHCSS---EEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHH-HS-------CCGCHHHHHHHHHHHHHHTSEEEEE
T ss_pred CCCCCc---eeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchh-cc-------ccchhhhhHHHHHHhhccCceEEEE
Confidence 355653 699999999999999999999999999999998763 33 3557777888899999988777666
Q ss_pred EEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccH
Q 002191 835 FGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQ 876 (955)
Q Consensus 835 ~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~ 876 (955)
..... +|+.+|+.++..|++|.+|++.|++++++|||++|+
T Consensus 70 ~~~~~-~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 70 EILLR-DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp EEECT-TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred EEEee-cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 65554 999999999999999999999999999999999875
No 29
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=99.31 E-value=2.3e-11 Score=112.94 Aligned_cols=112 Identities=29% Similarity=0.376 Sum_probs=88.4
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhc-C
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT-G 827 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~-g 827 (955)
++|++++++++. |++++|.+|+|+++|+++++++||+.++++|+++.+. .++++.......+.+.+. +
T Consensus 1 e~~~~i~~~~~~---~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~--------~~~~~~~~~~~~~~~~~~~~ 69 (113)
T PF00989_consen 1 ERYRAILENSPD---GIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDL--------IHPEDRRELRERLRQALSQG 69 (113)
T ss_dssp HHHHHHHHCSSS---EEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGG--------CSGGGHHHHHHHHHHHHHHC
T ss_pred CHHHHHHhcCCc---eEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHh--------cCchhhHHHHHHHHHHHHcC
Confidence 478999999975 6999999999999999999999999999999997753 334433334444444443 3
Q ss_pred CCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEecc
Q 002191 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQIL 871 (955)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DI 871 (955)
......+..+..++|+.+|+.+.++|+++.+|++.|++++++||
T Consensus 70 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 70 ESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp CHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred CCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 33445556666689999999999999999999999999999997
No 30
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.30 E-value=4.8e-11 Score=148.54 Aligned_cols=176 Identities=15% Similarity=0.127 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCeeeec-CCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHH
Q 002191 740 LMDKFIRLQGDYEAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFM 818 (955)
Q Consensus 740 ae~~L~~se~~lr~i~e~~~~~id~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~ 818 (955)
..+++++.+..++.++++++. |++++| .+|+++.+|+++.+++|+..-+-+.. . .+.. .
T Consensus 334 l~~~L~~~~~l~~~Ii~~lp~---Gilv~D~~~~~Ii~~N~aA~~ll~~~~l~~i~~------------~--~~~~---~ 393 (894)
T PRK10618 334 MSHELRILRALNEEIVSNLPL---GLLVYDFESNRTVISNKIADHLLPHLNLQKITT------------M--AEQH---Q 393 (894)
T ss_pred HHHHHHHHHHHHHHHHHhCCc---eEEEEECCCCeEEEEhHHHHHHhCccchhhHHH------------H--HHhc---c
Confidence 334678888889999999985 599999 78999999999999997532110000 0 0000 0
Q ss_pred HHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHH---HhHHHHHHHHHHHH
Q 002191 819 ILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEA---QGLEDMDIYAKIKE 895 (955)
Q Consensus 819 ~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~l---q~~aE~~~~ak~~f 895 (955)
..+... .++...++...... ....+.+.+++|+++++..+.++ +++++++.++|.+|
T Consensus 394 ~~i~~~---------------i~~~~~eir~~~~~-----~~~~~~l~~l~d~~~~~~~~~~L~~a~~~le~~~~~k~~f 453 (894)
T PRK10618 394 GVIQAT---------------INNELYEIRMFRSQ-----LAPRTQLFLLRDQDREVLVNKKLQQAQREYEKNQQARKAF 453 (894)
T ss_pred hhhhhh---------------ccCceeEEEEeecc-----ccCceEEEEEeehHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 000000 11222222221111 12234677889999877666555 34556677899999
Q ss_pred HHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 896 LAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 896 la~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+++|||||||||++|.|+.+++.....+++++++++.|..+++++.++|++ +|++|+|+|
T Consensus 454 la~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~ 514 (894)
T PRK10618 454 LQNIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQ 514 (894)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 999999999999999999999988777888999999999999999999999 999999976
No 31
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=99.26 E-value=8.8e-12 Score=105.01 Aligned_cols=65 Identities=35% Similarity=0.543 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhcc-CCCCHHH-HHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQ-RQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~-~~l~~~~-~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+|.+|++.+||||||||++|.++.+++.. ...++++ +++++.+..+++++..+|++ |+|+|+|+|
T Consensus 1 s~~~~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G 68 (68)
T PF00512_consen 1 SKGEFLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred CHHHHHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 47799999999999999999999999998 8888887 99999999999999999999 999999998
No 32
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=99.20 E-value=3.2e-10 Score=117.73 Aligned_cols=176 Identities=20% Similarity=0.216 Sum_probs=124.7
Q ss_pred HHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC-Ccc
Q 002191 753 AIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ-GTE 831 (955)
Q Consensus 753 ~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~-~~~ 831 (955)
.+++++.. +++..|.+|.|.|+|++++.+||.+...+.|..+.. +++. ... ....+.++...+ ...
T Consensus 11 ~~Ln~~~~---pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~-l~~~-----gs~----ll~ll~q~~~~~~~~~ 77 (363)
T COG3852 11 AILNNLIN---PVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSE-LLPF-----GSL----LLSLLDQVLERGQPVT 77 (363)
T ss_pred hHHhccCC---ceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHH-HcCC-----CcH----HHHHHHHHHHhcCCcc
Confidence 46666643 689999999999999999999999999999987653 3331 112 233444444433 233
Q ss_pred eeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhHhHH
Q 002191 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIR 911 (955)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~~I~ 911 (955)
.++..+. .+|....+...+.|+-...|.+. ..++-+....+...++. .....++-..+.++++|||||||.+|.
T Consensus 78 ~~~v~l~-~~g~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~ridre~~--q~a~~~a~~~L~r~LAHEIKNPL~GiR 151 (363)
T COG3852 78 EYEVTLV-ILGRSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRRLDREQT--QHAQQRAVKGLVRGLAHEIKNPLGGIR 151 (363)
T ss_pred cceeeee-ecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhHHHH--HHHHHHHHHHHHHHHHHHhcCcccchh
Confidence 4455555 78999999999999987777654 22343333222222211 111223455678899999999999999
Q ss_pred HHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhccc
Q 002191 912 FVHKLLESSSISENQRQYLETSDACERQIMTIIDGM 947 (955)
Q Consensus 912 g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~DL 947 (955)
|.++||++.--++..+.|.+.|.+.++|+..|++.|
T Consensus 152 GAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRm 187 (363)
T COG3852 152 GAAQLLERALPDEALRELTQLIIEEADRLRNLVDRL 187 (363)
T ss_pred hHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999985555559999999999999999999985
No 33
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=99.20 E-value=9.6e-10 Score=132.26 Aligned_cols=202 Identities=14% Similarity=0.147 Sum_probs=129.5
Q ss_pred EEEEEeecCCCCEEEEEEEEecchHhHHHH--------------------------------------HHHHHHHHHHHH
Q 002191 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLM--------------------------------------DKFIRLQGDYEA 753 (955)
Q Consensus 712 v~~~pi~d~~g~v~gvv~v~~DITerk~ae--------------------------------------~~L~~se~~lr~ 753 (955)
....|+++..|.++|++.+..++.+-...- .++....+.+++
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 355788888999999987766554432211 123344456788
Q ss_pred HHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCCh---hhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCc
Q 002191 754 IIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMR---HEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT 830 (955)
Q Consensus 754 i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~---eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~ 830 (955)
++++++. +|+++|.+|+|+++|+++++++|++. ++.+|+.... ...... +...+..+..
T Consensus 226 il~~~~~---gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~--------~~~~~~-------~~~~~~~~~~ 287 (542)
T PRK11086 226 MLQSIKE---GVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVES--------WMPVSR-------LKEVLRTGTP 287 (542)
T ss_pred HHHHhcC---cEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHH--------hCCchh-------HHHHHhcCCC
Confidence 9999875 69999999999999999999998763 3445544321 111111 2223333322
Q ss_pred ce-eeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhHh
Q 002191 831 EN-FPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNG 909 (955)
Q Consensus 831 ~~-~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~~ 909 (955)
.. .+.. .+|. ++.....|+.+ +|.+.|++++++|+|+.++.+.++... ....++++.++||+||||++
T Consensus 288 ~~~~~~~---~~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~-----~~~~~~l~~~sHel~npL~~ 356 (542)
T PRK11086 288 RRDEEIN---INGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGM-----VNYADALRAQSHEFMNKLHV 356 (542)
T ss_pred ccceEEE---ECCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHH-----HHHHHHHHhhchhhcCHHHH
Confidence 22 2222 2443 45667789988 899999999999999977665544322 23346678899999999999
Q ss_pred HHHHHHHhccCCCCHHHHHHHHH-HHHHHHHHHHhhcc
Q 002191 910 IRFVHKLLESSSISENQRQYLET-SDACERQIMTIIDG 946 (955)
Q Consensus 910 I~g~~~LL~~~~l~~~~~~~l~~-i~~~a~rl~~LI~D 946 (955)
|.|+.++... ++..+++.. +.....++..++++
T Consensus 357 I~g~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 390 (542)
T PRK11086 357 ILGLLHLKSY----DQLEDYILKTANNYQEEIGSLLGK 390 (542)
T ss_pred HHHHHHhCch----HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999887643 223334333 23333444444444
No 34
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=99.11 E-value=2.3e-09 Score=102.85 Aligned_cols=140 Identities=26% Similarity=0.403 Sum_probs=111.2
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCC
Q 002191 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (955)
Q Consensus 230 ~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~ 309 (955)
|++++++.+++.+.+++++||+.||.++++..+.....+......+..+..+|..+ ...+..+..+...++.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999888887777665544445667777666 5567778888888888876543
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhc-CceeEEEEEEEEcCCCCCceeEEEEeecC-CCCCCChhHHHHHHH
Q 002191 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNM-GSIASLVMAVIINSKDSMKLWGLVVCHHT-SPRYIPFPLRYACEF 387 (955)
Q Consensus 310 ~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~-gv~asl~v~i~~~~~~~~~LWGll~~hh~-~pr~~~~~~r~~~~~ 387 (955)
.+ . ..+...+ |+++.+++||..+| ++||+|++.++ .++.|+.+++..++.
T Consensus 79 ~~-----------------------~-~~~~~~~~~~~s~~~~Pl~~~~----~~~G~l~~~~~~~~~~~~~~~~~~l~~ 130 (149)
T smart00065 79 VF-----------------------A-LDLLGRYQGVRSFLAVPLVADG----ELVGVLALHNKDSPRPFTEEDEELLQA 130 (149)
T ss_pred cc-----------------------c-cccccceeceeeEEEeeeeecC----EEEEEEEEEecCCCCCCCHHHHHHHHH
Confidence 21 0 1122233 49999999999888 99999999999 699999999999999
Q ss_pred HHHHHHHHHHHH
Q 002191 388 LVQAFSLQLYME 399 (955)
Q Consensus 388 l~~~~~~~l~~~ 399 (955)
++++++..++..
T Consensus 131 ~~~~i~~~l~~~ 142 (149)
T smart00065 131 LANQLAIALANA 142 (149)
T ss_pred HHHHHHHHHHHH
Confidence 999998888643
No 35
>PRK10060 RNase II stability modulator; Provisional
Probab=99.11 E-value=2e-09 Score=132.10 Aligned_cols=167 Identities=13% Similarity=0.058 Sum_probs=123.7
Q ss_pred ccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHH
Q 002191 702 QKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAM 781 (955)
Q Consensus 702 ~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~ 781 (955)
+.+|...|+.+...++.+ ....|....+.|++. ....+......++.+++.++. +|+++|.+|+|+++|+++
T Consensus 69 ~~~g~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~v~~~~~~---gI~i~D~~g~I~~~N~a~ 140 (663)
T PRK10060 69 TLDGEPLSVHLVGRKINK--REWAGTASAWHDTPS---VARDLSHGLSFAEQVVSEANS---VIVILDSRGNIQRFNRLC 140 (663)
T ss_pred EeCCcEEEEEEeeeccCc--ccccchhhHHHHHHH---HHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEEcHHH
Confidence 458999999987777543 234444444455555 444455666778889999875 599999999999999999
Q ss_pred HHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCC-C
Q 002191 782 EKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEG-K 860 (955)
Q Consensus 782 ~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G-~ 860 (955)
++++||+.++++|+++.+.+. ++++...+...+...+..+..+..++.+.+++|+.+|+.....+ .+.+| .
T Consensus 141 ~~l~Gy~~~eliG~~~~~l~~-------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~~-~~~~g~~ 212 (663)
T PRK10060 141 EEYTGLKEHDVIGQSVFKLFM-------SRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKFV-HSGSGKN 212 (663)
T ss_pred HHHHCcCHHHHcCCCHHHHhC-------ChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeEE-EcCCCCc
Confidence 999999999999998654322 24444455556666677777888999999999999888765444 44444 4
Q ss_pred EEEEEEEEeccCcccHHHHHHHhH
Q 002191 861 VIGCFCFMQILVPDLQPALEAQGL 884 (955)
Q Consensus 861 v~g~v~i~~DITerk~~el~lq~~ 884 (955)
..+++++.+|||++|+++.++++.
T Consensus 213 ~~~~i~~~~DITe~k~~e~~l~~~ 236 (663)
T PRK10060 213 EIFLICSGTDITEERRAQERLRIL 236 (663)
T ss_pred eEEEEEEEEechHHHHHHHHHHHH
Confidence 566888999999999888776554
No 36
>PRK13559 hypothetical protein; Provisional
Probab=99.09 E-value=1.7e-09 Score=123.10 Aligned_cols=133 Identities=14% Similarity=0.030 Sum_probs=106.4
Q ss_pred HHHHHHHHHHHhcCccEEEEcC---CCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcce
Q 002191 615 SVACEMVRLIETATAPIFGVDS---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKN 691 (955)
Q Consensus 615 ~~~~~l~~lie~~~~~I~~~D~---dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~ 691 (955)
.....++.+++.++++++++|. +|.+++||+++++++||+.++++|+++. .+.++.........+...+.++....
T Consensus 40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~ 118 (361)
T PRK13559 40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCR-FLQGAATDPIAVAKIRAAIAAEREIV 118 (361)
T ss_pred hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChh-hhcCCCCCHHHHHHHHHHhccCCceE
Confidence 3456788899999999999997 5689999999999999999999999986 66655554444555566666665555
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHH
Q 002191 692 VELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYE 752 (955)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr 752 (955)
.+... .+++|..+|+.++..|+++.+|.+.+++++++|||++|++++..+..+..++
T Consensus 119 ~e~~~----~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~~~~~~l~~ 175 (361)
T PRK13559 119 VELLN----YRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALEAHERRLAR 175 (361)
T ss_pred EEEEE----EcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHHHHHHHHHH
Confidence 55444 6789999999999999999999999999999999999988766554444333
No 37
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=99.08 E-value=2.3e-09 Score=120.69 Aligned_cols=182 Identities=16% Similarity=0.220 Sum_probs=126.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHH
Q 002191 743 KFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLY 822 (955)
Q Consensus 743 ~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~ 822 (955)
++++....++++++.++. |++..|.+|++.-+|++++.++|.+.++++|..+.. +- |+ +...+.
T Consensus 364 ~~e~rr~f~E~VLsgvta---GVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa-~a--------p~----~~~vf~ 427 (712)
T COG5000 364 ALEQRRRFLEAVLSGLTA---GVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSA-IA--------PE----LEEVFA 427 (712)
T ss_pred HHHHHHHHHHHHHhcCce---eEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhh-hh--------hH----HHHHHH
Confidence 344444556678888764 599999999999999999999999999999998553 11 22 222232
Q ss_pred hhhc-CCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 002191 823 QGIT-GQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQ 901 (955)
Q Consensus 823 ~~~~-g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSH 901 (955)
..-. ++.....+..+ .+.|+.+.+.+.++-...++| -|++.++.|||+-..++ .+.+-.+-...++|
T Consensus 428 ~~~a~~~~~~~~ev~~-~r~g~~rtl~Vq~t~~~~d~~--~gyVvt~DDITdLV~AQ---------Rs~AW~dVArRIAH 495 (712)
T COG5000 428 EAGAAARTDKRVEVKL-AREGEERTLNVQATREPEDNG--NGYVVTFDDITDLVIAQ---------RSAAWGDVARRIAH 495 (712)
T ss_pred HhhhhcCCCccceeec-ccCCCceeeeeeeeecccccC--CceEEEecchHHHHHHH---------HHHHHHHHHHHHHH
Confidence 2222 23334444444 345666777776655433222 35778889999865543 23355566788999
Q ss_pred HhhhHhHhHHHHHHHhcc---CCCCHH---HHHHHHHHHHHHHHHHHhhcc-cCcccc
Q 002191 902 EVKNPLNGIRFVHKLLES---SSISEN---QRQYLETSDACERQIMTIIDG-MDLRCI 952 (955)
Q Consensus 902 ELRnPL~~I~g~~~LL~~---~~l~~~---~~~~l~~i~~~a~rl~~LI~D-Ld~SrI 952 (955)
||||||+.|.-+.+-|++ +.++++ -.+..++|.+.+..+.+++++ -+|.|+
T Consensus 496 EIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afARm 553 (712)
T COG5000 496 EIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFARM 553 (712)
T ss_pred HhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999977776663 445542 567889999999999999999 788875
No 38
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.05 E-value=3.5e-09 Score=130.68 Aligned_cols=136 Identities=19% Similarity=0.186 Sum_probs=114.1
Q ss_pred HHHHHHHhcCccEEEEc---CCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEE
Q 002191 619 EMVRLIETATAPIFGVD---SSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELK 695 (955)
Q Consensus 619 ~l~~lie~~~~~I~~~D---~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~ 695 (955)
.++.+++.++.+++.+| .+|++++||+++++++||+.++++|+++. .+.+++........+...+..+.....+++
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 227 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCR-FLQGEDTNEERVAELREAIDEERPTSVELR 227 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHH-HhcCCCccHHHHHHHHHHHhcCCCeEEEEE
Confidence 34678999999999997 47899999999999999999999999987 777766555555555556665555566666
Q ss_pred EEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcC
Q 002191 696 LRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVN 759 (955)
Q Consensus 696 ~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~ 759 (955)
. .+++|..+|+.++..|+++.+|.+.+++++.+|||++|++|+++++.+..++.+++.++
T Consensus 228 ~----~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~ 287 (665)
T PRK13558 228 N----YRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVE 287 (665)
T ss_pred E----ECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5 68999999999999999999999999999999999999999999988888877766543
No 39
>PRK13557 histidine kinase; Provisional
Probab=99.03 E-value=3.5e-09 Score=127.14 Aligned_cols=131 Identities=16% Similarity=0.114 Sum_probs=107.2
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcC---CCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCc
Q 002191 613 LSSVACEMVRLIETATAPIFGVDS---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED 689 (955)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~---dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~ 689 (955)
....+..|+.++++++++++++|. +|+|+++|+++++++||+.++++|+++. .+++++........+...+..+..
T Consensus 25 ~~~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~~ 103 (540)
T PRK13557 25 SDHRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCR-FLQGPETDRATVAEVRDAIAERRE 103 (540)
T ss_pred hhhhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChH-hhcCCCCCHHHHHHHHHHHHcCCC
Confidence 344567899999999999999995 7899999999999999999999999988 777766555444455555544444
Q ss_pred ceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHH
Q 002191 690 KNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQ 748 (955)
Q Consensus 690 ~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se 748 (955)
...++.. .+++|..+|+.+...|+++.+|.+++++++.+|||+++++++++...+
T Consensus 104 ~~~~~~~----~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~~ 158 (540)
T PRK13557 104 IATEILN----YRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQAQ 158 (540)
T ss_pred ceEEEEE----EeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHHH
Confidence 4444444 578999999999999999999999999999999999999988775443
No 40
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.99 E-value=1.6e-08 Score=114.07 Aligned_cols=224 Identities=21% Similarity=0.218 Sum_probs=154.0
Q ss_pred HHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeee
Q 002191 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFE 700 (955)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~ 700 (955)
..+++..+++++++|....+..+|..+..+++-....++|+++. ++.++...+.+. +++.. ......
T Consensus 4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~~~~-~i~~~~~~~~v~-------~~~~~-~~~~~~---- 70 (560)
T COG3829 4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGRPLR-EILETLGMERVE-------QSRDK-ELTERL---- 70 (560)
T ss_pred hhhhhhcccceEEEEcCCceeeechHHHHhhhcceEEEecccce-eeccccCcceee-------ccCcc-ceeeee----
Confidence 44889999999999999999999999999999999999999877 666654433222 22211 111121
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHH-HHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecH
Q 002191 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF-IRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNA 779 (955)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L-~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~ 779 (955)
..+ ... ..+...++.++.++++|+..++.|+++....-++. +...+.|+.+++.+.. +++++|.+|+++++|+
T Consensus 71 ~~~--~~~-~~~~~~~~~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~---~l~vvD~~G~~i~~N~ 144 (560)
T COG3829 71 KLK--VKR-IVVVGKTPVDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDD---GLLVVDEDGIIIYYNK 144 (560)
T ss_pred ecc--cee-EEEcCCceeecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhccC---ceEEEcCCCcEEEEcH
Confidence 111 233 33444455668899999999999999987766655 6677889999999875 6999999999999999
Q ss_pred HHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCC
Q 002191 780 AMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEG 859 (955)
Q Consensus 780 a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G 859 (955)
++.+++|++.++++|+++.+.+ .. .++ .....++..+.+.... .....|... ..+..|++ .+|
T Consensus 145 ~~~~~~gl~~e~~~gk~~~~v~-~~-----~~~------s~~l~vl~~~kp~~~~--~~~~~~~~~--i~~~~pv~-~~g 207 (560)
T COG3829 145 AYAKLLGLSPEEVLGKHLLDVV-SA-----GED------STLLEVLRTGKPIRDV--VQTYNGNKI--IVNVAPVY-ADG 207 (560)
T ss_pred HHHHHhCCCHHHHcCCcHHHHH-hc-----cCC------ceehhhhhcCCcceee--eeeecCCce--eEeeccEe-cCC
Confidence 9999999999999999765422 10 000 0112233333333222 222333332 33445555 567
Q ss_pred CEEEEEEEEeccCcccHHHHH
Q 002191 860 KVIGCFCFMQILVPDLQPALE 880 (955)
Q Consensus 860 ~v~g~v~i~~DITerk~~el~ 880 (955)
.++|.+++.+|+++-+....+
T Consensus 208 ~l~G~v~~~~~~~~l~~l~~~ 228 (560)
T COG3829 208 QLIGVVGISKDVSELERLTRE 228 (560)
T ss_pred cEEEEEEeecchHHHHHHHHH
Confidence 999999999999975544433
No 41
>PRK10060 RNase II stability modulator; Provisional
Probab=98.96 E-value=1.2e-08 Score=125.26 Aligned_cols=162 Identities=20% Similarity=0.208 Sum_probs=115.0
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCcccccc-ccccHHHHHHHHHHHHcCCCcce
Q 002191 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVV-HEESQGAVENLICRALLGEEDKN 691 (955)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~-~~~~~~~~~~~l~~~l~~~~~~~ 691 (955)
+......++.+++.++++|+++|.+|+|+++|+++++++||+.++++|+++. +++ ++++.......+...+..+..+.
T Consensus 106 ~~~~~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (663)
T PRK10060 106 LSHGLSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVF-KLFMSRREAAASRRNIRGFFRSGNAYE 184 (663)
T ss_pred HHHHHHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHH-HHhCChhhHHHHHHHHHHHHhcCCceE
Confidence 4445566788999999999999999999999999999999999999999987 554 55555555666666666666666
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCC-CEEEEEEEEecchHhHHHHHHHHHH---------------HHHHHHHH
Q 002191 692 VELKLRKFELQKQHSVVYILVNACTSRDYKN-NVKGVCFVGQDITHEKVLMDKFIRL---------------QGDYEAII 755 (955)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g-~v~gvv~v~~DITerk~ae~~L~~s---------------e~~lr~i~ 755 (955)
.+..+ .+++|..+|+.....+ .+..| ...+++++.+|||++|++++++++. .++++..+
T Consensus 185 ~e~~~----~~~~G~~~~~~~~~~~-~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~~l~~~l 259 (663)
T PRK10060 185 VERWI----KTRKGQRLFLFRNKFV-HSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAI 259 (663)
T ss_pred EEEEE----EeCCCCEEEEEeeeEE-EcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHHHHHHHH
Confidence 66665 6789988887655444 44444 4566788899999999999988763 33444444
Q ss_pred HhcCCCCCCeeeecCCCcEeeecHHH
Q 002191 756 QSVNPLIPPIFASDENACCSEWNAAM 781 (955)
Q Consensus 756 e~~~~~id~I~~~D~~g~i~~~N~a~ 781 (955)
........+++.+|.++- ..+|..+
T Consensus 260 ~~~~~~~~~ll~idld~f-k~iNd~~ 284 (663)
T PRK10060 260 NAADNNQVGIVYLDLDNF-KKVNDAY 284 (663)
T ss_pred HhCCCCcEEEEEEECcch-hHHHHhh
Confidence 332221124666776642 3455443
No 42
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=98.95 E-value=1.1e-08 Score=92.18 Aligned_cols=120 Identities=27% Similarity=0.344 Sum_probs=97.2
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCC-CcceEEEEE
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE-EDKNVELKL 696 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~-~~~~~e~~~ 696 (955)
+.++.+++.++.+++++|.+|+++++|+++.+++|++..+++|+.+. .++++.........+.....+. .....++.+
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVL-ELIPEEDREEVRERIERLLEGEREPVSEERRV 81 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchh-hhcChhhhHHHHHHHHHHHcCCCCCcceEeee
Confidence 45678899999999999999999999999999999999999999987 7777766666666666666533 222333333
Q ss_pred EeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHH
Q 002191 697 RKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (955)
Q Consensus 697 ~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~ 743 (955)
...+|..+|+.....|+. .+|...+++++..|||++++++++
T Consensus 82 ----~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 82 ----RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred ----EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhc
Confidence 367899999999999988 788899999999999999988754
No 43
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=98.92 E-value=6.1e-09 Score=92.91 Aligned_cols=90 Identities=13% Similarity=0.200 Sum_probs=74.5
Q ss_pred EeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHh-hhcCCCcceeeEEEEcCCCcEEEEEEEEe
Q 002191 774 CSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQ-GITGQGTENFPFGFFNRQGQFVEVALTAS 852 (955)
Q Consensus 774 i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~-~~~g~~~~~~e~~~~~~dG~~~~v~~~~~ 852 (955)
|++||+.+++++||+++++ +..... .+....||+|...+...+.+ ...++..+..++++++++|+++|+..++.
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~----~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~ 75 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFE----EWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGR 75 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHH----HHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHH----HHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEE
Confidence 5899999999999999999 654222 24568899999999999999 77788899999999999999999999999
Q ss_pred eeeCCCCCEEEEEEEE
Q 002191 853 RRTDAEGKVIGCFCFM 868 (955)
Q Consensus 853 pi~d~~G~v~g~v~i~ 868 (955)
+++|.+|+++.++|+.
