Query 023651
Match_columns 279
No_of_seqs 398 out of 3049
Neff 10.0
Searched_HMMs 46136
Date Fri Mar 29 05:37:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023651.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023651hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11091 aerobic respiration c 99.8 8.4E-20 1.8E-24 174.4 17.3 192 15-228 152-352 (779)
2 PF13426 PAS_9: PAS domain; PD 99.8 8.1E-18 1.8E-22 119.8 14.0 104 28-135 1-104 (104)
3 PRK13559 hypothetical protein; 99.7 3.3E-16 7.2E-21 136.7 16.4 183 15-220 40-227 (361)
4 PF08448 PAS_4: PAS fold; Int 99.7 1.6E-16 3.5E-21 114.3 11.9 110 24-138 1-110 (110)
5 PRK13557 histidine kinase; Pro 99.7 3.8E-16 8.2E-21 143.2 17.4 189 15-221 27-229 (540)
6 PF00989 PAS: PAS fold; Inter 99.7 3.9E-16 8.6E-21 112.8 12.4 112 18-133 1-113 (113)
7 PRK13560 hypothetical protein; 99.6 2.3E-14 4.9E-19 137.6 20.7 133 6-143 193-327 (807)
8 TIGR02938 nifL_nitrog nitrogen 99.6 6.8E-15 1.5E-19 133.2 14.6 122 18-143 4-125 (494)
9 PRK10060 RNase II stability mo 99.6 1.7E-14 3.7E-19 135.3 17.2 136 16-156 109-252 (663)
10 PRK09776 putative diguanylate 99.6 2.4E-14 5.2E-19 141.8 18.1 161 7-172 526-699 (1092)
11 PRK09776 putative diguanylate 99.6 1.3E-13 2.9E-18 136.6 17.4 125 15-143 280-405 (1092)
12 COG5002 VicK Signal transducti 99.5 2E-13 4.3E-18 112.9 12.4 179 15-229 108-297 (459)
13 TIGR02040 PpsR-CrtJ transcript 99.5 7.7E-13 1.7E-17 118.7 16.1 117 15-140 130-247 (442)
14 PRK13558 bacterio-opsin activa 99.5 8.8E-13 1.9E-17 124.2 16.1 125 19-144 149-273 (665)
15 TIGR02966 phoR_proteo phosphat 99.5 9.1E-13 2E-17 113.2 13.1 165 15-221 3-177 (333)
16 PRK11073 glnL nitrogen regulat 99.4 1.3E-12 2.9E-17 113.4 13.0 176 18-220 7-190 (348)
17 PRK11360 sensory histidine kin 99.4 4.1E-12 8.9E-17 117.8 15.4 184 15-221 259-451 (607)
18 TIGR02040 PpsR-CrtJ transcript 99.4 2.4E-12 5.2E-17 115.5 13.0 117 18-141 252-369 (442)
19 PRK11006 phoR phosphate regulo 99.4 1E-12 2.2E-17 117.6 10.1 163 15-221 95-266 (430)
20 TIGR00229 sensory_box PAS doma 99.4 1.3E-11 2.9E-16 87.1 13.3 120 18-142 3-123 (124)
21 PRK13560 hypothetical protein; 99.3 2.2E-11 4.9E-16 116.9 14.3 134 6-144 321-473 (807)
22 PRK11359 cyclic-di-GMP phospho 99.3 5.2E-11 1.1E-15 114.5 13.9 123 16-142 134-257 (799)
23 TIGR02938 nifL_nitrog nitrogen 99.3 6.1E-12 1.3E-16 113.9 6.2 161 8-185 121-293 (494)
24 PF08447 PAS_3: PAS fold; Int 99.3 4.3E-11 9.4E-16 83.0 8.6 86 43-130 1-91 (91)
25 PRK11359 cyclic-di-GMP phospho 99.2 2.5E-10 5.4E-15 109.8 14.6 117 19-141 13-133 (799)
26 PRK09959 hybrid sensory histid 99.2 1E-09 2.2E-14 110.1 17.0 195 15-226 573-780 (1197)
27 cd00130 PAS PAS domain; PAS mo 99.1 3.7E-09 8.1E-14 71.0 13.5 103 27-133 1-103 (103)
28 COG5000 NtrY Signal transducti 99.1 3.3E-09 7.2E-14 94.2 15.2 172 15-221 367-553 (712)
29 PF12860 PAS_7: PAS fold 99.1 7.7E-10 1.7E-14 80.4 8.4 105 24-141 1-115 (115)
30 PF13596 PAS_10: PAS domain; P 99.1 2.2E-09 4.8E-14 76.7 10.4 106 20-134 1-106 (106)
31 KOG0501 K+-channel KCNQ [Inorg 98.9 6.1E-09 1.3E-13 91.7 9.1 120 19-139 15-139 (971)
32 PRK11086 sensory histidine kin 98.9 1.8E-08 3.9E-13 92.7 12.1 136 15-185 218-356 (542)
33 COG3852 NtrB Signal transducti 98.8 1.1E-07 2.4E-12 78.1 12.4 216 21-271 10-239 (363)
34 PF14598 PAS_11: PAS domain; P 98.8 2.3E-07 4.9E-12 66.8 12.2 101 32-135 6-108 (111)
35 PRK10841 hybrid sensory kinase 98.6 7.2E-07 1.6E-11 87.0 14.0 176 15-228 331-516 (924)
36 PRK10820 DNA-binding transcrip 98.6 3.5E-07 7.6E-12 83.5 10.8 110 15-138 77-190 (520)
37 PRK15053 dpiB sensor histidine 98.5 4.3E-07 9.3E-12 83.8 9.8 110 17-143 221-332 (545)
38 PRK10618 phosphotransfer inter 98.5 5.9E-07 1.3E-11 86.8 10.0 171 15-229 340-520 (894)
39 COG3829 RocR Transcriptional r 98.5 6.8E-07 1.5E-11 79.3 9.1 116 15-143 114-229 (560)
40 COG2202 AtoS FOG: PAS/PAC doma 98.5 9.5E-06 2.1E-10 62.5 14.5 120 15-139 109-231 (232)
41 PF13188 PAS_8: PAS domain; PD 98.4 8.1E-07 1.8E-11 57.1 4.8 42 18-66 1-42 (64)
42 COG3290 CitA Signal transducti 98.3 3.3E-06 7.2E-11 74.9 8.7 113 16-143 213-327 (537)
43 KOG1229 3'5'-cyclic nucleotide 98.2 1.3E-06 2.8E-11 75.0 3.2 105 20-128 159-264 (775)
44 PRK11388 DNA-binding transcrip 98.0 0.00011 2.4E-09 69.2 12.9 108 19-138 204-311 (638)
45 KOG3558 Hypoxia-inducible fact 97.5 0.00017 3.7E-09 65.5 5.9 95 34-131 280-374 (768)
46 PF08670 MEKHLA: MEKHLA domain 97.5 0.004 8.7E-08 46.7 12.1 113 18-133 32-145 (148)
47 smart00091 PAS PAS domain. PAS 97.5 0.00039 8.5E-09 41.9 5.8 55 19-76 2-56 (67)
48 COG2461 Uncharacterized conser 97.2 0.0018 3.8E-08 55.5 7.7 115 17-141 289-403 (409)
49 TIGR02373 photo_yellow photoac 96.8 0.018 3.8E-07 41.5 9.0 67 21-90 19-86 (124)
50 COG3283 TyrR Transcriptional r 96.7 0.0059 1.3E-07 52.1 6.7 55 17-74 79-133 (511)
51 smart00086 PAC Motif C-termina 96.6 0.019 4.1E-07 30.5 6.9 40 96-136 4-43 (43)
52 COG3829 RocR Transcriptional r 95.8 0.12 2.5E-06 46.9 10.3 104 21-139 4-107 (560)
53 PF07310 PAS_5: PAS domain; I 95.6 0.24 5.1E-06 36.9 10.0 86 41-130 51-136 (137)
54 PRK11388 DNA-binding transcrip 94.7 0.84 1.8E-05 43.3 13.4 100 18-133 62-167 (638)
55 COG2205 KdpD Osmosensitive K+ 94.5 0.071 1.5E-06 50.4 5.3 153 113-275 597-777 (890)
56 KOG3560 Aryl-hydrocarbon recep 94.3 0.19 4.1E-06 45.1 7.3 93 41-135 293-385 (712)
57 KOG3561 Aryl-hydrocarbon recep 93.8 0.065 1.4E-06 50.9 3.7 54 19-75 96-149 (803)
58 PF00512 HisKA: His Kinase A ( 93.7 0.0079 1.7E-07 38.7 -1.7 53 171-223 5-68 (68)
59 KOG3558 Hypoxia-inducible fact 91.7 0.29 6.3E-06 45.3 4.8 57 23-82 124-180 (768)
60 COG4191 Signal transduction hi 89.4 0.26 5.7E-06 45.0 2.4 103 169-275 381-499 (603)
61 PF13188 PAS_8: PAS domain; PD 89.4 0.43 9.3E-06 29.9 2.8 32 243-278 3-34 (64)
62 KOG3559 Transcriptional regula 89.2 0.81 1.8E-05 39.7 5.0 84 31-117 228-311 (598)
63 PRK13837 two-component VirA-li 88.2 4.5 9.8E-05 39.7 10.2 52 170-221 452-512 (828)
64 PF08446 PAS_2: PAS fold; Int 85.7 0.75 1.6E-05 32.8 2.5 43 30-74 17-62 (110)
65 KOG3560 Aryl-hydrocarbon recep 85.7 0.9 2E-05 41.0 3.5 59 22-83 115-173 (712)
66 PF08348 PAS_6: YheO-like PAS 85.2 5.9 0.00013 28.6 7.0 48 92-142 68-115 (118)
67 KOG3753 Circadian clock protei 83.1 3.4 7.3E-05 39.7 6.1 74 39-112 339-415 (1114)
68 PRK09303 adaptive-response sen 82.7 1 2.2E-05 39.7 2.6 57 169-225 152-224 (380)
69 PRK13557 histidine kinase; Pro 82.2 1.6 3.5E-05 40.0 3.9 36 243-278 32-67 (540)
70 PRK10490 sensor protein KdpD; 81.4 5.1 0.00011 39.8 7.1 61 169-229 665-736 (895)
71 PRK13559 hypothetical protein; 80.0 2.3 5E-05 36.9 3.9 36 243-278 45-80 (361)
72 COG3887 Predicted signaling pr 78.8 5.6 0.00012 36.7 5.9 42 12-56 69-110 (655)
73 PF09884 DUF2111: Uncharacteri 76.6 17 0.00038 24.1 6.1 46 83-134 38-83 (84)
74 KOG3559 Transcriptional regula 75.0 3.4 7.3E-05 36.1 3.3 54 21-77 82-135 (598)
75 PRK14538 putative bifunctional 74.6 11 0.00024 37.0 6.9 46 17-68 101-147 (838)
76 COG4251 Bacteriophytochrome (l 74.4 2.7 5.9E-05 39.1 2.7 87 174-274 530-637 (750)
77 COG5388 Uncharacterized protei 73.0 27 0.00059 27.4 7.4 106 22-133 52-159 (209)
78 TIGR02956 TMAO_torS TMAO reduc 71.8 1 2.2E-05 44.9 -0.7 60 169-228 465-533 (968)
79 PRK13719 conjugal transfer tra 70.9 8.4 0.00018 31.0 4.4 39 17-58 18-56 (217)
80 COG4192 Signal transduction hi 70.1 1.9 4.2E-05 38.5 0.8 56 171-226 454-521 (673)
81 PRK11107 hybrid sensory histid 68.5 1.5 3.1E-05 43.4 -0.3 60 169-228 294-362 (919)
82 PRK15347 two component system 65.8 2.3 5E-05 42.1 0.4 61 169-229 399-468 (921)
83 PF06785 UPF0242: Uncharacteri 62.1 22 0.00048 30.4 5.4 88 20-115 285-378 (401)
84 COG3284 AcoR Transcriptional a 55.0 70 0.0015 30.1 7.8 102 18-130 77-179 (606)
85 PRK15053 dpiB sensor histidine 52.3 67 0.0014 29.6 7.6 33 243-278 224-256 (545)
86 KOG3753 Circadian clock protei 52.1 12 0.00026 36.2 2.6 43 31-76 195-237 (1114)
87 PRK10060 RNase II stability mo 49.9 17 0.00037 34.8 3.3 32 244-278 114-145 (663)
88 KOG3561 Aryl-hydrocarbon recep 49.6 17 0.00037 35.2 3.2 94 41-134 382-476 (803)
89 PRK11466 hybrid sensory histid 47.3 9 0.00019 38.0 1.1 55 169-223 445-508 (914)
90 PF09308 LuxQ-periplasm: LuxQ, 43.0 1.9E+02 0.0041 23.8 9.8 85 26-135 70-154 (238)
91 cd00082 HisKA Histidine Kinase 40.8 10 0.00023 22.6 0.3 19 202-220 47-65 (65)
92 COG4048 Uncharacterized protei 38.4 1.2E+02 0.0026 21.4 5.1 47 83-136 56-102 (123)
93 PF02743 Cache_1: Cache domain 34.8 1.3E+02 0.0027 19.4 5.3 34 105-139 11-44 (81)
94 COG2202 AtoS FOG: PAS/PAC doma 34.1 1.8E+02 0.0038 20.9 11.2 28 33-63 4-31 (232)
95 PRK10604 sensor protein RstB; 31.8 21 0.00045 32.0 0.8 51 170-221 214-268 (433)
96 PRK10337 sensor protein QseC; 31.4 34 0.00074 30.6 2.2 51 171-221 240-299 (449)
97 smart00388 HisKA His Kinase A 31.3 16 0.00034 21.9 -0.0 49 173-221 7-63 (66)
98 PF14827 Cache_3: Sensory doma 29.2 1E+02 0.0023 21.7 4.0 74 29-133 40-113 (116)
99 PRK11006 phoR phosphate regulo 27.9 47 0.001 29.6 2.4 33 243-278 100-132 (430)
100 PRK10549 signal transduction h 26.7 40 0.00087 30.2 1.8 57 170-226 242-306 (466)
101 PRK10755 sensor protein BasS/P 25.0 50 0.0011 28.4 2.0 51 170-222 139-194 (356)
102 PF12218 End_N_terminal: N ter 24.6 57 0.0012 20.5 1.6 19 255-273 48-66 (67)
103 PRK13558 bacterio-opsin activa 24.1 93 0.002 29.6 3.8 33 246-278 153-185 (665)
104 COG5001 Predicted signal trans 22.3 55 0.0012 29.3 1.6 23 151-173 238-263 (663)
105 PRK11086 sensory histidine kin 21.6 96 0.0021 28.4 3.3 33 243-278 223-255 (542)
106 PF10114 PocR: Sensory domain 21.4 3.6E+02 0.0079 20.3 9.0 28 16-46 10-37 (173)
107 PF12282 H_kinase_N: Signal tr 21.2 3.6E+02 0.0077 20.1 8.0 52 82-138 81-132 (145)
108 TIGR02916 PEP_his_kin putative 21.0 1.8E+02 0.0039 28.0 5.0 23 111-135 413-435 (679)
109 KOG1229 3'5'-cyclic nucleotide 20.7 31 0.00068 30.8 -0.1 33 243-278 159-191 (775)
110 PRK11091 aerobic respiration c 20.3 1.1E+02 0.0024 29.9 3.5 33 243-278 157-189 (779)
111 COG0093 RplN Ribosomal protein 20.1 1.1E+02 0.0025 21.9 2.6 28 98-126 69-96 (122)
No 1
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.84 E-value=8.4e-20 Score=174.43 Aligned_cols=192 Identities=13% Similarity=0.127 Sum_probs=150.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
+.+++++.+++++|++++++|.+ |+|+++|+++++++||+.++++|+++..+++++...............+.++..
T Consensus 152 ~~~~~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (779)
T PRK11091 152 QQSSLLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTY 228 (779)
T ss_pred HHHHHHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEE
Confidence 45567899999999999999999 999999999999999999999999988877765555555555666677778888
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcccee
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~ 174 (279)
+.+...++|..+|+.++..|+.+ .+|.+.|++++++|||++|++|+++.. + .+ ....++..
T Consensus 229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~l~~-------------a----~~-~~~~~~a~ 289 (779)
T PRK11091 229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQDALEK-------------A----SR-DKTTFIST 289 (779)
T ss_pred EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHHHHHHH-------------H----HH-HHHHHHHH
Confidence 88889999999999999999998 899999999999999999999766521 1 11 12457779
Q ss_pred ccccccccCCCC-----ccccccc---ccccHHHHHHHHhhhhhHhhhhhccccc-ccccccc
Q 023651 175 LDRVLALDSDDT-----GLEIEDS---CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCG 228 (279)
Q Consensus 175 ~~~~l~~~~~~~-----~~~~~~~---~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~ 228 (279)
++|++++|++.- .+..... .......+..+..++..+++++++++++ .+.+...
