Query 005722
Match_columns 681
No_of_seqs 301 out of 1193
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 12:46:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005722.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005722hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4251 Bacteriophytochrome (l 100.0 1E-127 2E-132 1052.7 47.4 485 61-581 9-505 (750)
2 PF00360 PHY: Phytochrome regi 100.0 5.6E-39 1.2E-43 317.5 13.3 159 421-581 19-180 (182)
3 PF08446 PAS_2: PAS fold; Int 99.9 5.5E-25 1.2E-29 200.9 7.7 108 68-182 3-110 (110)
4 PF01590 GAF: GAF domain; Int 99.4 6.7E-12 1.5E-16 117.1 13.0 152 215-389 1-153 (154)
5 smart00065 GAF Domain present 99.1 5.9E-09 1.3E-13 92.7 16.2 138 215-391 1-140 (149)
6 PF00989 PAS: PAS fold; Inter 99.0 6E-10 1.3E-14 98.1 7.3 66 611-676 1-66 (113)
7 PF08448 PAS_4: PAS fold; Int 98.6 6.6E-08 1.4E-12 84.6 6.1 63 617-679 1-63 (110)
8 PF13426 PAS_9: PAS domain; PD 98.5 1.5E-07 3.2E-12 81.3 6.0 57 621-677 1-57 (104)
9 COG2203 FhlA FOG: GAF domain [ 98.5 5.1E-07 1.1E-11 83.3 9.3 154 201-391 6-163 (175)
10 PF13492 GAF_3: GAF domain; PD 98.5 3.9E-06 8.5E-11 75.7 14.8 127 215-390 1-127 (129)
11 PF13185 GAF_2: GAF domain; PD 98.2 2.3E-05 4.9E-10 72.5 13.1 136 215-390 3-147 (148)
12 TIGR02040 PpsR-CrtJ transcript 98.2 2.7E-06 5.7E-11 94.9 8.0 73 604-676 126-199 (442)
13 TIGR01817 nifA Nif-specific re 98.1 0.00035 7.6E-09 80.5 23.5 226 200-470 6-242 (534)
14 TIGR00229 sensory_box PAS doma 98.1 1.2E-05 2.6E-10 66.1 6.9 67 611-677 3-69 (124)
15 PRK11091 aerobic respiration c 98.0 1.5E-05 3.3E-10 95.1 9.8 74 603-676 147-220 (779)
16 PF13188 PAS_8: PAS domain; PD 97.9 1E-05 2.2E-10 65.8 4.4 47 611-661 1-47 (64)
17 PRK09776 putative diguanylate 97.9 1.8E-05 4E-10 97.3 8.6 76 603-678 275-350 (1092)
18 PRK13560 hypothetical protein; 97.9 3.2E-05 6.8E-10 91.5 9.3 70 604-673 197-266 (807)
19 TIGR02966 phoR_proteo phosphat 97.9 1.5E-05 3.4E-10 83.1 5.7 57 608-664 3-59 (333)
20 PRK05022 anaerobic nitric oxid 97.9 0.0021 4.5E-08 73.9 22.8 215 202-457 7-222 (509)
21 TIGR02040 PpsR-CrtJ transcript 97.8 9.4E-06 2E-10 90.6 2.5 61 616-676 1-61 (442)
22 PRK13557 histidine kinase; Pro 97.8 4.1E-05 8.8E-10 86.1 7.6 68 607-674 26-96 (540)
23 smart00091 PAS PAS domain. PAS 97.8 8.3E-05 1.8E-09 53.9 6.7 63 613-675 3-65 (67)
24 PRK15429 formate hydrogenlyase 97.8 0.0037 7.9E-08 74.4 24.1 211 213-458 197-412 (686)
25 PRK11006 phoR phosphate regulo 97.7 3.8E-05 8.2E-10 85.2 6.0 61 604-664 91-151 (430)
26 cd00130 PAS PAS domain; PAS mo 97.7 6.8E-05 1.5E-09 58.3 5.8 57 620-676 1-57 (103)
27 PF13596 PAS_10: PAS domain; P 97.7 3.5E-05 7.6E-10 68.9 4.2 66 613-679 1-66 (106)
28 COG3604 FhlA Transcriptional r 97.7 0.0017 3.7E-08 73.0 18.0 206 214-458 47-259 (550)
29 PRK10060 RNase II stability mo 97.7 8.7E-05 1.9E-09 87.6 7.7 66 610-675 110-176 (663)
30 PRK10820 DNA-binding transcrip 97.6 6.9E-05 1.5E-09 86.1 6.0 60 607-666 76-135 (520)
31 PRK13558 bacterio-opsin activa 97.6 0.012 2.5E-07 69.4 23.9 135 213-391 300-436 (665)