T Consensus 76 ~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 76 PIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEETTTS-EEEEEEEE
T ss_pred EEECCCCCEEEEEEEC
Confidence 9999999999999874
No 44
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.92 E-value=3e-08 Score=125.25 Aligned_cols=126 Identities=17% Similarity=0.173 Sum_probs=101.6
Q ss_pred HHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccc-cccHHHHHHHHHHHHcCCCcceEE
Q 002191 615 SVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVH-EESQGAVENLICRALLGEEDKNVE 693 (955)
Q Consensus 615 ~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~-~~~~~~~~~~l~~~l~~~~~~~~e 693 (955)
+.++.+..+++.++++++++|.+|+++++|+++++++|++.++++|+.+. ++++ +.........+.....++.....+
T Consensus 133 ~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 211 (799)
T PRK11359 133 EQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPD-TLLNIPEFPADNRIRLQQLLWKTARDQDE 211 (799)
T ss_pred HHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChH-HhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence 34455677899999999999999999999999999999999999999887 5554 444444444455555555555555
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHH
Q 002191 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFI 745 (955)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~ 745 (955)
+.+ .+++|..+|+.++..|+.+.+|.+.+++++.+|||++|++++..+
T Consensus 212 ~~~----~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~~ 259 (799)
T PRK11359 212 FLL----LTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLEG 259 (799)
T ss_pred eEE----eCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHHH
Confidence 555 678999999999999999999999999999999999998876543
No 45
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.89 E-value=3.3e-08 Score=122.06 Aligned_cols=124 Identities=18% Similarity=0.209 Sum_probs=99.3
Q ss_pred HHHHHHhcCCCCCCeeeec---CCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcC
Q 002191 751 YEAIIQSVNPLIPPIFASD---ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (955)
Q Consensus 751 lr~i~e~~~~~id~I~~~D---~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g 827 (955)
++.+++..+. +++..| .+|++++||+++++++||+.++++|+.+.. +.+++........+...+.+
T Consensus 150 ~~~~~~~~~~---gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~--------l~~~~~~~~~~~~~~~~~~~ 218 (665)
T PRK13558 150 KERALDEAPV---GITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRF--------LQGEDTNEERVAELREAIDE 218 (665)
T ss_pred HHHHHhcCCc---cEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHH--------hcCCCccHHHHHHHHHHHhc
Confidence 4567888764 588887 479999999999999999999999997542 12233333334445555666
Q ss_pred CCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHH
Q 002191 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLE 885 (955)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~a 885 (955)
+.....++++.+++|..+|+..+..|+.+.+|.+.+++++.+|||++|+.|.++++..
T Consensus 219 ~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~ 276 (665)
T PRK13558 219 ERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRER 276 (665)
T ss_pred CCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHH
Confidence 6678899999999999999999999999999999999999999999999988776433
No 46
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=98.84 E-value=3.4e-07 Score=110.39 Aligned_cols=199 Identities=16% Similarity=0.182 Sum_probs=124.8
Q ss_pred EEEEEeecCCCCEEEEEEEEecchHhHHHH--------------------------------------HHHHHHHHHHHH
Q 002191 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLM--------------------------------------DKFIRLQGDYEA 753 (955)
Q Consensus 712 v~~~pi~d~~g~v~gvv~v~~DITerk~ae--------------------------------------~~L~~se~~lr~ 753 (955)
..+.|+++.+|+++|++.+...+.+..... .++......++.
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 478999999999999987766443332210 112223345667
Q ss_pred HHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCCh--hhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcc
Q 002191 754 IIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMR--HEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE 831 (955)
Q Consensus 754 i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~--eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~ 831 (955)
+++++++ |++.+|.+|+|+++|+++++++|++. ++++|+.+.+ +++ +... +. ...... ..
T Consensus 227 il~~~~e---gii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~-~~~-------~~~~--~~----~~~~~~-~~ 288 (545)
T PRK15053 227 LFSSVYE---GLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAE-VVR-------PADF--FT----EQIDEK-RQ 288 (545)
T ss_pred HHHHhCc---eEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHH-hCC-------Cchh--hh----hhcCCc-cc
Confidence 8888764 69999999999999999999999975 4688987543 221 1110 00 111111 11
Q ss_pred eeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhHhHH
Q 002191 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIR 911 (955)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~~I~ 911 (955)
..+ ...+| ..+..+..|+.+ +|++.|++.+++|+|+.++.+.++.... ...+.+..++||++|||++|.
T Consensus 289 ~~~---~~~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~-----~~~e~l~~~~he~~n~L~~i~ 357 (545)
T PRK15053 289 DVV---ANFNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIK-----QYVESLRTLRHEHLNWMSTLN 357 (545)
T ss_pred ceE---EEECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHH-----HHHHHHHHHHHHHhhhHHHHH
Confidence 111 12244 345566777765 5678899999999998766554433222 223557789999999999999
Q ss_pred HHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002191 912 FVHKLLESSSISENQRQYLETSDACERQIMTIIDG 946 (955)
Q Consensus 912 g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D 946 (955)
|+.++-+. .+.++.+...+.++..++++
T Consensus 358 g~l~~~~~-------~~~~~~i~~~s~~~~~l~~~ 385 (545)
T PRK15053 358 GLLQMKEY-------DRVLEMVQGESQAQQQLIDS 385 (545)
T ss_pred HHHhhchh-------hHHHHHHHHHHHHHHHHHHH
Confidence 98765322 23444555555555555544
No 47
>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=98.81 E-value=4.2e-08 Score=88.38 Aligned_cols=119 Identities=17% Similarity=0.180 Sum_probs=91.3
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~ 828 (955)
..++.++++++. +++++|.+|+++++|+++.+++|++..+++|+.+.. + .+++....+...+.....++
T Consensus 3 ~~~~~~~~~~~~---~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~-~-------~~~~~~~~~~~~~~~~~~~~ 71 (124)
T TIGR00229 3 ERYRAIFESSPD---AIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLE-L-------IPEEDREEVRERIERLLEGE 71 (124)
T ss_pred hHHHHHHhhCCc---eEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhh-h-------cChhhhHHHHHHHHHHHcCC
Confidence 456778888874 599999999999999999999999999999987553 2 22344444444455555533
Q ss_pred -CcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHH
Q 002191 829 -GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPAL 879 (955)
Q Consensus 829 -~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el 879 (955)
.....++.+...+|..+|+.....|+. .+|...+++++..|||++++.+.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 72 REPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred CCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 334455666688999999999999998 78889999999999999876653
No 48
>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=98.81 E-value=1.3e-08 Score=120.57 Aligned_cols=125 Identities=14% Similarity=0.124 Sum_probs=98.4
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~ 828 (955)
..|+.++++++. ++++.|.+|+++++|+++++++||++++++|+.... +.. +.........+.+.+..+
T Consensus 4 ~~~~~i~~~~~~---~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~-~~~-------~~~~~~~~~~~~~~~~~~ 72 (494)
T TIGR02938 4 EAYRQTVDQAPL---AISITDLKANILYANDAFTRITGYTKEEIIGKNESV-LSN-------HTTPPEVYQALWGSLAEQ 72 (494)
T ss_pred HHHHHHHHhCCc---eEEEECCCCcEEEEchhheeecCCCHHHHhCCCchh-hcC-------CCCCHHHHHHHHHHHHhC
Confidence 468899999874 599999999999999999999999999999986432 111 111112233333444455
Q ss_pred CcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhH
Q 002191 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGL 884 (955)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~ 884 (955)
..+..++...+++|+.+|+.....|+.+.+|.+.+++++++|||++|+++.++++.
T Consensus 73 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~ 128 (494)
T TIGR02938 73 KPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQ 128 (494)
T ss_pred CcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHH
Confidence 56777778889999999999999999999999999999999999999888776543
No 49
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=98.78 E-value=4.3e-08 Score=87.38 Aligned_cols=86 Identities=23% Similarity=0.276 Sum_probs=73.0
Q ss_pred EeeecHHHHHHhCCCchhhcCCC----ccccccccccHHHHHHHHHH-HHcCCCcceEEEEEEeeeeccCCcEEEEEEEE
Q 002191 640 INGWNAKVAELTGLPASEAMGKS----LIDEVVHEESQGAVENLICR-ALLGEEDKNVELKLRKFELQKQHSVVYILVNA 714 (955)
Q Consensus 640 i~~~N~~~~~l~G~~~eeliG~~----~~~~l~~~~~~~~~~~~l~~-~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~ 714 (955)
|++||+.+.+++||+++++ +.. +. .++||++.+.+.+.+.. ....+.....++++ ++++|+.+|+.+++
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~-~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~----~~~~G~~~wi~~~~ 74 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWL-ERIHPDDRERVRQAIQQAALQNGEPFEIEYRI----RRKDGEYRWIEVRG 74 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHH-HHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEE----EGTTSTEEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHH-hhcCHHHHHHHHHHHHHHhhccCcceEEEEEE----ECCCCCEEEEEEEE
Confidence 6899999999999999999 766 66 89999999999999999 77777788888888 78999999999999
Q ss_pred EEeecCCCCEEEEEEEE
Q 002191 715 CTSRDYKNNVKGVCFVG 731 (955)
Q Consensus 715 ~pi~d~~g~v~gvv~v~ 731 (955)
.+++|.+|++++++|++
T Consensus 75 ~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 75 RPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEETTTS-EEEEEEEE
T ss_pred EEEECCCCCEEEEEEEC
Confidence 99999999999998874
No 50
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.75 E-value=1.1e-07 Score=108.12 Aligned_cols=225 Identities=10% Similarity=0.131 Sum_probs=155.9
Q ss_pred HHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCC---------CcceE
Q 002191 622 RLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE---------EDKNV 692 (955)
Q Consensus 622 ~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~---------~~~~~ 692 (955)
.++++....+++++.||.++|+++.....+|++.-|+.|..++ |++||-|.+.+.+.+....... ....|
T Consensus 123 ~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvF-DfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRsF 201 (768)
T KOG3558|consen 123 HILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVF-DFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERSF 201 (768)
T ss_pred hHHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhh-hccCccCHHHHHHHhccccCCCcccccccCccceeE
Confidence 4567777788999999999999999999999999999999999 9999999998888775443311 12455
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEE---------eecCCCC----------EEEEEEEEecchHhHHHHHHHHHHHHHHHH
Q 002191 693 ELKLRKFELQKQHSVVYILVNACT---------SRDYKNN----------VKGVCFVGQDITHEKVLMDKFIRLQGDYEA 753 (955)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~p---------i~d~~g~----------v~gvv~v~~DITerk~ae~~L~~se~~lr~ 753 (955)
-+++++. +.+-|+...+.....- +++..+. ..+.+.+..-|---+-.|-
T Consensus 202 flRMKsT-LT~RGRtlnlKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~Ei----------- 269 (768)
T KOG3558|consen 202 FLRMKST-LTKRGRTLNLKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEI----------- 269 (768)
T ss_pred EEEeeee-eccCCceeeeeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCccccc-----------
Confidence 5666654 3455644333222111 1221111 2222222221111111100
Q ss_pred HHHhcCCCCCCee--eecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcc
Q 002191 754 IIQSVNPLIPPIF--ASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE 831 (955)
Q Consensus 754 i~e~~~~~id~I~--~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~ 831 (955)
+ +--..| ....|-+|+|+.+.+.+++||++++++|+... .++|..|...+.......+..|...
T Consensus 270 -----p-L~~~~FvtRhs~DmkityCedRisdlm~y~PeeLvGrS~Y--------e~~Ha~Ds~~v~KSh~dL~~KGQv~ 335 (768)
T KOG3558|consen 270 -----P-LDCHMFVTRHSLDMKITYCEDRISDLMDYEPEELVGRSCY--------EFVHALDSDRVRKSHHDLLTKGQVV 335 (768)
T ss_pred -----c-cCCceeEEeeecceeEEEEchhHHHHhcCCHHHhhchhHH--------HhhhHhhhhHHHHHHHHHHhcCccc
Confidence 0 000123 34567899999999999999999999999844 5888999999999999999988899
Q ss_pred eeeEEEEcCCCcEEEEEEEEeeeeCCC-CCEEEEEEEEeccCc
Q 002191 832 NFPFGFFNRQGQFVEVALTASRRTDAE-GKVIGCFCFMQILVP 873 (955)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~-G~v~g~v~i~~DITe 873 (955)
..-||+..++|.+.|++..++.+.+.. ++...++|+---|+.
T Consensus 336 TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS~ 378 (768)
T KOG3558|consen 336 TGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLSN 378 (768)
T ss_pred hhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeecc
Confidence 999999999999999999999987643 334456666555554
No 51
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=98.75 E-value=8.1e-07 Score=100.53 Aligned_cols=199 Identities=18% Similarity=0.191 Sum_probs=129.5
Q ss_pred CcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHH--------------------------------------HHHHH
Q 002191 705 HSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLM--------------------------------------DKFIR 746 (955)
Q Consensus 705 G~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae--------------------------------------~~L~~ 746 (955)
|..-+..--..|++|++|+++|++.+..-+++--..- .++..
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 4444444456899999999999998876555422111 13333
Q ss_pred HHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChh--hhccCCccchhcccchhccChhhHHHHHHHHHhh
Q 002191 747 LQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRH--EVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQG 824 (955)
Q Consensus 747 se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~e--eviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~ 824 (955)
.-+.-.++++++.. |++.+|..|.+..+|.++++++|+... +.+|+.+.+. ++ |+. .+...++
T Consensus 213 l~~er~A~l~si~E---GviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v-~~-------p~~--~l~~vl~-- 277 (537)
T COG3290 213 LLEERQAMLQSIKE---GVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEV-LP-------PDS--DLPEVLE-- 277 (537)
T ss_pred HHHHHHHHHHHhhc---eEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEe-ec-------ccc--CcHHHHh--
Confidence 34445677888765 599999999999999999999999765 6888876642 22 111 0112111
Q ss_pred hcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhh
Q 002191 825 ITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVK 904 (955)
Q Consensus 825 ~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELR 904 (955)
.+......+ .+-+| .++..+..|+. .+|+++|++.++||-||-++...++... +.-.+-|...+||+.
T Consensus 278 -~~~~~~~~e---~~~ng--~~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~v-----r~ya~aLRaq~HEfm 345 (537)
T COG3290 278 -TGKPQHDEE---IRING--RLLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGV-----RQYAEALRAQSHEFM 345 (537)
T ss_pred -cCCcccchh---hhcCC--eEEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHH-----HHHHHHHHHhhHHHH
Confidence 122122222 22234 36677778887 5789999999999999865554443211 122345778899999
Q ss_pred hHhHhHHHHHHHhccCCCCHHHHHHHHHHH
Q 002191 905 NPLNGIRFVHKLLESSSISENQRQYLETSD 934 (955)
Q Consensus 905 nPL~~I~g~~~LL~~~~l~~~~~~~l~~i~ 934 (955)
|-|.+|.|+.++=+- ++..+|+..+.
T Consensus 346 NkLhtI~GLlql~~y----d~a~~~I~~~~ 371 (537)
T COG3290 346 NKLHTILGLLQLGEY----DDALDYIQQES 371 (537)
T ss_pred HHHHHHHHHHhhccH----HHHHHHHHHHH
Confidence 999999999887653 34455555554
No 52
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.71 E-value=5.7e-08 Score=89.61 Aligned_cols=106 Identities=24% Similarity=0.314 Sum_probs=80.3
Q ss_pred HHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEee
Q 002191 620 MVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKF 699 (955)
Q Consensus 620 l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~ 699 (955)
+..++++++.++.++|.+++|.++|+++.++|++...+ +|+++. ++.++...+.+...+..+..++.. ..+...
T Consensus 1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~~~-iGr~l~-~~~~~~~~~~l~~~i~~~~~~~~~-~~~~~~--- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSPSD-IGRPLF-DIHPPLSYPNLKKIIEQVRSGKEE-EFEIVI--- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---GGG-TTSBCC-CSS-HHHHHHHHHHHHHHHTTSBS-EEEEEE---
T ss_pred ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCChHH-CCCCHH-HcCCccchHHHHHHHHHHHcCCCc-eEEEEe---
Confidence 46789999999999999999999999999999987655 599998 888887788888888888877653 233232
Q ss_pred eeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecch
Q 002191 700 ELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT 735 (955)
Q Consensus 700 ~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DIT 735 (955)
..+ .+|+.++..|+++.+|+..|++.++.|||
T Consensus 75 --~~~--~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 --PNG--GRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp --EET--TEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred --cCC--CEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 123 36788999999999999999999999998
No 53
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.71 E-value=6.7e-08 Score=95.92 Aligned_cols=154 Identities=18% Similarity=0.234 Sum_probs=110.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCC--eEEEEEecCCC----CCCccCCCCCCCCchH
Q 002191 215 LAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDH--GEVVSEIRRSD----LEPYLGIHFPANDIPQ 288 (955)
Q Consensus 215 ~~~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~--G~viaE~~~~~----~~s~lg~~~p~~dip~ 288 (955)
++..+...+.. +.+.+++++.+++.+.+.+|+||..||++++|+. +.++++..... ..+..+.. .....
T Consensus 5 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~- 79 (175)
T COG2203 5 LLNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLV--ILPAC- 79 (175)
T ss_pred HHHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhccc--Ccchh-
Confidence 34455566666 6699999999999999999999999999999995 66666554332 11111111 00111
Q ss_pred HHHHHHHhCCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEE
Q 002191 289 AARFLFKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVV 368 (955)
Q Consensus 289 ~~r~ly~~~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~ 368 (955)
............++.|+...+.. ..+|..++... ++|.+++||+.++ ++||.++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~-i~~~l~vPl~~~~----~~~G~l~ 133 (175)
T COG2203 80 LIGIALREGRPVVVEDILQDPRF---------------------RDNPLVLLEPP-IRSYLGVPLIAQG----ELLGLLC 133 (175)
T ss_pred hhhhhhcCCceEEeeccccCccc---------------------ccCHHHHHHHH-HHHheeeeeeECC----EeeEEee
Confidence 11222345566667776655431 12566555555 9999999999998 9999999
Q ss_pred eecCCCC-CCChhHHHHHHHHHHHHHHHHHHH
Q 002191 369 CHHTSPR-YIPFPLRYACEFLVQAFSLQLYME 399 (955)
Q Consensus 369 ~hh~~pr-~~~~~~r~~~~~l~~~~~~~l~~~ 399 (955)
+|+|.++ .|+.+++.+.+.++++++..+...
T Consensus 134 ~~~~~~~~~~~~~e~~ll~~la~~~a~ai~~~ 165 (175)
T COG2203 134 VHDSEPRRQWSEEELELLEELAEQVAIAIERA 165 (175)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999966 699999999999999999888644
No 54
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.67 E-value=5.7e-07 Score=85.49 Aligned_cols=128 Identities=19% Similarity=0.219 Sum_probs=91.6
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCC
Q 002191 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (955)
Q Consensus 230 ~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~ 309 (955)
|++++++.+++.+++++|+|++.||.++++..--.++... +..+.+...+| .+-| -....+.++++..+++....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~--~~~~~~~~~l~-~~~~-~~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW--GGDPRLSESLP-EDDP-LIGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE--SS-GCGHHCEE-TTSH-HHHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe--CCCccccccCC-CCcc-HHHHHHhhCCeEEeccccccc
Confidence 6899999999999999999999999999885434343333 21121222555 3333 333667777776666543211
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHH
Q 002191 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLV 389 (955)
Q Consensus 310 ~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~~~l~ 389 (955)
..+.++.|++||..++ +++|+|.++...++.|+......++.++
T Consensus 77 --------------------------------~~~~~s~~~vPl~~~~----~~~Gvl~~~~~~~~~~~~~d~~~l~~~a 120 (129)
T PF13492_consen 77 --------------------------------FLGIRSLLVVPLRSRD----RVIGVLCLDSREPEEFSDEDLQLLESLA 120 (129)
T ss_dssp --------------------------------TTTTCEEEEEEEEETT----EEEEEEEEEECTTCG-SHHHHHHHHHHH
T ss_pred --------------------------------CCCCCEEEEEEEeECC----EEEEEEEEEECCCCCCCHHHHHHHHHHH
Confidence 0566899999999988 9999999988888899999999999999
Q ss_pred HHHHHHHH
Q 002191 390 QAFSLQLY 397 (955)
Q Consensus 390 ~~~~~~l~ 397 (955)
.++|..|+
T Consensus 121 ~~~a~ale 128 (129)
T PF13492_consen 121 NQLAIALE 128 (129)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 99998874
No 55
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.57 E-value=6.9e-07 Score=108.62 Aligned_cols=131 Identities=18% Similarity=0.290 Sum_probs=102.4
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc-CCCc
Q 002191 611 DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL-GEED 689 (955)
Q Consensus 611 ~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~-~~~~ 689 (955)
..++..+..++.++++++++++++|.+|+++++|+++++++|++.++++|+++. ++++++.. . ...+..... +...
T Consensus 255 ~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~-~~~~~~~~-~-~~~~~~~~~~~~~~ 331 (607)
T PRK11360 255 QALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYS-ELFPPNTP-F-ASPLLDTLEHGTEH 331 (607)
T ss_pred HHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHH-HHcCCchh-H-HHHHHHHHhcCCCc
Confidence 445566677889999999999999999999999999999999999999999987 77665422 2 222333333 3333
Q ss_pred ceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHH
Q 002191 690 KNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (955)
Q Consensus 690 ~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~ 749 (955)
...++.+ ..++|... +.++..|+.+.+|++.|++++++|||++|++++++++.+.
T Consensus 332 ~~~~~~~----~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~~ 386 (607)
T PRK11360 332 VDLEISF----PGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQER 386 (607)
T ss_pred cceEEEE----EcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHHH
Confidence 3444444 45667665 8999999999999999999999999999999998876543
No 56
>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=98.55 E-value=1.5e-06 Score=74.20 Aligned_cols=103 Identities=29% Similarity=0.409 Sum_probs=84.9
Q ss_pred cCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCc
Q 002191 627 ATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHS 706 (955)
Q Consensus 627 ~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~ 706 (955)
++++++.+|.+|.++++|+.+.+++|++..+++|+.+. .++++.+...+...+............++.+ ...+|.
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~ 75 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLL-DLIHPEDREELRERLENLLSGGEPVTLEVRL----RRKDGS 75 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHH-HhcCCccchHHHHHHHHHHhcCcCeEEEEEE----EccCCC
Confidence 36789999999999999999999999999999999987 7888877766666666666554444455555 456789
Q ss_pred EEEEEEEEEEeecCCCCEEEEEEEEecc
Q 002191 707 VVYILVNACTSRDYKNNVKGVCFVGQDI 734 (955)
Q Consensus 707 ~~~v~v~~~pi~d~~g~v~gvv~v~~DI 734 (955)
..|+.+...++.+..|...+++++..||
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 76 VIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 9999999999998888999999998886
No 57
>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=98.53 E-value=1.7e-06 Score=84.32 Aligned_cols=137 Identities=15% Similarity=0.164 Sum_probs=90.4
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCC--CCC--CchHHHH-----HHHHhCCEE
Q 002191 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHF--PAN--DIPQAAR-----FLFKQNRVR 300 (955)
Q Consensus 230 ~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~--p~~--dip~~~r-----~ly~~~~~r 300 (955)
+++++++.+++.+.+++++|.+.||-+++++.-..++-+..+ ...++..+ |.. ..+...+ .++..++..
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDP--SEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEPI 80 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSS--CTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-E
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCc--hhhhhhhcccCcccccccchhhhhHHHHHHhcCceE
Confidence 789999999999999999999999999888732333333322 22222221 111 1111110 115667777
Q ss_pred EeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChh
Q 002191 301 MICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFP 380 (955)
Q Consensus 301 ~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~ 380 (955)
++. .+. +. .+. .......|++|.+++||+.+| ++||+|...+..++.++..
T Consensus 81 ~~~-~~~-~~----------------------~~~-~~~~~~~~~~s~l~vPl~~~~----~~~Gvl~l~~~~~~~f~~~ 131 (148)
T PF13185_consen 81 IIN-DDD-SS----------------------FPP-WELARHPGIRSILCVPLRSGG----EVIGVLSLYSKEPNAFSEE 131 (148)
T ss_dssp EES-CCC-GG----------------------GST-THHHCCTT-SEEEEEEEEETT----EEEEEEEEEESSTT---HH
T ss_pred EEe-Ccc-cc----------------------ccc-hhhhccccCCEEEEEEEeECC----EEEEEEEEeeCCCCCcCHH
Confidence 776 110 00 011 356889999999999999998 9999999999889999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q 002191 381 LRYACEFLVQAFSLQLY 397 (955)
Q Consensus 381 ~r~~~~~l~~~~~~~l~ 397 (955)
.+.+++.++.++|..|+
T Consensus 132 ~~~~l~~la~~~a~aie 148 (148)
T PF13185_consen 132 DLELLEALADQIAIAIE 148 (148)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999988763
No 58
>PF12860 PAS_7: PAS fold
Probab=98.46 E-value=6.8e-07 Score=83.72 Aligned_cols=104 Identities=21% Similarity=0.328 Sum_probs=71.8
Q ss_pred HHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhh-cCCCcccccc---------cccc-HHHHHHHHHHHHcCCCcceE
Q 002191 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEA-MGKSLIDEVV---------HEES-QGAVENLICRALLGEEDKNV 692 (955)
Q Consensus 624 ie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eel-iG~~~~~~l~---------~~~~-~~~~~~~l~~~l~~~~~~~~ 692 (955)
+++++.||+++|.+|++++||+++.+++|++.+.+ .|.++. +++ .+.+ ...+.+.+.... ......+
T Consensus 1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~-~l~~~~~~~g~~~~~~~~~~~~~~~~~~~-~~~~~~~ 78 (115)
T PF12860_consen 1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFR-DLLRRLAERGEFPPGDPEAWVRQRLARLR-RRQPRSF 78 (115)
T ss_pred CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHH-HHHHHHHHcCCCCCCCHHHHHHHHHHHHh-cCCCcee
Confidence 47889999999999999999999999999999988 788765 433 1122 222333332222 2333333
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHH
Q 002191 693 ELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMD 742 (955)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~ 742 (955)
+.. ..|| +|+.+...|..+ | |++.++.|||++|++|+
T Consensus 79 ~~~------~~dg--r~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 79 ELR------LPDG--RWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred EEE------CCCC--EEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 332 3555 567788888754 3 56788999999998874
No 59
>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=98.45 E-value=1.6e-06 Score=96.85 Aligned_cols=114 Identities=15% Similarity=0.201 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEE
Q 002191 614 SSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE 693 (955)
Q Consensus 614 ~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e 693 (955)
+...++++.++++++++++++|.+|++++||++++++||++.++.+|+++. ++.++++ +...+.. +.. ...
T Consensus 2 ~~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~-~~~~~~~---~~~~l~~---~~~--~~~ 72 (333)
T TIGR02966 2 SALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRIT-NLIRHPE---FVEYLAA---GRF--SEP 72 (333)
T ss_pred hhHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHH-HHccCHH---HHHHHHh---ccc--CCC
Confidence 345577899999999999999999999999999999999999999999987 6665432 2222221 111 112
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHH
Q 002191 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFI 745 (955)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~ 745 (955)
+.+ ..++|..+|+.+...|+.+.. ++++++|||++++.++..+
T Consensus 73 ~~~----~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~~ 115 (333)
T TIGR02966 73 LEL----PSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMRR 115 (333)
T ss_pred eEe----ecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHHH
Confidence 333 346788899999999987643 5678899999998876544
No 60
>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=98.43 E-value=3e-06 Score=72.33 Aligned_cols=101 Identities=19% Similarity=0.227 Sum_probs=81.6
Q ss_pred CCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCC
Q 002191 763 PPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQG 842 (955)
Q Consensus 763 d~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG 842 (955)
++++.+|.+|.++++|+++.+++|++.++++|+.+.. +.++++...+...+.....++.....++.+...+|
T Consensus 3 ~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (103)
T cd00130 3 DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLD--------LIHPEDREELRERLENLLSGGEPVTLEVRLRRKDG 74 (103)
T ss_pred ceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHH--------hcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCC
Confidence 3689999999999999999999999999999987553 22234444455555555555556777888888999
Q ss_pred cEEEEEEEEeeeeCCCCCEEEEEEEEecc
Q 002191 843 QFVEVALTASRRTDAEGKVIGCFCFMQIL 871 (955)
Q Consensus 843 ~~~~v~~~~~pi~d~~G~v~g~v~i~~DI 871 (955)
..+|+.....++.+.+|...+++++.+||
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 75 SVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred CEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 99999999999999999999999998886
No 61
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.43 E-value=1.5e-06 Score=92.10 Aligned_cols=130 Identities=16% Similarity=0.213 Sum_probs=103.9
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc
Q 002191 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (955)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~ 685 (955)
++.+++-++...+++.+++-.+.+|++..|..|+|+.+|..+.+++|.+.++++|+++. +++.-++.-.+.+.+ .