T Consensus 290 isHelrtPL~~I~g~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~ 352 (779)
T PRK11091 290 ISHELRTPLNGIVGLSRILLDTELTAEQRKYLKTIHVSAITLGNIFNDIIDMDKMERRKLQLD 352 (779)
T ss_pred hhHhhcCcHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhCCCcEEE
Confidence 999999999871 1111111 1112223456778899999999999988 6665443
No 2
>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=99.78 E-value=8.1e-18 Score=119.76 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=95.6
Q ss_pred CCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEE
Q 023651 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (279)
Q Consensus 28 ~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~ 107 (279)
|++++++|.+ |.|+++|+++++++||++++++|+++..++++.........+.+.+..+..+..+....+++|..+|
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 6899999999 9999999999999999999999999988888877888888899999989999999999999999999
Q ss_pred EEEEEEEeeecCCCcEEEEEEEEeccch
Q 023651 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (279)
Q Consensus 108 ~~~~~~pi~~~~~g~~~~~v~~~~DITe 135 (279)
+.+++.|+.+ ++|++.+++++++||||
T Consensus 78 ~~~~~~~i~~-~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 78 VEVSASPIRD-EDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEE-TTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEC-CCCCEEEEEEEEEECCC
Confidence 9999999999 89999999999999996
No 3
>PRK13559 hypothetical protein; Provisional
Probab=99.71 E-value=3.3e-16 Score=136.72 Aligned_cols=183 Identities=28% Similarity=0.406 Sum_probs=134.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
...+.++.+++.++++++++|.+.++|.++++|+++++++||+.++++|+++..+..+.........+...+..+..+..
T Consensus 40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (361)
T PRK13559 40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVV 119 (361)
T ss_pred hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEE
Confidence 34567888999999999999974223789999999999999999999999987776666666666667777777788888
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcccee
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~ 174 (279)
+....+++|..+|+.++..|+.+ .+|.+.+++++++|||++|+.+++.. . . ..++.+
T Consensus 120 e~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e~~~~--------------~---~-----~~l~~~ 176 (361)
T PRK13559 120 ELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVRALEA--------------H---E-----RRLARE 176 (361)
T ss_pred EEEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhHHHHH--------------H---H-----HHHHHH
Confidence 88888999999999999999998 89999999999999999998854321 1 1 112346
Q ss_pred ccccccccCCC-----CcccccccccccHHHHHHHHhhhhhHhhhhhcccc
Q 023651 175 LDRVLALDSDD-----TGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQ 220 (279)
Q Consensus 175 ~~~~l~~~~~~-----~~~~~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~ 220 (279)
++|.+++++.. ...............+...+.++.+++.+|++.++
T Consensus 177 l~H~~~n~L~~i~~~~~l~~~~~~~~~~~~~i~~~~~~l~~~~~~ll~~~~ 227 (361)
T PRK13559 177 VDHRSKNVFAVVDSIVRLTGRADDPSLYAAAIQERVQALARAHETLLDERG 227 (361)
T ss_pred HHHhhhhHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 78888888744 11111111111122334455667777777776554
No 4
>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=99.71 E-value=1.6e-16 Score=114.27 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=97.7
Q ss_pred HhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCC
Q 023651 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (279)
Q Consensus 24 l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG 103 (279)
++++|++++++|.+ |+|+++|+++.+++|++.++++|+++..++++...+.+...+.+++.++.+...+..... +|
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 76 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG 76 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence 57899999999999 999999999999999999999999988888777777788888888888777766655544 89
Q ss_pred ceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHH
Q 023651 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (279)
Q Consensus 104 ~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~ 138 (279)
..+|+.++..|+.+ .+|.+.|++++++|||++|+
T Consensus 77 ~~~~~~~~~~Pi~~-~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 77 EERWFEVSISPIFD-EDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp CEEEEEEEEEEEEC-TTTCEEEEEEEEEEECCHHH
T ss_pred CcEEEEEEEEEeEc-CCCCEEEEEEEEEECchhhC
Confidence 99999999999999 89999999999999999985
No 5
>PRK13557 histidine kinase; Provisional
Probab=99.71 E-value=3.8e-16 Score=143.18 Aligned_cols=189 Identities=29% Similarity=0.457 Sum_probs=141.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
....+|+.+++.++++++++|.+..+|+|+|+|++|++++||+.++++|+++..+.+++........+...+..+..+..
T Consensus 27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (540)
T PRK13557 27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIAT 106 (540)
T ss_pred hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceE
Confidence 44678999999999999999963223999999999999999999999999988888777777777777788888888888
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhcc-ccCCccce
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRR-EVCSDSLL 173 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r-~~~~~~l~ 173 (279)
+....+++|..+|+.++..|+.+ .+|.+.+++++.+|||+++++++++.. .++ +.....+.
T Consensus 107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~l~~-----------------~~~~~~l~~~~~ 168 (540)
T PRK13557 107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDALRQ-----------------AQKMEALGQLTG 168 (540)
T ss_pred EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHHHHH-----------------HHHHHHhhhhhh
Confidence 88888999999999999999998 899999999999999999998665421 111 11122344
Q ss_pred eccccccccCCCC-----ccc----ccccc----cccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 174 DLDRVLALDSDDT-----GLE----IEDSC----EASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 174 ~~~~~l~~~~~~~-----~~~----~~~~~----~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
.++|++++|+... .+. ..... ......+.....++..++.+|+.+++.
T Consensus 169 ~i~h~l~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~li~~l~~~~~~ 229 (540)
T PRK13557 169 GIAHDFNNLLQVMSGYLDVIQAALSHPDADRGRMARSVENIRAAAERAATLTQQLLAFARK 229 (540)
T ss_pred hhhHHhhhHHHHHHhHHHHHHHhhccCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 6788888877541 111 00011 111222345667888888888888764
No 6
>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=99.70 E-value=3.9e-16 Score=112.78 Aligned_cols=112 Identities=23% Similarity=0.363 Sum_probs=93.9
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE-EE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV-NL 96 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-e~ 96 (279)
++++.++++++++++++|.+ |+|+++|+++++++||++++++|+++..+.++++.......+...+..+..... +.
T Consensus 1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV 77 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence 47899999999999999999 999999999999999999999999988887766555566677777766665433 44
Q ss_pred EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEecc
Q 023651 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 97 ~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
....++|..+|+.+...|+.+ .+|.+.+++++++||
T Consensus 78 ~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 78 RFRLRDGRPRWVEVRASPVRD-EDGQIIGILVIFRDI 113 (113)
T ss_dssp EEEETTSCEEEEEEEEEEEEE-TTEEEEEEEEEEEE-
T ss_pred EEEecCCcEEEEEEEEEEEEe-CCCCEEEEEEEEEeC
Confidence 444469999999999999999 889999999999997
No 7
>PRK13560 hypothetical protein; Provisional
Probab=99.64 E-value=2.3e-14 Score=137.56 Aligned_cols=133 Identities=14% Similarity=0.112 Sum_probs=108.2
Q ss_pred hHHHHHhhHHHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHH
Q 023651 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREA 85 (279)
Q Consensus 6 ~~~~~~l~~~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~ 85 (279)
++.++.+. +.+++++.+++++|++++++|.+ |+++++|+++++++||++++++|+++..+.++.............
T Consensus 193 k~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~ 268 (807)
T PRK13560 193 KRAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAK 268 (807)
T ss_pred HHHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHH
Confidence 34455555 66789999999999999999999 999999999999999999999999988877655444443444455
Q ss_pred HHhCCCeEEEEEEEcCCCceEEEEEEE--EEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 86 IREERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 86 ~~~~~~~~~e~~~~~~dG~~~~~~~~~--~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
+..++....+....+++|..+|+.+.. .|+.+ .+|.+.+++++++|||++|++|+++
T Consensus 269 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e~~L 327 (807)
T PRK13560 269 FDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAEREL 327 (807)
T ss_pred hccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHHHHH
Confidence 556667778888899999999776554 55667 7899999999999999999997655
No 8
>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=99.62 E-value=6.8e-15 Score=133.19 Aligned_cols=122 Identities=25% Similarity=0.455 Sum_probs=106.1
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (279)
+.++.+++.++++++++|.+ |+++|+|+++++++||++++++|++...+..+.........+...+..+.++..+..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80 (494)
T ss_pred HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence 46899999999999999999 999999999999999999999999866666555555566666677777778877877
Q ss_pred EEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 98 ~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
..+++|..+|+.....|+.+ .+|.+.+++++++|||++|++++++
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~l 125 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQVV 125 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHHH
Confidence 88899999999999999998 8999999999999999999986544
No 9
>PRK10060 RNase II stability modulator; Provisional
Probab=99.62 E-value=1.7e-14 Score=135.28 Aligned_cols=136 Identities=13% Similarity=0.204 Sum_probs=108.5
Q ss_pred HHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCC-CCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 16 ~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
...+++.+++.++++|+++|.+ |+|+++|+++++++||+.++++|+++..++ ++.........+...+..+..+..
T Consensus 109 ~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (663)
T PRK10060 109 GLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV 185 (663)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence 3457788999999999999999 999999999999999999999999975544 444444455566667778888889
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCc-EEEEEEEEeccchhHHHHhcc--cccccc--C--Cchhhh
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGR-ATHFVAVQVPIVSRKHMRNSG--MSYSED--G--GGSRLR 156 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~-~~~~v~~~~DITerk~~e~~l--~~~~~d--g--NR~l~~ 156 (279)
+.+..+++|..+|+.....+. + ..|. ..+++++.+|||++|+.++++ .+.+|. | ||..|.
T Consensus 186 e~~~~~~~G~~~~~~~~~~~~-~-~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~ 252 (663)
T PRK10060 186 ERWIKTRKGQRLFLFRNKFVH-S-GSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQ 252 (663)
T ss_pred EEEEEeCCCCEEEEEeeeEEE-c-CCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHH
Confidence 999999999988876554444 3 3443 456889999999999999998 344555 5 999999
No 10
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.61 E-value=2.4e-14 Score=141.78 Aligned_cols=161 Identities=13% Similarity=0.166 Sum_probs=121.6
Q ss_pred HHHHHhhHHHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCC--CCHHHHHHHHH
Q 023651 7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR--TNRRTIMEIRE 84 (279)
Q Consensus 7 ~~~~~l~~~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~--~~~~~~~~~~~ 84 (279)
+.++.+. +.+++++.++++++++++.+|.+ |+++++|+++++++||+.++++|+++..+.+.. ........+..
T Consensus 526 ~~e~~L~-~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~ 601 (1092)
T PRK09776 526 QLNEALF-QEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYS 601 (1092)
T ss_pred HHHHHHH-HHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHH
Confidence 3444554 66778999999999999999999 999999999999999999999999865544321 11112222344
Q ss_pred HHHhCCC--eEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc--cccccc--C--Cchhhh
Q 023651 85 AIREERP--IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG--MSYSED--G--GGSRLR 156 (279)
Q Consensus 85 ~~~~~~~--~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l--~~~~~d--g--NR~l~~ 156 (279)
....... ...+....+++|..+|+..+..|+.+ .+|.+.|++++.+|||++|+.|+++ .+.||. | ||+.|.
T Consensus 602 ~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~L~~~a~~D~lTgl~nr~~f~ 680 (1092)
T PRK09776 602 CLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLST-LDGENIGSVLVIQDVTESRKMLRQLSYSASHDALTHLANRASFE 680 (1092)
T ss_pred HHhcCCCccccceEEEEeCCCcEEEEEEEeeeeec-CCCCEEEEEEEEEecchHHHHHHHHHhhcCCCcccCCccHHHHH
Confidence 4433333 44567778999999999999999999 8999999999999999999999998 344555 5 999998
Q ss_pred ---HHHHHhhccccCCccc
Q 023651 157 ---EIVFGSCRREVCSDSL 172 (279)
Q Consensus 157 ---~~~l~~~~r~~~~~~l 172 (279)
++.+....+.....++
T Consensus 681 ~~l~~~~~~~~~~~~~~~l 699 (1092)
T PRK09776 681 KQLRRLLQTVNSTHQRHAL 699 (1092)
T ss_pred HHHHHHHHHHHhcCCcEEE
Confidence 4455554444444444
No 11
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.56 E-value=1.3e-13 Score=136.56 Aligned_cols=125 Identities=17% Similarity=0.286 Sum_probs=107.4
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhC-CCeE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (279)
+.+++++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.++++.......+.....+. ..+.
T Consensus 280 ~~e~r~~~l~e~~~~~i~~~d~d---G~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~ 356 (1092)
T PRK09776 280 ESETRFRNAMEYSAIGMALVGTE---GQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYS 356 (1092)
T ss_pred HHHHHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCcccee
Confidence 56788999999999999999999 9999999999999999999999999888877776665555544444333 3456
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
.+.+..+++|+.+|+.....|+.+ .+|.+.+++++.+|||++|++|+++
T Consensus 357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l 405 (1092)
T PRK09776 357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVN 405 (1092)
T ss_pred eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHH
Confidence 788889999999999999999998 8999999999999999999997665
No 12
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=99.52 E-value=2e-13 Score=112.91 Aligned_cols=179 Identities=13% Similarity=0.165 Sum_probs=129.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
....++.+++..+.+|++.+|.. |+|+.+|..+.+++|.+.++++|++.-.+..-.+.-. +.+..........
T Consensus 108 ~Er~kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~----~~dL~e~~~s~ll 180 (459)
T COG5002 108 QERRKLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYT----FEDLVEKNDSLLL 180 (459)
T ss_pred HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee----HHHHHhcCCcEEE
Confidence 45578999999999999999999 9999999999999999999999998655543332222 2233333333332
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcccee
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~ 174 (279)
+. ...++...+.+..+.+.. +.|-+.|++++..|+||+.+.|++. ..|+++
T Consensus 181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~e~Er-------------------------Refvan 231 (459)
T COG5002 181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKVERER-------------------------REFVAN 231 (459)
T ss_pred ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHHHHHH-------------------------HHHHHh
Confidence 22 236777778888888888 8999999999999999999886543 457889
Q ss_pred ccccccccCCCC-----cccccccc-----cccHHHHHHHHhhhhhHhhhhhccccc-cccccccc
Q 023651 175 LDRVLALDSDDT-----GLEIEDSC-----EASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCGK 229 (279)
Q Consensus 175 ~~~~l~~~~~~~-----~~~~~~~~-----~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~~ 229 (279)
+||++|+|+... .++...+. .......+.-..+|-+++++|+..||+ .+...+.+
T Consensus 232 vSHElRTPltsmksyLEALe~ga~~d~eiAp~Fl~vt~~ETeRMiRlV~DLl~lsr~d~~~~qln~ 297 (459)
T COG5002 232 VSHELRTPLTSMKSYLEALEEGAWEDKEIAPRFLRVTLNETERMIRLVNDLLQLSRMDNARYQLNK 297 (459)
T ss_pred cchhhcCchHHHHHHHHHHhcCCccChhhhhHHHHHhHHHHHHHHHHHHHHHHHccCcchhhhhhH
Confidence 999999999761 12222222 111212234667999999999999999 44444333
No 13
>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=99.50 E-value=7.7e-13 Score=118.71 Aligned_cols=117 Identities=16% Similarity=0.163 Sum_probs=86.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEcC-CCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeE
Q 023651 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~-~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
..+++++.+++.+++++|++|. + |.|+++|+++++++||++++++|+++..++++++.......+......+....
T Consensus 130 ~~e~r~~~l~e~~~~~i~~~d~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~ 206 (442)
T TIGR02040 130 EMETRYRVVLEVSSDAVLLVDMST---GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAAP 206 (442)
T ss_pred HHHHHHHHHHhhCCceEEEEECCC---CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCcc
Confidence 4567899999999999999997 8 99999999999999999999999998777776666655666666665555544
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHH
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e 140 (279)
.++. .++|...| .+...++.. +|. ..+++...|||++++++
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~e 247 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPVG 247 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhhh
Confidence 4444 23343344 345566654 443 36778889999988763
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.49 E-value=8.8e-13 Score=124.22 Aligned_cols=125 Identities=38% Similarity=0.695 Sum_probs=108.3
Q ss_pred HHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 023651 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (279)
Q Consensus 19 ~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (279)
.++.+++.++.++++.|...++|.++|+|+++++++||++++++|+++..+.++.........+...+..+.++..++..
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 228 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRN 228 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEE
Confidence 45678999999999998532339999999999999999999999999877777666666666667777778888889999
Q ss_pred EcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccc
Q 023651 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM 144 (279)
Q Consensus 99 ~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~ 144 (279)
++++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++|+++.
T Consensus 229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L~ 273 (665)
T PRK13558 229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELALQ 273 (665)
T ss_pred ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHHH
Confidence 9999999999999999998 89999999999999999999988774
No 15
>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=99.46 E-value=9.1e-13 Score=113.21 Aligned_cols=165 Identities=11% Similarity=0.054 Sum_probs=115.5
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
+..++++.++++++++++++|.+ |.++++|+++++++|+++++.+|+++..+..+ +. +...+..+.. ..
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~---~~----~~~~l~~~~~-~~ 71 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRH---PE----FVEYLAAGRF-SE 71 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccC---HH----HHHHHHhccc-CC
Confidence 45568899999999999999999 99999999999999999999999987666442 22 2223322222 22
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcccee
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~ 174 (279)
......+.|..+|+.+...|+.+ +. ++++++|||++++.++.. ..++..
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~---~~---~~~~~~dit~~~~~~~~~-------------------------~~~~~~ 120 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE---EQ---KLLVARDVTRLRRLEQMR-------------------------RDFVAN 120 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC---Cc---eEEEEeCchHHHHHHHHH-------------------------HHHHHh
Confidence 24445578888999999999875 22 678899999998874432 123456
Q ss_pred ccccccccCCCC-----ccccc--ccc---cccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 175 LDRVLALDSDDT-----GLEIE--DSC---EASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 175 ~~~~l~~~~~~~-----~~~~~--~~~---~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
++|++++|++.- .+... ... ......+..+...+..++..++.++++
T Consensus 121 l~h~l~~pL~~i~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~l~~~i~~l~~~~~~ 177 (333)
T TIGR02966 121 VSHELRTPLTVLRGYLETLADGPDEDPEEWNRALEIMLEQSQRMQSLVEDLLTLSRL 177 (333)
T ss_pred hhhhhcccHHHHHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 888999888651 11111 111 111223455778889999999988876
No 16
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=99.45 E-value=1.3e-12 Score=113.42 Aligned_cols=176 Identities=12% Similarity=0.079 Sum_probs=118.6
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (279)
..++++++++++|++++|.+ |.|+++|+++++++||+.++++|.++..+++... .....+...+..+..+.....