32 PRK13559 hypothetical protein; 97.6 0.00016 3.6E-09 77.8 7.6 68 609-676 41-111 (361)
33 PRK11061 fused phosphoenolpyru 97.5 0.003 6.5E-08 75.7 17.6 149 203-391 7-155 (748)
34 PRK11073 glnL nitrogen regulat 97.5 0.00012 2.6E-09 78.3 4.9 54 611-664 7-60 (348)
35 TIGR02938 nifL_nitrog nitrogen 97.3 0.0004 8.6E-09 76.7 6.3 56 611-666 4-59 (494)
36 PRK15429 formate hydrogenlyase 97.3 0.28 6.1E-06 58.5 30.6 203 201-445 11-225 (686)
37 PRK11359 cyclic-di-GMP phospho 97.2 0.00035 7.6E-09 83.2 5.7 65 611-675 12-76 (799)
38 PF14598 PAS_11: PAS domain; P 97.1 0.00088 1.9E-08 61.4 6.0 53 624-676 5-59 (111)
39 COG3829 RocR Transcriptional r 97.1 0.00062 1.3E-08 77.2 5.7 55 606-660 112-166 (560)
40 PF12860 PAS_7: PAS fold 97.1 0.00031 6.8E-09 63.6 2.5 44 617-660 1-45 (115)
41 PRK09776 putative diguanylate 97.0 0.00076 1.6E-08 83.3 6.2 58 604-661 529-586 (1092)
42 PRK11360 sensory histidine kin 96.9 0.0016 3.5E-08 73.6 6.5 60 604-663 255-314 (607)
43 PF08447 PAS_3: PAS fold; Int 96.7 0.0015 3.2E-08 55.9 3.8 43 633-676 1-48 (91)
44 PRK11359 cyclic-di-GMP phospho 96.7 0.0032 7E-08 75.0 7.6 51 611-661 136-186 (799)
45 PRK11388 DNA-binding transcrip 96.7 0.002 4.4E-08 75.8 5.8 58 605-662 197-254 (638)
46 PRK11086 sensory histidine kin 96.7 0.0032 7E-08 71.2 6.8 61 604-664 214-277 (542)
47 PRK15053 dpiB sensor histidine 96.6 0.0027 5.9E-08 72.4 6.2 62 602-663 213-276 (545)
48 PRK13560 hypothetical protein; 96.6 0.004 8.8E-08 73.7 7.3 59 604-662 325-384 (807)
49 COG2202 AtoS FOG: PAS/PAC doma 96.5 0.0071 1.5E-07 54.3 6.9 60 604-663 105-164 (232)
50 PRK13558 bacterio-opsin activa 96.5 0.0051 1.1E-07 72.4 7.4 65 612-676 149-216 (665)
51 COG5002 VicK Signal transducti 96.4 0.0058 1.3E-07 66.0 6.2 67 606-672 106-172 (459)
52 TIGR02938 nifL_nitrog nitrogen 96.4 0.0036 7.8E-08 69.1 4.9 66 604-669 123-188 (494)
53 COG3283 TyrR Transcriptional r 96.2 0.0056 1.2E-07 66.4 5.2 56 612-667 81-136 (511)
54 COG3290 CitA Signal transducti 96.0 0.011 2.4E-07 67.2 6.1 65 604-668 208-275 (537)
55 TIGR02373 photo_yellow photoac 95.2 0.035 7.5E-07 52.0 5.3 57 616-672 21-78 (124)
56 TIGR02916 PEP_his_kin putative 94.9 1.3 2.8E-05 52.7 19.1 151 201-391 307-458 (679)
57 COG5000 NtrY Signal transducti 94.8 0.036 7.8E-07 63.8 5.3 70 601-675 360-429 (712)
58 KOG3561 Aryl-hydrocarbon recep 94.5 0.023 4.9E-07 67.8 2.7 54 616-669 100-153 (803)
59 COG3852 NtrB Signal transducti 93.2 0.07 1.5E-06 57.1 3.3 52 615-666 11-62 (363)
60 PRK09959 hybrid sensory histid 92.2 0.26 5.7E-06 62.0 7.1 50 604-653 569-618 (1197)
61 KOG3558 Hypoxia-inducible fact 91.7 0.17 3.6E-06 59.0 4.0 53 624-676 277-329 (768)
62 PF08446 PAS_2: PAS fold; Int 91.3 0.22 4.7E-06 45.6 3.7 52 623-674 17-72 (110)
63 KOG1229 3'5'-cyclic nucleotide 91.0 0.097 2.1E-06 57.9 1.3 51 611-661 157-207 (775)
64 TIGR02851 spore_V_T stage V sp 90.2 15 0.00033 36.8 15.9 126 214-390 52-179 (180)
65 KOG3559 Transcriptional regula 89.7 0.25 5.3E-06 54.3 2.9 58 616-673 84-141 (598)