T Consensus 99 ~~~aq~n~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~-elL~i~d~y~~~dL~----e 173 (459)
T COG5002 99 VQEAQANTEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSIL-ELLKIEDTYTFEDLV----E 173 (459)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHH-HHhCCccceeHHHHH----h
Confidence 34445566777788999999999999999999999999999999999999999999988 777655544444333 2
Q ss_pred CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHH
Q 002191 686 GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRL 747 (955)
Q Consensus 686 ~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~s 747 (955)
... ++.+. .+..++...+.++.+.++-+.|-+.|++.+..|+||+.+.|++.++.
T Consensus 174 ~~~----s~lld---~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErRef 228 (459)
T COG5002 174 KND----SLLLD---SSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERREF 228 (459)
T ss_pred cCC----cEEEe---ecCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHHHH
Confidence 222 22332 23367788889999999999999999999999999999999887664
No 62
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=98.43 E-value=2e-05 Score=94.33 Aligned_cols=153 Identities=10% Similarity=0.066 Sum_probs=109.6
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHH
Q 002191 214 KLAVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFL 293 (955)
Q Consensus 214 ~~~~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~l 293 (955)
+.+.++...+.+ +.+++++++.+++.+.+++|+||..||-+++++...+++ +....-+..-..+|+... --....
T Consensus 5 ~~L~~is~~l~~--~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~a-a~g~~~~~~~~~~~~~~~--gi~g~v 79 (534)
T TIGR01817 5 AALYEISKILSA--PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLVA-AIGWSEEGFAPIRYRVGE--GAIGQI 79 (534)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEEE-EeCCChhhcccccccCCc--cHHHHH
Confidence 344555666666 679999999999999999999999999998887654443 322111111113333221 224466
Q ss_pred HHhCCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002191 294 FKQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (955)
Q Consensus 294 y~~~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~ 373 (955)
+..+...+|.|+...|-.. .+. -+...+++|.|+|||..+| +++|.|..+...
T Consensus 80 ~~~~~pvii~Dv~~d~~~~---------------------~~~--~~~~~~~~S~l~VPL~~~g----~viGvL~v~s~~ 132 (534)
T TIGR01817 80 VATGNSLVVPDVAAEPLFL---------------------DRL--SLYDPGPVPFIGVPIKADS----ETIGVLAADRDF 132 (534)
T ss_pred HhcCCeEEecccccCchhh---------------------hcc--ccccCCcceEEEEEEcCCC----EEEEEEEEEecc
Confidence 7789999999987654311 000 0334678999999999888 999999999886
Q ss_pred -CCCCChhHHHHHHHHHHHHHHHHHH
Q 002191 374 -PRYIPFPLRYACEFLVQAFSLQLYM 398 (955)
Q Consensus 374 -pr~~~~~~r~~~~~l~~~~~~~l~~ 398 (955)
++.+..+...+++.+|.+++..|..
T Consensus 133 ~~~~ft~~d~~lL~~lA~~ia~aI~~ 158 (534)
T TIGR01817 133 RSRERLEEEVRFLEMVANLIGQTVRL 158 (534)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHH
Confidence 6777899999999999999988853
No 63
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.42 E-value=3.1e-05 Score=77.08 Aligned_cols=228 Identities=22% Similarity=0.288 Sum_probs=142.8
Q ss_pred EEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEE
Q 002191 632 FGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYIL 711 (955)
Q Consensus 632 ~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~ 711 (955)
+..+..+.+.+.|......+++......+ .. ............................... ...++...++.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 75 (232)
T COG2202 3 LVLDRDGRIIYANEAAEELLGYSAEELLG--LL-LALHPEDRDRLRELLRRLLAGEELLSEELRL----VRKDGEERWVE 75 (232)
T ss_pred EEEcccccEEEecccchhhcCCChHHhhh--hh-hccCccchhhhHHHHHHHhccCCcchhhHHh----hhcCCcEEEEE
Confidence 45667788888888888888877766655 11 1111111111111111112111111111111 23345555554
Q ss_pred EEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhh
Q 002191 712 VNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHE 791 (955)
Q Consensus 712 v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~ee 791 (955)
..........+........ .|+++.+..++.+...+.+++.++++.+. +++..|.+|++.++|+++.+++|++..+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~d~~~~~~~~n~~~~~~~g~~~~~ 151 (232)
T COG2202 76 LSAAPLRDGEGRVLGLLGL-RDITERKRAEEALRESEERLRALLEASPD---GIWVLDEDGRILYANPAAEELLGYSPEE 151 (232)
T ss_pred ecceEEEcCCCCEEEEEee-eecchHHHHHHHHHHHHHHHHHHHhhCCc---eEEEEeCCCCEEEeCHHHHHHhCCChHH
Confidence 4444444445555555555 89999999999999999999999999875 5999999999999999999999999888
Q ss_pred hccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcE-EEEEEEEeeeeCCCCCEEEEEEEEec
Q 002191 792 VIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQF-VEVALTASRRTDAEGKVIGCFCFMQI 870 (955)
Q Consensus 792 viGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~-~~v~~~~~pi~d~~G~v~g~v~i~~D 870 (955)
..+......... ...+.. ..................++....++|.. .+......+... .|.+.++.+...|
T Consensus 152 ~~~~~~~~~~~~-----~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d 224 (232)
T COG2202 152 ELGRGLSDLIHP-----EDEERR-ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVVGIARD 224 (232)
T ss_pred hcCCChhheEec-----CCCchh-hHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEec
Confidence 876654321111 111110 01111112222334577888899999996 888777777665 7889999999999
Q ss_pred cCcccHH
Q 002191 871 LVPDLQP 877 (955)
Q Consensus 871 ITerk~~ 877 (955)
++++++.
T Consensus 225 ~~~~~~~ 231 (232)
T COG2202 225 ITERKQA 231 (232)
T ss_pred hHHHhhc
Confidence 9987653
No 64
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.37 E-value=2.2e-06 Score=78.92 Aligned_cols=106 Identities=18% Similarity=0.173 Sum_probs=74.4
Q ss_pred HHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCc
Q 002191 751 YEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGT 830 (955)
Q Consensus 751 lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~ 830 (955)
++.++++++. ++..+|.++++.++|+++.++|+... ..+|+++.+ +..+...+.+...+..+..|+.
T Consensus 1 L~~il~s~~~---~i~~vD~~~~I~~~n~~a~~~f~~~~-~~iGr~l~~--------~~~~~~~~~l~~~i~~~~~~~~- 67 (106)
T PF13596_consen 1 LNNILDSMPI---GIIFVDRNLRIRYFNPAAARLFNLSP-SDIGRPLFD--------IHPPLSYPNLKKIIEQVRSGKE- 67 (106)
T ss_dssp HHHHHHHSSS---EEEEEETTSBEEEE-SCGC-SS---G-GGTTSBCCC--------SS-HHHHHHHHHHHHHHHTTSB-
T ss_pred ChHHHhcCCC---CEEEEcCCCeEEEeChhHhhhcCCCh-HHCCCCHHH--------cCCccchHHHHHHHHHHHcCCC-
Confidence 3578888875 59999999999999999999999775 457998764 3335566667777777777764
Q ss_pred ceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccC
Q 002191 831 ENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILV 872 (955)
Q Consensus 831 ~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DIT 872 (955)
...+... ..+| +|+.++..|+++.+|+..|++.++.|||
T Consensus 68 ~~~~~~~-~~~~--~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 68 EEFEIVI-PNGG--RWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp SEEEEEE-EETT--EEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred ceEEEEe-cCCC--EEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 2333333 2344 5778899999999999999999999998
No 65
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=98.35 E-value=1.1e-06 Score=103.26 Aligned_cols=66 Identities=17% Similarity=0.302 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHHHhhhHhHhHHHHHHHhcc--CCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLES--SSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 890 ~ak~~fla~iSHELRnPL~~I~g~~~LL~~--~~l~~~-~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+-++.+|+.+||||||||++|+|..+.|.. ..++++ +.+.+..|.+.+++|.++|++ ||+.||++|
T Consensus 658 ~lRsaLL~sISHDLRTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG 727 (890)
T COG2205 658 RLRSALLASISHDLRTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSG 727 (890)
T ss_pred HHHHHHHHHhhccccCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcC
Confidence 467789999999999999999999999874 456666 788999999999999999999 999999998
No 66
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.35 E-value=1.1e-05 Score=98.87 Aligned_cols=220 Identities=15% Similarity=0.174 Sum_probs=124.9
Q ss_pred HHHHHHHhcCccEEEEcCCCcEeeecHHHHHH-----hCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEE
Q 002191 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAEL-----TGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE 693 (955)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l-----~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e 693 (955)
.+..++...+..+.+.|.+|.++.++....-+ .|+. .|..|..+.+-. ..+..++..+.+..+.
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 44556677788999999999999875432211 1221 233333111111 1222333333221110
Q ss_pred EEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecch------------------HhHHHHH---HHHHHHHHHH
Q 002191 694 LKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT------------------HEKVLMD---KFIRLQGDYE 752 (955)
Q Consensus 694 ~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DIT------------------erk~ae~---~L~~se~~lr 752 (955)
-. -|-......+.+.+.|++|.+|+++|++.+..+.. .+..... ++......+.
T Consensus 132 --g~---EH~~~~~~~~~c~aaPI~d~~G~liGvl~l~~~~~~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~~~~~~~ 206 (638)
T PRK11388 132 --GD---QHFKQALHNWAFCATPVFDSKGRLTGTIALACPVEQTSAADLPLTLSIAREVGNLLLTDSLLAESNRHLNQLN 206 (638)
T ss_pred --cH---HHHHHhccCceEEeeEEEcCCCCEEEEEEEEecccccChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 00011223356788999999999999997765432 1111111 1122223344
Q ss_pred HHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcc-
Q 002191 753 AIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTE- 831 (955)
Q Consensus 753 ~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~- 831 (955)
.++++++ +||+++|.+|+|+++|+++++++|++.++++|+.+.+ +++ .+.. +.+++..+...
T Consensus 207 ~il~~~~---~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~-l~~------~~~~-------l~~vl~~~~~~~ 269 (638)
T PRK11388 207 ALLESMD---DGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITE-LLT------LPAV-------LQQAIKQAHPLK 269 (638)
T ss_pred HHHhccC---CcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHH-Hhc------cchH-------HHHHHhcCCcee
Confidence 5777765 4699999999999999999999999999999997653 222 0111 12223333222
Q ss_pred eeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcc
Q 002191 832 NFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPD 874 (955)
Q Consensus 832 ~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITer 874 (955)
..+.. ...+|..+++.++..|+.+..|. +++.+++|++..
T Consensus 270 ~~~~~-l~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~ 309 (638)
T PRK11388 270 HVEVT-FESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQM 309 (638)
T ss_pred eEEEE-EecCCceEEEEEEEEeecccCce--EEEEEehhhHHH
Confidence 22322 23457777888999999755553 355556787763
No 67
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.33 E-value=3.9e-06 Score=94.94 Aligned_cols=116 Identities=13% Similarity=0.125 Sum_probs=85.9
Q ss_pred HHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCc-ceEEEEEE
Q 002191 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED-KNVELKLR 697 (955)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~-~~~e~~~~ 697 (955)
.+..+++++++|++++|.+|+|+++|+++++++|++.++++|+++. ++++..... ...+...+..+.. ...++.
T Consensus 8 ~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-- 82 (348)
T PRK11073 8 DAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLP-ELLSYFSLN--IELMRESLQAGQGFTDNEVT-- 82 (348)
T ss_pred hHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHH-HHcCcchhh--HHHHHHHHHcCCcccccceE--
Confidence 5688999999999999999999999999999999999999999987 776543221 1223333333322 122222
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHH
Q 002191 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRL 747 (955)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~s 747 (955)
...+|+.+|+.++..|+. . .+++..++|+|++++.++++.+.
T Consensus 83 ---~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~~~ 124 (348)
T PRK11073 83 ---LVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQLQH 124 (348)
T ss_pred ---EEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHHHH
Confidence 345899999999999987 1 34567789999999887766443
No 68
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).
Probab=98.33 E-value=8.2e-07 Score=114.73 Aligned_cols=74 Identities=28% Similarity=0.445 Sum_probs=69.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 882 q~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+..+++++++|.+|++.|||||||||++|.|+.++|....++++++++++.|..++++|..+|++ ||++|+|+|
T Consensus 454 ~~~~~~~~~~~~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~ 528 (968)
T TIGR02956 454 RAEAEEANRAKSAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAG 528 (968)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 55677788899999999999999999999999999998888999999999999999999999999 999999875
No 69
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=98.29 E-value=1.1e-06 Score=72.38 Aligned_cols=64 Identities=39% Similarity=0.592 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 892 KIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 892 k~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+.++++.++||+||||++|.++.+++.....+++..++++.+..+++++..++++ ++++++++|
T Consensus 2 ~~~~~~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~ 66 (66)
T smart00388 2 KREFLANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRIEAG 66 (66)
T ss_pred HHHHHHHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3578899999999999999999988887566777789999999999999999999 899998865
No 70
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=98.29 E-value=1.2e-06 Score=112.73 Aligned_cols=74 Identities=26% Similarity=0.469 Sum_probs=68.5
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 882 q~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
++.+++++..|.+|++.+||||||||++|.|+.++|....++++++++++.+..++++|..+|++ ||++|+|+|
T Consensus 388 ~~~~~~~~~~~~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~ 462 (921)
T PRK15347 388 KQRAEQANKRKSEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESG 462 (921)
T ss_pred HHHHHHHHHHHHHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 45666777889999999999999999999999999998889999999999999999999999999 999999875
No 71
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=98.20 E-value=0.00017 Score=89.00 Aligned_cols=147 Identities=6% Similarity=0.007 Sum_probs=103.6
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEec--CCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecC
Q 002191 228 GGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIR--RSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDC 305 (955)
Q Consensus 228 ~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~--~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~ 305 (955)
..++++++..+++.+++++++|++.|+-++++...-++.-+. ..+.....+...|... --+...+..+...++.|.
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 679999999999999999999999999998887654443332 2222233343433321 123456777888888776
Q ss_pred CCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHH
Q 002191 306 HAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYAC 385 (955)
Q Consensus 306 ~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~ 385 (955)
...+.... .....+ +..-++++.++|||+.+| +.=|.|...++.++.++......+
T Consensus 275 ~~d~~~~~-------------------~~~~~~-~~~~~~~s~l~vPL~~~~----~v~GvL~l~~~~~~~F~~~dl~lL 330 (686)
T PRK15429 275 ERDDLAPY-------------------ERMLFD-TWGNQIQTLCLLPLMSGD----TMLGVLKLAQCEEKVFTTTNLKLL 330 (686)
T ss_pred cCcccchh-------------------hhhhhh-cccccceEEEEEeEEECC----EEEEEEEEeeCCCCcCCHHHHHHH
Confidence 64432100 000111 123468999999999988 999999998888888999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 002191 386 EFLVQAFSLQLYMEL 400 (955)
Q Consensus 386 ~~l~~~~~~~l~~~~ 400 (955)
..+|.++++.|+.+.
T Consensus 331 ~~iA~~~A~Aie~a~ 345 (686)
T PRK15429 331 RQIAERVAIAVDNAL 345 (686)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999887543
No 72
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=98.19 E-value=0.00017 Score=85.72 Aligned_cols=214 Identities=12% Similarity=0.068 Sum_probs=128.8
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHh
Q 002191 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (955)
Q Consensus 217 ~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~ 296 (955)
.++...|-+ +.+++++++.+++.+.+++++|.+-|+-++++ .....+..+......+..|+..+=|--. +....
T Consensus 7 ~eis~~L~~--s~d~~e~L~~vl~~l~~~l~~~~~~l~l~~~~---~l~~~as~gl~~~~~~~~~~~geGP~l~-av~~~ 80 (509)
T PRK05022 7 LPIALDLSR--GLPHQDRFQRLLTTLRQVLPCDASALLRLDGD---QLVPLAIDGLSPDVLGRRFALEEHPRLE-AILRA 80 (509)
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC---cEEEEEEcCCChHhhCCccCCCcchHHH-HHHhc
Confidence 455566666 78999999999999999999999999999753 2222233222233455577666544322 22243
Q ss_pred CCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCC
Q 002191 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRY 376 (955)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~ 376 (955)
+++..|+|...-|.++- |-... ...++|++|.|+|||.++| +.+|.|.+++..|..
T Consensus 81 g~~v~v~~~~~~p~~~~----------------~~~~~----~~~~~gi~S~l~vPL~~~~----~~~GvL~l~~~~~~~ 136 (509)
T PRK05022 81 GDPVRFPADSELPDPYD----------------GLIPG----VQESLPVHDCMGLPLFVDG----RLIGALTLDALDPGQ 136 (509)
T ss_pred CCeEEEecCCCCCcccc----------------ccccc----ccccCCcceEEEEEEEECC----EEEEEEEEeeCCCCc
Confidence 66666666543332110 00000 1345799999999999998 999999999988888
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc-CCcccccCCchhhhhccCCeEEEEECCeEE
Q 002191 377 IPFPLRYACEFLVQAFSLQLYMELQVAMQLAEKNILRTQVLLCDMLLRD-APFSIVTQSPSIMDLVKCDGAALYYGGRCW 455 (955)
Q Consensus 377 ~~~~~r~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~l~~~~g~a~~~~~~~~ 455 (955)
+......+++.++.+++..+...........+...+ ......+..+. .+..++.+++.+..+.+--..+--.+..+.
T Consensus 137 f~~~~~~~l~~~a~~~a~Al~~a~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~iig~s~~~~~~~~~i~~~a~~~~pVl 214 (509)
T PRK05022 137 FDAFSDEELRALAALAAATLRNALLIEQLESQAELP--QDVAEFLRQEALKEGEMIGQSPAMQQLKKEIEVVAASDLNVL 214 (509)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhhhhccCCceeecCHHHHHHHHHHHHHhCCCCcEE
Confidence 888888999999999998887543322221111111 11111111111 355677777666544432222222344455
Q ss_pred EecCCCC
Q 002191 456 LVGVTPT 462 (955)
Q Consensus 456 ~~G~~p~ 462 (955)
+.|.+=+
T Consensus 215 I~Ge~Gt 221 (509)
T PRK05022 215 ILGETGV 221 (509)
T ss_pred EECCCCc
Confidence 6665443
No 73
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.17 E-value=2.8e-06 Score=109.24 Aligned_cols=74 Identities=24% Similarity=0.413 Sum_probs=67.2
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 882 q~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
++.++++++.|.+|++.|||||||||++|.|+.+++....++++++++++.|..+++++..+|++ ||++|+|+|
T Consensus 283 ~~~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~ 357 (919)
T PRK11107 283 KKRAQEAARIKSEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAG 357 (919)
T ss_pred HHHHHHHHHHHHHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34566677788999999999999999999999999888788899999999999999999999999 999999875
No 74
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=98.14 E-value=0.00011 Score=82.56 Aligned_cols=205 Identities=18% Similarity=0.116 Sum_probs=122.5
Q ss_pred CCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHH-HHHHhCC-EEEe-ecC
Q 002191 229 GDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAAR-FLFKQNR-VRMI-CDC 305 (955)
Q Consensus 229 ~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r-~ly~~~~-~r~i-~d~ 305 (955)
.+++.++..+++.+..+.|||+++++++|.+. .+..+++.-..+.+|.+-+....|.+.- +.+..+. ++++ .|.
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 4444444444455665323333443332 3344444 4441 221
Q ss_pred CCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHH
Q 002191 306 HAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYAC 385 (955)
Q Consensus 306 ~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~ 385 (955)
..|++..+ -+--.+++++-|.|.+||.+++ ++||+|..-|+.|-...+..-..+
T Consensus 124 ------~~~~~~~~----------------l~~~~~~~~~~a~i~~PL~~~~----~~~G~Ltld~~~~~~f~~~~~~~l 177 (550)
T COG3604 124 ------LFPDPYDG----------------LLPDTEGNKKHACIGVPLKSGD----KLIGALTLDHTEPDQFDEDLDEEL 177 (550)
T ss_pred ------ccCCcccc----------------cccCccCCcceeEEeeeeeeCC----eeeeeEEeeeecccccchhHHHHH
Confidence 12222111 0111456788999999999998 999999999999888888888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhcc--cCCcccccCCchhhhhccCCeEEEEECCeEEEecCCCC
Q 002191 386 EFLVQAFSLQLYMELQVAMQLAEKNILRTQ-VLLCDMLLR--DAPFSIVTQSPSIMDLVKCDGAALYYGGRCWLVGVTPT 462 (955)
Q Consensus 386 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~l~~l~~~~g~a~~~~~~~~~~G~~p~ 462 (955)
++|+...+..+....-.+.....++.+..+ ..+..-+.. ....+|+.+++.++.+++.--++.-.+-.+.+.|.|-+
T Consensus 178 r~La~~a~la~~~~~l~~~l~~~~~~l~~e~~~~~~~~~~~~~~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGt 257 (550)
T COG3604 178 RFLAALAALAVANALLHRELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGT 257 (550)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccchhcccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCc
Confidence 888888877665332111111111111111 111111111 12356777777776666554444444555555666543
No 75
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.12 E-value=3e-05 Score=71.91 Aligned_cols=102 Identities=13% Similarity=0.138 Sum_probs=83.6
Q ss_pred eeeecCCCcEeeecHH-HHHHhCCChhhhccCCccchhcccchhccChhhHHH-HHHHHHhhhcCCCcceeeEEEEcCCC
Q 002191 765 IFASDENACCSEWNAA-MEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTK-FMILLYQGITGQGTENFPFGFFNRQG 842 (955)
Q Consensus 765 I~~~D~~g~i~~~N~a-~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~-~~~~l~~~~~g~~~~~~e~~~~~~dG 842 (955)
....+.+|+|+++-+. ...++||.++|++|+.+.+ +.||+|... +......++..+.....-+|++.++|
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~--------~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g 76 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYD--------FVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNG 76 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGG--------GBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTS
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHH--------hCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCC
Confidence 3456889999999999 6999999999999998664 778999997 77788888877777777899999999
Q ss_pred cEEEEEEEEeeeeC-CCCCEEEEEEEEeccCcc
Q 002191 843 QFVEVALTASRRTD-AEGKVIGCFCFMQILVPD 874 (955)
Q Consensus 843 ~~~~v~~~~~pi~d-~~G~v~g~v~i~~DITer 874 (955)
.++|+...+.++.+ ..+++..++|+-+-|+++
T Consensus 77 ~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vlse~ 109 (111)
T PF14598_consen 77 GYVWVQTKATLFYNPWTSKPEFIVCTNTVLSEE 109 (111)
T ss_dssp SEEEEEEEEEEEEETTTTCEEEEEEEEEEESCE
T ss_pred cEEEEEEEEEEEECCCCCCccEEEEEEEEeccC
Confidence 99999999999986 455777788877777763
No 76
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.11 E-value=1.6e-05 Score=92.82 Aligned_cols=119 Identities=13% Similarity=0.151 Sum_probs=83.2
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCC
Q 002191 608 QGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (955)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (955)
+..++|++.+++++.+++++|++++++|.+|+|++||+++++++|++.++..|+++. +++..++.. ..+.. ..
T Consensus 88 ~~~~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~-~~~~~~~~~---~~~~~---~~ 160 (430)
T PRK11006 88 KRRRELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNIL-NLLRYPEFT---QYLKT---RD 160 (430)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHH-HHhcCHHHH---HHHHh---cc
Confidence 346678888899999999999999999999999999999999999999999999987 665433211 11111 11
Q ss_pred CcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHH
Q 002191 688 EDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIR 746 (955)
Q Consensus 688 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~ 746 (955)
... ...+ ...++. ++.+...|..+ + +.+.+.+|||++++.+++.++
T Consensus 161 ~~~--~~~~----~~~~~~--~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~~~~ 206 (430)
T PRK11006 161 FSR--PLTL----VLNNGR--HLEIRVMPYTE--G---QLLMVARDVTQMHQLEGARRN 206 (430)
T ss_pred cCC--CeEE----EcCCCC--EEEEEEEEcCC--C---cEEEEEehhhHHHHHHHHHHH
Confidence 111 1122 123343 55666666543 2 245678999999988876543
No 77
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.11 E-value=5.6e-06 Score=106.31 Aligned_cols=72 Identities=28% Similarity=0.376 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 884 LEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 884 ~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
..++..++|..|++.|||||||||++|.|+.++|.....+++++++++.+..+++++..+|++ ||+++++.|
T Consensus 436 ~~~~~~~~~~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~ 508 (914)
T PRK11466 436 EAEKASQAKSAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAG 508 (914)
T ss_pred HHHHHHHHHHHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 455666789999999999999999999999999998888899999999999999999999999 999999865
No 78
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=98.07 E-value=8.7e-05 Score=91.25 Aligned_cols=151 Identities=11% Similarity=0.059 Sum_probs=109.7
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHh
Q 002191 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (955)
Q Consensus 217 ~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~ 296 (955)
.++...+.+ +.+++++++.+++.+++++|+|++.||-+++|+..-+++-+...+-+..-..+||... --+...+..
T Consensus 6 ~eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~ge--Gi~G~Va~t 81 (748)
T PRK11061 6 REIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDE--GIVGLVGRL 81 (748)
T ss_pred HHHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCc--chHHHHhcc
Confidence 344455555 6699999999999999999999999999999987666665543222222223444322 123455667
Q ss_pred CCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCC
Q 002191 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRY 376 (955)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~ 376 (955)
+..-.|.|+...|--. +...+...+++|.|+|||+.+| ++-|.|.+++..||.
T Consensus 82 g~pV~V~Dv~~dprf~-----------------------~~~~~~~~~~~S~L~VPL~~~g----eVIGVL~v~~~~~~~ 134 (748)
T PRK11061 82 AEPINLADAQKHPSFK-----------------------YIPSVKEERFRAFLGVPIIYRR----QLLGVLVVQQRELRQ 134 (748)
T ss_pred CceEEECCcccCcccc-----------------------cCccccCccceEEEEEEEeeCC----EEEEEEEEeeCCCCC
Confidence 8888889988654310 0001224689999999999877 999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHHHH
Q 002191 377 IPFPLRYACEFLVQAFSLQLYM 398 (955)
Q Consensus 377 ~~~~~r~~~~~l~~~~~~~l~~ 398 (955)
++......+..|+.+++..|+.