T Consensus 7 ~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 81 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEV 81 (348)
T ss_pred chHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccce
Confidence 35688999999999999999 9999999999999999999999999777764332 122334445555554443344
Q ss_pred EEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccceeccc
Q 023651 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (279)
Q Consensus 98 ~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~~~~ 177 (279)
...++|..+|+.++..|+.. .+++..++|+|++++.++++... .+......++..++|
T Consensus 82 ~~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~~~~~~~~----------------~~~~~~~~~~~~iaH 139 (348)
T PRK11073 82 TLVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRLSQEQLQH----------------AQQVAARDLVRGLAH 139 (348)
T ss_pred EEEECCceEEEEEEEEEccC------ceeEEEEechhHHHHHHHHHHHH----------------HHHHHHHHHHHhhhH
Confidence 45679999999999999853 24567799999999886554211 111111334557899
Q ss_pred cccccCCC-----Cccccccccc---ccHHHHHHHHhhhhhHhhhhhcccc
Q 023651 178 VLALDSDD-----TGLEIEDSCE---ASDLEKRKAATAIDNILSVLTHYSQ 220 (279)
Q Consensus 178 ~l~~~~~~-----~~~~~~~~~~---~~~~~~~~a~~~~~~i~~~l~~~s~ 220 (279)
++++||+. ..+....+.. .....+.....++..+++.|+.+++
T Consensus 140 elr~pL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~lv~~l~~~~~ 190 (348)
T PRK11073 140 EIKNPLGGLRGAAQLLSKALPDPALTEYTKVIIEQADRLRNLVDRLLGPQR 190 (348)
T ss_pred hhcChHHHHHHHHHHhhhcCCChHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 99999975 1122111111 1112234466778888888876654
No 17
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=99.42 E-value=4.1e-12 Score=117.79 Aligned_cols=184 Identities=10% Similarity=0.111 Sum_probs=129.5
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCe-E
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI-E 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~ 93 (279)
..+..++.++++++++++++|.+ |.++++|+++++++||++++++|+++..++++.. .....+......+... .
T Consensus 259 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 333 (607)
T PRK11360 259 ETRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVD 333 (607)
T ss_pred HHHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccc
Confidence 44567788999999999999999 9999999999999999999999998777765432 2233444455444433 3
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccce
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~ 173 (279)
.++....++|... +.++..|+.+ .+|.+.+++++++|||++|++|+++... ..++ .....+.
T Consensus 334 ~~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l~~~-----------~~~~-----~l~~~~~ 395 (607)
T PRK11360 334 LEISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRVARQ-----------ERLA-----ALGELVA 395 (607)
T ss_pred eEEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHHHHH-----------HHHH-----HHHHHHH
Confidence 4556667777766 8899999998 8999999999999999999997776321 1111 1123455
Q ss_pred eccccccccCCCCc-----cccc---ccccccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 174 DLDRVLALDSDDTG-----LEIE---DSCEASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 174 ~~~~~l~~~~~~~~-----~~~~---~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
+++|++++|++... +... .........+.....++..+++.++.+++.
T Consensus 396 ~~~hel~~~l~~i~~~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~~~l~~~~~~ 451 (607)
T PRK11360 396 GVAHEIRNPLTAIRGYVQIWRQQTSDPPSQEYLSVVLREVDRLNKVIDQLLEFSRP 451 (607)
T ss_pred HHHHHhhhHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 78889988886511 1111 111122223445667888888888888765
No 18
>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=99.42 E-value=2.4e-12 Score=115.50 Aligned_cols=117 Identities=18% Similarity=0.112 Sum_probs=88.6
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCC-cchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFS-RAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~-~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (279)
++++.++++++++|+++|.+ |+|+++|++|++++||+ .++++|+++..+.++... .....+......+.....+.
T Consensus 252 ~~~~~l~e~~~d~I~v~D~~---G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~~~-~~~~~~~~~~~~g~~~~~~~ 327 (442)
T TIGR02040 252 ENLARLYHEAPDAIVFSDAD---GTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRGGV-DLRVLLSNVRRTGQVRLYAT 327 (442)
T ss_pred HHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCCcc-cHHHHHHHHhhcCceEEEEE
Confidence 46899999999999999999 99999999999999997 578999987655443221 12112222223343344566
Q ss_pred EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHh
Q 023651 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (279)
Q Consensus 97 ~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~ 141 (279)
...+++|..+|+.+++.|+.+ ..+ ..++++++|||+||+.++
T Consensus 328 ~~~~~~G~~~~ve~s~~~i~~-~~~--~~~~~v~rDITeR~~~~~ 369 (442)
T TIGR02040 328 TLTGEFGAQTEVEISAAWVDQ-GER--PLIVLVIRDISRRLTMRD 369 (442)
T ss_pred EEEcCCCCEEEEEEEEEEecc-CCc--eEEEEEEecchhhccCCC
Confidence 678999999999999999976 333 468899999999988743
No 19
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=99.41 E-value=1e-12 Score=117.55 Aligned_cols=163 Identities=12% Similarity=0.126 Sum_probs=108.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
+..++++.+++++|++++++|.+ |+|+++|+++++++||+.++..|++...+...+ .... .+.... ...
T Consensus 95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~~----~~~~~~-~~~ 163 (430)
T PRK11006 95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFTQ----YLKTRD-FSR 163 (430)
T ss_pred HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHHH----HHHhcc-cCC
Confidence 45678999999999999999999 999999999999999999999999865554322 1111 111111 111
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcccee
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLD 174 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~ 174 (279)
.......+|. ++.+...|..+ + +++.+++|||++++.|+.. ..++..
T Consensus 164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e~~~-------------------------~~~~~~ 210 (430)
T PRK11006 164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLEGAR-------------------------RNFFAN 210 (430)
T ss_pred CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHHHHH-------------------------HHHHHH
Confidence 2222334454 55566666643 3 3567889999999884432 134567
Q ss_pred ccccccccCCCC-----ccccccc----ccccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 175 LDRVLALDSDDT-----GLEIEDS----CEASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 175 ~~~~l~~~~~~~-----~~~~~~~----~~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
++|++++|++.- .+..... .......+.....++..++++++++++.
T Consensus 211 isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~r~ 266 (430)
T PRK11006 211 VSHELRTPLTVLQGYLEMMQDQPLEGALREKALHTMREQTQRMEGLVKQLLTLSKI 266 (430)
T ss_pred hHHHhcchHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999761 1111111 1112223456778999999999999987
No 20
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=99.40 E-value=1.3e-11 Score=87.10 Aligned_cols=120 Identities=21% Similarity=0.347 Sum_probs=93.7
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhC-CCeEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (279)
+.++.+++.++.+++++|.+ |.++++|+++.+++|++..+++|.....+.++.........+......+ .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 45778999999999999999 9999999999999999999999998776665554444444444444422 2233444
Q ss_pred EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhc
Q 023651 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (279)
Q Consensus 97 ~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~ 142 (279)
.....+|..+|+.....|+.. +|...+++++..|||++++.+++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~~~ 123 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAEEA 123 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHHhc
Confidence 445789999999998888863 67888999999999999998765
No 21
>PRK13560 hypothetical protein; Provisional
Probab=99.33 E-value=2.2e-11 Score=116.94 Aligned_cols=134 Identities=16% Similarity=0.175 Sum_probs=102.2
Q ss_pred hHHHHHhhHHHHHHHHHHHhhCCCEEEEEcCCCCCCcEEec-chHHHHHhCCCcchhcCCCCCCCCCCCCCHHH------
Q 023651 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFA-SRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT------ 78 (279)
Q Consensus 6 ~~~~~~l~~~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~-N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~------ 78 (279)
++.++.+. +.+++++.++++++.+++++|.+ |.++++ |+++++++||+.++++|++...+.++......
T Consensus 321 k~~e~~L~-~se~~l~~l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~ 396 (807)
T PRK13560 321 RAAERELL-EKEDMLRAIIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKPLPGMDPELNEEFWCGDFQE 396 (807)
T ss_pred HHHHHHHH-HHHHHHHHHHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCCccccChhhhhhhhhchhhh
Confidence 34455555 67789999999999999999999 999986 68888899999999999886544322111110
Q ss_pred ---------H--HHHHHHHHhCCCeE-EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccc
Q 023651 79 ---------I--MEIREAIREERPIE-VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM 144 (279)
Q Consensus 79 ---------~--~~~~~~~~~~~~~~-~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~ 144 (279)
. ..+...+..+..+. .++...+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++|+++.
T Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~p~~d-~~g~~~~~~~~~~DITerk~~E~~L~ 473 (807)
T PRK13560 397 WYPDGRPMAFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEPLHD-ADGNIIGAIALLVDITERKQVEEQLL 473 (807)
T ss_pred cCCcCCcchhhhhhHHHHHhcCCcccCceEEEEcCCCCeEEEEEEEeeeEC-CCCCEEEEEEEeehhhhHHHHHHHHH
Confidence 0 01122344444433 467778899999999999999999 89999999999999999999998873
No 22
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.28 E-value=5.2e-11 Score=114.53 Aligned_cols=123 Identities=19% Similarity=0.291 Sum_probs=102.3
Q ss_pred HHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCC-CCCCHHHHHHHHHHHHhCCCeEE
Q 023651 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 16 ~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
.++.+..++++++++++++|.+ |.++++|+++++++||+.++++|+++..+.+ +.........+......+..+..
T Consensus 134 ~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (799)
T PRK11359 134 QTRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQD 210 (799)
T ss_pred HHHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcc
Confidence 3445667899999999999999 9999999999999999999999998665543 44444455555566666666777
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhc
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~ 142 (279)
+.+..+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++++.
T Consensus 211 e~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e~~ 257 (799)
T PRK11359 211 EFLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIRQL 257 (799)
T ss_pred eeEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHHHH
Confidence 88888999999999999999998 889999999999999999987653
No 23
>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=99.26 E-value=6.1e-12 Score=113.88 Aligned_cols=161 Identities=14% Similarity=0.136 Sum_probs=97.9
Q ss_pred HHHHhhHHHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHH
Q 023651 8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87 (279)
Q Consensus 8 ~~~~l~~~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~ 87 (279)
.++.+. +.+..++.++++++++++++|.+ |.++++|+++++++|+...+..+........+.... .+.....
T Consensus 121 ~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~----~~~~~~~ 192 (494)
T TIGR02938 121 LEQVVA-NQKLLIESVVDAAPVAFVLLDPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWRE----ALAENWP 192 (494)
T ss_pred HHHHHH-HHHHHHHHHHhcccceEEEEcCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhh----hhhhcch
Confidence 344444 56678999999999999999999 999999999999999987776655432222222111 1111111
Q ss_pred hCCCeE-EEEEEEcCCCc-eEEEEEEEEEeeecCCCcE---------EEEEEEEeccchhHHHHhccccccccCCchhhh
Q 023651 88 EERPIE-VNLLNYKKDGT-PFWMLFKMSLVFGKEDGRA---------THFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLR 156 (279)
Q Consensus 88 ~~~~~~-~e~~~~~~dG~-~~~~~~~~~pi~~~~~g~~---------~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~ 156 (279)
.+..+. .+......+|. .+|+.....|+.+ ..|.. .+++++++|||++|+.|+++.... +
T Consensus 193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~~~a-------l- 263 (494)
T TIGR02938 193 QQLAFSNREARFDRGGGRPARWLSCTGSVIGM-ESDCADSFFCAAEQPYLLLTIADISNLREEQERARLSA-------L- 263 (494)
T ss_pred hhhccccceeeeccCCCceeeEEEecCceEEe-ecchhhheeccCCCchheehHHHHHHHHHHHHHHHHHH-------H-
Confidence 111111 23333344444 7888888887765 45543 345668899999999987652100 0
Q ss_pred HHHHH-hhccccCCccceeccccccccCCC
Q 023651 157 EIVFG-SCRREVCSDSLLDLDRVLALDSDD 185 (279)
Q Consensus 157 ~~~l~-~~~r~~~~~~l~~~~~~l~~~~~~ 185 (279)
+..++ ..+.+....++..++|.+++|++.
T Consensus 264 ~~~~~~~~~~~~l~~~~~~~~h~lr~pL~~ 293 (494)
T TIGR02938 264 QALMAEEERLEAIRETLSAAIHRLQGPMNL 293 (494)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcHHHH
Confidence 01111 111111234456777999999976
No 24
>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=99.25 E-value=4.3e-11 Score=83.00 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=72.0
Q ss_pred EEecchHHHHHhCCCcchhcCCC----CCCCCCCCCCHHHHHHHHH-HHHhCCCeEEEEEEEcCCCceEEEEEEEEEeee
Q 023651 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (279)
Q Consensus 43 i~~~N~~~~~l~G~~~~e~~G~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~ 117 (279)
|+|||+.+++++||+++++ +.. +..+.+|++...+...+.. ....+..+..+++.++++|+.+|+...+.++.+
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d 79 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFD 79 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEET
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEEC
Confidence 6899999999999999999 665 5667889999988888888 677788899999999999999999999999998
Q ss_pred cCCCcEEEEEEEE
Q 023651 118 KEDGRATHFVAVQ 130 (279)
Q Consensus 118 ~~~g~~~~~v~~~ 130 (279)
++|.+.+++|+.
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999999874
No 25
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.21 E-value=2.5e-10 Score=109.81 Aligned_cols=117 Identities=21% Similarity=0.275 Sum_probs=90.7
Q ss_pred HHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCC----CeEE
Q 023651 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIEV 94 (279)
Q Consensus 19 ~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~~ 94 (279)
.+..+++.++.+++++|.+ |.|+++|+++++++||++++++|+++..+.+++........+......+. .+..
T Consensus 13 ~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (799)
T PRK11359 13 IFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSR 89 (799)
T ss_pred hHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccce
Confidence 4567889999999999999 99999999999999999999999998777766554433333333333222 2344
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHh
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~ 141 (279)
++...+++|..+|+.....|+.. +|. .+++++.+|||++++.++
T Consensus 90 e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~ 133 (799)
T PRK11359 90 ELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKE 133 (799)
T ss_pred eeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHH
Confidence 77888999999999999888753 555 467889999999887644
No 26
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.17 E-value=1e-09 Score=110.10 Aligned_cols=195 Identities=8% Similarity=-0.014 Sum_probs=106.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHH--HHHHhCCCe
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR--EAIREERPI 92 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~ 92 (279)
..+.+++.++++++.+++++|.+ |+|+++|+++++++|++.....+........+ .......... .........
T Consensus 573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 648 (1197)
T PRK09959 573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKNAMLPLENSDSP-FKDVFSNAHEVTAETKENRTI 648 (1197)
T ss_pred HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccccccccccccCc-hhhhHhHHHHHHHHHhhcccc
Confidence 44567788999999999999999 99999999999999987543333222111111 1111100000 111111111
Q ss_pred EEEEEEEcCCCceEEEEEE-EEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcc
Q 023651 93 EVNLLNYKKDGTPFWMLFK-MSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDS 171 (279)
Q Consensus 93 ~~e~~~~~~dG~~~~~~~~-~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~ 171 (279)
. .......+|...++... ..+... ..+...++++.+.|||++++.++++.... +++..+.. ....+
T Consensus 649 ~-~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dite~~~~~~~l~~~~---------~~~~~~~~--~~~~~ 715 (1197)
T PRK09959 649 Y-TQVFEIDNGIEKRCINHWHTLCNL-PASDHAVYICGWQDITETRDLIHALEVER---------NKAINATV--AKSQF 715 (1197)
T ss_pred c-eeeEeeecCccceeeeeeeeeecc-CCCCceEEEEEEEehhHHHHHHHHHHHHH---------HHHHHHHH--HHHHH
Confidence 1 11122233332222221 122222 23445678888999999999877663221 22222221 22456
Q ss_pred ceeccccccccCCCC-----ccccccc-cc---ccHHHHHHHHhhhhhHhhhhhccccc-ccccc
Q 023651 172 LLDLDRVLALDSDDT-----GLEIEDS-CE---ASDLEKRKAATAIDNILSVLTHYSQL-TGRLV 226 (279)
Q Consensus 172 l~~~~~~l~~~~~~~-----~~~~~~~-~~---~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~ 226 (279)
+..++|++++||+.- .+..... .. ........+...+..+++++++++++ .|...
T Consensus 716 ~~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~~l~~~~~~~~~l~~li~~ll~~~~~~~~~~~ 780 (1197)
T PRK09959 716 LATMSHEIRTPISSIMGFLELLSGSGLSKEQRVEAISLAYATGQSLLGLIGEILDVDKIESGNYQ 780 (1197)
T ss_pred HHhcChhhCccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCce
Confidence 778999999999761 1111111 11 11112234667888999999999988 55544
No 27
>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=99.13 E-value=3.7e-09 Score=70.96 Aligned_cols=103 Identities=21% Similarity=0.404 Sum_probs=83.7
Q ss_pred CCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceE
Q 023651 27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF 106 (279)
Q Consensus 27 ~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~ 106 (279)
++.+++++|.+ +.+.++|+.++.++|++..+++|.....+..+.........+......+.....+......+|...