66 KOG3558 Hypoxia-inducible fact 88.6 0.51 1.1E-05 55.1 4.7 63 613-675 120-183 (768)
67 PF00989 PAS: PAS fold; Inter 86.1 1.7 3.8E-05 37.5 5.7 51 81-142 12-66 (113)
68 PF13426 PAS_9: PAS domain; PD 85.6 1.8 3.9E-05 36.7 5.5 50 83-143 4-57 (104)
69 KOG3560 Aryl-hydrocarbon recep 85.0 0.94 2E-05 51.6 4.1 65 612-676 112-176 (712)
70 PF08670 MEKHLA: MEKHLA domain 82.2 3.5 7.6E-05 40.1 6.3 64 613-677 34-99 (148)
71 KOG3561 Aryl-hydrocarbon recep 77.9 1.7 3.6E-05 52.5 3.0 41 81-132 106-146 (803)
72 PRK10618 phosphotransfer inter 76.8 3.7 7.9E-05 50.8 5.7 44 604-647 336-380 (894)
73 PRK13837 two-component VirA-li 73.5 2.3E+02 0.005 34.8 20.2 132 215-390 293-425 (828)
74 PF08448 PAS_4: PAS fold; Int 73.3 3.1 6.7E-05 35.7 2.9 51 82-143 7-61 (110)
75 COG2461 Uncharacterized conser 73.0 6.5 0.00014 43.7 5.7 68 610-679 289-356 (409)
76 PF13596 PAS_10: PAS domain; P 67.6 10 0.00022 33.5 5.0 48 82-141 11-58 (106)
77 PF04340 DUF484: Protein of un 67.1 1.3E+02 0.0028 30.9 13.6 42 203-246 82-123 (225)
78 KOG3559 Transcriptional regula 64.6 6.6 0.00014 43.6 3.6 51 623-673 227-277 (598)
79 KOG3753 Circadian clock protei 62.8 8.7 0.00019 46.4 4.4 54 624-677 332-387 (1114)
80 COG1956 GAF domain-containing 60.0 1.9E+02 0.004 28.8 14.9 114 216-380 34-150 (163)
81 PRK10841 hybrid sensory kinase 57.1 20 0.00043 44.6 6.5 50 601-650 324-374 (924)
82 PRK13719 conjugal transfer tra 45.1 27 0.00059 36.1 4.2 46 610-657 18-63 (217)
83 COG3852 NtrB Signal transducti 43.4 1.2E+02 0.0026 33.3 8.7 91 83-184 20-115 (363)
84 PRK10490 sensor protein KdpD; 41.4 8.1E+02 0.017 30.6 19.7 39 203-244 517-555 (895)
85 KOG3753 Circadian clock protei 34.9 24 0.00052 42.9 2.2 50 623-672 194-243 (1114)
86 PRK11073 glnL nitrogen regulat 34.6 1.9E+02 0.0042 30.6 9.0 41 82-133 19-59 (348)
87 PF13192 Thioredoxin_3: Thiore 33.6 49 0.0011 27.8 3.4 24 441-464 52-75 (76)
88 KOG0387 Transcription-coupled 31.7 26 0.00056 42.4 1.8 27 229-277 614-640 (923)
89 KOG0501 K+-channel KCNQ [Inorg 29.5 75 0.0016 37.3 4.9 64 613-676 16-91 (971)
90 PF14827 Cache_3: Sensory doma 29.0 37 0.0008 30.9 2.0 52 213-272 19-70 (116)
91 PF10985 DUF2805: Protein of u 27.9 34 0.00074 29.4 1.4 19 541-559 37-55 (73)
92 COG3829 RocR Transcriptional r 25.9 42 0.00091 39.2 2.1 56 614-669 4-59 (560)
93 PRK14538 putative bifunctional 25.1 87 0.0019 38.7 4.7 50 608-660 99-149 (838)
94 PF12860 PAS_7: PAS fold 24.9 2.6E+02 0.0057 24.7 6.8 40 80-130 6-45 (115)
95 COG1098 VacB Predicted RNA bin 24.6 48 0.001 31.4 1.8 28 76-103 15-42 (129)
96 KOG3560 Aryl-hydrocarbon recep 24.3 94 0.002 36.2 4.4 56 76-142 116-172 (712)
97 PRK10234 DNA-binding transcrip 23.9 66 0.0014 30.2 2.7 55 619-677 51-115 (118)
98 PRK11360 sensory histidine kin 23.8 5.1E+02 0.011 29.1 10.5 40 82-132 274-313 (607)
99 PF11152 DUF2930: Protein of u 23.5 2.3E+02 0.005 28.9 6.6 79 430-514 87-172 (195)
100 PF03472 Autoind_bind: Autoind 23.3 5.6E+02 0.012 23.2 12.3 32 320-364 89-120 (149)