T Consensus 135 Fs~~d~~lL~~LA~~aAiAL~n 156 (748)
T PRK11061 135 FDESEESFLVTLATQLAAILSQ 156 (748)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999998888887754
No 79
>PF12860 PAS_7: PAS fold
Probab=98.06 E-value=1.4e-05 Score=74.70 Aligned_cols=105 Identities=11% Similarity=0.114 Sum_probs=66.0
Q ss_pred CCeeeecCCCcEeeecHHHHHHhCCChhhh-ccCCccchhcccch--hccChhhHHH-HHHHHHhhhcCCCcceeeEEEE
Q 002191 763 PPIFASDENACCSEWNAAMEKVTGWMRHEV-IGKMLPREIFGNFC--RMKGQDMLTK-FMILLYQGITGQGTENFPFGFF 838 (955)
Q Consensus 763 d~I~~~D~~g~i~~~N~a~~~l~G~~~eev-iGk~~~~~~~~~~~--~l~~~d~~~~-~~~~l~~~~~g~~~~~~e~~~~ 838 (955)
.||+++|.+|++++||+++.+++|++.+.+ .|.++.+ ++..+. ....+.+... +...+.. ....... .+.+.
T Consensus 6 ~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~-l~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~ 81 (115)
T PF12860_consen 6 QGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRD-LLRRLAERGEFPPGDPEAWVRQRLAR-LRRRQPR--SFELR 81 (115)
T ss_pred ceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHH-HHHHHHHcCCCCCCCHHHHHHHHHHH-HhcCCCc--eeEEE
Confidence 469999999999999999999999999998 6776443 332211 1111222222 2222222 2222232 33456
Q ss_pred cCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHH
Q 002191 839 NRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (955)
Q Consensus 839 ~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (955)
..||. |+.++..|.-+ | |++.+..|||+++++|
T Consensus 82 ~~dgr--~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 82 LPDGR--WLEVRAQPLPD--G---GFVLTFTDVTERRRAE 114 (115)
T ss_pred CCCCE--EEEEEeEECCC--C---CEEEEEEeCCHHHHhc
Confidence 67776 55666677643 4 4677889999988876
No 80
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.05 E-value=7.1e-05 Score=88.91 Aligned_cols=112 Identities=12% Similarity=0.119 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceE
Q 002191 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNV 692 (955)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~ 692 (955)
+++...++..+++++++||+++|.+|+|+++|++++++||++.++++|+++. ++++.... ...+..+.....
T Consensus 75 ~e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~-eli~~~~l-------~~~le~~~~~~~ 146 (520)
T PRK10820 75 SEREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAA-QLINGFNF-------LRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHH-HHcCcchH-------HHHHHcCCCccc
Confidence 4555677899999999999999999999999999999999999999999998 77765432 222332322111
Q ss_pred EEEEEeeeeccCCcEEEEEEEEEEee--cCCCCE--EEEEEEEecchHhHH
Q 002191 693 ELKLRKFELQKQHSVVYILVNACTSR--DYKNNV--KGVCFVGQDITHEKV 739 (955)
Q Consensus 693 e~~~~~~~~~~dG~~~~v~v~~~pi~--d~~g~v--~gvv~v~~DITerk~ 739 (955)
...+ ..+|..++ +...|+. +.+|.. .|++.+++|+++..+
T Consensus 147 ~~~v-----~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 NEHV-----VINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred eEEE-----EECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 1122 22465444 5667776 666654 899999999998643
No 81
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.05 E-value=4.8e-05 Score=70.54 Aligned_cols=101 Identities=14% Similarity=0.168 Sum_probs=81.1
Q ss_pred EEEEcCCCcEeeecHH-HHHHhCCCchhhcCCCccccccccccHHH-HHHHHHHHHcCCCcceEEEEEEeeeeccCCcEE
Q 002191 631 IFGVDSSGTINGWNAK-VAELTGLPASEAMGKSLIDEVVHEESQGA-VENLICRALLGEEDKNVELKLRKFELQKQHSVV 708 (955)
Q Consensus 631 I~~~D~dg~i~~~N~~-~~~l~G~~~eeliG~~~~~~l~~~~~~~~-~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~ 708 (955)
+...+.+|+|+++..+ ...++||.++|++|+++. +++||++... +.+....++..+.....-+++ +.++|..+
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y-~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~----~~k~g~~v 79 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIY-DFVHPDDLQRVLKQHHREVLQKGQSVSPYYRF----RTKNGGYV 79 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGG-GGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEE----E-TTSSEE
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchH-HhCCHhhhhhHHHHHHHHHhhCCCcCcceEEE----EecCCcEE
Confidence 4556899999999999 699999999999999999 9999999996 888888888777765555666 67999999
Q ss_pred EEEEEEEEeecC-CCCEEEEEEEEecchH
Q 002191 709 YILVNACTSRDY-KNNVKGVCFVGQDITH 736 (955)
Q Consensus 709 ~v~v~~~pi~d~-~g~v~gvv~v~~DITe 736 (955)
|+.....++.+. ++++..++++..=|++
T Consensus 80 wvqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 80 WVQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 999999999875 4566666666554443
No 82
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.98 E-value=9.3e-05 Score=84.23 Aligned_cols=167 Identities=19% Similarity=0.274 Sum_probs=112.4
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcc-e
Q 002191 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDK-N 691 (955)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~-~ 691 (955)
|......|..+++.+.++++++|.+|.++++|.++..++|++.++++|+++. +++..... .....++..+.+. .
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~-~v~~~~~~----s~~l~vl~~~kp~~~ 186 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLL-DVVSAGED----STLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHH-HHHhccCC----ceehhhhhcCCccee
Confidence 4556678999999999999999999999999999999999999999999887 66511000 1122233333321 2
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHH--------HHHHhc-----
Q 002191 692 VELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYE--------AIIQSV----- 758 (955)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr--------~i~e~~----- 758 (955)
....+ .|... ..+..|++ .+|.+.|++++++|+++-+....++.+++...+ .|+-..
T Consensus 187 ~~~~~-------~~~~~--i~~~~pv~-~~g~l~G~v~~~~~~~~l~~l~~~~~~~~~~~~~~a~y~f~~Iig~S~~m~~ 256 (560)
T COG3829 187 VVQTY-------NGNKI--IVNVAPVY-ADGQLIGVVGISKDVSELERLTRELEESEGLLRLKAKYTFDDIIGESPAMLR 256 (560)
T ss_pred eeeee-------cCCce--eEeeccEe-cCCcEEEEEEeecchHHHHHHHHHHHHHhhhhccccccchhhhccCCHHHHH
Confidence 11111 22222 45556666 567999999999999999999888877766544 222111
Q ss_pred --------CCCCCCeeeecCCC-------------------cEeeecHHH-------HHHhCCChhhhcc
Q 002191 759 --------NPLIPPIFASDENA-------------------CCSEWNAAM-------EKVTGWMRHEVIG 794 (955)
Q Consensus 759 --------~~~id~I~~~D~~g-------------------~i~~~N~a~-------~~l~G~~~eeviG 794 (955)
...-..|.+..+.| -++.+|=++ .++|||....+-|
T Consensus 257 ~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye~GAFTG 326 (560)
T COG3829 257 VLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYEKGAFTG 326 (560)
T ss_pred HHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCHHHHHHHHhCcCCccccc
Confidence 00012466665544 477777665 6799998877765
No 83
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=97.98 E-value=8.2e-05 Score=89.54 Aligned_cols=122 Identities=14% Similarity=0.195 Sum_probs=87.8
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCC---chhhcCCCccccccccccHHHHHHHHHHHHcCC
Q 002191 611 DELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLP---ASEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (955)
Q Consensus 611 ~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~---~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (955)
.|+....++++.+++++++|++++|.+|+|+++|+++++++|++ ..+.+|+.+. .+.+.. .+...+..+
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~-~~~~~~-------~~~~~~~~~ 285 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVE-SWMPVS-------RLKEVLRTG 285 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHH-HhCCch-------hHHHHHhcC
Confidence 46666777889999999999999999999999999999999865 3455666655 444322 223333333
Q ss_pred Ccc-eEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHH
Q 002191 688 EDK-NVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGD 750 (955)
Q Consensus 688 ~~~-~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~ 750 (955)
... ..+... +| .++.++..|+.+ +|.+.|++.+++|+|+.++.++++......
T Consensus 286 ~~~~~~~~~~-------~g--~~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~~~~~~ 339 (542)
T PRK11086 286 TPRRDEEINI-------NG--RLLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLDGMVNY 339 (542)
T ss_pred CCccceEEEE-------CC--EEEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHHHHHHH
Confidence 322 222221 34 345667789998 889999999999999999988887665543
No 84
>PRK09303 adaptive-response sensory kinase; Validated
Probab=97.85 E-value=2.9e-05 Score=88.97 Aligned_cols=69 Identities=16% Similarity=0.200 Sum_probs=57.7
Q ss_pred HHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCC-------HHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 887 MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSIS-------ENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 887 ~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~-------~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
+..+.+.+|++++||||||||++|.++.++|.....+ +..+++++.+..++++|.++|++ |+++|.+.+
T Consensus 146 e~~~~~~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~ 222 (380)
T PRK09303 146 EQLKFKDRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWE 222 (380)
T ss_pred HHHHHHHHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 3445688999999999999999999999999853322 33778999999999999999999 899887653
No 85
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.82 E-value=6.2e-05 Score=80.56 Aligned_cols=208 Identities=17% Similarity=0.185 Sum_probs=127.1
Q ss_pred HHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHH---cCCCcceEEEEEEe
Q 002191 622 RLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRAL---LGEEDKNVELKLRK 698 (955)
Q Consensus 622 ~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l---~~~~~~~~e~~~~~ 698 (955)
.+++.....|++++++|.|+|+++.+.--+|++.-|+.|..+. +++|+.+.+.+...+...- +-+....+..+.++
T Consensus 83 hlLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~-eYIH~~D~demna~L~~h~H~qeyeIErsfflrmkC 161 (598)
T KOG3559|consen 83 HLLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIY-EYIHPQDHDEMNAVLTAHQHLQEYEIERSFFLRMKC 161 (598)
T ss_pred hHHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhh-hhhcccchHHHHHHHhhhhhhhhhhhhhhhhhhhhh
Confidence 4567777889999999999999999999999999999999999 9999988887766553222 11111112222221
Q ss_pred eeeccC------CcE-E----EEEEEEEEeecC-CC---CEEEEEEEEec-----chHhHHHHHHHHHHHHHHHHHHHhc
Q 002191 699 FELQKQ------HSV-V----YILVNACTSRDY-KN---NVKGVCFVGQD-----ITHEKVLMDKFIRLQGDYEAIIQSV 758 (955)
Q Consensus 699 ~~~~~d------G~~-~----~v~v~~~pi~d~-~g---~v~gvv~v~~D-----ITerk~ae~~L~~se~~lr~i~e~~ 758 (955)
....++ |.. + ++.+...++.-. ++ ..+|++.+..- ||+.| +-.
T Consensus 162 vlakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteik---------------l~s-- 224 (598)
T KOG3559|consen 162 VLAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIK---------------LHS-- 224 (598)
T ss_pred hheeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEE---------------ecc--
Confidence 111111 110 0 111222222111 11 34566666432 33332 111
Q ss_pred CCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEE
Q 002191 759 NPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFF 838 (955)
Q Consensus 759 ~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~ 838 (955)
+. -+|....|-++++......+++||++.+++++.+... +|..|...+...-.-.+..|....--+|+.
T Consensus 225 Nm---FmfraslDlkliF~D~rv~qltgYepqdliektLY~~--------ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l 293 (598)
T KOG3559|consen 225 NM---FMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHH--------IHGCDSFHLRCAHHLLLVKGQVTTKYYRFL 293 (598)
T ss_pred ce---EEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHH--------hhhhhHHHHHHHHHHHHhccccccHHHHHH
Confidence 22 2667778999999999999999999999999987652 333333222222222222332333446888
Q ss_pred cCCCcEEEEEEEEeeeeCCC
Q 002191 839 NRQGQFVEVALTASRRTDAE 858 (955)
Q Consensus 839 ~~dG~~~~v~~~~~pi~d~~ 858 (955)
.+.|.+.|+....+.+.+..
T Consensus 294 ~k~ggwvwvqsyat~vHnSr 313 (598)
T KOG3559|consen 294 LKQGGWVWVQSYATFVHNSR 313 (598)
T ss_pred HcCCceEEEEEeeEEEeccc
Confidence 89999999988887776543
No 86
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=97.74 E-value=0.0023 Score=73.60 Aligned_cols=59 Identities=25% Similarity=0.279 Sum_probs=46.2
Q ss_pred HHHHHHHHHHhhhHhHhHHHHHH---HhccCCCCHHHHHHHHHHHHHHHHHHHhhccc-Cccc
Q 002191 893 IKELAYIRQEVKNPLNGIRFVHK---LLESSSISENQRQYLETSDACERQIMTIIDGM-DLRC 951 (955)
Q Consensus 893 ~~fla~iSHELRnPL~~I~g~~~---LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~DL-d~Sr 951 (955)
.+..+.+|||||+||++|..+.+ +|-+....++..+.+..|..-++||.+|...| .|+|
T Consensus 385 GQmSA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FAr 447 (603)
T COG4191 385 GQMSAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFAR 447 (603)
T ss_pred HHHHHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44567889999999999995533 33334677889999999999999999999885 4443
No 87
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=97.69 E-value=8.7e-05 Score=60.47 Aligned_cols=61 Identities=34% Similarity=0.479 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccC-CCCHHHHHHHHHHHHHHHHHHHhhcc-cCccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESS-SISENQRQYLETSDACERQIMTIIDG-MDLRC 951 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~-~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~Sr 951 (955)
.+.++.+.++||+||||++|.++.+.+... ...++...+++.+..++.++..++++ ++++|
T Consensus 3 ~~~~~~~~~~hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ 65 (65)
T cd00082 3 AKGEFLANVSHELRTPLTAIRGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLDLSR 65 (65)
T ss_pred HHHHHHHHHhHHhcchHHHHHHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 355788999999999999999988888753 33577888999999999999999999 77764
No 88
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.67 E-value=0.00051 Score=78.60 Aligned_cols=132 Identities=23% Similarity=0.284 Sum_probs=96.7
Q ss_pred ccccccccccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHH
Q 002191 599 NTQQNGSKMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVEN 678 (955)
Q Consensus 599 ~~rl~~~l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~ 678 (955)
++.+.++++++..++++..+.++.+++..+.|++.+|.+|++..+|+++++++|.+.++++|.++. .+.+. +..
T Consensus 351 L~~qq~~l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~ls-a~ap~-----~~~ 424 (712)
T COG5000 351 LSSQQEALERAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLS-AIAPE-----LEE 424 (712)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhh-hhhhH-----HHH
Confidence 444455677778888898899999999999999999999999999999999999999999999976 44332 222
Q ss_pred HHHHHHc-CCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHH
Q 002191 679 LICRALL-GEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (955)
Q Consensus 679 ~l~~~l~-~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~ 743 (955)
.+...-. .+..+..++.+ .+.|+.+.+.+..+-...+ +--|++.++.|||+...++..
T Consensus 425 vf~~~~a~~~~~~~~ev~~-----~r~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~AQRs 483 (712)
T COG5000 425 VFAEAGAAARTDKRVEVKL-----AREGEERTLNVQATREPED--NGNGYVVTFDDITDLVIAQRS 483 (712)
T ss_pred HHHHhhhhcCCCccceeec-----ccCCCceeeeeeeeecccc--cCCceEEEecchHHHHHHHHH
Confidence 3322222 23444555554 3457777777777654433 334678999999998887764
No 89
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.62 E-value=0.00095 Score=66.12 Aligned_cols=126 Identities=23% Similarity=0.309 Sum_probs=88.4
Q ss_pred chHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHH-HHHHHHHHH-cC
Q 002191 609 GVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGA-VENLICRAL-LG 686 (955)
Q Consensus 609 ~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~-~~~~l~~~l-~~ 686 (955)
...++.....++..+++..+++++.+|.+|.++++|+.+.+++|++..+..+.... .+........ ......... ..
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 181 (232)
T COG2202 103 AEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLS-DLIHPEDEERRELELARALAEGR 181 (232)
T ss_pred HHHHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChh-heEecCCCchhhHHHHHHhhccC
Confidence 35556666667899999999999999999999999999999999998887777655 4443322211 111222222 22
Q ss_pred CCcceEEEEEEeeeeccCCcE-EEEEEEEEEeecCCCCEEEEEEEEecchHhHHH
Q 002191 687 EEDKNVELKLRKFELQKQHSV-VYILVNACTSRDYKNNVKGVCFVGQDITHEKVL 740 (955)
Q Consensus 687 ~~~~~~e~~~~~~~~~~dG~~-~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~a 740 (955)
......+... ..++|.. .+......+... .|.+.++.....|++++++.
T Consensus 182 ~~~~~~~~~~----~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 182 GGPLEIEYRV----RRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred CCCcceEEEE----EecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 2233445554 5678885 777777766654 78888889999999998764
No 90
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=97.61 E-value=0.00031 Score=78.28 Aligned_cols=225 Identities=13% Similarity=0.086 Sum_probs=146.9
Q ss_pred HHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCc-ceEEEEEEe-
Q 002191 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEED-KNVELKLRK- 698 (955)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~-~~~e~~~~~- 698 (955)
+.++++....++++..+|.|-|++...+..+|+...+++.++++ +++|.+|++.+.+.+.-++.-... .......++
T Consensus 114 e~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVY-dlIHseDR~dfqrQLhwa~~ppq~~~s~q~~~e~~ 192 (712)
T KOG3560|consen 114 ELLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVY-DLIHSEDRQDFQRQLHWAMDPPQVVFSQQPPLETG 192 (712)
T ss_pred HHHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHH-HHhhhhhHHHHHHHHhhccCCchhhccCCCccccc
Confidence 55788888999999999999999999999999999999999999 999999999988877544421100 000000000
Q ss_pred ------eeeccCCc--------EEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHH----------------------
Q 002191 699 ------FELQKQHS--------VVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMD---------------------- 742 (955)
Q Consensus 699 ------~~~~~dG~--------~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~---------------------- 742 (955)
.-...|+. .+.+.++...+.|... |++. .|+-.+.+.-.
T Consensus 193 ~~~~~~~~~~~d~~ppens~yleRcficR~RCLLDnTs---GFLa--mdfqGklk~LhGqkkk~~~g~~lpP~LaLf~ia 267 (712)
T KOG3560|consen 193 DDAILRAQEWGDGTPPENSAYLERCFICRFRCLLDNTS---GFLA--MDFQGKLKFLHGQKKKAPSGAMLPPRLALFCIA 267 (712)
T ss_pred cccceeeeccCccCCcccchHHhhhheeeEEEeecCCc---ceee--eecccceeeecCCcccCCCCccCCCceeEEEEe
Confidence 00011111 2345555666665443 3222 35443221100
Q ss_pred ---------HHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhh
Q 002191 743 ---------KFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDM 813 (955)
Q Consensus 743 ---------~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~ 813 (955)
+++.- ..|+.+-+. .|+..+.+......++||...|+.|..- +.++|-+|
T Consensus 268 tP~~pPS~lEi~~k----~~i~rtKhk---------lDfa~vs~Dak~k~~lgy~eaEL~~m~g--------Y~lvH~~D 326 (712)
T KOG3560|consen 268 TPFLPPSALEIKMK----SAILRTKHK---------LDFALVSMDAKVKATLGYCEAELHGMPG--------YNLVHVED 326 (712)
T ss_pred cCCCCchhhhhhhh----hhhhhcccc---------cccceeccchhhhhhhccchhhccCCCc--------cceeehhh
Confidence 00000 112221111 1344455566677889999999998653 34778888
Q ss_pred HHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCc
Q 002191 814 LTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (955)
Q Consensus 814 ~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (955)
...+.+.-.+.++.+++--..||..+++|++.||..++.-++ .+|++-.+++.-+-.++
T Consensus 327 ~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 327 KVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred hhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee-ecCCCCEEEecCCCccc
Confidence 887888888899999898999999999999999999887665 56777766665555554
No 91
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.59 E-value=0.00056 Score=78.03 Aligned_cols=122 Identities=20% Similarity=0.344 Sum_probs=91.2
Q ss_pred hHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCch--hhcCCCccccccccccHHHHHHHHHHHHcC-
Q 002191 610 VDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPAS--EAMGKSLIDEVVHEESQGAVENLICRALLG- 686 (955)
Q Consensus 610 ~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~e--eliG~~~~~~l~~~~~~~~~~~~l~~~l~~- 686 (955)
=.|+...-++..++++++..|++.+|..|.|..+|.++++|+|+... +.+|+++. ++++|+.. +...++.
T Consensus 207 P~EIa~l~~er~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~-~v~~p~~~------l~~vl~~~ 279 (537)
T COG3290 207 PEEIATLLEERQAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIV-EVLPPDSD------LPEVLETG 279 (537)
T ss_pred HHHHHHHHHHHHHHHHHhhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccce-EeeccccC------cHHHHhcC
Confidence 35566666777899999999999999999999999999999998765 68899998 77776221 1222222
Q ss_pred CCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHH
Q 002191 687 EEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQ 748 (955)
Q Consensus 687 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se 748 (955)
....+-++++ +| .++.++..|++ .+|+++|.+.+++|-||-++..++|....
T Consensus 280 ~~~~~~e~~~-------ng--~~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~vr 331 (537)
T COG3290 280 KPQHDEEIRI-------NG--RLLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTGVR 331 (537)
T ss_pred Ccccchhhhc-------CC--eEEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHHHH
Confidence 2223333333 23 46778888988 58899999999999999998887765443
No 92
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.41 E-value=0.0025 Score=76.80 Aligned_cols=123 Identities=16% Similarity=0.244 Sum_probs=85.8
Q ss_pred hHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCc--hhhcCCCccccccccccHHHHHHHHHHHHcCC
Q 002191 610 VDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPA--SEAMGKSLIDEVVHEESQGAVENLICRALLGE 687 (955)
Q Consensus 610 ~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~--eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~ 687 (955)
..++.....+++.+++++++|++++|.+|+|+++|+++++++|++. ++++|+++. +++++... +..... .
T Consensus 214 ~~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~-~~~~~~~~------~~~~~~-~ 285 (545)
T PRK15053 214 PKQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIA-EVVRPADF------FTEQID-E 285 (545)
T ss_pred HHHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHH-HhCCCchh------hhhhcC-C
Confidence 3445555567889999999999999999999999999999999875 468899887 66654311 111111 1
Q ss_pred CcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHH
Q 002191 688 EDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGD 750 (955)
Q Consensus 688 ~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~ 750 (955)
........ .+| ..+.++..|+.. ++++.|++.+++|+|+.++.+.++...+..
T Consensus 286 ~~~~~~~~-------~~~--~~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~~~~~ 338 (545)
T PRK15053 286 KRQDVVAN-------FNG--LSVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQIKQY 338 (545)
T ss_pred cccceEEE-------ECC--EEEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHHHHHH
Confidence 11111222 134 345567778775 567789999999999998888777665543
No 93
>PRK10490 sensor protein KdpD; Provisional
Probab=97.39 E-value=0.00033 Score=88.78 Aligned_cols=67 Identities=13% Similarity=0.159 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHHhhhHhHhHHHHHHHhccC--CCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 889 IYAKIKELAYIRQEVKNPLNGIRFVHKLLESS--SISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 889 ~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~--~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
.+.+.+|++.+||||||||++|.|+.+++... ....+..+.++.+.+...++.++|++ |+++|+++|
T Consensus 661 e~lr~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~ 730 (895)
T PRK10490 661 EQLRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSG 730 (895)
T ss_pred HHHHHHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 34567899999999999999999999988642 22334456788899999999999999 899998875
No 94
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=97.39 E-value=0.00044 Score=79.24 Aligned_cols=72 Identities=11% Similarity=0.158 Sum_probs=62.2
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhcc---CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 882 QGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLES---SSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 882 q~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~---~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
.+..|+.+....+|...+||++|+||+.|.++.++|.+ ..++++.++++..+.+.+..|.+||+| +.+|++.
T Consensus 514 ~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~ 589 (750)
T COG4251 514 RRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLG 589 (750)
T ss_pred HHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 44456666666777777799999999999999999985 578899999999999999999999999 8998874
No 95
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.37 E-value=0.00084 Score=79.85 Aligned_cols=110 Identities=10% Similarity=0.105 Sum_probs=74.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHh
Q 002191 744 FIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQ 823 (955)
Q Consensus 744 L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~ 823 (955)
+++.+..+++++++++. ||+.+|.+|+|+++|++++++||++.++++|+++.+ +++ .... ..
T Consensus 75 ~e~e~~~L~aIL~sm~e---GVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~e-li~-------~~~l---~~---- 136 (520)
T PRK10820 75 SEREHRALSALLEALPE---PVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQ-LIN-------GFNF---LR---- 136 (520)
T ss_pred HHHHHHHHHHHHHhCCC---cEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHH-HcC-------cchH---HH----
Confidence 34456678899999975 699999999999999999999999999999998653 222 1111 12
Q ss_pred hhcCCCcceeeEEEEcCCCcEEEEEEEEeeee--CCCCCE--EEEEEEEeccCcc
Q 002191 824 GITGQGTENFPFGFFNRQGQFVEVALTASRRT--DAEGKV--IGCFCFMQILVPD 874 (955)
Q Consensus 824 ~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~--d~~G~v--~g~v~i~~DITer 874 (955)
.+..+...... .....+|..++ +...|+. +++|.. +|++.+++|+++.
T Consensus 137 ~le~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l 188 (520)
T PRK10820 137 WLESEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARM 188 (520)
T ss_pred HHHcCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHH
Confidence 22222221111 12234565444 5567776 666664 8999999999864
No 96
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=97.33 E-value=0.00043 Score=87.66 Aligned_cols=64 Identities=16% Similarity=0.077 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhcc-CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~-~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
++.+|++.+||||||||++|.++.+++.. ...+++..++++.|..+++++..+|++ |+++|...
T Consensus 449 ~l~~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~~~ 514 (828)
T PRK13837 449 AVGTLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRKGE 514 (828)
T ss_pred HHHHHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 55689999999999999999999998764 334567889999999999999999999 89998654
No 97
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.30 E-value=0.00036 Score=78.25 Aligned_cols=100 Identities=16% Similarity=0.227 Sum_probs=77.8
Q ss_pred CCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEE
Q 002191 771 NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALT 850 (955)
Q Consensus 771 ~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~ 850 (955)
+--|+|+|+.|+++.||.+.|++.|.-.--+. ..++.+.+..++ +++.+++.+...+|.-+..++...+|+.+.
T Consensus 39 D~PiVY~NdgFcKlsGY~RAevMQKs~tc~FM--yGEltdk~ti~k----~~~t~eN~~~~qfEillyKKN~TPvW~~vq 112 (971)
T KOG0501|consen 39 DWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFM--YGELTDKGTIEK----VRQTLENYETNQFEILLYKKNRTPVWLLVQ 112 (971)
T ss_pred ccceEEecCcchhccCccHHHHhcccceeeee--eccccchhhHHH----HHHHHHhhhhcceeeEeeecCCCceEEEEE
Confidence 45689999999999999999999886321111 112333344444 455555666778999999999999999999
Q ss_pred EeeeeCCCCCEEEEEEEEeccCcccH
Q 002191 851 ASRRTDAEGKVIGCFCFMQILVPDLQ 876 (955)
Q Consensus 851 ~~pi~d~~G~v~g~v~i~~DITerk~ 876 (955)
+.||+++...++-++|.+.|||.-||
T Consensus 113 iAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 113 IAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred eecccCCCceEEEEEeecccchhhcC
Confidence 99999999999999999999998664
No 98
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.29 E-value=0.00033 Score=57.80 Aligned_cols=43 Identities=23% Similarity=0.256 Sum_probs=36.0
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCcc
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLI 664 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~ 664 (955)
++|+.+++++|+||+++| +++|+++|+++++++||+ ..|+.+.