T Consensus 1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (103)
T cd00130 1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77 (103)
T ss_pred CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence 36789999999 999999999999999999999999876666666655555555555555556667777778889999
Q ss_pred EEEEEEEEeeecCCCcEEEEEEEEecc
Q 023651 107 WMLFKMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 107 ~~~~~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
|+.+...|+.+ ..|...+++++..||
T Consensus 78 ~~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 78 WVLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEec-CCCCEEEEEEEEecC
Confidence 99999999987 678888999988886
No 28
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=99.11 E-value=3.3e-09 Score=94.20 Aligned_cols=172 Identities=11% Similarity=0.115 Sum_probs=113.8
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCC-eE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~ 93 (279)
+..+.++.+++..+.|++.+|.+ |.+.-+|++++.|+|.+-++++|++...+.+ .+...+...-..++. ..
T Consensus 367 ~rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap-----~~~~vf~~~~a~~~~~~~ 438 (712)
T COG5000 367 QRRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAP-----ELEEVFAEAGAAARTDKR 438 (712)
T ss_pred HHHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhh-----HHHHHHHHhhhhcCCCcc
Confidence 34567788999999999999999 9999999999999999999999998654432 222222222222222 22
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccce
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~ 173 (279)
.++. ....|+.+.+.+..+.... ++| .|++.++.|||+...+|. ..++..--|.
T Consensus 439 ~ev~-~~r~g~~rtl~Vq~t~~~~-d~~--~gyVvt~DDITdLV~AQR---------------s~AW~dVArR------- 492 (712)
T COG5000 439 VEVK-LAREGEERTLNVQATREPE-DNG--NGYVVTFDDITDLVIAQR---------------SAAWGDVARR------- 492 (712)
T ss_pred ceee-cccCCCceeeeeeeeeccc-ccC--CceEEEecchHHHHHHHH---------------HHHHHHHHHH-------
Confidence 3333 3445666666666665543 222 478999999999999865 3455544444
Q ss_pred eccccccccCCCCc-----------ccccc---cccccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 174 DLDRVLALDSDDTG-----------LEIED---SCEASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 174 ~~~~~l~~~~~~~~-----------~~~~~---~~~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
++|++++||..-. -+..+ .-......+.+.+..+++++++.-.|+|+
T Consensus 493 -IAHEIKNPLTPIQLSAERl~rk~gk~i~eDrevfd~~tdTIirQV~dI~rMVdeF~afARm 553 (712)
T COG5000 493 -IAHEIKNPLTPIQLSAERLLRKLGKEIDEDREVFDRCTDTIIRQVEDIKRMVDEFRAFARM 553 (712)
T ss_pred -HHHHhcCCCchhhhhHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7999999996511 11111 11222233456777888888888888865
No 29
>PF12860 PAS_7: PAS fold
Probab=99.07 E-value=7.7e-10 Score=80.37 Aligned_cols=105 Identities=21% Similarity=0.356 Sum_probs=73.5
Q ss_pred HhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchh-cCCCCCCCC---------CCCCCHHHHHHHHHHHHhCCCeE
Q 023651 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 24 l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~-~G~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
++++++||+++|.+ +++++||+.|.+++|++.+.+ .|.+...+. .+.....................
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRRRQPRS 77 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhcCCCce
Confidence 47899999999999 999999999999999999887 677754432 11222233333333333333333
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHh
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~ 141 (279)
.+ ....+|. |+.+...|+. +| |++.++.|||++|++|+
T Consensus 78 ~~--~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 78 FE--LRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred eE--EECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhcC
Confidence 33 3456675 7788888884 45 57889999999999864
No 30
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=99.06 E-value=2.2e-09 Score=76.75 Aligned_cols=106 Identities=21% Similarity=0.253 Sum_probs=72.7
Q ss_pred HHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 023651 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (279)
Q Consensus 20 ~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (279)
+..++++++.+++++|.+ ++|.++|+++.++++..+. .+|++...+.++...+.... +.+.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~-~iGr~l~~~~~~~~~~~l~~-~i~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPS-DIGRPLFDIHPPLSYPNLKK-IIEQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GG-GTTSBCCCSS-HHHHHHHHH-HHHHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChH-HCCCCHHHcCCccchHHHHH-HHHHHHcCCCceEEEEe-
Confidence 467899999999999999 9999999999999998754 47999888875533333333 33444455544444333
Q ss_pred cCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccc
Q 023651 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (279)
Q Consensus 100 ~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DIT 134 (279)
..+| .|+.+...|+++ ++|...|++.++.|||
T Consensus 75 ~~~~--~~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGG--RWYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETT--EEEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCC--EEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 2444 477889999999 8999999999999998
No 31
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.91 E-value=6.1e-09 Score=91.69 Aligned_cols=120 Identities=27% Similarity=0.539 Sum_probs=99.8
Q ss_pred HHHHHHhhCC--C-EEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCC--CCCCCCCCCCHHHHHHHHHHHHhCCCeE
Q 023651 19 WVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 19 ~~~~~l~~~~--~-~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
+++.++..+. + .+++.+++..|..|+|+|.+||++.||.+.|++.++ +.+++++..+....+.+++.+...+.-.
T Consensus 15 FLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~q 94 (971)
T KOG0501|consen 15 FLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQ 94 (971)
T ss_pred HHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcc
Confidence 4555554433 3 344455555568999999999999999999999886 5667777777888888888888888888
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHH
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~ 139 (279)
+|+..+.|+.++.|+.+.+.|+++ +...++-|++++.|||..|+-
T Consensus 95 fEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 95 FEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred eeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence 999999999999999999999999 899999999999999998863
No 32
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.89 E-value=1.8e-08 Score=92.69 Aligned_cols=136 Identities=10% Similarity=0.093 Sum_probs=92.2
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCc---chhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERP 91 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~---~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 91 (279)
+..+.++.+++++++||+++|.+ |+|+++|+++++++|++. .+.+|.....+.+. ..+...+..+.+
T Consensus 218 ~l~~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~ 287 (542)
T PRK11086 218 TLFEQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPV-------SRLKEVLRTGTP 287 (542)
T ss_pred HHHHHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCc-------hhHHHHHhcCCC
Confidence 34456788999999999999999 999999999999998753 35556554433321 122334444444
Q ss_pred eEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCcc
Q 023651 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDS 171 (279)
Q Consensus 92 ~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~ 171 (279)
...... ..+|. ++.+...|+.+ +|.+.|++.+++|+|+.++.++++... ... ..+
T Consensus 288 ~~~~~~--~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~~l~~~-----------------~~~--~~~ 342 (542)
T PRK11086 288 RRDEEI--NINGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQRLDGM-----------------VNY--ADA 342 (542)
T ss_pred ccceEE--EECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHHHHHHH-----------------HHH--HHH
Confidence 332211 22443 44566789986 889999999999999999986665221 100 223
Q ss_pred ceeccccccccCCC
Q 023651 172 LLDLDRVLALDSDD 185 (279)
Q Consensus 172 l~~~~~~l~~~~~~ 185 (279)
+..++|++++|+..
T Consensus 343 l~~~sHel~npL~~ 356 (542)
T PRK11086 343 LRAQSHEFMNKLHV 356 (542)
T ss_pred HHhhchhhcCHHHH
Confidence 44578999999866
No 33
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=98.81 E-value=1.1e-07 Score=78.07 Aligned_cols=216 Identities=13% Similarity=0.092 Sum_probs=128.2
Q ss_pred HHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeE-EEEEEE
Q 023651 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY 99 (279)
Q Consensus 21 ~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~ 99 (279)
..++++.+..++++|.+ +.|.|+|++++.+||.+...+.|.....+++.. ......+.+....+.++. .++...
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~ 84 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV 84 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee
Confidence 46889999999999999 999999999999999999999999877776433 233445555665555543 333333
Q ss_pred cCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccceeccccc
Q 023651 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVL 179 (279)
Q Consensus 100 ~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~~~~~~l 179 (279)
.+|....++.++.|+.. ..|.+ +..+..+....+...++. ..+.........-.++|+|
T Consensus 85 -~~g~~~~v~~~v~~v~~-~~G~v---lle~~~~~~~~ridre~~----------------q~a~~~a~~~L~r~LAHEI 143 (363)
T COG3852 85 -ILGRSHIVDLTVAPVPE-EPGSV---LLEFHPRDMQRRLDREQT----------------QHAQQRAVKGLVRGLAHEI 143 (363)
T ss_pred -ecCccceEEEEEeeccC-CCCeE---EEEechhHHHhHhhHHHH----------------HHHHHHHHHHHHHHHHHHh
Confidence 68889999999999976 56654 345555555555533220 1111111133344799999
Q ss_pred cccCCC-----CcccccccccccHHHHHHHHhhhhhHhhhhhccccccccccccccccCCCCCccchhhhhhhhhcc---
Q 023651 180 ALDSDD-----TGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIK--- 251 (279)
Q Consensus 180 ~~~~~~-----~~~~~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~--- 251 (279)
++||.+ .+++...|.+......+-.....+++.+.+.++-- ++.. .+.+-+..++-.++++++
T Consensus 144 KNPL~GiRGAAQLLe~~lpd~~~~~lt~lIieE~DRl~~LVDRme~----~~~~-----rp~~r~~~NIH~VLerV~~lv 214 (363)
T COG3852 144 KNPLGGIRGAAQLLERALPDEALRELTQLIIEEADRLRNLVDRLEV----LGPQ-----RPGDRVPVNIHEVLERVRALV 214 (363)
T ss_pred cCcccchhhHHHHHHhhCCChHHHHHHHHHHHHHHHHHHHHHHHHh----cCCC-----CCcccccchHHHHHHHHHHHH
Confidence 999976 33444445443333333444444444444443210 0011 122222334556666655
Q ss_pred -----cceEeeCCCCCCCCEEEech
Q 023651 252 -----QSFVLIDPHLPDMPMVYASD 271 (279)
Q Consensus 252 -----~~~~~~~~~~p~~p~~~~~~ 271 (279)
.++.+...==|..|=||+|.
T Consensus 215 ~~e~~~~i~l~rdYDPSLP~v~~d~ 239 (363)
T COG3852 215 EAEFADNVRLIRDYDPSLPEVLGDR 239 (363)
T ss_pred hcccCCceEEeecCCCCCccccCCH
Confidence 33444432225566678775
No 34
>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=98.78 E-value=2.3e-07 Score=66.75 Aligned_cols=101 Identities=17% Similarity=0.262 Sum_probs=82.5
Q ss_pred EEEcCCCCCCcEEecchH-HHHHhCCCcchhcCCCCCCCCCCCCCHH-HHHHHHHHHHhCCCeEEEEEEEcCCCceEEEE
Q 023651 32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (279)
Q Consensus 32 ~~~d~~~~~g~i~~~N~~-~~~l~G~~~~e~~G~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~ 109 (279)
.-.+.+ |+|+++.+. ...++||.++|++|+++..+.+|++... ..+.....+..|.....-+++..++|...|+.
T Consensus 6 trhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq 82 (111)
T PF14598_consen 6 TRHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ 82 (111)
T ss_dssp EEEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred EEECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence 345677 999999999 6999999999999999999999998886 66778888888887777799999999999999
Q ss_pred EEEEEeeecCCCcEEEEEEEEeccch
Q 023651 110 FKMSLVFGKEDGRATHFVAVQVPIVS 135 (279)
Q Consensus 110 ~~~~pi~~~~~g~~~~~v~~~~DITe 135 (279)
....++.++..+++..++++-+=|++
T Consensus 83 t~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 83 TKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEEEECCCCCCccEEEEEEEEecc
Confidence 99999886345677777777655554
No 35
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=98.62 E-value=7.2e-07 Score=86.98 Aligned_cols=176 Identities=10% Similarity=0.063 Sum_probs=105.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEc-CCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeE
Q 023651 15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d-~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
..++.++.+++.+|.++++++ .+ |.++++|+.+..++|+...+. .. .+........ ..
T Consensus 331 e~e~~~r~iv~~~p~gi~i~~~~~---g~~~~~N~~a~~~~~l~~~~~-------------~~----~~~~~~~~~~-~~ 389 (924)
T PRK10841 331 EHEQFNRKIVASAPVGICILRTSD---GTNILSNELAHNYLNMLTHED-------------RQ----RLTQIICGQQ-VN 389 (924)
T ss_pred HHHHHHHHHHHhCCccEEEEEcCC---CcEEEehHHHHHHhccCChhH-------------HH----HHHHHHhccc-cc
Confidence 556788999999999999997 56 999999999999988743321 01 1111111111 11
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccce
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~ 173 (279)
. ......++... .+...+... .+. ...++++.|||++++.|+++... .+.+..+.+ .+..++.
T Consensus 390 ~-~~~~~~~~~~~--~i~~~~~~~--~~~-~~~i~~~~Dit~r~~~e~~L~~~----------~~~~e~a~~-~k~~fla 452 (924)
T PRK10841 390 F-VDVLTSNNTNL--QISFVHSRY--RNE-NVAICVLVDVSARVKMEESLQEM----------AQAAEQASQ-SKSMFLA 452 (924)
T ss_pred e-eeEEcCCCcEE--EEEEEeeee--cCc-eEEEEEEEEhhHHHHHHHHHHHH----------HHHHHHHHH-HHHHHHH
Confidence 1 11123344433 333333333 233 24678899999999998887432 122222111 1244788
Q ss_pred eccccccccCCCC-----ccccccc---ccccHHHHHHHHhhhhhHhhhhhccccc-ccccccc
Q 023651 174 DLDRVLALDSDDT-----GLEIEDS---CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCG 228 (279)
Q Consensus 174 ~~~~~l~~~~~~~-----~~~~~~~---~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~ 228 (279)
.++|++++||+.- .+..... .......+..+...+.+++++|++++++ .|.+...
T Consensus 453 ~iSHELRTPL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~srie~~~~~l~ 516 (924)
T PRK10841 453 TVSHELRTPLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFSKIESEQLKIE 516 (924)
T ss_pred HhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceee
Confidence 9999999999761 1211111 1112223456778899999999999997 5555433
No 36
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.60 E-value=3.5e-07 Score=83.53 Aligned_cols=110 Identities=14% Similarity=0.138 Sum_probs=79.0
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
+....+..+++++++||+++|.+ |+|+++|+++++++|++.++++|+++..+.+... +...+..+.....
T Consensus 77 ~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~ 146 (520)
T PRK10820 77 REHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccc
Confidence 34567899999999999999999 9999999999999999999999999777665332 2233334433111
Q ss_pred EEEEEcCCCceEEEEEEEEEee--ecCCCc--EEEEEEEEeccchhHH
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRKH 138 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~--~~~~g~--~~~~v~~~~DITerk~ 138 (279)
. .....+|..++ +...|+. + ++|. ..|.+.+++|+++..+
T Consensus 147 ~-~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 147 N-EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred e-EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHHH
Confidence 1 12234566554 5567776 5 4554 3899999999998643
No 37
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=98.54 E-value=4.3e-07 Score=83.78 Aligned_cols=110 Identities=14% Similarity=0.082 Sum_probs=76.5
Q ss_pred HHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCc--chhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 17 ~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~--~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
...++.+++++++|++++|.+ |+|+++|+++++++|++. ++++|++...+.++... . ..... ......
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~--~----~~~~~-~~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF--F----TEQID-EKRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh--h----hhhcC-Ccccce
Confidence 345678999999999999999 999999999999999975 46889886655543211 0 11111 111111
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
. ...+| ..+.+...|+.. .|.+.|.+.+++|+|+.++.++++
T Consensus 291 ~---~~~~~--~~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l~~~l 332 (545)
T PRK15053 291 V---ANFNG--LSVIANREAIRS--GDDLLGAIISFRSKDEISTLNAQL 332 (545)
T ss_pred E---EEECC--EEEEEEeeeEEE--CCeEEEEEEEEEchHHHHHHHHHH
Confidence 1 12234 344567788875 677889999999999999886665
No 38
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.51 E-value=5.9e-07 Score=86.77 Aligned_cols=171 Identities=8% Similarity=-0.019 Sum_probs=99.9
Q ss_pred HHHHHHHHHHhhCCCEEEEEc-CCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeE
Q 023651 15 RYTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d-~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
..++..+.+++++|+|++++| .+ |+++++|+++.+++|+..-.-+ . .... ...+..
T Consensus 340 ~~~~l~~~Ii~~lp~Gilv~D~~~---~~Ii~~N~aA~~ll~~~~l~~i-------~------~~~~------~~~~~i- 396 (894)
T PRK10618 340 ILRALNEEIVSNLPLGLLVYDFES---NRTVISNKIADHLLPHLNLQKI-------T------TMAE------QHQGVI- 396 (894)
T ss_pred HHHHHHHHHHHhCCceEEEEECCC---CeEEEEhHHHHHHhCccchhhH-------H------HHHH------hcchhh-
Confidence 456688999999999999999 55 9999999999999975321100 0 0000 000000
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhccccccccCCchhhhHHHHHhhccccCCccce
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l~~~~~dgNR~l~~~~~l~~~~r~~~~~~l~ 173 (279)
....++..+++...... ....+++.+.+|+++.+..++++... ...+.... ..+..++.
T Consensus 397 ----~~~i~~~~~eir~~~~~------~~~~~~l~~l~d~~~~~~~~~~L~~a----------~~~le~~~-~~k~~fla 455 (894)
T PRK10618 397 ----QATINNELYEIRMFRSQ------LAPRTQLFLLRDQDREVLVNKKLQQA----------QREYEKNQ-QARKAFLQ 455 (894)
T ss_pred ----hhhccCceeEEEEeecc------ccCceEEEEEeehHHHHHHHHHHHHH----------HHHHHHHH-HHHHHHHH
Confidence 00112333332222222 22235677889999988876666322 11111111 12246778
Q ss_pred eccccccccCCCC-----cccccc---cccccHHHHHHHHhhhhhHhhhhhccccc-cccccccc
Q 023651 174 DLDRVLALDSDDT-----GLEIED---SCEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCGK 229 (279)
Q Consensus 174 ~~~~~l~~~~~~~-----~~~~~~---~~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~~ 229 (279)
.++|++++||+.. .+.... ........+..+...+.++++++++++++ .|++....