101 PF06923 GutM: Glucitol operon 22.0 36 0.00078 31.4 0.5 38 619-660 50-94 (109)
102 PF14598 PAS_11: PAS domain; P 21.0 78 0.0017 28.8 2.5 37 90-136 11-48 (111)
103 TIGR03643 conserved hypothetic 20.9 56 0.0012 28.0 1.4 18 542-559 39-56 (72)
104 TIGR00229 sensory_box PAS doma 20.8 1.5E+02 0.0032 23.1 4.0 42 82-134 15-56 (124)
No 1
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=100.00 E-value=1e-127 Score=1052.67 Aligned_cols=485 Identities=35% Similarity=0.630 Sum_probs=433.8
Q ss_pred ccchhhh-hhcccCCCCCCCCceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchHHHHHH
Q 005722 61 SSTVSAY-LQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQ 139 (681)
Q Consensus 61 ~~~~t~~-~~~I~~pG~IQp~G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~~~l~ 139 (681)
..+++.| .+|||+||+||||||||++|+.++.|+|+|+||..+||+.|++ ++|+++.++|+..+...++
T Consensus 9 ~v~l~nce~ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~----------l~~~tl~~vl~~~qv~~l~ 78 (750)
T COG4251 9 HVTLTNCEREPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPED----------LLGRTLGAVLTSEQVPPLQ 78 (750)
T ss_pred cCcccccccCCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhh----------hhcCCHHHhcchhhccHHH
Confidence 5678899 9999999999999999999999999999999999999999976 5899999999999999999
Q ss_pred HHhccCCCccCCceeeeccCCCceEEEEEEeeCCeEEEEeccCCCCCCccchhhhhHHHHHHHHHHHHHhcCCCCCHHHH
Q 005722 140 KAANFGEVNLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPVNPDDVPVTAAGALKSYKLAAKAISRLQSLPSGNISLL 219 (681)
Q Consensus 140 ~~l~~~~~~~~~p~~~~~~~~~~~f~~~~Hr~~~~lviElEp~~~~~~~~~~~g~~~~~~l~~~~i~rl~~~~~~~l~~l 219 (681)
.++..+.....||..+-.+. +..|++++||+++.+|+||||+...+. . ..+.++.++..++.+||+.+ ++.++
T Consensus 79 ~~l~~~~~~~~np~~~w~~~-~~~fDv~~HR~~~llIlEfEp~~t~e~-~---~~l~f~h~~k~a~~~lq~a~--~l~~l 151 (750)
T COG4251 79 SALTVGGLTTLNPTKMWTRK-GGSFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDL 151 (750)
T ss_pred HhccccCcccCCchhhhhhc-CCceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHH
Confidence 99998888888884432222 338999999999999999999754442 1 23456788888999999955 99999
Q ss_pred HHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCCCceeec
Q 005722 220 CDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPPVKVIQ 299 (681)
Q Consensus 220 ~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~pv~lv~ 299 (681)
|+.++++||++|||||||+|||++||+|+||||+++++|+||||+||||||||+|||+||.+|++|+|+|+.|+||||+|
T Consensus 152 ~~~~tqeVr~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~P 231 (750)
T COG4251 152 LSRTTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLP 231 (750)
T ss_pred HHHHHHHHHHhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred --CCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCCCChhHHH
Q 005722 300 --DKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFPLRY 377 (681)
Q Consensus 300 --~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~v~~~~R~ 377 (681)
+|.++.|+|||+|.|||+||||+|||+||||.||||||||+| |+|||||+|||.+||.+||++|.