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~ 43 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIG 43 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHH
Confidence 468999999999999999 889999999999999998 4565543
No 99
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.13 E-value=0.02 Score=70.42 Aligned_cols=113 Identities=15% Similarity=0.222 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCC-cce
Q 002191 613 LSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEE-DKN 691 (955)
Q Consensus 613 L~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~-~~~ 691 (955)
+......+..+++++++|++++|.+|+|+++|+++++++|++.++++|+++. +++.... .+..++..+. ...
T Consensus 198 ~~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~-~l~~~~~------~l~~vl~~~~~~~~ 270 (638)
T PRK11388 198 SNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAIT-ELLTLPA------VLQQAIKQAHPLKH 270 (638)
T ss_pred HHHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHH-HHhccch------HHHHHHhcCCceee
Confidence 3344455677899999999999999999999999999999999999999987 6654221 1222333332 222
Q ss_pred EEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHH
Q 002191 692 VELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKV 739 (955)
Q Consensus 692 ~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 739 (955)
.+..+ ..+|..+++.+...|+.+..|. +++.+..|++..++
T Consensus 271 ~~~~l-----~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 271 VEVTF-----ESQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EEEEE-----ecCCceEEEEEEEEeecccCce--EEEEEehhhHHHHH
Confidence 22222 2346667888899998754443 35666778887654
No 100
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.10 E-value=0.01 Score=78.83 Aligned_cols=136 Identities=10% Similarity=-0.071 Sum_probs=77.7
Q ss_pred cccchHHHHHHHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHH---H
Q 002191 606 KMQGVDELSSVACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLIC---R 682 (955)
Q Consensus 606 l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~---~ 682 (955)
++..+.+++.....++.++++++++++++|.+|+|+++|++++++||++.....+.... . ..+...+.+..... .
T Consensus 564 r~~~~~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~ 641 (1197)
T PRK09959 564 RKVIQGDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAMLPLE-N-SDSPFKDVFSNAHEVTAE 641 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccccccc-c-ccCchhhhHhHHHHHHHH
Confidence 35567788888889999999999999999999999999999999999775443332221 1 11111111111111 1
Q ss_pred HHcCCCcceEEEEEEeeeeccCCcEEEE-EEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHH
Q 002191 683 ALLGEEDKNVELKLRKFELQKQHSVVYI-LVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQG 749 (955)
Q Consensus 683 ~l~~~~~~~~e~~~~~~~~~~dG~~~~v-~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~ 749 (955)
...........+. ..+|...++ .....+.....+...++++..+|||++++.+++++....
T Consensus 642 ~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dite~~~~~~~l~~~~~ 703 (1197)
T PRK09959 642 TKENRTIYTQVFE------IDNGIEKRCINHWHTLCNLPASDHAVYICGWQDITETRDLIHALEVERN 703 (1197)
T ss_pred HhhccccceeeEe------eecCccceeeeeeeeeeccCCCCceEEEEEEEehhHHHHHHHHHHHHHH
Confidence 1111111111111 122322222 122222222334455677888999999988877765433
No 101
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.08 E-value=0.0016 Score=73.22 Aligned_cols=116 Identities=23% Similarity=0.253 Sum_probs=83.3
Q ss_pred HHHHHHHhcC--ccEEEEc-C---CCcEeeecHHHHHHhCCCchhhcCCCccccccccc--cHHHHHHHHHHHHcCCCcc
Q 002191 619 EMVRLIETAT--APIFGVD-S---SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEE--SQGAVENLICRALLGEEDK 690 (955)
Q Consensus 619 ~l~~lie~~~--~~I~~~D-~---dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~--~~~~~~~~l~~~l~~~~~~ 690 (955)
.++.++..+. +.-|++. . |.-|+|+|+.++++.||.+.|++.++..-.+.+.+ +.+.+ +.++..+...+..
T Consensus 15 FLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti-~k~~~t~eN~~~~ 93 (971)
T KOG0501|consen 15 FLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTI-EKVRQTLENYETN 93 (971)
T ss_pred HHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhH-HHHHHHHHhhhhc
Confidence 3445554443 4444442 2 56799999999999999999999887542344432 22222 2334445445555
Q ss_pred eEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHH
Q 002191 691 NVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKV 739 (955)
Q Consensus 691 ~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ 739 (955)
.+|+-+ .+++..++|+.+...|++++.+.++-+.+.+.|||..|+
T Consensus 94 qfEill----yKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQ 138 (971)
T KOG0501|consen 94 QFEILL----YKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQ 138 (971)
T ss_pred ceeeEe----eecCCCceEEEEEeecccCCCceEEEEEeecccchhhcC
Confidence 667766 688999999999999999999999999999999999875
No 102
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=96.84 E-value=0.051 Score=67.27 Aligned_cols=203 Identities=11% Similarity=0.034 Sum_probs=116.3
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHH
Q 002191 216 AVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFK 295 (955)
Q Consensus 216 ~~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~ 295 (955)
+..+...+-+ ..|++++++.+-..++++.-+|||-|.-+|+.. +.+.-=....+-++. .| + ......
T Consensus 11 l~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~---~~----~---~~~~~~ 77 (686)
T PRK15429 11 LFDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV---KY----E---DETVLA 77 (686)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch---hc----c---chhhhc
Confidence 3344444444 569999999999999999999999999999976 555421111111110 00 0 112233
Q ss_pred hCCEEEeecCCCCCcccccccccCCccccccccccCCChhhH--HHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002191 296 QNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHL--QYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (955)
Q Consensus 296 ~~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~--~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~ 373 (955)
.+++.++-- +++|+-+++...+-..|--. .+... +++.+.|||.+.| +..|-|..-.+.
T Consensus 78 ~g~~g~vl~-------------~~~~l~~~~~~~~~~~~~l~~~~~~~~--~~~~lgvPl~~~~----~v~G~l~l~~~~ 138 (686)
T PRK15429 78 HGPVRRILS-------------RPDTLHCSYEEFCETWPQLAAGGLYPK--FGHYCLMPLAAEG----HIFGGCEFIRYD 138 (686)
T ss_pred cCcceEEee-------------cCceEEEchHHhhhccHHHhhcccccC--ccceEEeceeeCC----eeEEEEEEEEcC
Confidence 333333322 23333333322222111111 11123 3568899999998 999999998888
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH---HHHHHHHHHhhc----ccCCcccccC-CchhhhhccCC
Q 002191 374 PRYIPFPLRYACEFLVQAFSLQLYMELQVA-MQLAEKNI---LRTQVLLCDMLL----RDAPFSIVTQ-SPSIMDLVKCD 444 (955)
Q Consensus 374 pr~~~~~~r~~~~~l~~~~~~~l~~~~~~~-~~~~~~~~---~~~~~~~~~~~~----~~~~~~~~~~-~~~l~~l~~~~ 444 (955)
+..++.++..++..|+++.++.++.....+ .+.++... ......+.++.. ...+..+... ...+..+++++
T Consensus 139 ~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~eIs~~l~s~~dl~ell~~I~~~i~~~~~a~ 218 (686)
T PRK15429 139 DRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVAITNAVLSRLDMDELVSEVAKEIHYYFDID 218 (686)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhCCC
Confidence 899999999999999999999997543211 11111111 011222333221 1122222222 35677789999
Q ss_pred eEEEEE
Q 002191 445 GAALYY 450 (955)
Q Consensus 445 g~a~~~ 450 (955)
.+.|+.
T Consensus 219 ~~~I~L 224 (686)
T PRK15429 219 AISIVL 224 (686)
T ss_pred EEEEEE
Confidence 977764
No 103
>PRK10604 sensor protein RstB; Provisional
Probab=96.68 E-value=0.0027 Score=74.18 Aligned_cols=63 Identities=17% Similarity=0.278 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 888 ~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
....+.+|++.+||||||||+.|.+..++++. .+++..+ .+.+..++|..++++ +.++|++.+
T Consensus 208 ~~~~~~~l~~~vsHeLrtPL~~i~~~l~~l~~--~~~~~~~---~i~~~~~~l~~li~~ll~~~rl~~~ 271 (433)
T PRK10604 208 LIASKKQLIDGIAHELRTPLVRLRYRLEMSDN--LSAAESQ---ALNRDIGQLEALIEELLTYARLDRP 271 (433)
T ss_pred HHHHHHHHHHHhhHhhcChHHHHHHHHHHhcC--CCcHHHH---HHHHHHHHHHHHHHHHHHHHhccCC
Confidence 33466789999999999999999999999874 2333332 267778899999999 899998753
No 104
>PRK10815 sensor protein PhoQ; Provisional
Probab=96.67 E-value=0.0034 Score=74.35 Aligned_cols=63 Identities=16% Similarity=0.083 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHhhhHhHhHHHHHHHhccCC-CCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLESSS-ISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 890 ~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~-l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
....+|++.+||||||||+.|.+..+.|.... .+.+ +....+.+...++.++|++ |++++.++
T Consensus 264 ~~~~~~l~~isHELRTPLt~I~~~l~~L~~~~~~~~~--~~~~~~~~~i~ri~~~i~~ll~~~~~~~ 328 (485)
T PRK10815 264 TKYRTTLTDLTHSLKTPLAVLQSTLRSLRSGKQMSVE--QAEPIMLEQISRISQQIGYYLHRASMRS 328 (485)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34567899999999999999999999887533 3332 2334456667788888888 77766554
No 105
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=96.58 E-value=0.0026 Score=52.34 Aligned_cols=36 Identities=19% Similarity=0.279 Sum_probs=31.1
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCC
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWM 788 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~ 788 (955)
++|+.++++++. ||+++| +++|+++|+++++++||+
T Consensus 1 e~~~~l~~~~~~---~i~i~d-~~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 1 ERYRSLFDNSPD---GILIID-GGRIIYVNPAFEELFGYS 36 (64)
T ss_dssp HHHHHHHCCSSS---EEEEEE-TSBEEEE-HHHHHHHCS-
T ss_pred CHHHHHHHcCcc---ceEEEE-CCChHHhhHHHHHHhCCC
Confidence 478999999985 599999 889999999999999998
No 106
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.57 E-value=0.0056 Score=66.81 Aligned_cols=115 Identities=20% Similarity=0.165 Sum_probs=90.1
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEE
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLR 697 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~ 697 (955)
+++.+++++.|.-|-.+|.++++.++|.. .++|-.++..+ |++.. ...+|.+...+...+.....|... ..++-+
T Consensus 290 ~e~naif~~lP~Ditfvdk~diV~ffs~~-~rif~rt~svi-Gr~v~-~chpPksv~iv~ki~~~fksG~kd-~~efw~- 364 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKNDIVRFFSGG-ERIFPRTPSVI-GRRVQ-LCHPPKSVHIVEKILKDFKSGEKD-FAEFWI- 364 (409)
T ss_pred HHHHHHHhhCCCceEEecccceEEecCCc-ceecccChHhh-CCccc-CCCCCchHHHHHHHHHHhhcCCcc-hHHHhc-
Confidence 56789999999999999999999999988 88998888765 99987 666677777777777776666543 222222
Q ss_pred eeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHH
Q 002191 698 KFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDK 743 (955)
Q Consensus 698 ~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~ 743 (955)
+ .....+.++..+++|++|+..|++-+.+|||..|..+-+
T Consensus 365 ----~--~~~~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ge 404 (409)
T COG2461 365 ----N--MGDKFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELEGE 404 (409)
T ss_pred ----c--CCCceEEEEEEEEEcCCCceeeeehhhhhhHHHHhccch
Confidence 1 223467788899999999999999999999998876643
No 107
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.56 E-value=0.0023 Score=69.71 Aligned_cols=115 Identities=15% Similarity=0.103 Sum_probs=88.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHH
Q 002191 741 MDKFIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMIL 820 (955)
Q Consensus 741 e~~L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~ 820 (955)
.-+++.....|.++ +.... +|-+.|.+..|.|+|++|++++||-..|++|+...+. ......+..+...
T Consensus 150 afkiRAcnalFaaL-D~c~e---AiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adl-------pkkdknradlldt 218 (775)
T KOG1229|consen 150 AFKIRACNALFAAL-DECDE---AIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADL-------PKKDKNRADLLDT 218 (775)
T ss_pred HHHHhhhHHHHHHH-hhhhh---hheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhc-------cccccchhhhhhh
Confidence 33444444444333 33343 4888999999999999999999999999999986642 1223345557778
Q ss_pred HHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEE
Q 002191 821 LYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFC 866 (955)
Q Consensus 821 l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~ 866 (955)
++..++.+..+..++.-+++.|......+..+|+.+..|++..++.
T Consensus 219 intcikkgke~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfvs 264 (775)
T KOG1229|consen 219 INTCIKKGKEAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFVS 264 (775)
T ss_pred hhHhhhcCccccchHHHhhccCCcccceEEEeeecCCCCceeeehh
Confidence 8889998889999998899999998888999999999999887664
No 108
>PRK10364 sensor protein ZraS; Provisional
Probab=96.51 E-value=0.0063 Score=71.63 Aligned_cols=62 Identities=16% Similarity=0.205 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhcc-CCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLES-SSISENQRQYLETSDACERQIMTIIDG-MDLRCI 952 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~-~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrI 952 (955)
...++.+.++||+||||++|.++.+++.. ...+++.+++++.+.+..+++..++++ ++++|.
T Consensus 236 ~~~~~~~~laHelrtpL~~i~~~~~~l~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~ll~~~~~ 299 (457)
T PRK10364 236 ALGHLAAGVAHEIRNPLSSIKGLAKYFAERAPAGGEAHQLAQVMAKEADRLNRVVSELLELVKP 299 (457)
T ss_pred HHHHHHHHhhHHhccHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 44578899999999999999999999875 334466778899999999999999999 788764
No 109
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=96.50 E-value=0.009 Score=45.94 Aligned_cols=63 Identities=32% Similarity=0.481 Sum_probs=52.4
Q ss_pred HHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHH
Q 002191 619 EMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICR 682 (955)
Q Consensus 619 ~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~ 682 (955)
+++.+++.++++++.+|.++.+.++|+.+..++|++..++.|+.+. .+.++.+...+...+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 64 (67)
T smart00091 2 RLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLL-ELIHPEDREEVQEALQR 64 (67)
T ss_pred hHHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHH-HhcCcccHHHHHHHHHH
Confidence 3567889999999999999999999999999999999999998877 77777766655554443
No 110
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=96.31 E-value=0.16 Score=63.02 Aligned_cols=152 Identities=16% Similarity=0.099 Sum_probs=90.6
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHh
Q 002191 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (955)
Q Consensus 217 ~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~ 296 (955)
.+..++|.+ +.+.+++++.+++.+.+++++++..+|-.++|+ +....... .+++. .+...|. +.|-. ..+-..
T Consensus 308 l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~~-~~~~~~~~-~~~~~-~~~~~~~-~~~~~-~~~~~~ 380 (679)
T TIGR02916 308 LRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGND-GLYRPAAR-WNQPL-AQAFEPS-DSAFC-QFLQES 380 (679)
T ss_pred HHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCCC-CEEeeehh-cCCCC-cccCCCC-CCHHH-HHHHhC
Confidence 456677776 568999999999999999999999999665544 43333321 11111 1112222 22211 112222
Q ss_pred CCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC-CC
Q 002191 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS-PR 375 (955)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~-pr 375 (955)
+++--+.+....|. .. ++.+..+..+...++.+.+||..+| ++.|.+.+.+.. ++
T Consensus 381 ~~v~~~~~~~~~~~--~~------------------~~~~~~~~~~~~~~~~l~vPL~~~~----~~~G~l~l~~~~~~~ 436 (679)
T TIGR02916 381 GWIINLEEARSEPD--HY------------------SGLVLPEWLREIPNAWLIVPLISGE----ELVGFVVLARPRTAG 436 (679)
T ss_pred CCcccchhhcCCcc--cc------------------cccccchhhhcCCCceEEEEeccCC----EEEEEEEEecCCCCC
Confidence 33322122111111 00 0000111222234678999999888 999999987764 77
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHH
Q 002191 376 YIPFPLRYACEFLVQAFSLQLYME 399 (955)
Q Consensus 376 ~~~~~~r~~~~~l~~~~~~~l~~~ 399 (955)
.++++++...+.++.+++..++..
T Consensus 437 ~~~~e~~~lL~~l~~q~a~~l~~~ 460 (679)
T TIGR02916 437 EFNWEVRDLLKTAGRQAASYLAQM 460 (679)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 889999999999999999888654
No 111
>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=96.28 E-value=0.064 Score=51.85 Aligned_cols=109 Identities=13% Similarity=0.026 Sum_probs=83.5
Q ss_pred HHHHHHHhcCccEEEEcC--CCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEE-EE
Q 002191 619 EMVRLIETATAPIFGVDS--SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVE-LK 695 (955)
Q Consensus 619 ~l~~lie~~~~~I~~~D~--dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e-~~ 695 (955)
.++.+++ .|.+|+..+. +-.++|.|.++.++++++-+++.+.+.. ....+..++.....+.++.+.+-..++. ++
T Consensus 33 ~~~~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 33 LAKALWH-APFAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSR-LSAEEPERKERQSLLAQVMQQGYIDNYSGIR 110 (148)
T ss_pred HHHHHHc-CCCEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHh-hccChhhHHHHHHHHHHHHHhCCccCCCeEE
Confidence 3455555 8999998875 5599999999999999999999999987 5666777777788888888776654432 22
Q ss_pred EEeeeeccCCcEEEEE-EEEEEeecCCCCEEEEEEEEecc
Q 002191 696 LRKFELQKQHSVVYIL-VNACTSRDYKNNVKGVCFVGQDI 734 (955)
Q Consensus 696 ~~~~~~~~dG~~~~v~-v~~~pi~d~~g~v~gvv~v~~DI 734 (955)
..+.|+.++++ ..+-.+.|++|...|...++.+-
T Consensus 111 -----iss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~W 145 (148)
T PF08670_consen 111 -----ISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSNW 145 (148)
T ss_pred -----EcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEeee
Confidence 46778877765 34556789999999988877653
No 112
>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase. This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase.
Probab=96.18 E-value=0.014 Score=72.21 Aligned_cols=68 Identities=15% Similarity=0.245 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 887 MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 887 ~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
+......++.+.++||+||||+.|.+..+.+.....+++..++++.+..+++++..++++ ++++|+|.
T Consensus 480 ~~~~~l~~~s~~lSHELrtPL~~I~~~le~L~~~~~~~~~~~~le~i~~~i~~L~~li~~l~~~arle~ 548 (703)
T TIGR03785 480 QYTHYLENMSSRLSHELRTPVAVVRSSLENLELQALEQEKQKYLERAREGTERLSMILNNMSEATRLEQ 548 (703)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 334455678899999999999999999999987777888888999999999999999999 78888764
No 113
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=95.95 E-value=0.013 Score=67.93 Aligned_cols=100 Identities=18% Similarity=0.179 Sum_probs=80.5
Q ss_pred EEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEE
Q 002191 631 IFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYI 710 (955)
Q Consensus 631 I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v 710 (955)
+...+.|-+|+||.+++.+++||.+++++|++++ +++|..|.+.+..-...++..+....-.+++ ..+.|+.+|+
T Consensus 277 vtRhs~DmkityCedRisdlm~y~PeeLvGrS~Y-e~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~----lak~GGyvWl 351 (768)
T KOG3558|consen 277 VTRHSLDMKITYCEDRISDLMDYEPEELVGRSCY-EFVHALDSDRVRKSHHDLLTKGQVVTGYYRL----LAKNGGYVWL 351 (768)
T ss_pred EEeeecceeEEEEchhHHHHhcCCHHHhhchhHH-HhhhHhhhhHHHHHHHHHHhcCccchhHHHH----HHhcCCeEEE
Confidence 3345678899999999999999999999999999 9999999999999888888887776666676 7899999999
Q ss_pred EEEEEEeecCCC-CEEEEEEEEecch
Q 002191 711 LVNACTSRDYKN-NVKGVCFVGQDIT 735 (955)
Q Consensus 711 ~v~~~pi~d~~g-~v~gvv~v~~DIT 735 (955)
...++.+.+..+ +...+++|..=|+
T Consensus 352 QTqATVi~~tkn~q~q~IicVnYVlS 377 (768)
T KOG3558|consen 352 QTQATVIYNTKNPQEQNIICVNYVLS 377 (768)
T ss_pred EeeeEEEecCCCCCcceEEEEEeeec
Confidence 999988876532 3333444443333
No 114
>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=95.75 E-value=0.047 Score=50.52 Aligned_cols=62 Identities=18% Similarity=0.267 Sum_probs=52.4
Q ss_pred HHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc
Q 002191 624 IETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL 685 (955)
Q Consensus 624 ie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~ 685 (955)
++..|-|++-+|.+|+|+..|.+-..+.|++++.++|+++..++.+-.....+...+....+
T Consensus 22 lD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~ 83 (124)
T TIGR02373 22 FDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVA 83 (124)
T ss_pred hhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhh
Confidence 78899999999999999999999999999999999999988667666666656655555443
No 115
>PRK10337 sensor protein QseC; Provisional
Probab=95.72 E-value=0.025 Score=66.34 Aligned_cols=64 Identities=13% Similarity=0.207 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHH-HHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~-~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
...+|++.++||+||||+.|.+..+.+.....+++ ...+++.+...++++..++++ ++++|++.
T Consensus 236 ~~~~~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~~~ 301 (449)
T PRK10337 236 RERRFTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRLDS 301 (449)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 34568999999999999999988887765444443 567899999999999999999 89988764
No 116
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=95.67 E-value=0.023 Score=62.97 Aligned_cols=61 Identities=13% Similarity=0.268 Sum_probs=47.6
Q ss_pred HHHHHHHHHhhhHhHhHHHH---HHHhccCCCCHHHHHHHHHHHHHHHHHHHhhccc-Ccccccc
Q 002191 894 KELAYIRQEVKNPLNGIRFV---HKLLESSSISENQRQYLETSDACERQIMTIIDGM-DLRCIEE 954 (955)
Q Consensus 894 ~fla~iSHELRnPL~~I~g~---~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~DL-d~SrIea 954 (955)
+-+..++|||+.|||++..+ ..+.-...-+.....++++|+.-.+|+.+||+.| .|+|=.+
T Consensus 453 qTmTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s 517 (673)
T COG4192 453 QTMTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNS 517 (673)
T ss_pred HHHHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 34567799999999999844 4444344667778899999999999999999984 7776443
No 117
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=95.53 E-value=0.087 Score=65.37 Aligned_cols=55 Identities=15% Similarity=0.259 Sum_probs=44.3
Q ss_pred HHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHH-HHHHHHHHHHHHHHHHHhhccc
Q 002191 893 IKELAYIRQEVKNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDGM 947 (955)
Q Consensus 893 ~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~-~~~~l~~i~~~a~rl~~LI~DL 947 (955)
.++.+.++||||||++.+....+.++....+++ ..++++.+.++.+++.+++++|
T Consensus 476 ~~~~a~i~HdLrn~l~~l~~~l~~~~~~~~~~~~~~~~l~~i~~~~~rl~~ll~~l 531 (679)
T TIGR02916 476 NRMSAFVVHDLKNLVAQLSLLLRNAERHKDNPEFQDDMLETVENAVNRMKKLLAQL 531 (679)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556788999999999999888777665444444 6678899999999999998873
No 118
>PRK09467 envZ osmolarity sensor protein; Provisional
Probab=95.37 E-value=0.034 Score=64.86 Aligned_cols=63 Identities=14% Similarity=0.190 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 886 DMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 886 E~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
++..+.+..|++.+||||||||+.|.+..+++... .....+.+....++|..++++ +++.|.+
T Consensus 223 ~~~~~~~~~~~~~lsHeLrtPL~~i~~~~e~~~~~-----~~~~~~~i~~~~~~~~~~i~~~l~~~r~~ 286 (435)
T PRK09467 223 KQLEDDRTLLMAGVSHDLRTPLTRIRLATEMMSEE-----DGYLAESINKDIEECNAIIEQFIDYLRTG 286 (435)
T ss_pred HHHHHHHHHHHHHhhhhccchHHHHHHHHHhcccc-----hHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34445677899999999999999999888877531 223445677788889999988 7777654
No 119
>PRK09835 sensor kinase CusS; Provisional
Probab=95.11 E-value=0.054 Score=64.05 Aligned_cols=67 Identities=10% Similarity=0.095 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccC-CCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESS-SISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 888 ~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~-~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
....+.+|++.++|||||||+.|.+..+.+... ....+..+.+..+.....++..++++ ++++|++.
T Consensus 258 ~~~~~~~~~~~laheL~tpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~ll~~~~~~~ 326 (482)
T PRK09835 258 VFTRQSNFSADIAHEIRTPITNLITQTEIALSQSRSQKELEDVLYSNLEELTRMAKMVSDMLFLAQADN 326 (482)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 334567889999999999999999888876542 33344667777777788899999999 88888765
No 120
>TIGR01386 cztS_silS_copS heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.
Probab=95.04 E-value=0.047 Score=63.99 Aligned_cols=65 Identities=15% Similarity=0.150 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHhhhHhHhHHHHHHHhccCC-CCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 890 YAKIKELAYIRQEVKNPLNGIRFVHKLLESSS-ISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 890 ~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~-l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
....++.+.++||+||||+.+.+..+++.... ..++..++++.+.....++.+++++ |+++++|.
T Consensus 239 ~~~~~~~~~~~h~l~tpl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~ll~~~~~~~ 305 (457)
T TIGR01386 239 QRLSQFSADLAHELRTPLTNLLGQTQVALSQPRTGEEYREVLESNLEELERLSRMVSDMLFLARADN 305 (457)
T ss_pred HHHHHHHHhhhhhhcCcHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34556889999999999999998888875433 3455677888888889999999999 88888764
No 121
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=95.00 E-value=0.042 Score=64.50 Aligned_cols=64 Identities=17% Similarity=0.270 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 887 MDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 887 ~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
+....+.+|++.+|||+||||+.|.+...++.....+. ..+..+...++++.++|++ ++++|.+
T Consensus 238 ~~~~~~~~~~~~~shel~tpl~~i~~~~~~~~~~~~~~---~~~~~i~~~~~~l~~~i~~l~~~~~~~ 302 (461)
T PRK09470 238 RMMTSQQRLLSDISHELRTPLTRLQLATALLRRRQGES---KELERIETEAQRLDSMINDLLVLSRNQ 302 (461)
T ss_pred HHHHHHHHHHHhhhHhhCCHHHHHHHHHHHHhhccCCh---HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33345567899999999999999999988887643332 2456677889999999999 8888864
No 122
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=94.99 E-value=0.05 Score=61.67 Aligned_cols=58 Identities=24% Similarity=0.264 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIE 953 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIe 953 (955)
.+.+|++.++|||||||++|.+..+++.... .++... +....+++..++++ ++++|.+
T Consensus 136 ~~~~~~~~~sHelrtPL~~i~~~~e~l~~~~-~~~~~~----~~~~~~~l~~~i~~ll~~~r~~ 194 (356)
T PRK10755 136 QERLFTADVAHELRTPLAGIRLHLELLEKQH-HIDVAP----LIARLDQMMHTVEQLLQLARAG 194 (356)
T ss_pred HHHHHHHHhhHhhcChHHHHHHHHHHHHhcc-chhHHH----HHHHHHHHHHHHHHHHHHHHcc
Confidence 4456899999999999999999999887532 222222 23334566667777 6666643
No 123
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=94.86 E-value=0.049 Score=64.17 Aligned_cols=64 Identities=20% Similarity=0.324 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
...++++.++||+|||++.|.+..+++......++..++++.+...++++..++++ +++++++.