T Consensus 456 ~iSHELRtPL~aI~g~~elL~~~~~~~~~~~~l~~I~~~~~~L~~lI~dILdlsrle~~~~~l~~ 520 (894)
T PRK10618 456 NIGDELKQPLQSLAQLAAQLRQTSDEEQQQPELDQLAEQSDVLVRLVDNIQLLNMLETQDWKPEQ 520 (894)
T ss_pred HHHHHHhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccc
Confidence 9999999999761 111111 11122223456778999999999999998 67666544
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.49 E-value=6.8e-07 Score=79.26 Aligned_cols=116 Identities=16% Similarity=0.347 Sum_probs=88.5
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEE
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (279)
+..+.|+.+++.+.++++++|.+ |.++++|+++..++|++.++++|++..++...... ....+++..+.+...
T Consensus 114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~~~ 186 (560)
T COG3829 114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCccee
Confidence 55678999999999999999999 99999999999999999999999986665411111 122456667777665
Q ss_pred EEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 95 e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
....+..+. . ..+..|+.. +|.+.|.+++.+|+++.+....++
T Consensus 187 ~~~~~~~~~--~--i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l~~~~ 229 (560)
T COG3829 187 VVQTYNGNK--I--IVNVAPVYA--DGQLIGVVGISKDVSELERLTREL 229 (560)
T ss_pred eeeeecCCc--e--eEeeccEec--CCcEEEEEEeecchHHHHHHHHHH
Confidence 554433222 2 455667764 789999999999999998876666
No 40
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.47 E-value=9.5e-06 Score=62.52 Aligned_cols=120 Identities=24% Similarity=0.357 Sum_probs=86.6
Q ss_pred HHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHH-HHHHHHHH-HHhCCCe
Q 023651 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREA-IREERPI 92 (279)
Q Consensus 15 ~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~-~~~~~~~~-~~~~~~~ 92 (279)
....+++.+++..+++++..|.+ |.+.++|+.+.+++|++..+..+.....+........ ........ .......
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (232)
T COG2202 109 ESEERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPL 185 (232)
T ss_pred HHHHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCc
Confidence 34455899999999999999999 9999999999999999988777776544433222211 11111111 2223345
Q ss_pred EEEEEEEcCCCce-EEEEEEEEEeeecCCCcEEEEEEEEeccchhHHH
Q 023651 93 EVNLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (279)
Q Consensus 93 ~~e~~~~~~dG~~-~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~ 139 (279)
..+.....++|.. .|......+... .|.+..+.+...|++++++.
T Consensus 186 ~~~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 186 EIEYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred ceEEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence 6677788899996 777777777653 68888899999999998864
No 41
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.36 E-value=8.1e-07 Score=57.10 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.6
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCC
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~ 66 (279)
++++.+++++|.+|+++| + ++|+++|+++++++||+ ..|...
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence 478999999999999999 9 99999999999999998 455543
No 42
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=98.30 E-value=3.3e-06 Score=74.90 Aligned_cols=113 Identities=12% Similarity=0.165 Sum_probs=85.9
Q ss_pred HHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcc--hhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeE
Q 023651 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (279)
Q Consensus 16 ~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~--e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (279)
.-+...++++++.+|++.+|.. |.|+.+|.++++|+|+... +.+|++...+++|+.. +...++.+.+..
T Consensus 213 l~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~ 283 (537)
T COG3290 213 LLEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQH 283 (537)
T ss_pred HHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCccc
Confidence 3345678999999999999999 9999999999999999765 6889987777765322 123344455443
Q ss_pred EEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhcc
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~l 143 (279)
.+.. +-+|. ++.....|+.. +|+++|++.+++|=||-++.-+++
T Consensus 284 ~~e~--~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L~eqL 327 (537)
T COG3290 284 DEEI--RINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKLTEQL 327 (537)
T ss_pred chhh--hcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHHHHHH
Confidence 3321 23443 66778889986 899999999999999999987766
No 43
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=98.17 E-value=1.3e-06 Score=74.99 Aligned_cols=105 Identities=23% Similarity=0.377 Sum_probs=88.2
Q ss_pred HHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCC-CCHHHHHHHHHHHHhCCCeEEEEEE
Q 023651 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLLN 98 (279)
Q Consensus 20 ~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (279)
+-.+++....+|-+.|.+ ..|.|+||+|++|+||-..|++|+...++...+ ....+.+.+..+++.|..+.++...
T Consensus 159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~a 235 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA 235 (775)
T ss_pred HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence 345678888899999999 999999999999999999999999987775433 3456777788889999999999888
Q ss_pred EcCCCceEEEEEEEEEeeecCCCcEEEEEE
Q 023651 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128 (279)
Q Consensus 99 ~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~ 128 (279)
+++.|...-..+..+|+.. ..|++..|+.
T Consensus 236 RRksgdS~dqh~~itP~~g-qggkirhfvs 264 (775)
T KOG1229|consen 236 RRKSGDSCDQHFIITPFAG-QGGKIRHFVS 264 (775)
T ss_pred hhccCCcccceEEEeeecC-CCCceeeehh
Confidence 8999988877888899987 7788887764
No 44
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.99 E-value=0.00011 Score=69.19 Aligned_cols=108 Identities=12% Similarity=0.228 Sum_probs=77.0
Q ss_pred HHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEE
Q 023651 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (279)
Q Consensus 19 ~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (279)
.+..++++.+++|+++|.+ |+|+++|+++++++|++.++++|++...++... ..+..++..+.........
T Consensus 204 ~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~~ 274 (638)
T PRK11388 204 QLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEVT 274 (638)
T ss_pred HHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEEE
Confidence 3456889999999999999 999999999999999999999999876665321 1223444555544332223
Q ss_pred EcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHH
Q 023651 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (279)
Q Consensus 99 ~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~ 138 (279)
...+|..+++.+...|+.+ ..|. +++.+..|++..++
T Consensus 275 l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 275 FESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 3445777788888999865 3443 46666788887554
No 45
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.53 E-value=0.00017 Score=65.51 Aligned_cols=95 Identities=11% Similarity=0.252 Sum_probs=79.6
Q ss_pred EcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEEEEEEEE
Q 023651 34 TDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMS 113 (279)
Q Consensus 34 ~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~ 113 (279)
...+ .+|+||.+.+..++||.+++++|+.+..++++.+...+.....+.+.+|.....-+++..+.|.+.|+...++
T Consensus 280 hs~D---mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqAT 356 (768)
T KOG3558|consen 280 HSLD---MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQAT 356 (768)
T ss_pred eecc---eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeE
Confidence 3456 8999999999999999999999999999999998888888888999999988888999999999999999988
Q ss_pred EeeecCCCcEEEEEEEEe
Q 023651 114 LVFGKEDGRATHFVAVQV 131 (279)
Q Consensus 114 pi~~~~~g~~~~~v~~~~ 131 (279)
.+.+..+++...++++-.
T Consensus 357 Vi~~tkn~q~q~IicVnY 374 (768)
T KOG3558|consen 357 VIYNTKNPQEQNIICVNY 374 (768)
T ss_pred EEecCCCCCcceEEEEEe
Confidence 887512334445555543
No 46
>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=97.51 E-value=0.004 Score=46.71 Aligned_cols=113 Identities=11% Similarity=0.096 Sum_probs=77.0
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (279)
..++.++. .|.+|+--+.. ++-.++|.|.++.+|++++-+++.+.+...-..+...+.....+.++...|-.....-.
T Consensus 32 ~~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~Gi 109 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGI 109 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence 34555555 88888776543 33689999999999999999999999877665555555555555555555543333333
Q ss_pred EEcCCCceEEEEE-EEEEeeecCCCcEEEEEEEEecc
Q 023651 98 NYKKDGTPFWMLF-KMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 98 ~~~~dG~~~~~~~-~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
...+.|..++++- .+=.+.| ++|...|...++.+-
T Consensus 110 Riss~Grrf~ie~a~vW~l~D-~~g~~~GqAa~F~~W 145 (148)
T PF08670_consen 110 RISSTGRRFRIERATVWNLID-EDGNYCGQAAMFSNW 145 (148)
T ss_pred EEcCCCCeEEEeceEEEEEEc-CCCCEEEEEEEEeee
Confidence 4578898888753 3334567 789888877776654
No 47
>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=97.50 E-value=0.00039 Score=41.91 Aligned_cols=55 Identities=24% Similarity=0.412 Sum_probs=45.3
Q ss_pred HHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCH
Q 023651 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR 76 (279)
Q Consensus 19 ~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~ 76 (279)
+++.+++.++.++++++.. +.+.++|+.+..++|++..++.|..+..+.++.+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (67)
T smart00091 2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRE 56 (67)
T ss_pred hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHH
Confidence 3567888999999999999 999999999999999999888888665555544433
No 48
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=97.18 E-value=0.0018 Score=55.46 Aligned_cols=115 Identities=16% Similarity=0.201 Sum_probs=88.6
Q ss_pred HHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 023651 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (279)
Q Consensus 17 ~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (279)
.+.+..++.+.|.-+-.+|.+ +.+.|.|+. .++|-.++. ++|+.+...+ |+........+.+.+++|..-..++
T Consensus 289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~~ch-pPksv~iv~ki~~~fksG~kd~~ef 362 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQLCH-PPKSVHIVEKILKDFKSGEKDFAEF 362 (409)
T ss_pred HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCcccCCC-CCchHHHHHHHHHHhhcCCcchHHH
Confidence 357889999999667778999 999999998 888877665 4688776544 4456667778888888888777777
Q ss_pred EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHh
Q 023651 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (279)
Q Consensus 97 ~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~ 141 (279)
|. ...+. .+.++-.+++| ++|...|.+-+.+|||.-|+.+-
T Consensus 363 w~-~~~~~--~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l~g 403 (409)
T COG2461 363 WI-NMGDK--FIHIRYFAVKD-EEGEYLGTLEVVQDITRIKELEG 403 (409)
T ss_pred hc-cCCCc--eEEEEEEEEEc-CCCceeeeehhhhhhHHHHhccc
Confidence 73 33333 44567778899 89999999999999999988754
No 49
>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=96.81 E-value=0.018 Score=41.53 Aligned_cols=67 Identities=19% Similarity=0.107 Sum_probs=52.1
Q ss_pred HHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCC-CCHHHHHHHHHHHHhCC
Q 023651 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREER 90 (279)
Q Consensus 21 ~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~-~~~~~~~~~~~~~~~~~ 90 (279)
..-++..|-|++-+|.+ |.|+..|.+-..+.|++++.++|++...=+.|. ..+.+...+.+..+.+.
T Consensus 19 ~eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 19 DAQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred HhHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 34588999999999999 999999999999999999999999854434443 34446666666554443
No 50
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.69 E-value=0.0059 Score=52.14 Aligned_cols=55 Identities=15% Similarity=0.177 Sum_probs=48.7
Q ss_pred HHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCC
Q 023651 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74 (279)
Q Consensus 17 ~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~ 74 (279)
.-.+.++++++|+.++.+|.. |.+..+|++++.++|.+++++.|.+...++....
T Consensus 79 hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n 133 (511)
T COG3283 79 HLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN 133 (511)
T ss_pred hHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence 345788999999999999999 9999999999999999999999998777765444
No 51
>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=96.62 E-value=0.019 Score=30.52 Aligned_cols=40 Identities=30% Similarity=0.452 Sum_probs=33.2
Q ss_pred EEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchh
Q 023651 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (279)
Q Consensus 96 ~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITer 136 (279)
+.....+|..+|+.....++.+ ..|.+.+++++..|||++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 4 YRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence 4456778888999888888887 788899999999999863
No 52
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=95.78 E-value=0.12 Score=46.88 Aligned_cols=104 Identities=19% Similarity=0.114 Sum_probs=70.7
Q ss_pred HHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEc
Q 023651 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (279)
Q Consensus 21 ~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (279)
+.+++..++++++++.. ..+.++|..+..+.+-....++|+++..+.++...+... .+..+........
T Consensus 4 ~~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~ 72 (560)
T COG3829 4 EGILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKL 72 (560)
T ss_pred hhhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeec
Confidence 44889999999999998 999999999999999999999999877665443322211 1222222222222
Q ss_pred CCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHH
Q 023651 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (279)
Q Consensus 101 ~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~ 139 (279)
+ + ...+.+...|+ + +.+.+.|++.++.|+++....
T Consensus 73 ~-~-~~~~~~~~~~~-~-~~~~~~g~~~~~~~~~e~~~~ 107 (560)
T COG3829 73 K-V-KRIVVVGKTPV-D-EQGRVVGVLEVFLDISEALEL 107 (560)
T ss_pred c-c-eeEEEcCCcee-e-cCCceeeeehhhhhhHHHHHH
Confidence 3 2 22333334455 4 588999999999999985544
No 53
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=95.56 E-value=0.24 Score=36.91 Aligned_cols=86 Identities=13% Similarity=0.147 Sum_probs=69.9
Q ss_pred CcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEEEEEEEEEeeecCC
Q 023651 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (279)
Q Consensus 41 g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~~~~ 120 (279)
.++-.+-...++++|+. +-|++...++.+.........+..++....+..........+|....++....|+.+ ++
T Consensus 51 ~r~RLaGt~i~~~~G~d---~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~ 126 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGRD---LTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG 126 (137)
T ss_pred eEEEEecHHHHHHhCCC---CCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence 45666888999999984 458888888777777777777888888888888777777888988888999999998 77
Q ss_pred CcEEEEEEEE
Q 023651 121 GRATHFVAVQ 130 (279)
Q Consensus 121 g~~~~~v~~~ 130 (279)
|.+..++|..
T Consensus 127 ~~v~rilG~~ 136 (137)
T PF07310_consen 127 GTVDRILGAL 136 (137)
T ss_pred CCccEEEEec
Confidence 8888888864
No 54
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=94.74 E-value=0.84 Score=43.29 Aligned_cols=100 Identities=18% Similarity=0.130 Sum_probs=53.1
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHH-----hCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCe
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKM-----SGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l-----~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (279)
+.+..++...+..++++|.+ |.++.++..-..+ .|.. .|..|..-... -..+--++..+.+.
T Consensus 62 ~~l~~~l~~~~~~~~l~D~~---G~vL~~~g~~~~~~~~~~~~~~----~G~~w~E~~~G------Tnaig~al~~~~pv 128 (638)
T PRK11388 62 EDAWEYMADRECALLILDET---GCILSRNGDPQTLQQLSALGFN----DGTYCAEGIIG------TNALSLAAISGQPV 128 (638)
T ss_pred HHHHHHhcCCCcEEEEEcCC---ceEEEEeCCHHHHHHHHHcCCc----cCCccchhccC------cCHHHHHHhcCCce
Confidence 34455666778889999999 9999865432211 1221 12222111000 01223344444443
Q ss_pred EEEE-EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEecc
Q 023651 93 EVNL-LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 93 ~~e~-~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
...- .++.. ....+.+...|+++ .+|+++|++.+..+.