T Consensus 232 avNp~t~~p~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~-------------g~LWGLIACHH~sPk~ip~~vR~ 298 (750)
T COG4251 232 AVNPETNEPLDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD-------------GKLWGLIACHHQSPKVIPYEVRK 298 (750)
T ss_pred ccCcccCCcccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC-------------CeeEEeeeeccCCCccCCHHHHH
Confidence 688999999999999999999999999999999999999998 89999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHhhccCC-ccccccCChhhhhhccCCeEEEEECCeEEEe
Q 005722 378 ACEFLIQVFGVQVNKEVE-----LSAQLREKHILRTQTVLCDMLLRDS-PVGIVTQTPNVMDLVKCDGAALYYRGKLWLL 451 (681)
Q Consensus 378 a~e~l~q~~s~ql~~~~e-----l~~q~~e~~~~~~~~~l~~~l~~~~-~~~i~~~~~~ll~L~~adGaal~~~~~~~~~ 451 (681)
+||||+|++|.+|+.+.+ ...++.+.+ ..++..|...++ ..++..+.++|++|+.|||++++++|++.++
T Consensus 299 acef~gq~~s~~i~~~e~~~~~d~r~~l~~~~----arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~v 374 (750)
T COG4251 299 ACEFFGQVLSMEISALEQSEDADYRVQLTEHH----ARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLV 374 (750)
T ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHH----HHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEe
Confidence 999999999999976422 222222211 123344444444 4567888899999999999999999999999
Q ss_pred ccCCCHHHHHHHHHHHHHhcCCCeeeeeccccccCCCCccccccccccEEEEEeCC--CcEEEEeecCcceEEeecCCCC
Q 005722 452 GVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGIAAVKITS--KDFLFWFRSHTAKEIKWGGAKH 529 (681)
Q Consensus 452 G~tP~~~~i~~l~~wl~~~~~~~~~~~td~L~~~~~p~a~~~~~~~~G~lav~i~~--~~~l~wFR~e~~~~v~WaG~p~ 529 (681)
|.||+..++..|+.||.+... ..+|+||+|+.. ||++..++..+||+||+||+. ++||+|||+|..++|+|||||+
T Consensus 375 G~tP~~~~v~~Ll~wl~~~~~-~~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~ 452 (750)
T COG4251 375 GETPPRPAVQRLLQWLAEREE-GDVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPE 452 (750)
T ss_pred cCCCChHHHHHHHHHHhcCCc-ccEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCC
Confidence 999999999999999988754 468999999985 999999999999999999997 8999999999999999999999
Q ss_pred CCCC-CCCCCCccCCchhhhHHhhhccccCCCCHHHHHHHHHHHHHHHHHHHH
Q 005722 530 DSGG-KDGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRGSLQD 581 (681)
Q Consensus 530 k~~~-~~~g~~l~PR~SFe~w~E~v~~~s~pW~~~Ei~aa~~L~l~l~~~l~~ 581 (681)
||.+ .+.|.||+||+||+.|+|+|+++|.||++.|+++|.+||..|.+.+..
T Consensus 453 k~~e~~~~~~rL~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~ 505 (750)
T COG4251 453 KPYEAGPMGIRLTPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLR 505 (750)
T ss_pred CccccCCCCcccCCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9976 456889999999999999999999999999999999998777666544
No 2
>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []. The protein undergoes reversible photochemical conversion between a biologically-inactive red light-absorbing form and the active far-red light-absorbing form. Phytochrome is a dimer of identical 124 kDa subunits, each of which contains a linear tetrapyrrole chromophore, covalently-attached via a Cys residue. This domain represents a region specific to phytochrome proteins.; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3C2W_G 3NHQ_B 3G6O_B 3IBR_A 2VEA_A 3ZQ5_A.