T Consensus 255 ~~~~~~~~~~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~ 319 (475)
T PRK11100 255 YVEQYVQTLTHELKSPLAAIRGAAELLQEDPPPEDRARFTGNILTQSARLQQLIDRLLELARLEQ 319 (475)
T ss_pred HHHHHHHHhhhhhcCcHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34568899999999999999999999887545666888999999999999999999 78877654
No 124
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=94.83 E-value=0.045 Score=64.44 Aligned_cols=67 Identities=16% Similarity=0.233 Sum_probs=51.8
Q ss_pred HHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 888 DIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 888 ~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
....+.++++.++||++|||+.|.+..+.+.. ...+...+.+..+...++++..++++ +++++.+.|
T Consensus 236 ~~~~~~~~~~~~shel~~pL~~i~~~~~~l~~-~~~~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~ 303 (466)
T PRK10549 236 NEQMRRDFMADISHELRTPLAVLRGELEAIQD-GVRKFTPESVASLQAEVGTLTKLVDDLHQLSLSDEG 303 (466)
T ss_pred HHHHHHHHHHHHhHHhCChHHHHHHHHHHHHh-ccccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence 34456689999999999999999999998875 23333455677888888999999998 677766543
No 125
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=94.68 E-value=0.61 Score=45.19 Aligned_cols=110 Identities=14% Similarity=0.027 Sum_probs=79.0
Q ss_pred HHHHHHHHhcCCCCCCeeeec--CCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhc
Q 002191 749 GDYEAIIQSVNPLIPPIFASD--ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT 826 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D--~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~ 826 (955)
..++.+.+. | ++|+..+ .+-.++|.|.++.++|+++-+++.+.+..- ...+.+++.....+.++..
T Consensus 32 ~~~~~L~~a-p---~ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr~--------sae~~~r~er~~lL~~v~~ 99 (148)
T PF08670_consen 32 ELAKALWHA-P---FAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSRL--------SAEEPERKERQSLLAQVMQ 99 (148)
T ss_pred HHHHHHHcC-C---CEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHhh--------ccChhhHHHHHHHHHHHHH
Confidence 445666663 3 2466654 456899999999999999999999987431 2224445555666777777
Q ss_pred CCCcceeeEEEEcCCCcEEEEE-EEEeeeeCCCCCEEEEEEEEec
Q 002191 827 GQGTENFPFGFFNRQGQFVEVA-LTASRRTDAEGKVIGCFCFMQI 870 (955)
Q Consensus 827 g~~~~~~e~~~~~~dG~~~~v~-~~~~pi~d~~G~v~g~v~i~~D 870 (955)
.+-...+.-.-..+.|+.+++. ..+-.+.|++|...|...++.+
T Consensus 100 qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 100 QGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAMFSN 144 (148)
T ss_pred hCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEEEee
Confidence 7766666656678899988775 4567889999999987766554
No 126
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=94.37 E-value=0.22 Score=33.79 Aligned_cols=40 Identities=20% Similarity=0.390 Sum_probs=35.1
Q ss_pred eEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCc
Q 002191 834 PFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVP 873 (955)
Q Consensus 834 e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITe 873 (955)
++.+...+|..+|+.....++.+.+|.+.+++++..|||+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 4566778999999999999999988999999999999986
No 127
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=94.33 E-value=0.41 Score=51.16 Aligned_cols=111 Identities=15% Similarity=0.096 Sum_probs=78.8
Q ss_pred HHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCC-CcceEEEEEEee
Q 002191 621 VRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGE-EDKNVELKLRKF 699 (955)
Q Consensus 621 ~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~-~~~~~e~~~~~~ 699 (955)
..++++.+.+++++|.+|.|.|+|++++.+||.+...+.|.++. .+++.... ....+.+....+ ....++..+
T Consensus 10 ~~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~-~l~~~gs~--ll~ll~q~~~~~~~~~~~~v~l--- 83 (363)
T COG3852 10 GAILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLS-ELLPFGSL--LLSLLDQVLERGQPVTEYEVTL--- 83 (363)
T ss_pred HhHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChH-HHcCCCcH--HHHHHHHHHHhcCCcccceeee---
Confidence 36789999999999999999999999999999999999999987 77665432 233444444333 333444444
Q ss_pred eeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHH
Q 002191 700 ELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMD 742 (955)
Q Consensus 700 ~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~ 742 (955)
..+|....+.....|+....|-++ ..++-+....+...
T Consensus 84 --~~~g~~~~v~~~v~~v~~~~G~vl---le~~~~~~~~ridr 121 (363)
T COG3852 84 --VILGRSHIVDLTVAPVPEEPGSVL---LEFHPRDMQRRLDR 121 (363)
T ss_pred --eecCccceEEEEEeeccCCCCeEE---EEechhHHHhHhhH
Confidence 257889999999999987666543 44445554444433
No 128
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=94.04 E-value=2.3 Score=42.96 Aligned_cols=126 Identities=12% Similarity=0.172 Sum_probs=90.9
Q ss_pred CHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCC
Q 002191 230 DIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIP 309 (955)
Q Consensus 230 ~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~ 309 (955)
++....+.+++-+.+.||+ -|+|-- .-.|+|=+ ..+-.. |-|.+ +.+..++.+..+++.+..+.....
T Consensus 53 ~~~~~A~~~aeII~~~t~~-aVaITD-----r~~ILA~~-G~g~d~----~~~~~-is~~t~~~i~~gk~~~~~~~~~~~ 120 (180)
T TIGR02851 53 ELGDFAKEYAESLYQSLGH-IVLITD-----RDTVIAVA-GVSKKE----YLNKP-ISDELEDTMEERKTVILSDTKDGP 120 (180)
T ss_pred chHHHHHHHHHHHHHHhCC-EEEEEC-----CCcEEEEE-CCChhh----cCCCc-cCHHHHHHHHcCCEEEecCCccce
Confidence 5677778888889999999 888862 33566644 222222 33444 999999999999999998744222
Q ss_pred cccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCC--CCChhHHHHHHH
Q 002191 310 VMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPR--YIPFPLRYACEF 387 (955)
Q Consensus 310 ~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr--~~~~~~r~~~~~ 387 (955)
+++... .+....+.+++||+.+| +.=|.|... ...+ .++..++.+.+-
T Consensus 121 i~c~~~-------------------------~~~~l~s~ii~Pl~~~g----~viGtLkly-~k~~~~~~~~~e~~la~g 170 (180)
T TIGR02851 121 IEIIDG-------------------------QEFEYTSQVIAPIIAEG----DPIGAVIIF-SKEPGEKLGEVEQKAAET 170 (180)
T ss_pred eccccC-------------------------CCCCcceEEEEEEEECC----eEEEEEEEE-ECCccCCCCHHHHHHHHH
Confidence 322100 12224789999999998 999987777 6566 788999999999
Q ss_pred HHHHHHHHHH
Q 002191 388 LVQAFSLQLY 397 (955)
Q Consensus 388 l~~~~~~~l~ 397 (955)
||+.||.||+
T Consensus 171 lA~lLS~QLE 180 (180)
T TIGR02851 171 AAAFLGKQME 180 (180)
T ss_pred HHHHHHHhhC
Confidence 9999999873
No 129
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=94.02 E-value=0.1 Score=57.30 Aligned_cols=114 Identities=15% Similarity=0.119 Sum_probs=78.1
Q ss_pred HHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcC
Q 002191 748 QGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (955)
Q Consensus 748 e~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g 827 (955)
...+.++++..|.- |-.+|.++++.++|+. .++|-+++ .++|+.... ..+|.....+...+. .+..
T Consensus 289 ~~e~naif~~lP~D---itfvdk~diV~ffs~~-~rif~rt~-sviGr~v~~--------chpPksv~iv~ki~~-~fks 354 (409)
T COG2461 289 LEELNAIFKHLPVD---ITFVDKNDIVRFFSGG-ERIFPRTP-SVIGRRVQL--------CHPPKSVHIVEKILK-DFKS 354 (409)
T ss_pred HHHHHHHHhhCCCc---eEEecccceEEecCCc-ceecccCh-HhhCCcccC--------CCCCchHHHHHHHHH-Hhhc
Confidence 34577899998732 6778999999999998 88887776 456887542 122333333333333 3444
Q ss_pred CCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccHHH
Q 002191 828 QGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQPA 878 (955)
Q Consensus 828 ~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~~e 878 (955)
|.....++. .+..+ ..+.++..+++|++|+..|++-+.+|||.-++.+
T Consensus 355 G~kd~~efw-~~~~~--~~i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 355 GEKDFAEFW-INMGD--KFIHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred CCcchHHHh-ccCCC--ceEEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 445666665 33333 3566778889999999999999999999855443
No 130
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=93.79 E-value=0.19 Score=38.10 Aligned_cols=45 Identities=33% Similarity=0.397 Sum_probs=37.5
Q ss_pred HHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCcc
Q 002191 751 YEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (955)
Q Consensus 751 lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (955)
++.+++..+. +++.+|.++.+.++|+.+.+++|++..++.++.+.
T Consensus 3 ~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (67)
T smart00091 3 LRAILESLPD---GIFVLDLDGRILYANPAAEELLGYSPEELIGKSLL 47 (67)
T ss_pred HHHHHhhCCc---eEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHH
Confidence 4567777664 58999999999999999999999999888887543
No 131
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=93.71 E-value=0.96 Score=58.06 Aligned_cols=115 Identities=15% Similarity=0.109 Sum_probs=69.6
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEc-CCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcC
Q 002191 608 QGVDELSSVACEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLG 686 (955)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D-~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~ 686 (955)
+...+|++.++.++.+++++|.++++++ .+|.++.+|+.+..++|+...+. ...+.. ....
T Consensus 324 ~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~~--------------~~~~~~----~~~~ 385 (924)
T PRK10841 324 SNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHED--------------RQRLTQ----IICG 385 (924)
T ss_pred HHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChhH--------------HHHHHH----HHhc
Confidence 3455788888889999999999999997 69999999999999888643221 111111 1111
Q ss_pred CCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHH
Q 002191 687 EEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGD 750 (955)
Q Consensus 687 ~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~ 750 (955)
......+ . ...++....+. ....+. .+.. ..++++.|||+++++++++++..+.
T Consensus 386 ~~~~~~~--~----~~~~~~~~~i~--~~~~~~-~~~~-~~i~~~~Dit~r~~~e~~L~~~~~~ 439 (924)
T PRK10841 386 QQVNFVD--V----LTSNNTNLQIS--FVHSRY-RNEN-VAICVLVDVSARVKMEESLQEMAQA 439 (924)
T ss_pred cccceee--E----EcCCCcEEEEE--EEeeee-cCce-EEEEEEEEhhHHHHHHHHHHHHHHH
Confidence 1111111 1 12234333333 333222 2222 3467788999999999888765443
No 132
>PRK11644 sensory histidine kinase UhpB; Provisional
Probab=93.25 E-value=0.28 Score=58.32 Aligned_cols=59 Identities=7% Similarity=0.120 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCC-CHHHHHHHHHHHHHHHHHHHhhcc-cCc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSI-SENQRQYLETSDACERQIMTIIDG-MDL 949 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l-~~~~~~~l~~i~~~a~rl~~LI~D-Ld~ 949 (955)
.+.++.+.++||++|||++|.+..+++++... +++..+..+.+++.+.++.+.+++ ++.
T Consensus 301 ~r~~ia~elhdeI~~pLtaI~~~a~ll~~~~~~~~~~~~~~~~I~~~~~~l~~~vr~LL~~ 361 (495)
T PRK11644 301 VRRDVARELHDEIGQTITAIRTQAGIIKRLAADNASVKQSAQLIEQLSLGVYDTVRRLLGR 361 (495)
T ss_pred HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34567788899999999999999999876433 344667888888888888888887 543
No 133
>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=93.14 E-value=0.48 Score=44.04 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=40.1
Q ss_pred HHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcc
Q 002191 755 IQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFG 803 (955)
Q Consensus 755 ~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~ 803 (955)
++.+| -|++-+|.+|+|+..|.+-.++.|++++.++|+++..++-+
T Consensus 22 lD~lp---FGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAP 67 (124)
T TIGR02373 22 FDALP---FGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAP 67 (124)
T ss_pred hhcCC---cceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhccc
Confidence 45554 47999999999999999999999999999999998776655
No 134
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=93.14 E-value=0.069 Score=58.58 Aligned_cols=104 Identities=11% Similarity=0.099 Sum_probs=75.5
Q ss_pred HHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccc-cHHHHHHHHHHHHcCCCcceEEEEEEe
Q 002191 620 MVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEE-SQGAVENLICRALLGEEDKNVELKLRK 698 (955)
Q Consensus 620 l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~-~~~~~~~~l~~~l~~~~~~~~e~~~~~ 698 (955)
+-..++....+|-+.|.+..|.|+|+++++++|+...|++|+... ++-..+ .+..+.+.+...+..+..+..+...
T Consensus 159 lFaaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~a-dlpkkdknradlldtintcikkgke~qG~~~a-- 235 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEA-DLPKKDKNRADLLDTINTCIKKGKEAQGEEEA-- 235 (775)
T ss_pred HHHHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchh-hccccccchhhhhhhhhHhhhcCccccchHHH--
Confidence 345678888899999999999999999999999999999999987 554332 2334445555555555444333333
Q ss_pred eeeccCCcEEEEEEEEEEeecCCCCEEEEE
Q 002191 699 FELQKQHSVVYILVNACTSRDYKNNVKGVC 728 (955)
Q Consensus 699 ~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv 728 (955)
+++.|......+...|+....|++..++
T Consensus 236 --RRksgdS~dqh~~itP~~gqggkirhfv 263 (775)
T KOG1229|consen 236 --RRKSGDSCDQHFIITPFAGQGGKIRHFV 263 (775)
T ss_pred --hhccCCcccceEEEeeecCCCCceeeeh
Confidence 5677777777777888888888776554
No 135
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=92.46 E-value=0.66 Score=55.59 Aligned_cols=199 Identities=15% Similarity=0.215 Sum_probs=112.4
Q ss_pred cEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHc-------CC--------CcceEEE
Q 002191 630 PIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALL-------GE--------EDKNVEL 694 (955)
Q Consensus 630 ~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~-------~~--------~~~~~e~ 694 (955)
.+++-+.+|+|+|+...+..++|+.++-+.+..|. +++++.+...+...+....- +. ....+..
T Consensus 194 ~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~Fv-dflapqD~~vF~sfta~~~lp~ws~~s~~ds~~~~c~~~ks~fc 272 (1114)
T KOG3753|consen 194 VVAVSFLDGRILYISEQAALILGCKRDVLSSAKFV-DFLAPQDVGVFYSFTARYKLPLWSMGSSADSFTQECAEEKSFFC 272 (1114)
T ss_pred EEEEeccCCcEEEeechhhhhccCchhhhccchhh-hhcchhhhhhhhhccccccCccccccccccchhhhhhhhcceee
Confidence 34455679999999999999999999999999999 99999887766554432210 00 0011111
Q ss_pred EEEeeeeccCCcEEEEEEEE----EEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCCCCeeeec-
Q 002191 695 KLRKFELQKQHSVVYILVNA----CTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLIPPIFASD- 769 (955)
Q Consensus 695 ~~~~~~~~~dG~~~~v~v~~----~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~id~I~~~D- 769 (955)
++.. +.......++--++. +-+++..|-..+.+.+. +- .++..-|++= ...+.- -||.+-
T Consensus 273 Risg-r~~~~~~~~y~PFRl~pyl~ev~~~~~~~s~~ccLl--la---------erihSgYeAP-rIps~K--riFtT~H 337 (1114)
T KOG3753|consen 273 RISG-RKDRENEIRYHPFRLTPYLVEVRDQQGAESQPCCLL--LA---------ERIHSGYEAP-RIPSNK--RIFTTTH 337 (1114)
T ss_pred eeec-ccCCcCccccCcccccceeEEeccccccCcCcceee--hh---------hhhhcccccC-cCCccc--ceeEecc
Confidence 1110 000011111111111 11222111111111111 00 0112222211 111111 255544
Q ss_pred -CCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhc-CCCc--ceeeEEEEcCCCcEE
Q 002191 770 -ENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGIT-GQGT--ENFPFGFFNRQGQFV 845 (955)
Q Consensus 770 -~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~-g~~~--~~~e~~~~~~dG~~~ 845 (955)
..+-+..+..++.-++||=+.++||+.+.. +.|++|+..+.+...++++ ++.+ ..-.+||...+|.++
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil~--------f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv 409 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSILA--------FVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYV 409 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchhh--------hhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEE
Confidence 456677889999999999999999998764 5678887777776666665 3333 345678999999998
Q ss_pred EEEEEEe
Q 002191 846 EVALTAS 852 (955)
Q Consensus 846 ~v~~~~~ 852 (955)
.+....+
T Consensus 410 ~ldTeWS 416 (1114)
T KOG3753|consen 410 RLDTEWS 416 (1114)
T ss_pred EEechhh
Confidence 7765543
No 136
>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=92.38 E-value=0.18 Score=55.32 Aligned_cols=63 Identities=30% Similarity=0.449 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCcccccc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEE 954 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIea 954 (955)
.+..+++.++||+|||++.+.+..+++.... .+...+++..+....+++..++++ +++++++.
T Consensus 114 ~~~~~~~~~~hel~~pl~~i~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~ 177 (336)
T COG0642 114 AKREFLANISHELRTPLTAIRGLLELLLEGL-LDPQRELLEIIEEEAERLLRLVNDLLDLSRLEA 177 (336)
T ss_pred HHHHHHHhhhhhhcCcHHHHHHHHHHhccCC-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3678999999999999999999888666542 222778899998889999999999 89988865
No 137
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=92.04 E-value=0.66 Score=50.67 Aligned_cols=55 Identities=18% Similarity=0.317 Sum_probs=49.1
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccH
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQ 673 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~ 673 (955)
.++.++++++|++++.+|..|.+..+|++++++||.+.+++.|.+.. .++.....
T Consensus 80 l~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~-~l~~~~nf 134 (511)
T COG3283 80 LALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA-QLINGFNF 134 (511)
T ss_pred HHHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHH-HhcCcCCH
Confidence 45788999999999999999999999999999999999999999987 67665443
No 138
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=90.68 E-value=12 Score=47.71 Aligned_cols=143 Identities=13% Similarity=0.043 Sum_probs=85.1
Q ss_pred HHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEE
Q 002191 221 SRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVR 300 (955)
Q Consensus 221 ~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r 300 (955)
..+.......++..++.+++.+..++|.+++.++-|+.++...+... + |.. |..+.+...+.+-...
T Consensus 284 ~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---~------~~~-~~~~~~~~~~~~~~~~--- 350 (828)
T PRK13837 284 RCFEAASPHELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---P------GLT-PDPVWPDRLRALASTV--- 350 (828)
T ss_pred HHHhcCCchhhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---C------ccC-CCCCchHHHHHHHHHH---
Confidence 33444222345689999999999999999999999988775544221 1 111 2333333333321110
Q ss_pred EeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCC-CCCCCh
Q 002191 301 MICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTS-PRYIPF 379 (955)
Q Consensus 301 ~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~-pr~~~~ 379 (955)
...+-.++.. .+..++....++...+..+.+++|+...+ ++.|++.+.... ...++.
T Consensus 351 -----~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~g~l~~~~~~~~~~~~~ 408 (828)
T PRK13837 351 -----KAAERDVVFV-------------DRNGPVRKRSCLTRRGPALWACLAFKSGD----RIVALLGLGRQRYGLRPPA 408 (828)
T ss_pred -----hccCCceEEe-------------ecccchhhhcccccCCcceEEEEEeccCC----ceEEEEEecccccCCCCCh
Confidence 0000000000 01112233344556788999999998887 999999998775 334456
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 002191 380 PLRYACEFLVQAFSLQLYM 398 (955)
Q Consensus 380 ~~r~~~~~l~~~~~~~l~~ 398 (955)
.+...++.++..++..+..
T Consensus 409 ~~~~~l~~~~~~~~~~~~~ 427 (828)
T PRK13837 409 GELQLLELALDCLAHAIER 427 (828)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 7777888888877776653
No 139
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=90.67 E-value=11 Score=36.87 Aligned_cols=118 Identities=18% Similarity=0.216 Sum_probs=83.7
Q ss_pred HHHHHHHHHHh-CCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHH---HHHHHHhCCEEEeecCCCCCcc
Q 002191 236 DTVVEDVQKLT-GYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQA---ARFLFKQNRVRMICDCHAIPVM 311 (955)
Q Consensus 236 ~~~v~~vr~~~-g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~---~r~ly~~~~~r~i~d~~~~~~~ 311 (955)
..+..-+.+.+ .+|=|=.|.++ +++-|-+ ||-|. -+-.+||-- .-.--..|++..|.||++-|=
T Consensus 38 an~sall~~~l~~~nW~GFYl~~---~~~LvLg-------PFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~g- 105 (163)
T COG1956 38 ANASALLKERLPDVNWVGFYLLE---GDELVLG-------PFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHAFPG- 105 (163)
T ss_pred HHHHHHHHhhccCCceEEEEEec---CCeEEEe-------cccCC-cceEEeccCcchhHHHHhcCCeEEecccccCCC-
Confidence 34444455544 48888888888 6666644 78886 444556632 233456799999999997554
Q ss_pred cccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHH
Q 002191 312 VIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQA 391 (955)
Q Consensus 312 l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~~~l~~~ 391 (955)
|+.- .--++|-+++||+.+| ++-|.|=.-..+|-+++...+..++.++..
T Consensus 106 ------------------------hiaC--D~as~SEIVvPi~~~g----~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~~ 155 (163)
T COG1956 106 ------------------------HIAC--DAASNSEIVVPIFKDG----KLIGVLDIDSPTPGRFDEEDEAGLEKLAAL 155 (163)
T ss_pred ------------------------cccc--ccccCceEEEEEEECC----EEEEEEecCCCCcccCCHHHHHHHHHHHHH
Confidence 3321 2345899999999998 999999999888888898888888887776
Q ss_pred HHHH
Q 002191 392 FSLQ 395 (955)
Q Consensus 392 ~~~~ 395 (955)
+...
T Consensus 156 l~~~ 159 (163)
T COG1956 156 LEKS 159 (163)
T ss_pred HHHH
Confidence 6543
No 140
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=90.19 E-value=1.4 Score=29.45 Aligned_cols=36 Identities=36% Similarity=0.481 Sum_probs=31.4
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchH
Q 002191 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITH 736 (955)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITe 736 (955)
...+|...|+.....++.+..+.+.+++++..|||+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 7 RRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred EecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 456788899999999999888999999999999986
No 141
>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]
Probab=90.15 E-value=0.043 Score=68.41 Aligned_cols=69 Identities=23% Similarity=0.495 Sum_probs=59.6
Q ss_pred HHHHHHHHHH--HHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc-cCccccccC
Q 002191 885 EDMDIYAKIK--ELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG-MDLRCIEEG 955 (955)
Q Consensus 885 aE~~~~ak~~--fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D-Ld~SrIeaG 955 (955)
.+.+...+.+ |++.++||||+||++ |....+..+..+.+++.+++..+.++.....++++ +|.+++++|
T Consensus 212 ~e~~~~~~sq~~~~~~~sHeir~p~~~--~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~s~ln~i~d~~~v~~g 283 (786)
T KOG0519|consen 212 DEAAVWSPSQKGFLATLSHEIRTPLNG--GMLGGLSDTDLDSDQRLILNTDRVSAKSLLSLLNDILDLSKVESG 283 (786)
T ss_pred chhcccCccchhhcccccceeeccccc--CcceEEeccccchHHHHHHHHHhhhccccchhHHHhhcccccccc
Confidence 3444445556 999999999999998 67777777889999999999999999999999999 999999887
No 142
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=89.31 E-value=5.4 Score=50.89 Aligned_cols=46 Identities=13% Similarity=-0.016 Sum_probs=40.8
Q ss_pred cchHHHHHHHHHHHHHHHhcCccEEEEc-CCCcEeeecHHHHHHhCC
Q 002191 608 QGVDELSSVACEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGL 653 (955)
Q Consensus 608 ~~~~eL~~~~~~l~~lie~~~~~I~~~D-~dg~i~~~N~~~~~l~G~ 653 (955)
+..+++++.+...+.+++++|+|++++| .+|+++.+|+++.+++|.
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 3346788888899999999999999999 688999999999999974
No 143
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=88.76 E-value=2.6 Score=49.88 Aligned_cols=179 Identities=15% Similarity=0.137 Sum_probs=89.3
Q ss_pred ccchHHHHHHHHHHHHHHH---hcCccEEEEcCCCcEeeecHHHHHHhCCCchh-hcCCCccccccccccHHHHHHHHHH
Q 002191 607 MQGVDELSSVACEMVRLIE---TATAPIFGVDSSGTINGWNAKVAELTGLPASE-AMGKSLIDEVVHEESQGAVENLICR 682 (955)
Q Consensus 607 ~~~~~eL~~~~~~l~~lie---~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~ee-liG~~~~~~l~~~~~~~~~~~~l~~ 682 (955)
++...-|......|..++. ..+..++..|.+|.++..+-.-.....++.-- ..|..|. +-.-. .+.+-.
T Consensus 63 E~~~~LL~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~~~~~~~~rk~gl~~Ga~WS-E~~~G------TNgIGT 135 (606)
T COG3284 63 ERAEALLTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGDPRDDEDFRKAGLWLGAVWS-EPREG------TNGIGT 135 (606)
T ss_pred HHHHHHHHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecChhhhhhhhhhccccccccc-ccccc------ccchhh
Confidence 3333334444455555554 45667888999999998764422222221111 1222222 11000 111222
Q ss_pred HHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEEeecCCCCEEEEEEEE---ecchHhHH------HHHHHHHHHHH-HH
Q 002191 683 ALLGEEDKNVELKLRKFELQKQHSVVYILVNACTSRDYKNNVKGVCFVG---QDITHEKV------LMDKFIRLQGD-YE 752 (955)
Q Consensus 683 ~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~---~DITerk~------ae~~L~~se~~-lr 752 (955)
++..++.. .+.-. .|-......+.+++.|++|..|+++|++-+. .|+++.-. ....-+..|.. |.
T Consensus 136 cLve~~aV--tI~~~---qHF~~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~~~~~~s~~~~~~iV~~~ar~IE~~~~~ 210 (606)
T COG3284 136 CLVEGEAV--TIHGD---QHFIQAHHGLSCSAAPIFDEQGELVGVLDISSCRSDLSEASQPLTLAIVTDAARRIEAELFL 210 (606)
T ss_pred hhccCcce--EEehh---hhHhhcccCceeeeeccccCCCcEEEEEEeccCCcchhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 22222221 11100 1112333457889999999999999887554 23333221 01111111111 11
Q ss_pred --------HHHHhcC----CCCCCeeeecCCCcEeeecHHHHHHhCCC-hhhhccCCc
Q 002191 753 --------AIIQSVN----PLIPPIFASDENACCSEWNAAMEKVTGWM-RHEVIGKML 797 (955)
Q Consensus 753 --------~i~e~~~----~~id~I~~~D~~g~i~~~N~a~~~l~G~~-~eeviGk~~ 797 (955)
..+...| ....+.+.+|.+|+++..|+++..+++.+ ...++|.+.