T Consensus 129 ~v~g~EH~~~--~~~~~~c~aaPI~d-~~G~liGvl~l~~~~ 167 (638)
T PRK11388 129 KTMGDQHFKQ--ALHNWAFCATPVFD-SKGRLTGTIALACPV 167 (638)
T ss_pred EEecHHHHHH--hccCceEEeeEEEc-CCCCEEEEEEEEecc
Confidence 2210 00111 11234677899999 899999999877654
No 55
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=94.49 E-value=0.071 Score=50.40 Aligned_cols=153 Identities=12% Similarity=0.097 Sum_probs=84.4
Q ss_pred EEeeecCCCcEEEEEEEEec----cchhHHHHhccc-ccccc--C--Cchhhh---HHHHHhhccccCCccc-eeccccc
Q 023651 113 SLVFGKEDGRATHFVAVQVP----IVSRKHMRNSGM-SYSED--G--GGSRLR---EIVFGSCRREVCSDSL-LDLDRVL 179 (279)
Q Consensus 113 ~pi~~~~~g~~~~~v~~~~D----ITerk~~e~~l~-~~~~d--g--NR~l~~---~~~l~~~~r~~~~~~l-~~~~~~l 179 (279)
.|+.. .+.+.|++++..+ ++.+.+ +++ +.... . -|..|. +++...++++....+| ..+||.|
T Consensus 597 lPl~~--~~~~~gvlgv~~~~~~ll~p~~~---rlL~a~~~q~AlAler~~L~~~~~~a~l~~e~E~lRsaLL~sISHDL 671 (890)
T COG2205 597 LPLKS--GGKVLGVLGVEPGLSPLLAPEQR---RLLDAVLTQIALALERVTLAEEAEQARLAAERERLRSALLASISHDL 671 (890)
T ss_pred eeccc--CCceEEEEEecCCCCccCChHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 47763 6788899998877 332221 110 00000 0 112222 4445555555544444 4899999
Q ss_pred cccCCC------Cccccc----cc-ccccHHHHHHHHhhhhhHhhhhhccccc-cccccccccccCCCCCccchhhhhhh
Q 023651 180 ALDSDD------TGLEIE----DS-CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCGKRCSLPGMGFISSSLYISL 247 (279)
Q Consensus 180 ~~~~~~------~~~~~~----~~-~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~~~~~~~~~~~~~~~l~~~~ 247 (279)
|+||.. .+.... .+ .......+..-...+.+++.-||+++|+ +|.+..++ .... +..-+.+.+
T Consensus 672 RTPLt~i~Gaa~tL~~~~~~l~~~~~aeLl~~I~ees~~L~rlV~NLLdmTRi~sG~~~l~~----~~~~-veEvVg~Al 746 (890)
T COG2205 672 RTPLTAIMGAAETLLLDGEALSPEDRAELLSSIREESERLTRLVTNLLDMTRLQSGGVNLKL----DWVL-VEEVVGEAL 746 (890)
T ss_pred cCcHHHHhhhHHHhhhcccccCcHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcCCccccc----chhh-HHHHHHHHH
Confidence 999954 111111 11 1222223455677999999999999999 88888776 3322 111133334
Q ss_pred hhcc---cceEeeCCCCCCCCEEEechhhhh
Q 023651 248 GRIK---QSFVLIDPHLPDMPMVYASDAFLK 275 (279)
Q Consensus 248 ~~~~---~~~~~~~~~~p~~p~~~~~~~~~~ 275 (279)
+++. ....+.-.-.+|+|.|.+|....+
T Consensus 747 ~r~~k~~~~~~i~v~~~~dl~li~~D~~Lie 777 (890)
T COG2205 747 QRLRKRFTGHKIVVSVPVDLPLIHVDSPLIE 777 (890)
T ss_pred HHhhhhcCCceEEEecCCCCceEecCHHHHH
Confidence 4333 223333333468899999987654
No 56
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=94.29 E-value=0.19 Score=45.10 Aligned_cols=93 Identities=14% Similarity=0.170 Sum_probs=73.7
Q ss_pred CcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEEEEEEEEEeeecCC
Q 023651 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (279)
Q Consensus 41 g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~~~~ 120 (279)
+..+.+......++||...|+.|.+...+++.++..-......+.++.|.+...-++..+|+|++.|+..+..-+. .+
T Consensus 293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly--kn 370 (712)
T KOG3560|consen 293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY--KN 370 (712)
T ss_pred cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee--ec
Confidence 5666677778899999999999887777777776666666677788888887778888999999999887776665 48
Q ss_pred CcEEEEEEEEeccch
Q 023651 121 GRATHFVAVQVPIVS 135 (279)
Q Consensus 121 g~~~~~v~~~~DITe 135 (279)
|+...++.+.+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 888877877776665
No 57
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=93.78 E-value=0.065 Score=50.88 Aligned_cols=54 Identities=19% Similarity=0.313 Sum_probs=45.7
Q ss_pred HHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCC
Q 023651 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTN 75 (279)
Q Consensus 19 ~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~ 75 (279)
+=..+++++...+|++..+ |+|+||++....++||..++++|+++..+.++.+.
T Consensus 96 L~~LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~ 149 (803)
T KOG3561|consen 96 LTHLILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDN 149 (803)
T ss_pred HHHHHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCcccc
Confidence 3345677777778899999 99999999999999999999999997777766543
No 58
>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=93.73 E-value=0.0079 Score=38.72 Aligned_cols=53 Identities=21% Similarity=0.190 Sum_probs=35.5
Q ss_pred cceeccccccccCCC-----Ccccc---cccc--cccHHHHHHHHhhhhhHhhhhhccccc-cc
Q 023651 171 SLLDLDRVLALDSDD-----TGLEI---EDSC--EASDLEKRKAATAIDNILSVLTHYSQL-TG 223 (279)
Q Consensus 171 ~l~~~~~~l~~~~~~-----~~~~~---~~~~--~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g 223 (279)
++..++|++++|++. ..+.. ..+. ......+..+..++..+++++++|++. +|
T Consensus 5 ~~~~isHelr~PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr~~~G 68 (68)
T PF00512_consen 5 FLASISHELRNPLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSRIESG 68 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 456789999999976 11111 1111 233334567889999999999999987 44
No 59
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=91.73 E-value=0.29 Score=45.31 Aligned_cols=57 Identities=16% Similarity=0.183 Sum_probs=49.0
Q ss_pred HHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHH
Q 023651 23 ALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEI 82 (279)
Q Consensus 23 ~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~ 82 (279)
+++.+...|++++.+ |.++|+++.....+|++.-|+.|..+.++.+|.+...+.+.+
T Consensus 124 iLqsLDGFVm~l~~d---G~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL 180 (768)
T KOG3558|consen 124 ILQSLDGFVMALTQD---GDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQL 180 (768)
T ss_pred HHhhccceEEEEccC---CCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHh
Confidence 556666667889999 999999999999999999999999999999988877766544
No 60
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=89.43 E-value=0.26 Score=45.02 Aligned_cols=103 Identities=17% Similarity=0.126 Sum_probs=58.1
Q ss_pred CccceeccccccccCCC-------------Cccccccc--ccccHHHHHHHHhhhhhHhhhhhccccccccccccccccC
Q 023651 169 SDSLLDLDRVLALDSDD-------------TGLEIEDS--CEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSL 233 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~-------------~~~~~~~~--~~~~~~~~~~a~~~~~~i~~~l~~~s~~~g~~~~~~~~~~ 233 (279)
...|..|+-.+.|.+|. ..++.... .......+..-.++|..|.+.|-.|+|....-....
T Consensus 381 LA~LGQmSA~iaHElNQPLaaiRt~adna~~lLergr~e~a~~Nl~~I~~LteRma~It~~Lk~FArk~~~a~~~v---- 456 (603)
T COG4191 381 LAALGQMSAGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSFARKSRDAAGPV---- 456 (603)
T ss_pred HHHHHHHHHHHHHHhcCcHHHHHhHHHHHHHHHHcCChHHHHhHHHHHHHHHHHHHHHHHHHHHHhccCccccCCc----
Confidence 34455677667776665 11222222 222333344566788888888888887632221111
Q ss_pred CCCCccchhhhhhhhhcccceEeeCCCCCC-CCEEEechhhhh
Q 023651 234 PGMGFISSSLYISLGRIKQSFVLIDPHLPD-MPMVYASDAFLK 275 (279)
Q Consensus 234 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~p~-~p~~~~~~~~~~ 275 (279)
..-+++...|...-.++++.-+..+-++|+ .|+|.+|+.-|+
T Consensus 457 ~l~~ai~~Al~ll~~R~~~~~~~l~~~~~~~~~~V~~~~iRLe 499 (603)
T COG4191 457 SLREAIEGALELLRGRLRAAGVELELDLPDAPLWVMANEIRLE 499 (603)
T ss_pred cHHHHHHHHHHHHHHhhhccCceeeccCCCCCceeecchhhHH
Confidence 111334445666666777766666666654 788999987665
No 61
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=89.41 E-value=0.43 Score=29.92 Aligned_cols=32 Identities=22% Similarity=0.371 Sum_probs=25.0
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+..+++.+..++.+.| +.-|+++|++|++++|
T Consensus 3 ~~~l~~~~~~~i~i~d----~~~i~~~N~~~~~l~g 34 (64)
T PF13188_consen 3 YRSLFDNSPDGILIID----GGRIIYVNPAFEELFG 34 (64)
T ss_dssp HHHHHCCSSSEEEEEE----TSBEEEE-HHHHHHHC
T ss_pred HHHHHHcCccceEEEE----CCChHHhhHHHHHHhC
Confidence 4566777788888887 2379999999999998
No 62
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=89.22 E-value=0.81 Score=39.74 Aligned_cols=84 Identities=8% Similarity=0.062 Sum_probs=57.8
Q ss_pred EEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEEEEE
Q 023651 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF 110 (279)
Q Consensus 31 i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~ 110 (279)
+|....| -.++|......+++||.+.+++|++....++..+...........+..|....--+++..+.|...|+.-
T Consensus 228 mfraslD---lkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvqs 304 (598)
T KOG3559|consen 228 MFRASLD---LKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQS 304 (598)
T ss_pred EEEeecc---eEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEEE
Confidence 4555667 8899999999999999999999998666665555444443333444455443334556677888888876
Q ss_pred EEEEeee
Q 023651 111 KMSLVFG 117 (279)
Q Consensus 111 ~~~pi~~ 117 (279)
...-+.+
T Consensus 305 yat~vHn 311 (598)
T KOG3559|consen 305 YATFVHN 311 (598)
T ss_pred eeEEEec
Confidence 6655543
No 63
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=88.18 E-value=4.5 Score=39.71 Aligned_cols=52 Identities=8% Similarity=-0.061 Sum_probs=33.4
Q ss_pred ccceeccccccccCCCC------cc---cccccccccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 170 DSLLDLDRVLALDSDDT------GL---EIEDSCEASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 170 ~~l~~~~~~l~~~~~~~------~~---~~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
.++..++|++++|++.- .. ............+.....++.+++++++++++.
T Consensus 452 ~~~~~iaHeLrtPL~~I~~~~~~l~~~~~~~~~~~~~l~~i~~~~~rl~~li~~ll~~sr~ 512 (828)
T PRK13837 452 TLASGIAHNFNNILGAILGYAEMALNKLARHSRAARYIDEIISAGARARLIIDQILAFGRK 512 (828)
T ss_pred HHHHHhhHHhhhHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 35568999999998761 11 111111222333456778999999999999974
No 64
>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=85.70 E-value=0.75 Score=32.77 Aligned_cols=43 Identities=26% Similarity=0.397 Sum_probs=34.2
Q ss_pred EEEEEcCCCCCCcEEecchHHHHHhCCC---cchhcCCCCCCCCCCCC
Q 023651 30 SFTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPRT 74 (279)
Q Consensus 30 ~i~~~d~~~~~g~i~~~N~~~~~l~G~~---~~e~~G~~~~~l~~~~~ 74 (279)
.++++|.+ +++|+.++.....++|.+ .++++|++...++.+..
T Consensus 17 ~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~ 62 (110)
T PF08446_consen 17 ALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES 62 (110)
T ss_dssp EEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred EEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence 34567653 399999999999999999 99999999888776543
No 65
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=85.70 E-value=0.9 Score=41.00 Aligned_cols=59 Identities=12% Similarity=0.147 Sum_probs=50.7
Q ss_pred HHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHH
Q 023651 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (279)
Q Consensus 22 ~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~ 83 (279)
-+++++..-++++..+ |.|.|++...+..+|+...+++-+++.++++.++.+.+.+.+.
T Consensus 115 ~lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLh 173 (712)
T KOG3560|consen 115 LLLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLH 173 (712)
T ss_pred HHHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHh
Confidence 3566777778888999 9999999999999999999999999888888888877766654
No 66
>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=85.21 E-value=5.9 Score=28.61 Aligned_cols=48 Identities=17% Similarity=0.213 Sum_probs=36.7
Q ss_pred eEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHHHhc
Q 023651 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (279)
Q Consensus 92 ~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~e~~ 142 (279)
....+....++|+ .+..+...+++ ++|.++|++++-.|+|....+++-
T Consensus 68 ~~~nY~~~~~~Gk--~lrSsT~~Ird-~~g~~iG~LCIN~D~s~~~~~~~~ 115 (118)
T PF08348_consen 68 YIINYKTKTKDGK--ILRSSTFFIRD-ENGKLIGALCINFDISALEQAQNF 115 (118)
T ss_pred ccccccccCCCCC--EEEEEEEEEEC-CCCCEEEEEEEEeccHHHHHHHHH
Confidence 3344555677886 44566778888 899999999999999998887443
No 67
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=83.07 E-value=3.4 Score=39.73 Aligned_cols=74 Identities=8% Similarity=0.106 Sum_probs=58.1
Q ss_pred CCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCe---EEEEEEEcCCCceEEEEEEE
Q 023651 39 SGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI---EVNLLNYKKDGTPFWMLFKM 112 (279)
Q Consensus 39 ~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~~e~~~~~~dG~~~~~~~~~ 112 (279)
+.+.+..|..++..++||-+.+++|+.+..++++++.....+....+++.++.. ...++++..+|.++.+....
T Consensus 339 ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTeW 415 (1114)
T KOG3753|consen 339 PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTEW 415 (1114)
T ss_pred CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEechh
Confidence 448889999999999999999999999888888888887777777777665432 23567778889887665443
No 68
>PRK09303 adaptive-response sensory kinase; Validated
Probab=82.73 E-value=1 Score=39.72 Aligned_cols=57 Identities=18% Similarity=0.135 Sum_probs=35.6
Q ss_pred CccceeccccccccCCCC-----cccccccc----------cccHHHHHHHHhhhhhHhhhhhccccc-cccc
Q 023651 169 SDSLLDLDRVLALDSDDT-----GLEIEDSC----------EASDLEKRKAATAIDNILSVLTHYSQL-TGRL 225 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~~-----~~~~~~~~----------~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~ 225 (279)
..++..++|++++|++.. .+...... ..........+..+..++++++.+++. .+..
T Consensus 152 ~~l~~~iaHeLrtPLt~i~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~ll~~~~~~~~~~ 224 (380)
T PRK09303 152 DRVLAMLAHDLRTPLTAASLALETLELGQIDEDTELKPALIEQLQDQARRQLEEIERLITDLLEVGRTRWEAL 224 (380)
T ss_pred HHHHHHHhHhhcchHHHHHHHHHHHhccCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 445678999999999761 11111111 111123456777899999999999987 4444
No 69
>PRK13557 histidine kinase; Provisional
Probab=82.18 E-value=1.6 Score=39.98 Aligned_cols=36 Identities=33% Similarity=0.793 Sum_probs=31.6
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.+...+++.|++-++.+|+|+|++|++++|
T Consensus 32 ~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G 67 (540)
T PRK13557 32 FFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTG 67 (540)
T ss_pred HHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhC
Confidence 566777778888999988788999999999999998
No 70
>PRK10490 sensor protein KdpD; Provisional
Probab=81.36 E-value=5.1 Score=39.76 Aligned_cols=61 Identities=15% Similarity=0.089 Sum_probs=37.5
Q ss_pred CccceeccccccccCCCC-----ccc-----ccccccccHHHHHHHHhhhhhHhhhhhccccc-cccccccc
Q 023651 169 SDSLLDLDRVLALDSDDT-----GLE-----IEDSCEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCGK 229 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~~-----~~~-----~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~~ 229 (279)
..++..++|++++|++.. .+. ...+.......+.....++.++++.|++++++ .|.+....
T Consensus 665 ~~lla~isHELrtPLt~I~g~~~lL~~~l~~~~~~~~~~~~~i~~~~~~l~~li~~LL~~srl~~~~~~l~~ 736 (895)
T PRK10490 665 NALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQQVLNTTRLVNNLLDMARIQSGGFNLRK 736 (895)
T ss_pred HHHHHHhHHHHhHHHHHHHHHHHHHhhcccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccc
Confidence 345668999999999751 111 11111122233455677888999999999988 56554443
No 71
>PRK13559 hypothetical protein; Provisional
Probab=79.99 E-value=2.3 Score=36.94 Aligned_cols=36 Identities=39% Similarity=0.782 Sum_probs=30.5
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.....++++|+.-++.+|+|+|++|.+++|
T Consensus 45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G 80 (361)
T PRK13559 45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTG 80 (361)
T ss_pred HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhC
Confidence 455667777788999987788899999999999998
No 72
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=78.83 E-value=5.6 Score=36.74 Aligned_cols=42 Identities=12% Similarity=0.125 Sum_probs=36.3
Q ss_pred hhHHHHHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCC
Q 023651 12 FNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (279)
Q Consensus 12 l~~~~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~ 56 (279)
+..+.+..+..++.++|.||++++.+ +.+.|+||-+..+++-
T Consensus 69 ls~~~~~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~~ 110 (655)
T COG3887 69 LSYQAEKSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcCh
Confidence 44456677889999999999999988 9999999999998864
No 73
>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=76.57 E-value=17 Score=24.15 Aligned_cols=46 Identities=15% Similarity=0.134 Sum_probs=30.9
Q ss_pred HHHHHhCCCeEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccc
Q 023651 83 REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (279)
Q Consensus 83 ~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DIT 134 (279)
.+++..+... +.....|.+.-+-+...|+++ .+|++++.+|+. |+|
T Consensus 38 e~vl~~g~v~----r~~P~~G~Y~G~PViV~PI~~-~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 38 EEVLETGKVI----RVTPIEGPYKGVPVIVAPIKD-EDGEVIAAIGVV-DLT 83 (84)
T ss_pred HHHHHcCCEE----EeccCCcccCCeeEEEEEEEc-CCCCEEEEEEEE-Ecc
Confidence 4455555432 223445665556678899998 789999999986 665
No 74
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=74.96 E-value=3.4 Score=36.08 Aligned_cols=54 Identities=19% Similarity=0.273 Sum_probs=44.3
Q ss_pred HHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHH
Q 023651 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR 77 (279)
Q Consensus 21 ~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~ 77 (279)
..+++.+...|++++++ |.|.|+++.+.-.+|++.-|+-|....+.+++.+...
T Consensus 82 shlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~de 135 (598)
T KOG3559|consen 82 SHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDE 135 (598)
T ss_pred HhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHH
Confidence 44566666778899999 9999999999999999999999998777666665443
No 75
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=74.56 E-value=11 Score=37.01 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=37.3
Q ss_pred HHHHHHHHhhCCCEEEEEc-CCCCCCcEEecchHHHHHhCCCcchhcCCCCCC
Q 023651 17 TLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68 (279)
Q Consensus 17 ~~~~~~~l~~~~~~i~~~d-~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~ 68 (279)
...-..++..+|.|++++| .+ |.|.|+|+.|..++| .+ ++|++...