Probab=100.00 E-value=5.6e-39 Score=317.48 Aligned_cols=159 Identities=38% Similarity=0.739 Sum_probs=136.6
Q ss_pred ccccccCChhhhhhccCCeEEEEECCeEEEeccCCCHHHHHHHHHHHHHhcCCCeeeeeccccccCCCCccccccccccE
Q 005722 421 PVGIVTQTPNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEYHRGSTGLSTDSLVEAGYPGALALGDAVCGI 500 (681)
Q Consensus 421 ~~~i~~~~~~ll~L~~adGaal~~~~~~~~~G~tP~~~~i~~l~~wl~~~~~~~~~~~td~L~~~~~p~a~~~~~~~~G~ 500 (681)
..++..+.++||+|++|||+||+++|+++++|.+|++.+|.+|++||.... +..+|+||+|.+. ||++.++.+.+|||
T Consensus 19 ~~~l~~~~~~ll~l~~AdG~al~~~g~~~~~G~~P~~~~i~~L~~wl~~~~-~~~v~~T~~L~~~-~p~~~~~~~~aaGv 96 (182)
T PF00360_consen 19 LEALISQAPDLLDLVDADGVALVIDGEVYTFGETPPEEQIRALAEWLREQA-DGEVFATDSLSED-YPDAAALAERAAGV 96 (182)
T ss_dssp HHHHCTTCCCHHHCTT-SEEEEEETTEEEEEESS--HHHHHHHHHHCCCTT-T-SEEEESBGGGT-SGGGGGGCCCHSEE
T ss_pred hHhhHhccHHHHhhccCCEEEEEECCEEEEecCCcCHHHHHHHHHHHHhhC-CCccchhhhHhHh-ChhhhhhcccCCCc
Confidence 456788999999999999999999999999999999999999999999774 4578999999985 99999999999999
Q ss_pred EEEEeCC--CcEEEEeecCcceEEeecCCCCCCCCC-CCCCCccCCchhhhHHhhhccccCCCCHHHHHHHHHHHHHHHH
Q 005722 501 AAVKITS--KDFLFWFRSHTAKEIKWGGAKHDSGGK-DGGRKMHPRSSFKAFLEVVKQRSLPWEDVEMDAIHSLQLILRG 577 (681)
Q Consensus 501 lav~i~~--~~~l~wFR~e~~~~v~WaG~p~k~~~~-~~g~~l~PR~SFe~w~E~v~~~s~pW~~~Ei~aa~~L~l~l~~ 577 (681)
|+++|++ ++||+|||+|+.++|+|||||+|++.. +++.+|+||+||++|+|+|+|+|.||++.|+++|..|+..|.+
T Consensus 97 Lai~l~~~~~~~l~wFR~E~~~~v~WaG~P~k~~~~~~~~~~l~PR~SF~~W~E~v~g~S~pW~~~d~~~A~~lr~~l~~ 176 (182)
T PF00360_consen 97 LAIPLSSEPRDYLLWFRPEQVQTVNWAGNPEKPVEVDPGGVRLSPRKSFEAWRETVRGRSLPWSDADLEAAERLRRALLE 176 (182)
T ss_dssp EEEEECTTCCEEEEEEE-S--ECEEECSSCGGSCEEECTCCCCCCHCHHHCCCCCCTTBBS---HHHHHHHHHHHHHHHH
T ss_pred EEEECCCCCCceEEEEecCcceEEEeCCCCCccccCCCCCCCCCChHHHHHHHhHhcCcCCCCCHHHHHHHHHHHHHHHH
Confidence 9999985 689999999999999999999999764 4588999999999999999999999999999999999887776
Q ss_pred HHHH
Q 005722 578 SLQD 581 (681)
Q Consensus 578 ~l~~ 581 (681)
.+..
T Consensus 177 ~~~~ 180 (182)
T PF00360_consen 177 VILR 180 (182)
T ss_dssp HHHH
T ss_pred HHHh
Confidence 6554
No 3
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=99.91 E-value=5.5e-25 Score=200.87 Aligned_cols=108 Identities=31% Similarity=0.515 Sum_probs=91.6
Q ss_pred hhcccCCCCCCCCceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchHHHHHHHHhccCCC
Q 005722 68 LQRVQRGRLIQPFGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAANFGEV 147 (681)
Q Consensus 68 ~~~I~~pG~IQp~G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~~~l~~~l~~~~~ 147 (681)
.||||+||+|||||+|||+|+++++|+++|+|++++||++|. + ...++|+++.++|+....+.+++++.....