T Consensus 211 ~~~~~~~~lr~~~~p~~~d~~~~~~lavd~~grvl~at~aA~~~La~~~~~~l~g~p~ 268 (606)
T COG3284 211 AAFEGHWLLRIALAPDYLDSQSEALLAVDQDGRVLGATRAARQLLALTDRQRLIGQPV 268 (606)
T ss_pred HhcCcchHHHHhcCccccCcccceeeeecCcchhhhccHHHHHhhccchhhHhhcCCc
Confidence 1111111 12246888999999999999999999888 444455443
No 144
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=88.23 E-value=1.6 Score=49.79 Aligned_cols=94 Identities=14% Similarity=0.046 Sum_probs=77.1
Q ss_pred CCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEEEEEEEEEE
Q 002191 637 SGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVVYILVNACT 716 (955)
Q Consensus 637 dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~~v~v~~~p 716 (955)
|+..+.+..+...++||...|+.|.+.+ +++|-++.....+.-.+.+..++..-.-+++ ..++|++.|+..++..
T Consensus 292 Dfa~vs~Dak~k~~lgy~eaEL~~m~gY-~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~----qtk~grw~wvqssarl 366 (712)
T KOG3560|consen 292 DFALVSMDAKVKATLGYCEAELHGMPGY-NLVHVEDKVYMAEAHSEGIKTGESGMLVYRE----QTKAGRWAWVQSSARL 366 (712)
T ss_pred ccceeccchhhhhhhccchhhccCCCcc-ceeehhhhhhhhHHHHHHhhcCCcceEEEEE----eecCCcEEEeecccee
Confidence 5666777788889999999999999988 9999999877777778888888777777776 7899999999998887
Q ss_pred eecCCCCEEEEEEEEecchH
Q 002191 717 SRDYKNNVKGVCFVGQDITH 736 (955)
Q Consensus 717 i~d~~g~v~gvv~v~~DITe 736 (955)
++ .+|++..++.+-+-.++
T Consensus 367 ly-kngkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 367 LY-KNGKPDLVIDTHRGLGD 385 (712)
T ss_pred ee-ecCCCCEEEecCCCccc
Confidence 76 57777777777666665
No 145
>PRK10490 sensor protein KdpD; Provisional
Probab=87.07 E-value=30 Score=44.44 Aligned_cols=49 Identities=10% Similarity=0.076 Sum_probs=39.4
Q ss_pred eeEEEEEEEEcCCCCCceeEEEEeecCCC-CCCChhHHHHHHHHHHHHHHHHHH
Q 002191 346 IASLVMAVIINSKDSMKLWGLVVCHHTSP-RYIPFPLRYACEFLVQAFSLQLYM 398 (955)
Q Consensus 346 ~asl~v~i~~~~~~~~~LWGll~~hh~~p-r~~~~~~r~~~~~l~~~~~~~l~~ 398 (955)
.+.+.+||...+ +++|++.+..+.+ +.++++.+...+.++.+++..++.
T Consensus 595 ~~~~~lPl~~~~----~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler 644 (895)
T PRK10490 595 VPYQILPLKSAQ----KTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALER 644 (895)
T ss_pred CceEEEEEEECC----EEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHH
Confidence 346789999888 9999999977764 567888888888888888887764
No 146
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=85.92 E-value=6.2 Score=37.96 Aligned_cols=93 Identities=15% Similarity=0.064 Sum_probs=72.5
Q ss_pred EEEEcCCC--cEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcEE
Q 002191 631 IFGVDSSG--TINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSVV 708 (955)
Q Consensus 631 I~~~D~dg--~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~~ 708 (955)
|+.++.+| ++..+-...++++|.+ +.|+++. +++.++....+...+..+.......-..... ...+|...
T Consensus 42 ile~~~~~~~r~RLaGt~i~~~~G~d---~tG~~~~-el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~----~~~~g~~~ 113 (137)
T PF07310_consen 42 ILEVDDPGDFRYRLAGTRIVELFGRD---LTGRRLS-ELFPPEDRERVRRAYRAVVERPAPVRARGRA----EDADGRYL 113 (137)
T ss_pred EEEEeCCCceEEEEecHHHHHHhCCC---CCCCCHH-HhcChHhHHHHHHHHHHHHcCCceEEEEEEE----ecCCCCee
Confidence 33344434 6667889999999984 5699998 8999988888999999998877665555554 45678888
Q ss_pred EEEEEEEEeecCCCCEEEEEEEE
Q 002191 709 YILVNACTSRDYKNNVKGVCFVG 731 (955)
Q Consensus 709 ~v~v~~~pi~d~~g~v~gvv~v~ 731 (955)
.++....|+.+.+|.+..++|++
T Consensus 114 ~~e~l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 114 EYERLLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred EEEEEEcccCCCCCCccEEEEec
Confidence 89999999999989888877764
No 147
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=85.37 E-value=0.43 Score=58.17 Aligned_cols=98 Identities=11% Similarity=0.085 Sum_probs=67.5
Q ss_pred eecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcC-CCcceeeEEEEcCCCcEE
Q 002191 767 ASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG-QGTENFPFGFFNRQGQFV 845 (955)
Q Consensus 767 ~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g-~~~~~~e~~~~~~dG~~~ 845 (955)
-.+.+|.++++-.....+.||...++.|+.... ..|+++...+...+..+... ......-++++.++|.+.
T Consensus 377 r~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~--------s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~ 448 (803)
T KOG3561|consen 377 RSSSDGSFTFVDQRASAILGYQPQELLGRSSYE--------SSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSI 448 (803)
T ss_pred ccCcCCceeccccccccccccCchhhcCccccc--------ccCccccchhhchHHHHHHhcccccccccccccCCCCcc
Confidence 345678888888889999999999999997542 44566665555555444432 224556678899999999
Q ss_pred EEEEEEeeeeCC-CCCEEEEEEEEeccC
Q 002191 846 EVALTASRRTDA-EGKVIGCFCFMQILV 872 (955)
Q Consensus 846 ~v~~~~~pi~d~-~G~v~g~v~i~~DIT 872 (955)
|.........+. ...+.+++|.-..+.
T Consensus 449 ~~~~~~~~~~n~~s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 449 PNKSSAYLFSNPGSDEVEYIVCTNSNVP 476 (803)
T ss_pred ccccccccccCCCccccceeeecccccc
Confidence 887776655543 345666777666655
No 148
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=84.98 E-value=5.8 Score=32.39 Aligned_cols=48 Identities=19% Similarity=0.186 Sum_probs=38.1
Q ss_pred HHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhc
Q 002191 894 KELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIID 945 (955)
Q Consensus 894 ~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~ 945 (955)
+.+....||++|-|+.|.|++++=+ .++..+|++.+....+....+++
T Consensus 14 ~~lR~~RHD~~NhLqvI~gllqlg~----~~~a~eYi~~~~~~~~~~s~l~~ 61 (62)
T PF14689_consen 14 DSLRAQRHDFLNHLQVIYGLLQLGK----YEEAKEYIKELSKDLQQESELLK 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHhHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHHHHHHHHHHHHc
Confidence 4466679999999999999988644 36788999999888888776653
No 149
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=84.18 E-value=2.1 Score=46.89 Aligned_cols=88 Identities=16% Similarity=0.127 Sum_probs=67.2
Q ss_pred CccEEEEcCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeeccCCcE
Q 002191 628 TAPIFGVDSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQKQHSV 707 (955)
Q Consensus 628 ~~~I~~~D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~dG~~ 707 (955)
...++....|-++++...+..+++||.+.++++++++ ..++..+...+..+-..++..+....--+++ ..+.|++
T Consensus 225 NmFmfraslDlkliF~D~rv~qltgYepqdliektLY-~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~----l~k~ggw 299 (598)
T KOG3559|consen 225 NMFMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLY-HHIHGCDSFHLRCAHHLLLVKGQVTTKYYRF----LLKQGGW 299 (598)
T ss_pred ceEEEEeecceEEEeehhhHHHhhCCCchhhhhHHHH-HHhhhhhHHHHHHHHHHHHhccccccHHHHH----HHcCCce
Confidence 3456667788999999999999999999999999999 8888888777776666666555443333444 5677899
Q ss_pred EEEEEEEEEeecC
Q 002191 708 VYILVNACTSRDY 720 (955)
Q Consensus 708 ~~v~v~~~pi~d~ 720 (955)
.|+......+.+.
T Consensus 300 vwvqsyat~vHnS 312 (598)
T KOG3559|consen 300 VWVQSYATFVHNS 312 (598)
T ss_pred EEEEEeeEEEecc
Confidence 9988877766543
No 150
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=82.92 E-value=0.71 Score=56.32 Aligned_cols=45 Identities=22% Similarity=0.283 Sum_probs=39.5
Q ss_pred cceEEEEeCCCceEEEEecChhhhhCCCCcccccccccccCCccccccCCchH
Q 002191 96 FGCMLAVEEPTFRIIGYSENCLEMLDLRSRSEDFELNGLIGIDARTLFTPPSG 148 (955)
Q Consensus 96 ~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~g~~~~~~~~~~~~ 148 (955)
=|||+||.-+ |+|++||+|+..+||..+ ++++|+.|-+++.+...
T Consensus 105 DGF~fvV~cd-G~IvyVSeSVT~~L~y~Q-------sDL~~qSly~ilhp~d~ 149 (803)
T KOG3561|consen 105 DGFLFVVNCD-GRIVYVSESVTSVLGYLQ-------SDLMGQSLYDILHPLDN 149 (803)
T ss_pred cCeEEEEecC-ceEEEEecchHHhhCcCH-------HHHhcchHHHhcCcccc
Confidence 4999999987 999999999999999988 68999999888865443
No 151
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=80.77 E-value=5.1 Score=44.07 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=41.8
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCcc
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (955)
-.+.+++++++ +|++.+|..|.+..+|++++++||.+.+++.|++..
T Consensus 80 l~L~aLL~al~---~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~ 126 (511)
T COG3283 80 LALSALLEALP---EPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAA 126 (511)
T ss_pred HHHHHHHHhCC---CceEEecccCceeecCHHHHHHhCCChhhhcCccHH
Confidence 34678888887 479999999999999999999999999999999755
No 152
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=80.01 E-value=12 Score=43.84 Aligned_cols=147 Identities=15% Similarity=0.165 Sum_probs=99.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCC-eEEEEEecCCCCCCccCCCCCCCCchHHHHHHH
Q 002191 216 AVSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDH-GEVVSEIRRSDLEPYLGIHFPANDIPQAARFLF 294 (955)
Q Consensus 216 ~~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~-G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly 294 (955)
+.++.+...+ ..++++-++..|++|..-..++=+-||=.+.|++ =+..| ..|+...-+
T Consensus 5 Lr~i~E~va~--~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~A---TeGLnk~av---------------- 63 (756)
T COG3605 5 LRRIVEKVAS--ALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELMA---TEGLNKPAV---------------- 63 (756)
T ss_pred HHHHHHHHhc--ccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEe---ccccCcccc----------------
Confidence 3455566666 6699999999999999999999999999999984 33333 123322222
Q ss_pred HhCCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcC---ceeEEEEEEEEcCCCCCceeEEEEeec
Q 002191 295 KQNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMG---SIASLVMAVIINSKDSMKLWGLVVCHH 371 (955)
Q Consensus 295 ~~~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~g---v~asl~v~i~~~~~~~~~LWGll~~hh 371 (955)
..+++-.| ..-|.++ ....+||+|+.+. -||. -.|+..-| -.|-|.+||+..+ ++-|.++.++
T Consensus 64 --~~~~l~~~--eGLVG~v--~~~aePlNLsdAq---sHPs-F~Y~petgEE~Y~sFLGvPIi~~~----r~lGVLVVQq 129 (756)
T COG3605 64 --HLVQLAFG--EGLVGLV--GRSAEPLNLADAQ---SHPS-FKYLPETGEERYHSFLGVPIIRRG----RLLGVLVVQQ 129 (756)
T ss_pred --ceEEecCC--Cchhhhh--hhccCCCChhhhh---hCCc-cccccccchHHHHHhhccceeecC----ceeEEEEEec
Confidence 12222222 1122222 2345788887654 2333 23554444 2577889999888 9999999999
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHH
Q 002191 372 TSPRYIPFPLRYACEFLVQAFSLQLY 397 (955)
Q Consensus 372 ~~pr~~~~~~r~~~~~l~~~~~~~l~ 397 (955)
.++|.+...+-.+++.++.+++.-++
T Consensus 130 k~~R~y~E~Eve~L~T~A~~lA~iva 155 (756)
T COG3605 130 RELRQYDEDEVEFLVTLAMQLAEIVA 155 (756)
T ss_pred ccccccchHHHHHHHHHHHHHHHHHH
Confidence 99999999998888877776665443
No 153
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=79.70 E-value=12 Score=35.91 Aligned_cols=85 Identities=8% Similarity=0.004 Sum_probs=68.5
Q ss_pred cEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEe
Q 002191 773 CCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQGQFVEVALTAS 852 (955)
Q Consensus 773 ~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~ 852 (955)
++..+-...++++|+ |+.|+.+.+ +..++....+...+..+.....+.....+....+|....++...-
T Consensus 52 r~RLaGt~i~~~~G~---d~tG~~~~e--------l~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~L 120 (137)
T PF07310_consen 52 RYRLAGTRIVELFGR---DLTGRRLSE--------LFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLL 120 (137)
T ss_pred EEEEecHHHHHHhCC---CCCCCCHHH--------hcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEc
Confidence 455677888888886 455776553 344677777888899999988888888888899999999999999
Q ss_pred eeeCCCCCEEEEEEEE
Q 002191 853 RRTDAEGKVIGCFCFM 868 (955)
Q Consensus 853 pi~d~~G~v~g~v~i~ 868 (955)
|+.+.+|.+..++|.+
T Consensus 121 PL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 121 PLRSDGGTVDRILGAL 136 (137)
T ss_pred ccCCCCCCccEEEEec
Confidence 9999999998888864
No 154
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=78.10 E-value=32 Score=36.15 Aligned_cols=137 Identities=15% Similarity=0.063 Sum_probs=73.3
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHh
Q 002191 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQ 296 (955)
Q Consensus 217 ~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~ 296 (955)
..+.-+|-. +.++++++++..+.+++..+.|-|-+.-|++++.- +++.. .++..++ ........
T Consensus 81 ~~l~l~LL~--a~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~~---~~~~~--------~~~~~~~---~~~~~~~~ 144 (225)
T PF04340_consen 81 HRLVLALLA--ARSLQELLQALDDGLREDFDVDAVRLRLFDDDAAP---GPSLT--------DHVWLSR---DAFAQVFI 144 (225)
T ss_dssp HHHHHHHHC----SHHHHHHHHHHHHHHTS--SEEEEEEE-SS------SEE--------------E-H---HHHHHHHC
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHhcCCCeEEEEeecccccc---ccchh--------hcccccH---HHHHHHHH
Confidence 344445555 56999999999999999999999999999987662 11110 1111111 11111110
Q ss_pred CCEEEeecCCCCCcccccccccCCccccccccccCCChhhH-HHHh--hcCceeEEEEEEEEcCCCCCceeEEEEeecCC
Q 002191 297 NRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHL-QYMT--NMGSIASLVMAVIINSKDSMKLWGLVVCHHTS 373 (955)
Q Consensus 297 ~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~-~yl~--n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~ 373 (955)
... .. +.|.+ -.++..-. ..+- .-+|+|.-.+|+. .+ +.+|+|+.=+..
T Consensus 145 ~~l-------~~----------~~p~~------G~~~~~~~~~lF~~~~~~v~S~AlipL~-~~----~~~G~LalGS~D 196 (225)
T PF04340_consen 145 DLL-------GL----------QQPYC------GRLSEEEAALLFGDEAAQVGSVALIPLG-SG----RPIGLLALGSRD 196 (225)
T ss_dssp CCH-------TT-------------CC------CS--HHHHHHHHHHCHCC-SEEEEEEEE-SS----SEEEEEEEEESS
T ss_pred HHh-------CC----------CCcee------CCCCcchhHHhcCCCCccccchheeecc-CC----CceEEEEecCCC
Confidence 000 00 00111 11112222 2222 3568999999998 66 999999987777
Q ss_pred CCCCCh-hHHHHHHHHHHHHHHHHH
Q 002191 374 PRYIPF-PLRYACEFLVQAFSLQLY 397 (955)
Q Consensus 374 pr~~~~-~~r~~~~~l~~~~~~~l~ 397 (955)
|.++.+ ---.++++|+++++..|.
T Consensus 197 ~~rF~p~mgT~fL~~La~vv~~~L~ 221 (225)
T PF04340_consen 197 PDRFQPDMGTDFLEQLAEVVSAALE 221 (225)
T ss_dssp TTCCCSTTTTHHHHHHHHHHHHHGG
T ss_pred hhhCCCCccHHHHHHHHHHHHHHHh
Confidence 654444 447888888888887663
No 155
>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=75.95 E-value=11 Score=35.28 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=36.5
Q ss_pred CcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccCcccH
Q 002191 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILVPDLQ 876 (955)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DITerk~ 876 (955)
......|....++|+ .+..+...++|++|+++|++|+-.|+|.-.+
T Consensus 66 ~~~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~ 111 (118)
T PF08348_consen 66 EDYIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQ 111 (118)
T ss_pred CCccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHH
Confidence 345556667888885 5567778899999999999999999997443
No 156
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=74.59 E-value=1.2e+02 Score=36.84 Aligned_cols=124 Identities=16% Similarity=0.146 Sum_probs=76.9
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHHHhCCCeEEEEeecCCCCeEEE-EEecCCCCCCccCCCCCCCCchHHHHHHHH
Q 002191 217 VSAISRLQALPGGDIGLLCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVV-SEIRRSDLEPYLGIHFPANDIPQAARFLFK 295 (955)
Q Consensus 217 ~~~~~~l~~~~~~~~~~~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~vi-aE~~~~~~~s~lg~~~p~~dip~~~r~ly~ 295 (955)
..+..++.. +..+.+.|+.+.+++.++++.+.+.+.-+++++..... -.+..+ . +.++
T Consensus 223 y~~~~~l~~--~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~----~~~~------------ 281 (569)
T PRK10600 223 WQANRRLHS--RAPLCERLSPVLNGLQNLTLLRDIELRVYETDDEENHQEFTCQSD---M----TCDD------------ 281 (569)
T ss_pred HHHHHHHhc--CcchHHHHHHHHHHHHHhcCCCceEEEEeccccccceeeccCCCc---c----Cccc------------
Confidence 334456655 55788899999999999999999999887765544221 111110 0 0000
Q ss_pred hCCEEEeecCCCCCcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCC
Q 002191 296 QNRVRMICDCHAIPVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPR 375 (955)
Q Consensus 296 ~~~~r~i~d~~~~~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr 375 (955)
..|..-+... .|.. .+ ...+..||..++ +.-|.+...-..++
T Consensus 282 -------~~~~~~~~~~--------------------~~~~------~~-~~~~~~~l~~~~----~~~G~~~~~~~~~~ 323 (569)
T PRK10600 282 -------KGCQLCPRGV--------------------LPVG------DR-GTTLKWRLSDKH----GQYGILLATLPQGR 323 (569)
T ss_pred -------cccccccccC--------------------CCcC------CC-CceEEEEeecCC----cceEEEEEEcCCCC
Confidence 0011000000 0000 00 366789998776 89998876644467
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHH
Q 002191 376 YIPFPLRYACEFLVQAFSLQLYME 399 (955)
Q Consensus 376 ~~~~~~r~~~~~l~~~~~~~l~~~ 399 (955)
.++++.+.+++.++.+++..++.+
T Consensus 324 ~l~~~~~~ll~~l~~~l~~~l~~~ 347 (569)
T PRK10600 324 HLSHDQQQLVDTLVEQLTATLALE 347 (569)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 789999999999999988777543
No 157
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=68.15 E-value=16 Score=31.15 Aligned_cols=48 Identities=23% Similarity=0.245 Sum_probs=38.2
Q ss_pred HHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002191 899 IRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDACERQIMTIIDG 946 (955)
Q Consensus 899 iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~~a~rl~~LI~D 946 (955)
+.|.+||.|+.|.++..+-.+...+++.++.+..+..-..-|..+=+.
T Consensus 2 ~~HRVkNnLq~i~sll~lq~~~~~~~e~~~~L~~~~~RI~aia~vh~~ 49 (76)
T PF07568_consen 2 LHHRVKNNLQIISSLLRLQARRSEDPEAREALEDAQNRIQAIALVHEQ 49 (76)
T ss_pred hHHhHHhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999988777788888888777766555555443
No 158
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=67.93 E-value=58 Score=38.57 Aligned_cols=38 Identities=5% Similarity=0.024 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCC
Q 002191 616 VACEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGL 653 (955)
Q Consensus 616 ~~~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~ 653 (955)
.+.-++.++.++|.||+.+|.++.+.++|+-+..+|+-
T Consensus 73 ~~~~~~~al~nmPiGii~~~e~~~veW~Npf~~~if~~ 110 (655)
T COG3887 73 AEKSLEEALTNMPIGIILFNETNKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHhCCceEEEEcCCCceEEecHHHHHhcCh
Confidence 34557889999999999999999999999999999863
No 159
>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=62.63 E-value=24 Score=36.97 Aligned_cols=58 Identities=21% Similarity=0.071 Sum_probs=38.6
Q ss_pred eccCcccHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHH
Q 002191 869 QILVPDLQPALEAQGLEDMDIYAKIKELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETS 933 (955)
Q Consensus 869 ~DITerk~~el~lq~~aE~~~~ak~~fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i 933 (955)
.|+|++++.+..+... .+..++..+.|.++|-|+.|.+++.+-.+...++ ..+++...
T Consensus 2 ~~~~~~~~~e~~~~~~------~~~~ll~Ei~HRVKNnLqiIsSll~lq~r~~~~~-~~~~~~~~ 59 (221)
T COG3920 2 LLTTARKETEERLAES------EKELLLREIHHRVKNNLQIISSLLRLQARKFEDE-VLEALRES 59 (221)
T ss_pred chHHHHHHHHHHHHHH------HHHHHHHHhhhhhhhHHHHHHHHHHHHHhhcCCH-HHHHHHHH
Confidence 3556666555443221 4556789999999999999999999887655453 33444433
No 160
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=58.87 E-value=36 Score=31.79 Aligned_cols=42 Identities=14% Similarity=0.121 Sum_probs=35.1
Q ss_pred eccCCcEEEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHH
Q 002191 701 LQKQHSVVYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKF 744 (955)
Q Consensus 701 ~~~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L 744 (955)
..++|+ .+..+...++|++|+++|++++-.|+|....+..-|
T Consensus 75 ~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~~~L 116 (118)
T PF08348_consen 75 KTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQAQNFL 116 (118)
T ss_pred cCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHHHHHH
Confidence 456774 577888899999999999999999999988776554
No 161
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=58.46 E-value=44 Score=42.19 Aligned_cols=44 Identities=16% Similarity=0.059 Sum_probs=37.3
Q ss_pred HHHHHHHHhcCccEEEEc-CCCcEeeecHHHHHHhCCCchhhcCCCcc
Q 002191 618 CEMVRLIETATAPIFGVD-SSGTINGWNAKVAELTGLPASEAMGKSLI 664 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D-~dg~i~~~N~~~~~l~G~~~eeliG~~~~ 664 (955)
+--+.++..+|.|++++| .+|.|++.|+.+.+++| .+ ++|+++.
T Consensus 102 ~~~~~~l~~~p~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 102 QIGEEVLNELPIGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHHHHhCCceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 445677899999999999 79999999999999988 22 7898877
No 162
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=57.58 E-value=12 Score=34.39 Aligned_cols=47 Identities=28% Similarity=0.468 Sum_probs=37.5
Q ss_pred cEEEEcC-CCcEeeecHHHHHHhCCC---chhhcCCCccccccccccHHHHH
Q 002191 630 PIFGVDS-SGTINGWNAKVAELTGLP---ASEAMGKSLIDEVVHEESQGAVE 677 (955)
Q Consensus 630 ~I~~~D~-dg~i~~~N~~~~~l~G~~---~eeliG~~~~~~l~~~~~~~~~~ 677 (955)
.++++|. +++|+.++..+..++|.+ .++++|+++. +++.+.....+.
T Consensus 17 ~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~-~ll~~~~~~~l~ 67 (110)
T PF08446_consen 17 ALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLS-ELLGAESAERLR 67 (110)
T ss_dssp EEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHH-HHSCCCCHHHHH
T ss_pred EEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHH-HHhCHHHHHHHH
Confidence 3466665 689999999999999999 9999999998 888776655433
No 163
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=52.35 E-value=22 Score=36.83 Aligned_cols=39 Identities=13% Similarity=0.007 Sum_probs=34.9
Q ss_pred HHHHHHHHhcCccEEEEcCCCcEeeecHHHHHHhCCCch
Q 002191 618 CEMVRLIETATAPIFGVDSSGTINGWNAKVAELTGLPAS 656 (955)
Q Consensus 618 ~~l~~lie~~~~~I~~~D~dg~i~~~N~~~~~l~G~~~e 656 (955)
+.+..+++..+.|+++-+.+|.++++|..+.++|.-...
T Consensus 19 ~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~~ 57 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQ 57 (217)
T ss_pred HHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcCC
Confidence 467889999999999999999999999999999975443
No 164
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=45.99 E-value=38 Score=31.32 Aligned_cols=73 Identities=18% Similarity=0.181 Sum_probs=41.9
Q ss_pred CCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCCCcceeeEEEEcCCC
Q 002191 763 PPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQGTENFPFGFFNRQG 842 (955)
Q Consensus 763 d~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~~~~~~e~~~~~~dG 842 (955)
+-|++.|.+|++++-+ ..+.+|+.+.+ .+ ..+++.|+ .+... ...++
T Consensus 40 ~~i~v~D~~g~~l~~s----------~~~~iG~~~~~------------~~-------~~~aL~G~-~~~~~---~~~~~ 86 (116)
T PF14827_consen 40 DYIVVTDRDGIVLAHS----------DPERIGDRYSD------------ED-------VRKALQGK-SYTSV---SQGTG 86 (116)
T ss_dssp SEEEEECTTSBECE-S----------SCCCTTSB-SS------------CC-------HCHHCCT---EEEE---EECTT
T ss_pred eEEEEEcCCCCEEEcC----------ChHHcCCcccC------------CC-------hhhhhcCC-ceEEe---eecCC
Confidence 4589999999987643 34556776442 11 23445453 32222 22222
Q ss_pred cEEEEEEEEeeeeCCCCCEEEEEEEEec
Q 002191 843 QFVEVALTASRRTDAEGKVIGCFCFMQI 870 (955)
Q Consensus 843 ~~~~v~~~~~pi~d~~G~v~g~v~i~~D 870 (955)
.+......|++|.+|+++|++.+...