T Consensus 101 ~~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~ 147 (838)
T PRK14538 101 SQIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQ 147 (838)
T ss_pred hHHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHH
Confidence 3445678889999999999 68 999999999999987 23 78887654
No 76
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=74.36 E-value=2.7 Score=39.08 Aligned_cols=87 Identities=15% Similarity=0.149 Sum_probs=47.9
Q ss_pred eccccccccCCC-----Cccc-c--cccccccHH---HHHHHHhhhhhHhhhhhccccccccccccccccCCCCCccchh
Q 023651 174 DLDRVLALDSDD-----TGLE-I--EDSCEASDL---EKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSS 242 (279)
Q Consensus 174 ~~~~~l~~~~~~-----~~~~-~--~~~~~~~~~---~~~~a~~~~~~i~~~l~~~s~~~g~~~~~~~~~~~~~~~~~~~ 242 (279)
.++|.++.|++. .++. . ........+ .+.+....|++++++++.||++.- ...++-.++
T Consensus 530 v~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l~~----------~~~~l~~td 599 (750)
T COG4251 530 VASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKLGL----------TEAPLQPTD 599 (750)
T ss_pred HhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcc----------ccCCCCCcc
Confidence 567777777754 1111 1 222222222 344577799999999999996521 111111223
Q ss_pred hhhhhhhcccce----------EeeCCCCCCCCEEEechhhh
Q 023651 243 LYISLGRIKQSF----------VLIDPHLPDMPMVYASDAFL 274 (279)
Q Consensus 243 l~~~~~~~~~~~----------~~~~~~~p~~p~~~~~~~~~ 274 (279)
+..++.++.... +-++ | +|.|++|+.-+
T Consensus 600 ~~~vv~~vl~~l~~ri~dtgaei~i~---~-lp~v~~d~~~l 637 (750)
T COG4251 600 VQKVVDKVLLELSQRIADTGAEIRIA---P-LPVVAADATQL 637 (750)
T ss_pred hHHHHHHHHHhcccccccccceEEec---c-cceeecCHHHH
Confidence 555555555332 2233 4 88999998643
No 77
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.01 E-value=27 Score=27.40 Aligned_cols=106 Identities=16% Similarity=0.210 Sum_probs=69.8
Q ss_pred HHHhhCCCEEEEEcCCCCCCcEE--ecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEE
Q 023651 22 EALDELPDSFTITDPSISGHPIV--FASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (279)
Q Consensus 22 ~~l~~~~~~i~~~d~~~~~g~i~--~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (279)
.+-..+++.+++-+... |.+. .+-...|.++|- |+-|.....+..+.+.......+..+.....+.-......
T Consensus 52 ~l~slL~d~FiL~~~~~--G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~ 126 (209)
T COG5388 52 KLKSLLPDVFILERDGR--GKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGR 126 (209)
T ss_pred HHHhhcCceEEEeccCC--CCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchh
Confidence 35566777555433221 4443 356667777764 6677776666666666666666666666666766666666
Q ss_pred cCCCceEEEEEEEEEeeecCCCcEEEEEEEEecc
Q 023651 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 100 ~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
...|...-+++-..|+.. ..|+...++|...-+
T Consensus 127 s~~G~sl~fEmLl~PL~~-~~g~~~R~LGais~~ 159 (209)
T COG5388 127 SHGGRSLGFEMLLAPLQG-ASGETDRFLGAISPI 159 (209)
T ss_pred hccCcccceeeeeecccC-CCCCccchhhhcccc
Confidence 777888888999999987 788866777765443
No 78
>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=71.82 E-value=1 Score=44.88 Aligned_cols=60 Identities=15% Similarity=0.133 Sum_probs=40.1
Q ss_pred CccceeccccccccCCC-----Cccccccc---ccccHHHHHHHHhhhhhHhhhhhccccc-ccccccc
Q 023651 169 SDSLLDLDRVLALDSDD-----TGLEIEDS---CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCG 228 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~-----~~~~~~~~---~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~ 228 (279)
..++..++|++++|++. ..+..... .......+.....++..+++++++|+++ .|.+...
T Consensus 465 ~~~~~~~sHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~~~~e~~~~~~~ 533 (968)
T TIGR02956 465 SAFLATMSHEIRTPLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDYSKIEAGHLSIS 533 (968)
T ss_pred HHHHHHhHHHhhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeee
Confidence 56778999999999976 11221111 1122234456788999999999999998 6655443
No 79
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=70.87 E-value=8.4 Score=30.99 Aligned_cols=39 Identities=18% Similarity=0.065 Sum_probs=34.0
Q ss_pred HHHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCc
Q 023651 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (279)
Q Consensus 17 ~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~ 58 (279)
.+.+..+++..+..+++-+.+ |.+++.|.+|...+.-.-
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhcC
Confidence 346778999999999999999 999999999999987643
No 80
>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]
Probab=70.07 E-value=1.9 Score=38.46 Aligned_cols=56 Identities=13% Similarity=0.145 Sum_probs=36.8
Q ss_pred cceeccccccccCCCC---------ccccccc--ccccHHHHHHHHhhhhhHhhhhhccccc-ccccc
Q 023651 171 SLLDLDRVLALDSDDT---------GLEIEDS--CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLV 226 (279)
Q Consensus 171 ~l~~~~~~l~~~~~~~---------~~~~~~~--~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~ 226 (279)
.+..++|++-.|+|++ .++..+. ...+...+.....+|..|+..|..|+|. ++..+
T Consensus 454 TmTslaHEinQPLnAmsaYLFsA~~A~e~~~s~qa~~~L~kie~L~eR~~~Iv~sLRqF~Rk~s~~~~ 521 (673)
T COG4192 454 TMTSLAHEINQPLNAMSAYLFSARLALEEAPSAQAATSLDKIENLTERMGKIVNSLRQFARKNSSDES 521 (673)
T ss_pred HHHHHHHHhcCchHHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 3457899999999871 1222222 1223334556778999999999999987 55533
No 81
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=68.53 E-value=1.5 Score=43.44 Aligned_cols=60 Identities=17% Similarity=0.160 Sum_probs=39.4
Q ss_pred CccceeccccccccCCCC-----ccccccc---ccccHHHHHHHHhhhhhHhhhhhccccc-ccccccc
Q 023651 169 SDSLLDLDRVLALDSDDT-----GLEIEDS---CEASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCG 228 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~~-----~~~~~~~---~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~ 228 (279)
..++..++|++++|++.. .+..... .......+......+..+++++++++++ .|++...
T Consensus 294 ~~~l~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~ 362 (919)
T PRK11107 294 SEFLANMSHELRTPLNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDFSKLEAGKLVLE 362 (919)
T ss_pred HHHHHHhhHhhcccHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEE
Confidence 467889999999999761 1111111 1112223456778899999999999998 6665543
No 82
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=65.84 E-value=2.3 Score=42.09 Aligned_cols=61 Identities=13% Similarity=0.169 Sum_probs=39.7
Q ss_pred CccceeccccccccCCC-----Ccccccccc---cccHHHHHHHHhhhhhHhhhhhccccc-cccccccc
Q 023651 169 SDSLLDLDRVLALDSDD-----TGLEIEDSC---EASDLEKRKAATAIDNILSVLTHYSQL-TGRLVCGK 229 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~-----~~~~~~~~~---~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~~~~ 229 (279)
..++..++|++++||+. ..+...... ......+.....++..++++|++++++ .|.+....
T Consensus 399 ~~~~~~isHelrtPL~~i~~~~~~l~~~~~~~~~~~~~~~i~~~~~~l~~li~~ll~~~~~~~~~~~~~~ 468 (921)
T PRK15347 399 SEHLTTISHEIRTPLNGVLGALELLQNTPLTAEQMDLADTARQCTLSLLAIINNLLDFSRIESGQMTLSL 468 (921)
T ss_pred HHHHHHhHHHhchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccee
Confidence 45677899999999976 111111111 112223445777899999999999998 66665443
No 83
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=62.11 E-value=22 Score=30.40 Aligned_cols=88 Identities=14% Similarity=0.303 Sum_probs=54.4
Q ss_pred HHHHHhhCC----CEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHH--hCCCeE
Q 023651 20 VHEALDELP----DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR--EERPIE 93 (279)
Q Consensus 20 ~~~~l~~~~----~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~ 93 (279)
++.++|+.. .++++..+. +.+.+|+|..+..++||+.++++......+.. ....+...+. ......
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV~e------Gl~qW~~dL~~~s~~E~~ 356 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIVQE------GLAQWETDLQLLSRQERS 356 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHHHh------hHHHHHHHHHhhhhhhhh
Confidence 455666543 356666644 37899999999999999999887553322221 1112222221 222334
Q ss_pred EEEEEEcCCCceEEEEEEEEEe
Q 023651 94 VNLLNYKKDGTPFWMLFKMSLV 115 (279)
Q Consensus 94 ~e~~~~~~dG~~~~~~~~~~pi 115 (279)
+.+...+|.|....+......+
T Consensus 357 grlviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 357 GRLVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred ceEEEEecCCCceeeEEEEeec
Confidence 5677788999888877766655
No 84
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=55.02 E-value=70 Score=30.08 Aligned_cols=102 Identities=12% Similarity=0.031 Sum_probs=52.8
Q ss_pred HHHHHHHhhCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcch-hcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEE
Q 023651 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE-IIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (279)
Q Consensus 18 ~~~~~~l~~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e-~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (279)
+++-..+...+..++++|.+ |.++..+-.-......+.-- ..|..|..-... -..+-.++..+++...--
T Consensus 77 ~~L~~~v~~~~~~vLLtD~~---GViL~~~G~~~~~~~~rk~gl~~Ga~WSE~~~G------TNgIGTcLve~~aVtI~~ 147 (606)
T COG3284 77 DRLFQAVAGSGCCVLLTDAD---GVILERRGDPRDDEDFRKAGLWLGAVWSEPREG------TNGIGTCLVEGEAVTIHG 147 (606)
T ss_pred HHHHHHhcCCCeEEEEEcCc---eeEEEeecChhhhhhhhhhcccccccccccccc------ccchhhhhccCcceEEeh
Confidence 34444556677889999999 99987654322222221111 123333221100 112233444444433210
Q ss_pred EEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEE
Q 023651 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQ 130 (279)
Q Consensus 97 ~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~ 130 (279)
. .+-.-....+.+++.|++| ++|.+.|++.+.
T Consensus 148 ~-qHF~~~~~~lsCsAaPI~D-~qG~L~gVLDIS 179 (606)
T COG3284 148 D-QHFIQAHHGLSCSAAPIFD-EQGELVGVLDIS 179 (606)
T ss_pred h-hhHhhcccCceeeeecccc-CCCcEEEEEEec
Confidence 0 0111223345788999999 899999887654
No 85
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=52.32 E-value=67 Score=29.62 Aligned_cols=33 Identities=12% Similarity=0.182 Sum_probs=27.7
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.+..+++++|+ +.-|+++|+++.+++|
T Consensus 224 ~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~ 256 (545)
T PRK15053 224 QEALFSSVYEGLIAVDP---HGYITAINRNARKMLG 256 (545)
T ss_pred HHHHHHHhCceEEEECC---CCeEEeecHHHHHHhC
Confidence 45577777888899987 6789999999999987
No 86
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=52.08 E-value=12 Score=36.18 Aligned_cols=43 Identities=14% Similarity=0.117 Sum_probs=35.3
Q ss_pred EEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCH
Q 023651 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR 76 (279)
Q Consensus 31 i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~ 76 (279)
+++-+.+ |+|+|+.+.+..++||+++-+.|..+.+++++.+..
T Consensus 195 ~~vS~~d---G~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~ 237 (1114)
T KOG3753|consen 195 VAVSFLD---GRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVG 237 (1114)
T ss_pred EEEeccC---CcEEEeechhhhhccCchhhhccchhhhhcchhhhh
Confidence 3445567 999999999999999999999999887777665543
No 87
>PRK10060 RNase II stability modulator; Provisional
Probab=49.85 E-value=17 Score=34.78 Aligned_cols=32 Identities=13% Similarity=0.102 Sum_probs=25.3
Q ss_pred hhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
..+++.....++++|+ +.-|+|+|++|+++||
T Consensus 114 ~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~G 145 (663)
T PRK10060 114 EQVVSEANSVIVILDS---RGNIQRFNRLCEEYTG 145 (663)
T ss_pred HHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHC
Confidence 3445556667888887 5679999999999998
No 88
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=49.58 E-value=17 Score=35.19 Aligned_cols=94 Identities=11% Similarity=0.096 Sum_probs=66.1
Q ss_pred CcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCC-CeEEEEEEEcCCCceEEEEEEEEEeeecC
Q 023651 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKDGTPFWMLFKMSLVFGKE 119 (279)
Q Consensus 41 g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~dG~~~~~~~~~~pi~~~~ 119 (279)
|.++++-.++..+.||...++.|..+..+.++++.......+..+..... ....-++.+.++|...|......-..+..
T Consensus 382 g~~~~~dqr~~~i~~~~~~~~~g~ss~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~~~~~~~~~~n~~ 461 (803)
T KOG3561|consen 382 GSFTFVDQRASAILGYQPQELLGRSSYESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIPNKSSAYLFSNPG 461 (803)
T ss_pred CceeccccccccccccCchhhcCcccccccCccccchhhchHHHHHHhcccccccccccccCCCCccccccccccccCCC
Confidence 89999999999999999999999998888777777766666655544333 23344666778998887766554443313
Q ss_pred CCcEEEEEEEEeccc
Q 023651 120 DGRATHFVAVQVPIV 134 (279)
Q Consensus 120 ~g~~~~~v~~~~DIT 134 (279)
...+.+++++-..+.
T Consensus 462 s~~~~~~~~~ns~~~ 476 (803)
T KOG3561|consen 462 SDEVEYIVCTNSNVP 476 (803)
T ss_pred ccccceeeecccccc
Confidence 455667777665555
No 89
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=47.34 E-value=9 Score=37.99 Aligned_cols=55 Identities=15% Similarity=0.100 Sum_probs=36.2
Q ss_pred CccceeccccccccCCCC-----cccccccc---cccHHHHHHHHhhhhhHhhhhhccccc-cc
Q 023651 169 SDSLLDLDRVLALDSDDT-----GLEIEDSC---EASDLEKRKAATAIDNILSVLTHYSQL-TG 223 (279)
Q Consensus 169 ~~~l~~~~~~l~~~~~~~-----~~~~~~~~---~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g 223 (279)
..++..++|++++|++.. .+...... ......+.....++..+++++++|++. .|
T Consensus 445 ~~~l~~isHelrtPL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~s~~~~~ 508 (914)
T PRK11466 445 SAFLAAMSHEIRTPLYGILGTAQLLADNPALNAQRDDLRAITDSGESLLTILNDILDYSAIEAG 508 (914)
T ss_pred HHHHHHhHHHHhhHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 457779999999999761 12111111 112223456778899999999999987 44
No 90
>PF09308 LuxQ-periplasm: LuxQ, periplasmic; InterPro: IPR015387 This entry represents the periplasmic sensor domain of the prokaryotic protein LuxQ, that assumes a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds []. ; GO: 0004673 protein histidine kinase activity, 0016791 phosphatase activity; PDB: 2HJ9_C 2HJE_A 1ZHH_B 3C30_A 3C38_A.
Probab=42.96 E-value=1.9e+02 Score=23.79 Aligned_cols=85 Identities=12% Similarity=0.154 Sum_probs=49.5
Q ss_pred hCCCEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCce
Q 023651 26 ELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTP 105 (279)
Q Consensus 26 ~~~~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~ 105 (279)
++|+--|+.+.+ | .+|..+-..++|.+...+ ..+......+..|.... .......
T Consensus 70 ~~pDfRFi~~~~---~--~~WdDgN~~FYGi~~~~L------------------~~ls~~~~~~~~W~~i~--~~s~~g~ 124 (238)
T PF09308_consen 70 NAPDFRFISSHD---G--VIWDDGNAPFYGISESSL------------------QHLSQKVAFSNNWHYIQ--TPSSMGN 124 (238)
T ss_dssp CS-SEEEEEETT---C--EEEE-SHHHHCT--HHHH------------------HHHHHHT-STTS-EEEE--EEETTCE
T ss_pred CCCCEEEEEeCC---C--cEEeCCCCcccCcCHHHH------------------HHHhhcccccCceeEEE--ecCCCCc
Confidence 467777888776 5 356777778888765432 23333334455555432 2445667
Q ss_pred EEEEEEEEEeeecCCCcEEEEEEEEeccch
Q 023651 106 FWMLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (279)
Q Consensus 106 ~~~~~~~~pi~~~~~g~~~~~v~~~~DITe 135 (279)
+.+.+..+|+.+...|++.|+.-+..-.-.