T Consensus 3 ~EPIH~pG~IQphG~LLa~d~~~~~I~~~S~N~~~~lg~~~~-~------~~~llG~~l~~ll~~~~~~~l~~~~~~~~~ 75 (110)
T PF08446_consen 3 REPIHIPGSIQPHGALLALDPDDLRIVQASENIAELLGIPPE-L------PEELLGRPLSELLGAESAERLREALQSESL 75 (110)
T ss_dssp GS-TTC-SEE-TTSEEEEEETTTTBEEEEETTHHHHHSS-----------HHHHTTCBHHHHSCCCCHHHHHHHCTCCCC
T ss_pred cccccCCCccCCCEEEEEEECCCCEEEEEcCCHHHHhCCccc-c------chhhcccCHHHHhCHHHHHHHHHhhhccCc
Confidence 799999999999999999999999999999999999999842 0 113699999999999999999999887777
Q ss_pred ccCCceeeeccCCCceEEEEEEeeCCeEEEEeccC
Q 005722 148 NLLNPILIHCKTSGKPFYAILHRIDVGLVIDLEPV 182 (681)
Q Consensus 148 ~~~~p~~~~~~~~~~~f~~~~Hr~~~~lviElEp~ 182 (681)
...+|+.+++..+++.|++++||+++++||||||+
T Consensus 76 ~~~~~~~~~~~~~~~~f~~~~H~~~~~lilElEp~ 110 (110)
T PF08446_consen 76 SLSNPIALRLRIGGRPFDAIAHRSGGLLILELEPA 110 (110)
T ss_dssp CCCCCEEEEEEEEEEEEEEEEEEETTEEEEEEEE-
T ss_pred cccCCeEEEeccCCeeEEEEEEEECCEEEEEEeeC
Confidence 77788888776778999999999999999999995
No 4
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=99.37 E-value=6.7e-12 Score=117.12 Aligned_cols=152 Identities=18% Similarity=0.186 Sum_probs=109.1
Q ss_pred CHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCCC
Q 005722 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (681)
Q Consensus 215 ~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~p 294 (681)
|++++++.+++++++++|+||++||.+++++..-...-.....-.+..+..++.. -+ ...+....+..-.|.|+...|
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~i~d~~~~~ 78 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMD-ES-ICGQVLQSREPIVISDVAADP 78 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETT-SS-HHHHHHHHTSCEEESSSGGST
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccccccccccc-cc-HHHHHHhCCCeEeeccccccc
Confidence 6899999999999999999999999999999866333333222122222222221 11 255666667777888887543
Q ss_pred ceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCC-CCCCh
Q 005722 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSP-RFVPF 373 (681)
Q Consensus 295 v~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~sp-r~v~~ 373 (681)
- ..+.......+|+.++++.+|+..+|+++.|.+||..+ |++||+|+++++.+ |.|+.
T Consensus 79 ~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~-------------g~~~G~l~l~~~~~~~~~~~ 137 (154)
T PF01590_consen 79 R--------FAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISG-------------GRLIGVLSLYRTRPGRPFTE 137 (154)
T ss_dssp T--------SSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEET-------------TEEEEEEEEEEESSSSS--H
T ss_pred c--------ccccccccccccccccccccccccccCceeeEeeeecc-------------cCcEEEEEEEECCCCCCcCH
Confidence 1 11222233457788999999999999999999998866 89999999999987 99999
Q ss_pred hHHHHHHHHHHHHHHH
Q 005722 374 PLRYACEFLIQVFGVQ 389 (681)
Q Consensus 374 ~~R~a~e~l~q~~s~q 389 (681)
+.+..++.+++.++..
T Consensus 138 ~d~~ll~~~a~~~a~a 153 (154)
T PF01590_consen 138 EDLALLESFAQQLAIA 153 (154)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhh
Confidence 8888888777766654
No 5
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=99.08 E-value=5.9e-09 Score=92.70 Aligned_cols=138 Identities=23% Similarity=0.331 Sum_probs=105.0
Q ss_pred CHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCCC
Q 005722 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (681)
Q Consensus 215 ~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~p 294 (681)
+++++++.+++.+.+++|+||+.||.++++..+............+..+..+|..+ ...+.++..+...++.|....+
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~ 78 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGE--GLAGRVAETGRPLNIPDVEADP 78 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCC--ChHHHHHHcCCeEEeechhhCC
Confidence 46889999999999999999999999999888888777665544446677788776 4566777777777777776332
Q ss_pred ceeecCCCCCCCcccccccccCCChHHHHHHHhc-CCeeEEEEEEEecCccccccccccccCceeEEEEeecC-CCCCCC
Q 005722 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENM-GSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHT-SPRFVP 372 (681)
Q Consensus 295 v~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NM-GV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~-spr~v~ 372 (681)
. +. ..+...+ |+++.+.+||..+ +++||+|.+.++ .++.|+
T Consensus 79 ~-----------------------~~-~~~~~~~~~~~s~~~~Pl~~~-------------~~~~G~l~~~~~~~~~~~~ 121 (149)
T smart00065 79 V-----------------------FA-LDLLGRYQGVRSFLAVPLVAD-------------GELVGVLALHNKDSPRPFT 121 (149)
T ss_pred c-----------------------cc-cccccceeceeeEEEeeeeec-------------CEEEEEEEEEecCCCCCCC
Confidence 1 00 1122223 4999999999976 899999999998 689999
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q 005722 373 FPLRYACEFLIQVFGVQVN 391 (681)
Q Consensus 373 ~~~R~a~e~l~q~~s~ql~ 391 (681)
.+.+..++.+++.++..+.