T Consensus 87 --~~~~~~~~PV~d~~g~viG~V~VG~~ 112 (116)
T PF14827_consen 87 --GPSLRAFAPVYDSDGKVIGVVSVGVS 112 (116)
T ss_dssp --CEEEEEEEEEE-TTS-EEEEEEEEEE
T ss_pred --ceEEEEEEeeECCCCcEEEEEEEEEE
Confidence 45566678999999999999987654
No 165
>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.33 E-value=40 Score=32.96 Aligned_cols=41 Identities=12% Similarity=0.250 Sum_probs=32.5
Q ss_pred HHHHHHHHhhhHhHhHHHHHHHhccCCCCHHHHHHHHHHHH
Q 002191 895 ELAYIRQEVKNPLNGIRFVHKLLESSSISENQRQYLETSDA 935 (955)
Q Consensus 895 fla~iSHELRnPL~~I~g~~~LL~~~~l~~~~~~~l~~i~~ 935 (955)
+.+.++||+-.|..+|..-++||+....+++...++....+
T Consensus 18 LcsRvCHDiISPvgAInnGLeLLdeg~addDAm~LIrsSAr 58 (214)
T COG5385 18 LCSRVCHDIISPVGAINNGLELLDEGGADDDAMDLIRSSAR 58 (214)
T ss_pred HHHHHHhhccCcHHHhhchhhhhccCCccHHHHHHHHHHhh
Confidence 35778999999999999999999987777766655555443
No 166
>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=43.65 E-value=2.3e+02 Score=31.21 Aligned_cols=68 Identities=15% Similarity=0.137 Sum_probs=41.6
Q ss_pred HHHHHHHHhcCCCCCCe-eeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcC
Q 002191 749 GDYEAIIQSVNPLIPPI-FASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITG 827 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I-~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g 827 (955)
++.++++.++..+.||. |++|.+|+-+.- -...+..|++++. +.+|+...-+...+.++.+|
T Consensus 80 ~evk~iLt~ldyG~DGYFF~YD~~G~NlvH---------PrQpelvG~nlw~--------L~D~rGd~~Iq~Li~kAq~G 142 (459)
T COG4564 80 QEVKAILTNLDYGSDGYFFVYDYQGTNLVH---------PRQPELVGQNLWQ--------LTDPRGDRVIQALIAKAQEG 142 (459)
T ss_pred HHHHHHHhhcccCCCceEEEEecCCccccC---------CCCccccccchhh--------ccCCCcChHHHHHHHHHHhC
Confidence 34556666665555554 668888864321 1224566777553 66666666677777888888
Q ss_pred CCccee
Q 002191 828 QGTENF 833 (955)
Q Consensus 828 ~~~~~~ 833 (955)
|....+
T Consensus 143 GG~~qY 148 (459)
T COG4564 143 GGLHQY 148 (459)
T ss_pred CCeEEE
Confidence 755444
No 167
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=38.95 E-value=99 Score=35.80 Aligned_cols=118 Identities=21% Similarity=0.214 Sum_probs=79.4
Q ss_pred HHHHHHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccC----CCCCCCCchHHH-HHHHHhCCEEEeecCCCC
Q 002191 234 LCDTVVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLG----IHFPANDIPQAA-RFLFKQNRVRMICDCHAI 308 (955)
Q Consensus 234 ~~~~~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg----~~~p~~dip~~~-r~ly~~~~~r~i~d~~~~ 308 (955)
=+..+++-|.+.+|.+=|.+ .-+..+-.|.| .|.|-.+|--.. +.-...|.+-. .|-.+.
T Consensus 226 s~~~va~Ii~~~~~~~AVai--------------Td~e~ilA~vg~g~dhhi~g~~i~s~~t~~ai~~g~vv~-~~~~e~ 290 (557)
T COG3275 226 SLMKVAEIIYEELGAGAVAI--------------TDREKLLAFVGIGDDHHIPGKPIISSLTRKAIKTGEVVY-ADGNEV 290 (557)
T ss_pred hHHHHHHHHHHHhCCCeEEe--------------cCHHHHHHhhcccccccCCCCeeccHHHHHHHhhCCEEE-Eccchh
Confidence 34556677888888876654 33444444444 466777755443 44444455433 333322
Q ss_pred CcccccccccCCccccccccccCCChhhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHH
Q 002191 309 PVMVIQSKELKQPLCLVNSTLRSPHGCHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFL 388 (955)
Q Consensus 309 ~~~l~~~~~~~~~ldl~~s~lRs~s~~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~~~l 388 (955)
... . | .+-.+.|.+++|+--+| +.=|-|--.-+.|+.++.-+|.+.+-+
T Consensus 291 -~~c---------------s----h-------~~c~l~s~lViPL~~~g----~ViGTiK~y~~~~~lis~~~r~la~Gi 339 (557)
T COG3275 291 -YEC---------------S----H-------PTCKLGSALVIPLRGKG----RVIGTIKLYEAKARLISSINRELAEGI 339 (557)
T ss_pred -hcc---------------C----C-------CCCCcCCceEeecccCC----ceeeeEEEEeccHhHhhHHHHHHHHHH
Confidence 100 0 1 12245899999997666 999999999999999999999999999
Q ss_pred HHHHHHHHH
Q 002191 389 VQAFSLQLY 397 (955)
Q Consensus 389 ~~~~~~~l~ 397 (955)
++.+|.|++
T Consensus 340 a~l~SaQie 348 (557)
T COG3275 340 AQLLSAQIE 348 (557)
T ss_pred HHHHHHHHH
Confidence 999999996
No 168
>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=38.38 E-value=56 Score=27.77 Aligned_cols=56 Identities=14% Similarity=0.116 Sum_probs=35.4
Q ss_pred EEEEEEEEEeecCCCCEEEEEEEEecchHhHHHHHHHHHHHHHHHHHHHhcCCCC-CCeeeecCCCcEeee
Q 002191 708 VYILVNACTSRDYKNNVKGVCFVGQDITHEKVLMDKFIRLQGDYEAIIQSVNPLI-PPIFASDENACCSEW 777 (955)
Q Consensus 708 ~~v~v~~~pi~d~~g~v~gvv~v~~DITerk~ae~~L~~se~~lr~i~e~~~~~i-d~I~~~D~~g~i~~~ 777 (955)
.++..-..|+++.+|+++|++++-.++.. +..++......- .-++++|.+|.++.-
T Consensus 12 ~~vi~~s~pi~~~~g~~~Gvv~~di~l~~--------------l~~~i~~~~~~~~g~~~ivd~~G~ii~h 68 (81)
T PF02743_consen 12 QPVITISVPIYDDDGKIIGVVGIDISLDQ--------------LSEIISNIKFGNNGYAFIVDKNGTIIAH 68 (81)
T ss_dssp EEEEEEEEEEEETTTEEEEEEEEEEEHHH--------------HHHHHTTSBBTTTBEEEEEETTSBBCE-
T ss_pred cEEEEEEEEEECCCCCEEEEEEEEeccce--------------eeeEEEeeEECCCEEEEEEECCCCEEEe
Confidence 45777789999999999999887544332 222333321110 126788999988753
No 169
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=37.39 E-value=2.3e+02 Score=33.93 Aligned_cols=37 Identities=14% Similarity=0.058 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhC
Q 002191 747 LQGDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTG 786 (955)
Q Consensus 747 se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G 786 (955)
.+.-++.++.++|. ||+.+|.++++.++||-+..+|+
T Consensus 73 ~~~~~~~al~nmPi---Gii~~~e~~~veW~Npf~~~if~ 109 (655)
T COG3887 73 AEKSLEEALTNMPI---GIILFNETNKVEWVNPFASKIFN 109 (655)
T ss_pred HHHHHHHHHHhCCc---eEEEEcCCCceEEecHHHHHhcC
Confidence 34456677888774 69999999999999999999986
No 170
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=37.26 E-value=2.4e+02 Score=34.06 Aligned_cols=37 Identities=14% Similarity=0.111 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCCeeeecCCCcEeeecHH
Q 002191 744 FIRLQGDYEAIIQSVNPLIPPIFASDENACCSEWNAA 780 (955)
Q Consensus 744 L~~se~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a 780 (955)
|+..+..+..++..+...-..++..|.+|.++..+-.
T Consensus 69 L~iA~~~L~~L~~~v~~~~~~vLLtD~~GViL~~~G~ 105 (606)
T COG3284 69 LTIAQPELDRLFQAVAGSGCCVLLTDADGVILERRGD 105 (606)
T ss_pred HHHhHHHHHHHHHHhcCCCeEEEEEcCceeEEEeecC
Confidence 4445556666766665544568899999999987544
No 171
>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=37.01 E-value=1.2e+02 Score=26.27 Aligned_cols=32 Identities=19% Similarity=0.047 Sum_probs=26.4
Q ss_pred cCCcEEEEEEEEEEeecCCCCEEEEEEEEecch
Q 002191 703 KQHSVVYILVNACTSRDYKNNVKGVCFVGQDIT 735 (955)
Q Consensus 703 ~dG~~~~v~v~~~pi~d~~g~v~gvv~v~~DIT 735 (955)
..|.+.=+-+...|+++.+|++++.+++. |+|
T Consensus 52 ~~G~Y~G~PViV~PI~~~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 52 IEGPYKGVPVIVAPIKDEDGEVIAAIGVV-DLT 83 (84)
T ss_pred CCcccCCeeEEEEEEEcCCCCEEEEEEEE-Ecc
Confidence 44666666778899999999999999998 876
No 172
>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=35.79 E-value=1.1e+02 Score=26.35 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=34.3
Q ss_pred HHHhhhcCCCcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEeccC
Q 002191 820 LLYQGITGQGTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQILV 872 (955)
Q Consensus 820 ~l~~~~~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~DIT 872 (955)
.+++++..+.. .+-.-..|.+.=+-+...|+++.+|++++.+|+. |+|
T Consensus 36 VLe~vl~~g~v----~r~~P~~G~Y~G~PViV~PI~~~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 36 VLEEVLETGKV----IRVTPIEGPYKGVPVIVAPIKDEDGEVIAAIGVV-DLT 83 (84)
T ss_pred HHHHHHHcCCE----EEeccCCcccCCeeEEEEEEEcCCCCEEEEEEEE-Ecc
Confidence 34555554432 2335567888778888999999999999999984 544
No 173
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=34.38 E-value=63 Score=39.72 Aligned_cols=76 Identities=13% Similarity=0.198 Sum_probs=56.7
Q ss_pred cCCCcEeeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcc---eEEEEEEeeeeccCCcEEEEE
Q 002191 635 DSSGTINGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDK---NVELKLRKFELQKQHSVVYIL 711 (955)
Q Consensus 635 D~dg~i~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~---~~e~~~~~~~~~~dG~~~~v~ 711 (955)
.+.+.+..+..++..++||-+.+++|+++. .++|++++..+.+.-..+++.+... .-.+++ ...+|.++.+.
T Consensus 338 TptClf~hVDeaAVp~LGyLPqDLIG~sil-~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf----~aqNG~yv~ld 412 (1114)
T KOG3753|consen 338 TPTCLFQHVDEAAVPLLGYLPQDLIGTSIL-AFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRF----CAQNGSYVRLD 412 (1114)
T ss_pred CCcceeeecchhhhhhhccCchhhhccchh-hhhcCCchHHHHHHHHHHHHhCCCCcccccceee----eecCCcEEEEe
Confidence 457788889999999999999999999999 9999999888888877777644221 123344 45678776655
Q ss_pred EEEE
Q 002191 712 VNAC 715 (955)
Q Consensus 712 v~~~ 715 (955)
..-.
T Consensus 413 TeWS 416 (1114)
T KOG3753|consen 413 TEWS 416 (1114)
T ss_pred chhh
Confidence 5433
No 174
>PRK04158 transcriptional repressor CodY; Validated
Probab=34.18 E-value=4e+02 Score=28.52 Aligned_cols=49 Identities=8% Similarity=0.089 Sum_probs=39.0
Q ss_pred eeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhHHHHHHHHHHHHHHHHHHH
Q 002191 346 IASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPLRYACEFLVQAFSLQLYME 399 (955)
Q Consensus 346 ~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~r~~~~~l~~~~~~~l~~~ 399 (955)
+=.+++||..+| ..-|-|++-.+.. .+..+...++|..|.+++++|-..
T Consensus 110 ~~~tIvPI~ggG----eRLGTLvl~r~~~-~f~~dDliL~EyaATVVgLEIlR~ 158 (256)
T PRK04158 110 KLTTIVPIIGGG----ERLGTLILARFDK-EFTDDDLILAEYAATVVGMEILRE 158 (256)
T ss_pred ceEEEEEEecCC----eEEEEEEEEecCC-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 446889999888 8889888887762 356677889999999999988654
No 175
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=33.46 E-value=4.1e+02 Score=24.92 Aligned_cols=110 Identities=12% Similarity=0.119 Sum_probs=57.1
Q ss_pred HHHHHHHHhCCCeEEEEeecCCCCeEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCEEEeecCCCCCcccccc-c
Q 002191 238 VVEDVQKLTGYDRVMLYNFHDDDHGEVVSEIRRSDLEPYLGIHFPANDIPQAARFLFKQNRVRMICDCHAIPVMVIQS-K 316 (955)
Q Consensus 238 ~v~~vr~~~g~DRV~iy~f~~d~~G~viaE~~~~~~~s~lg~~~p~~dip~~~r~ly~~~~~r~i~d~~~~~~~l~~~-~ 316 (955)
++..+.+.+|||++++.....+..+ .-... + -+..|....+.|.++....+ -|++.. .
T Consensus 8 ~l~~~~~~~Gf~~~~~~~~~~~~~~-~~~~~-------~------~~~~p~~w~~~Y~~~~~~~~-------DPv~~~~~ 66 (149)
T PF03472_consen 8 LLERLAARLGFDRFAYGAPSPDPRG-DSDFL-------L------ISNYPDEWLEHYEERGYFRI-------DPVVRHAR 66 (149)
T ss_dssp HHHHHHHCTTTSEEEEEEEETTSCE-CEEEE-------E------EESS-HHHHHHHHHTTGGGT--------HHHHHHC
T ss_pred HHHHHHHHcCCCEEEEEeccCCCCC-CccEE-------E------EecCCHHHHHHHHHcCCcCC-------CHHHHHHH
Confidence 4556788899999999922222211 11110 1 12445677777776653211 122210 1
Q ss_pred ccCCccccccccccC-CCh---hhHHHHhhcCceeEEEEEEEEcCCCCCceeEEEEeecC
Q 002191 317 ELKQPLCLVNSTLRS-PHG---CHLQYMTNMGSIASLVMAVIINSKDSMKLWGLVVCHHT 372 (955)
Q Consensus 317 ~~~~~ldl~~s~lRs-~s~---~h~~yl~n~gv~asl~v~i~~~~~~~~~LWGll~~hh~ 372 (955)
....|+.=+....+. .+| ...+..+.+|+++-+++|+--.+ +.. |+|+....
T Consensus 67 ~~~~p~~W~~~~~~~~~~~~~~~~~~~a~~~Gl~~G~~~p~~~~~---g~~-~~~s~~~~ 122 (149)
T PF03472_consen 67 RSSGPFFWSDLFERDALSPEQRRFFDEARDFGLRSGVSVPLHGPD---GRF-GALSFAGD 122 (149)
T ss_dssp HTSSEEEEECHCTSSSSSHHHHHHHHHHHHTTTSEEEEEEEEECC---GCE-EEEEEEES
T ss_pred hCCCCEEEccchhhhhhhHHHHHHHHHHHHcCCCceEEEEeEcCC---CCE-EEEEEECC
Confidence 111222222222221 144 34456789999999999997554 355 88876433
No 176
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=30.45 E-value=26 Score=42.61 Aligned_cols=16 Identities=44% Similarity=0.723 Sum_probs=14.2
Q ss_pred HHhCCCeEEEEeecCCCC
Q 002191 244 KLTGYDRVMLYNFHDDDH 261 (955)
Q Consensus 244 ~~~g~DRV~iy~f~~d~~ 261 (955)
.|||++||+| ||||||
T Consensus 614 NLTgAnRVII--fDPdWN 629 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN 629 (923)
T ss_pred ccccCceEEE--ECCCCC
Confidence 6899999999 589987
No 177
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=29.84 E-value=34 Score=31.85 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=19.6
Q ss_pred CCCccceEEEEeCCCceEEEEecC
Q 002191 92 LIQPFGCMLAVEEPTFRIIGYSEN 115 (955)
Q Consensus 92 ~iQp~G~ll~~~~~~~~i~~~S~N 115 (955)
-|||||+.+.++..+-=.+|+|+=
T Consensus 15 gI~~yGAFV~l~~g~tGLVHISEI 38 (129)
T COG1098 15 GITPYGAFVELEGGKTGLVHISEI 38 (129)
T ss_pred eeEecceEEEecCCCcceEEehHh
Confidence 489999999999864447889973
No 178
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=26.31 E-value=1.7e+02 Score=32.08 Aligned_cols=90 Identities=11% Similarity=0.099 Sum_probs=52.9
Q ss_pred HHHHHHhcC-CCCCCeeeecC-CCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC
Q 002191 751 YEAIIQSVN-PLIPPIFASDE-NACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (955)
Q Consensus 751 lr~i~e~~~-~~id~I~~~D~-~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~ 828 (955)
.|.++|++. .-..+++++.. +.+.+++|.-+..++||+.++++... .+ +. .+........+... ..
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k~qRllFAN~~fk~wtGy~~edFl~~~-~d-IV--------~eGl~qW~~dL~~~--s~ 352 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPKSQRLLFANSQFKTWTGYSSEDFLKDF-SD-IV--------QEGLAQWETDLQLL--SR 352 (401)
T ss_pred HHHHHhhhcccccceEEEecchhhHHHHhHHHHHHHhccCHHHHHhcc-hH-HH--------HhhHHHHHHHHHhh--hh
Confidence 455565541 11135777764 57899999999999999999987542 11 11 22232223333211 12
Q ss_pred CcceeeEEEEcCCCcEEEEEEEEe
Q 002191 829 GTENFPFGFFNRQGQFVEVALTAS 852 (955)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~ 852 (955)
...+....+.+|+|...++.....
T Consensus 353 ~E~~grlviKTK~~g~ipf~ycL~ 376 (401)
T PF06785_consen 353 QERSGRLVIKTKNGGNIPFYYCLG 376 (401)
T ss_pred hhhhceEEEEecCCCceeeEEEEe
Confidence 233455667889988776655543
No 179
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=24.74 E-value=5.7e+02 Score=32.57 Aligned_cols=41 Identities=15% Similarity=0.067 Sum_probs=31.3
Q ss_pred HHHHHhcCCCCCCeeeec-CCCcEeeecHHHHHHhCCChhhhccCCcc
Q 002191 752 EAIIQSVNPLIPPIFASD-ENACCSEWNAAMEKVTGWMRHEVIGKMLP 798 (955)
Q Consensus 752 r~i~e~~~~~id~I~~~D-~~g~i~~~N~a~~~l~G~~~eeviGk~~~ 798 (955)
+.++..+| -|++++| .+|.|.++|+.|.+++| .+ ++|+++.
T Consensus 105 ~~~l~~~p---~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~ 146 (838)
T PRK14538 105 EEVLNELP---IGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLA 146 (838)
T ss_pred HHHHHhCC---ceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHH
Confidence 34555555 3689999 79999999999999987 23 7888754
No 180
>PRK10963 hypothetical protein; Provisional
Probab=23.61 E-value=8.6e+02 Score=25.41 Aligned_cols=49 Identities=6% Similarity=-0.098 Sum_probs=36.3
Q ss_pred CceeEEEEEEEEcCCCCCceeEEEEeecCCCCCCChhH-HHHHHHHHHHHHHHHH
Q 002191 344 GSIASLVMAVIINSKDSMKLWGLVVCHHTSPRYIPFPL-RYACEFLVQAFSLQLY 397 (955)
Q Consensus 344 gv~asl~v~i~~~~~~~~~LWGll~~hh~~pr~~~~~~-r~~~~~l~~~~~~~l~ 397 (955)
+|+|.-.+|+.- + +..|+|+.=...|.++.+.. -.++++|+++++..|.
T Consensus 168 ~v~S~AllpL~~-~----~~~GlLalGS~D~~rF~~~mgT~fL~~la~vvs~~L~ 217 (223)
T PRK10963 168 AVGSVAMSLLGS-D----GDLGVLLFSSRDAQHYQQGQGTQLLQHLALMLPELLE 217 (223)
T ss_pred cCceeEEEeccC-C----CceEEEEEeCCChhhcCCCccHHHHHHHHHHHHHHHH
Confidence 578888888843 2 45999999888876666554 6778888888887664
No 181
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=23.37 E-value=4.4e+02 Score=31.65 Aligned_cols=91 Identities=14% Similarity=0.219 Sum_probs=53.4
Q ss_pred HHHHHHHHhcCCCCCCeeeecCCCcEeeecHHHHHHhCCChhhhccCCccchhcccchhccChhhHHHHHHHHHhhhcCC
Q 002191 749 GDYEAIIQSVNPLIPPIFASDENACCSEWNAAMEKVTGWMRHEVIGKMLPREIFGNFCRMKGQDMLTKFMILLYQGITGQ 828 (955)
Q Consensus 749 ~~lr~i~e~~~~~id~I~~~D~~g~i~~~N~a~~~l~G~~~eeviGk~~~~~~~~~~~~l~~~d~~~~~~~~l~~~~~g~ 828 (955)
..++.+-..+.. ..++++|.+|..+..+.. + .+..++|.++. |..++..+++|+
T Consensus 89 ~~L~~in~~a~s--s~iYlid~~G~~iaASNw-----~-~p~SFVG~nya------------------fRpYf~~Am~gg 142 (603)
T COG4191 89 RYLEQINEAAGS--SAIYLIDPTGLTLAASNW-----N-LPTSFVGRNYA------------------FRPYFQDAMAGG 142 (603)
T ss_pred HHHHHHHhhccC--CeEEEECCCCcEEeeccC-----C-CCCcccccCcc------------------cHHHHHHHHhcC
Confidence 334444444432 369999999998876542 1 13345666532 566788888888
Q ss_pred CcceeeEEEEcCCCcEEEEEEEEeeeeCCCCCEEEEEEEEec
Q 002191 829 GTENFPFGFFNRQGQFVEVALTASRRTDAEGKVIGCFCFMQI 870 (955)
Q Consensus 829 ~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~i~~D 870 (955)
....+-... -.|+ +-...+.|+.+.+| ++|++++--|
T Consensus 143 ~~r~yalGt--ts~~--pGyy~a~pV~~~~~-ilGvivvKvd 179 (603)
T COG4191 143 SGRFYALGT--TSGR--PGYYLAAPVDDGGG-ILGVIVVKVD 179 (603)
T ss_pred CceeEeecc--ccCC--CceeEeeeeccCCc-eeEEEEEEEe
Confidence 555443322 2232 22334567776555 9998887444
No 182
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.74 E-value=1.9e+02 Score=29.25 Aligned_cols=97 Identities=9% Similarity=0.007 Sum_probs=68.8
Q ss_pred cCcc-EEEEcCCCcE--eeecHHHHHHhCCCchhhcCCCccccccccccHHHHHHHHHHHHcCCCcceEEEEEEeeeecc
Q 002191 627 ATAP-IFGVDSSGTI--NGWNAKVAELTGLPASEAMGKSLIDEVVHEESQGAVENLICRALLGEEDKNVELKLRKFELQK 703 (955)
Q Consensus 627 ~~~~-I~~~D~dg~i--~~~N~~~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~~~~~~~~~ 703 (955)
.++- |+..|.+|.+ ..+-...|.+|| .|+-|..+. .++.+.+......++..+.....+.-+.... ...
T Consensus 57 L~d~FiL~~~~~G~~~FRLAGTriC~LfG---RELr~~~F~-sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg----~s~ 128 (209)
T COG5388 57 LPDVFILERDGRGKLPFRLAGTRICDLFG---RELRGRDFL-SLWAEADRLELKRAADGVRKRRTPVLVTADG----RSH 128 (209)
T ss_pred cCceEEEeccCCCCceEEecccchhhhhc---hhhcCCchh-HhccccchHHHHHHHHHHhhccCceEEecch----hhc
Confidence 3443 3333455644 446677788887 467788888 8899988888888888888776665444444 445
Q ss_pred CCcEEEEEEEEEEeecCCCCEEEEEEEE
Q 002191 704 QHSVVYILVNACTSRDYKNNVKGVCFVG 731 (955)
Q Consensus 704 dG~~~~v~v~~~pi~d~~g~v~gvv~v~ 731 (955)
.|...-+++-..|+....|+-..+.|.+
T Consensus 129 ~G~sl~fEmLl~PL~~~~g~~~R~LGai 156 (209)
T COG5388 129 GGRSLGFEMLLAPLQGASGETDRFLGAI 156 (209)
T ss_pred cCcccceeeeeecccCCCCCccchhhhc
Confidence 6777889999999998888865556555
No 183
>PF02070 NMU: Neuromedin U; InterPro: IPR008199 Neuromedin U (NmU) [, ] is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved.; GO: 0006940 regulation of smooth muscle contraction
Probab=22.53 E-value=60 Score=21.00 Aligned_cols=16 Identities=38% Similarity=0.372 Sum_probs=13.5
Q ss_pred hccCCCCCCccceEEE
Q 002191 86 KIQRGGLIQPFGCMLA 101 (955)
Q Consensus 86 ~i~~~g~iQp~G~ll~ 101 (955)
..|-||.||+-|..|.
T Consensus 6 e~QgP~~~qsrgyFlf 21 (25)
T PF02070_consen 6 EFQGPGGIQSRGYFLF 21 (25)
T ss_pred hccCCcccccccEEEe
Confidence 4688999999999874
No 184
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=21.88 E-value=2.2e+02 Score=34.08 Aligned_cols=56 Identities=14% Similarity=0.153 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhhhHhHhHHHHHHH----hcc--CCCCHHHHHHHHHHHHHHHHHHHhhcc
Q 002191 891 AKIKELAYIRQEVKNPLNGIRFVHKL----LES--SSISENQRQYLETSDACERQIMTIIDG 946 (955)
Q Consensus 891 ak~~fla~iSHELRnPL~~I~g~~~L----L~~--~~l~~~~~~~l~~i~~~a~rl~~LI~D 946 (955)
+..+....++||+++|++.++.+..+ +.. ....++..+.+..+.....++...+.+
T Consensus 359 ~~~~~~~~la~el~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~ 420 (565)
T PRK10935 359 LLMEERATIARELHDSLAQVLSYLKIQLTLLKRSLDEDNAKAQSIIAEFDQALSDAYRQLRE 420 (565)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456677999999999988866543 332 122345556666666666666666555
No 185
>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=21.43 E-value=1.1e+02 Score=25.71 Aligned_cols=24 Identities=33% Similarity=0.631 Sum_probs=17.7
Q ss_pred EEEECCeEEEecCCCCHHHHHHHH
Q 002191 447 ALYYGGRCWLVGVTPTESQLKDIA 470 (955)
Q Consensus 447 a~~~~~~~~~~G~~p~~~~~~~l~ 470 (955)
+++.||+..+.|..|+.+++..++
T Consensus 52 alvIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 52 ALVINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EEEETTEEEEESS--HHHHHHHHH
T ss_pred EEEECCEEEEEecCCCHHHHHHHh
Confidence 457899999999999988776654
No 186
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=20.65 E-value=94 Score=25.84 Aligned_cols=47 Identities=19% Similarity=0.360 Sum_probs=29.3
Q ss_pred hhHhHhHHHHHHHhccCCCCHH-HHHHHHHHHHHHHHHHHhhcc--cCcccccc
Q 002191 904 KNPLNGIRFVHKLLESSSISEN-QRQYLETSDACERQIMTIIDG--MDLRCIEE 954 (955)
Q Consensus 904 RnPL~~I~g~~~LL~~~~l~~~-~~~~l~~i~~~a~rl~~LI~D--Ld~SrIea 954 (955)
.|||.++....+| .+.++ .+..+...-..-.-+..-++. |||||.|+
T Consensus 27 ~NPl~AMa~i~qL----Gip~eKLQ~lm~~VMqnP~LikeAv~ELgLDFsKve~ 76 (82)
T PF11212_consen 27 QNPLAAMATIQQL----GIPQEKLQQLMAQVMQNPALIKEAVEELGLDFSKVEA 76 (82)
T ss_pred hCHHHHHHHHHHc----CCCHHHHHHHHHHHhcChHHHHHHHHHhCCcHHHHHH
Confidence 4888877655443 34444 444555544445556666777 89999985
Done!