T Consensus 125 ~~lLvRR~pIi~~~tGEVlG~Ly~gvVLNn 154 (238)
T PF09308_consen 125 RYLLVRRTPIIDPKTGEVLGYLYIGVVLNN 154 (238)
T ss_dssp EEEEEEEEEEE-TTTSBEEEEEEEEEE-TT
T ss_pred eEEEEeecceeeCCCCeEEEEEEEEEEEcC
Confidence 888899999987578999997655543333
No 91
>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=40.75 E-value=10 Score=22.56 Aligned_cols=19 Identities=21% Similarity=0.302 Sum_probs=13.3
Q ss_pred HHHHhhhhhHhhhhhcccc
Q 023651 202 RKAATAIDNILSVLTHYSQ 220 (279)
Q Consensus 202 ~~a~~~~~~i~~~l~~~s~ 220 (279)
..+...+..+++.++.|++
T Consensus 47 ~~~~~~~~~l~~~l~~~~~ 65 (65)
T cd00082 47 REEAERLLRLINDLLDLSR 65 (65)
T ss_pred HHHHHHHHHHHHHHHHHhC
Confidence 4466777888888877653
No 92
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.44 E-value=1.2e+02 Score=21.40 Aligned_cols=47 Identities=6% Similarity=0.069 Sum_probs=29.0
Q ss_pred HHHHHhCCCeEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchh
Q 023651 83 REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (279)
Q Consensus 83 ~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITer 136 (279)
.++++.|+.... ....|-+.-.-+...|+.+ +|++++.+|+. |+|.-
T Consensus 56 eevle~gevvr~----vP~~GpY~G~pVVV~Pik~--~g~viaAiGiV-Dlt~g 102 (123)
T COG4048 56 EEVLEKGEVVRE----VPIIGPYRGLPVVVAPIKD--EGEVIAAIGIV-DLTAG 102 (123)
T ss_pred HHHHhhCceeee----CCCCCccCCceEEEEEecc--CCeEEEEEEee-ehhhh
Confidence 445555553321 2334444444567889986 89999999976 66643
No 93
>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=34.84 E-value=1.3e+02 Score=19.44 Aligned_cols=34 Identities=9% Similarity=0.206 Sum_probs=25.3
Q ss_pred eEEEEEEEEEeeecCCCcEEEEEEEEeccchhHHH
Q 023651 105 PFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (279)
Q Consensus 105 ~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~~ 139 (279)
..++.....|+.+ .+|++.|++++-.++....+.
T Consensus 11 ~~~vi~~s~pi~~-~~g~~~Gvv~~di~l~~l~~~ 44 (81)
T PF02743_consen 11 GQPVITISVPIYD-DDGKIIGVVGIDISLDQLSEI 44 (81)
T ss_dssp TEEEEEEEEEEEE-TTTEEEEEEEEEEEHHHHHHH
T ss_pred CcEEEEEEEEEEC-CCCCEEEEEEEEeccceeeeE
Confidence 3466677889998 899999999987666554433
No 94
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=34.07 E-value=1.8e+02 Score=20.90 Aligned_cols=28 Identities=25% Similarity=0.549 Sum_probs=21.2
Q ss_pred EEcCCCCCCcEEecchHHHHHhCCCcchhcC
Q 023651 33 ITDPSISGHPIVFASRGFLKMSGFSRAEIIG 63 (279)
Q Consensus 33 ~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G 63 (279)
..+.. +.+.+.|......+++......+
T Consensus 4 ~~~~~---~~~~~~~~~~~~~~~~~~~~~~~ 31 (232)
T COG2202 4 VLDRD---GRIIYANEAAEELLGYSAEELLG 31 (232)
T ss_pred EEccc---ccEEEecccchhhcCCChHHhhh
Confidence 44555 78888888888888888776655
No 95
>PRK10604 sensor protein RstB; Provisional
Probab=31.80 E-value=21 Score=32.03 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=33.5
Q ss_pred ccceeccccccccCCCCc----ccccccccccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 170 DSLLDLDRVLALDSDDTG----LEIEDSCEASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 170 ~~l~~~~~~l~~~~~~~~----~~~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
..+..++|++++|+.... +.. ................+..++++|+.++++
T Consensus 214 ~l~~~vsHeLrtPL~~i~~~l~~l~-~~~~~~~~~i~~~~~~l~~li~~ll~~~rl 268 (433)
T PRK10604 214 QLIDGIAHELRTPLVRLRYRLEMSD-NLSAAESQALNRDIGQLEALIEELLTYARL 268 (433)
T ss_pred HHHHHhhHhhcChHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345688999999996621 111 111111223556778999999999999987
No 96
>PRK10337 sensor protein QseC; Provisional
Probab=31.40 E-value=34 Score=30.55 Aligned_cols=51 Identities=14% Similarity=0.050 Sum_probs=31.6
Q ss_pred cceeccccccccCCCCc-----cc--ccccc--cccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 171 SLLDLDRVLALDSDDTG-----LE--IEDSC--EASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 171 ~l~~~~~~l~~~~~~~~-----~~--~~~~~--~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
++..++|++++|+.... .. ...+. ............++..+++.|+.+++.
T Consensus 240 ~~~~~ahelrtpl~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~ll~~~r~ 299 (449)
T PRK10337 240 FTSDAAHELRSPLAALKVQTEVAQLSDDDPQARKKALLQLHAGIDRATRLVDQLLTLSRL 299 (449)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45679999999986511 11 11111 111222344678899999999999987
No 97
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=31.30 E-value=16 Score=21.95 Aligned_cols=49 Identities=16% Similarity=0.063 Sum_probs=27.3
Q ss_pred eeccccccccCCCC-----cccccc-cc--cccHHHHHHHHhhhhhHhhhhhccccc
Q 023651 173 LDLDRVLALDSDDT-----GLEIED-SC--EASDLEKRKAATAIDNILSVLTHYSQL 221 (279)
Q Consensus 173 ~~~~~~l~~~~~~~-----~~~~~~-~~--~~~~~~~~~a~~~~~~i~~~l~~~s~~ 221 (279)
..++|++++|+... .+.... +. .............+..++..++.|++.
T Consensus 7 ~~i~Hel~~pl~~i~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~ 63 (66)
T smart00388 7 ANLSHELRTPLTAIRGYLELLEDTELSEEQREYLETILRSAERLLRLINDLLDLSRI 63 (66)
T ss_pred HHHHHhccCcHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34678888887541 111111 11 111122345677888888888888764
No 98
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=29.17 E-value=1e+02 Score=21.73 Aligned_cols=74 Identities=23% Similarity=0.274 Sum_probs=40.9
Q ss_pred CEEEEEcCCCCCCcEEecchHHHHHhCCCcchhcCCCCCCCCCCCCCHHHHHHHHHHHHhCCCeEEEEEEEcCCCceEEE
Q 023651 29 DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWM 108 (279)
Q Consensus 29 ~~i~~~d~~~~~g~i~~~N~~~~~l~G~~~~e~~G~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~ 108 (279)
+-++++|.+ |.+++-+ ..+.+|+.... .+ ...++ .|+++... ....+ -+.
T Consensus 40 ~~i~v~D~~---g~~l~~s----------~~~~iG~~~~~---~~--------~~~aL-~G~~~~~~---~~~~~--~~~ 89 (116)
T PF14827_consen 40 DYIVVTDRD---GIVLAHS----------DPERIGDRYSD---ED--------VRKAL-QGKSYTSV---SQGTG--GPS 89 (116)
T ss_dssp SEEEEECTT---SBECE-S----------SCCCTTSB-SS---CC--------HCHHC-CT--EEEE---EECTT--CEE
T ss_pred eEEEEEcCC---CCEEEcC----------ChHHcCCcccC---CC--------hhhhh-cCCceEEe---eecCC--ceE
Confidence 457889999 9887633 33456775432 11 12334 44444332 12222 355
Q ss_pred EEEEEEeeecCCCcEEEEEEEEecc
Q 023651 109 LFKMSLVFGKEDGRATHFVAVQVPI 133 (279)
Q Consensus 109 ~~~~~pi~~~~~g~~~~~v~~~~DI 133 (279)
.....|+.+ .+|+++|++.+...+
T Consensus 90 ~~~~~PV~d-~~g~viG~V~VG~~~ 113 (116)
T PF14827_consen 90 LRAFAPVYD-SDGKVIGVVSVGVSL 113 (116)
T ss_dssp EEEEEEEE--TTS-EEEEEEEEEEH
T ss_pred EEEEEeeEC-CCCcEEEEEEEEEEc
Confidence 567789998 799999998876543
No 99
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=27.88 E-value=47 Score=29.64 Aligned_cols=33 Identities=12% Similarity=0.198 Sum_probs=26.9
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.+...+++.|+ +.-|+|+|++|.+++|
T Consensus 100 ~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g 132 (430)
T PRK11006 100 FRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLG 132 (430)
T ss_pred HHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhC
Confidence 45566777777888885 6779999999999998
No 100
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=26.72 E-value=40 Score=30.22 Aligned_cols=57 Identities=14% Similarity=0.109 Sum_probs=31.3
Q ss_pred ccceeccccccccCCCC-----ccccc--ccccccHHHHHHHHhhhhhHhhhhhccccc-ccccc
Q 023651 170 DSLLDLDRVLALDSDDT-----GLEIE--DSCEASDLEKRKAATAIDNILSVLTHYSQL-TGRLV 226 (279)
Q Consensus 170 ~~l~~~~~~l~~~~~~~-----~~~~~--~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~-~g~~~ 226 (279)
.++.+++|++++|+... .+... ................+..+++.+..+++. .|.+.
T Consensus 242 ~~~~~~shel~~pL~~i~~~~~~l~~~~~~~~~~~l~~~~~~~~~l~~li~~l~~l~~~~~~~~~ 306 (466)
T PRK10549 242 DFMADISHELRTPLAVLRGELEAIQDGVRKFTPESVASLQAEVGTLTKLVDDLHQLSLSDEGALA 306 (466)
T ss_pred HHHHHHhHHhCChHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc
Confidence 45568899999998651 11111 111112223344556777788887777655 44433
No 101
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=25.03 E-value=50 Score=28.44 Aligned_cols=51 Identities=10% Similarity=-0.040 Sum_probs=30.1
Q ss_pred ccceeccccccccCCCCc-----ccccccccccHHHHHHHHhhhhhHhhhhhcccccc
Q 023651 170 DSLLDLDRVLALDSDDTG-----LEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLT 222 (279)
Q Consensus 170 ~~l~~~~~~l~~~~~~~~-----~~~~~~~~~~~~~~~~a~~~~~~i~~~l~~~s~~~ 222 (279)
.++..++|++++|+.... +....+ ...........++...++.++.+++..
T Consensus 139 ~~~~~~sHelrtPL~~i~~~~e~l~~~~~--~~~~~~~~~~~~l~~~i~~ll~~~r~~ 194 (356)
T PRK10755 139 LFTADVAHELRTPLAGIRLHLELLEKQHH--IDVAPLIARLDQMMHTVEQLLQLARAG 194 (356)
T ss_pred HHHHHhhHhhcChHHHHHHHHHHHHhccc--hhHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 356689999999997521 111111 111122334567777788888888763
No 102
>PF12218 End_N_terminal: N terminal extension of bacteriophage endosialidase; InterPro: IPR024429 This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain [].; PDB: 3JU4_A 3GVL_A 3GVK_B 3GVJ_A 1V0E_B 1V0F_E.
Probab=24.58 E-value=57 Score=20.45 Aligned_cols=19 Identities=26% Similarity=0.693 Sum_probs=12.0
Q ss_pred EeeCCCCCCCCEEEechhh
Q 023651 255 VLIDPHLPDMPMVYASDAF 273 (279)
Q Consensus 255 ~~~~~~~p~~p~~~~~~~~ 273 (279)
+....++|.-|.-|+++.|
T Consensus 48 rF~~eri~gqpl~y~s~~f 66 (67)
T PF12218_consen 48 RFVYERIPGQPLYYVSEGF 66 (67)
T ss_dssp EEEE-SSTT--EEEE-BTS
T ss_pred eEEEeecCCCceEeeeccc
Confidence 4444579999999999988
No 103
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.07 E-value=93 Score=29.64 Aligned_cols=33 Identities=36% Similarity=0.731 Sum_probs=25.4
Q ss_pred hhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 246 ~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
.++.....+.+.+...++..++|+|++|.+++|
T Consensus 153 ~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G 185 (665)
T PRK13558 153 ALDEAPVGITIADATLPDEPLIYINDAFERITG 185 (665)
T ss_pred HHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhC
Confidence 444555556677766678889999999999998
No 104
>COG5001 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]
Probab=22.27 E-value=55 Score=29.30 Aligned_cols=23 Identities=13% Similarity=0.031 Sum_probs=17.3
Q ss_pred Cchhhh---HHHHHhhccccCCccce
Q 023651 151 GGSRLR---EIVFGSCRREVCSDSLL 173 (279)
Q Consensus 151 NR~l~~---~~~l~~~~r~~~~~~l~ 173 (279)
||+.|. +..+++++.++....+.
T Consensus 238 NRr~ffa~Ldarlaaar~~g~rl~lg 263 (663)
T COG5001 238 NRRRFFAELDARLAAARQSGRRLVLG 263 (663)
T ss_pred chhHHHHHHHHHHhhhhhcCCceEEE
Confidence 999998 66778887777666554
No 105
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=21.57 E-value=96 Score=28.38 Aligned_cols=33 Identities=18% Similarity=0.181 Sum_probs=28.3
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.+..+++++|+ +.-|+|+|+++++++|
T Consensus 223 ~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg 255 (542)
T PRK11086 223 RQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFN 255 (542)
T ss_pred HHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhC
Confidence 56677888888999996 7789999999999985
No 106
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=21.44 E-value=3.6e+02 Score=20.32 Aligned_cols=28 Identities=14% Similarity=-0.019 Sum_probs=20.3
Q ss_pred HHHHHHHHHhhCCCEEEEEcCCCCCCcEEec
Q 023651 16 YTLWVHEALDELPDSFTITDPSISGHPIVFA 46 (279)
Q Consensus 16 ~~~~~~~~l~~~~~~i~~~d~~~~~g~i~~~ 46 (279)
.++......+.+..++.++|.+ |..+..
T Consensus 10 lq~i~~~fs~~tgl~~~i~d~~---G~~l~~ 37 (173)
T PF10114_consen 10 LQEIQDSFSKATGLSIVIVDPD---GNPLTQ 37 (173)
T ss_pred HHHHHHHHHHHHCCcEEEEeCC---CCEEee
Confidence 3445556666777889999999 988843
No 107
>PF12282 H_kinase_N: Signal transduction histidine kinase; InterPro: IPR022066 This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with PF07568 from PFAM, PF08448 from PFAM, PF02518 from PFAM. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this. ; PDB: 2YKH_B 2YKF_A.
Probab=21.24 E-value=3.6e+02 Score=20.13 Aligned_cols=52 Identities=12% Similarity=0.185 Sum_probs=22.6
Q ss_pred HHHHHHhCCCeEEEEEEEcCCCceEEEEEEEEEeeecCCCcEEEEEEEEeccchhHH
Q 023651 82 IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (279)
Q Consensus 82 ~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~~~~~g~~~~~v~~~~DITerk~ 138 (279)
+.+++..|........ ...+| ..+.....|+++ +|++++++..-.++...+.
T Consensus 81 v~~a~~tg~~~~~~~~-~~~~~--~~v~~~~~PI~~--~~~vIaVl~~~~~~~~~~~ 132 (145)
T PF12282_consen 81 VDRALETGRPVRGGRA-VWQGG--VPVRQEVVPIRR--NGRVIAVLIRETNLSASRT 132 (145)
T ss_dssp HHHHHH---------------------EEEEEEEEE--TTEEEEEEEEE--GGGS--
T ss_pred HHHHHHhCCceecCCc-cccCC--ceeEEEEEEEEE--CCEEEEEEEEEcccccccC
Confidence 4555666655432211 11122 356788999998 6798888886666665554
No 108
>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=21.01 E-value=1.8e+02 Score=27.95 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=16.9
Q ss_pred EEEEeeecCCCcEEEEEEEEeccch
Q 023651 111 KMSLVFGKEDGRATHFVAVQVPIVS 135 (279)
Q Consensus 111 ~~~pi~~~~~g~~~~~v~~~~DITe 135 (279)
...|+.. .|++.|++.+..+.++
T Consensus 413 l~vPL~~--~~~~~G~l~l~~~~~~ 435 (679)
T TIGR02916 413 LIVPLIS--GEELVGFVVLARPRTA 435 (679)
T ss_pred EEEEecc--CCEEEEEEEEecCCCC
Confidence 3478875 7888999888776553
No 109
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=20.70 E-value=31 Score=30.81 Aligned_cols=33 Identities=24% Similarity=0.484 Sum_probs=26.6
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
|-.+++...+.+.|++. |--|-|+|++|+.|+|
T Consensus 159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG 191 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMG 191 (775)
T ss_pred HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhc
Confidence 55667777788888885 5557899999999998
No 110
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=20.33 E-value=1.1e+02 Score=29.86 Aligned_cols=33 Identities=21% Similarity=0.067 Sum_probs=26.9
Q ss_pred hhhhhhhcccceEeeCCCCCCCCEEEechhhhhhhC
Q 023651 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTG 278 (279)
Q Consensus 243 l~~~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~~~~ 278 (279)
+...++.+...+.+.|+ +.-|+++|++|.+++|
T Consensus 157 l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G 189 (779)
T PRK11091 157 LRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTG 189 (779)
T ss_pred HHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhC
Confidence 55566777777888886 6779999999999998
No 111
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=20.13 E-value=1.1e+02 Score=21.93 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=23.2
Q ss_pred EEcCCCceEEEEEEEEEeeecCCCcEEEE
Q 023651 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHF 126 (279)
Q Consensus 98 ~~~~dG~~~~~~~~~~pi~~~~~g~~~~~ 126 (279)
++++||+...+.-.+..+.+ .+|++.|.
T Consensus 69 ~rR~DGs~i~FddNA~Viin-~~g~P~Gt 96 (122)
T COG0093 69 VRRPDGSYIKFDDNAAVIIN-PDGEPRGT 96 (122)
T ss_pred eEcCCCCEEEeCCceEEEEC-CCCCcccc
Confidence 46889999999988888888 78888763
Done!