T Consensus 122 ~~~~~~l~~~~~~i~~~l~ 140 (149)
T smart00065 122 EEDEELLQALANQLAIALA 140 (149)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9888877777777666554
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=99.02 E-value=6e-10 Score=98.05 Aligned_cols=66 Identities=24% Similarity=0.395 Sum_probs=58.0
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
++++++++++++||+++|.+|+|++||++++++|||+.+|++|+++.+++++++.......+.+.+
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~ 66 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQAL 66 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHH
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHH
Confidence 468899999999999999999999999999999999999999999999999987765555555554
No 7
>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=98.61 E-value=6.6e-08 Score=84.58 Aligned_cols=63 Identities=25% Similarity=0.393 Sum_probs=59.0
Q ss_pred HHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHccc
Q 005722 617 IETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLAI 679 (681)
Q Consensus 617 ie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~G~ 679 (681)
+|+++++|+++|.+|+|++||+++++++|+++++++|+++.++++++..+.+...+.+++.|.
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGG 63 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHT
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccC
Confidence 589999999999999999999999999999999999999999999999999999999998764
No 8
>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=98.52 E-value=1.5e-07 Score=81.28 Aligned_cols=57 Identities=18% Similarity=0.269 Sum_probs=48.7
Q ss_pred CccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHc
Q 005722 621 AVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFL 677 (681)
Q Consensus 621 ~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~ 677 (681)
|++|+++|.+|+|++||+++++++||+++|++|+++.+++++++.......+.+++.
T Consensus 1 p~~i~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 57 (104)
T PF13426_consen 1 PDGIFILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALE 57 (104)
T ss_dssp -SEEEEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHH
T ss_pred CEEEEEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHh
Confidence 689999999999999999999999999999999999999998877777777776654
No 9
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.50 E-value=5.1e-07 Score=83.29 Aligned_cols=154 Identities=18% Similarity=0.248 Sum_probs=97.3
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCC--eEEEEeecCCCCCCcCCCcCCCCCchHH-HHH
Q 005722 201 AAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEH--GEVVAECRRPDLEPYLGFHYPATDIPQA-SRF 277 (681)
Q Consensus 201 ~~~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~--GeVVAEs~~~~l~s~LGlhfPasDIP~q-aR~ 277 (681)
.......+.. ..+.+++++.+++.+.+.+|.||..||++++++. +.++++.........+.-.+.....|.- ...
T Consensus 6 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (175)
T COG2203 6 LNELAAKIAQ--DLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAGLEQLIDELFGLVILPACLIGI 83 (175)
T ss_pred HHHHHHHHHH--HCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcchhhhhHHHHhcccCcchhhhhh
Confidence 3445555665 5699999999999999999999999999999995 6666665544300111000100000000 001
Q ss_pred HHHcCCeEEeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCce
Q 005722 278 LIMKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKL 357 (681)
Q Consensus 278 Ly~~n~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kL 357 (681)
........++.|+...+ | ...+|..++... +++.+.+||+.+ +++
T Consensus 84 ~~~~~~~~~~~~~~~~~--------------------~-~~~~~~~~~~~~-i~~~l~vPl~~~-------------~~~ 128 (175)
T COG2203 84 ALREGRPVVVEDILQDP--------------------R-FRDNPLVLLEPP-IRSYLGVPLIAQ-------------GEL 128 (175)
T ss_pred hhcCCceEEeeccccCc--------------------c-cccCHHHHHHHH-HHHheeeeeeEC-------------CEe
Confidence 11222333333433221 0 122666666665 899999999987 799
Q ss_pred eEEEEeecCCCC-CCChhHHHHHHHHHHHHHHHHH
Q 005722 358 WGLVVCHHTSPR-FVPFPLRYACEFLIQVFGVQVN 391 (681)
Q Consensus 358 WGLi~cHh~spr-~v~~~~R~a~e~l~q~~s~ql~ 391 (681)
||.++.||+.++ .|+.+.....+.+++.++..|.
T Consensus 129 ~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ai~ 163 (175)
T COG2203 129 LGLLCVHDSEPRRQWSEEELELLEELAEQVAIAIE 163 (175)
T ss_pred eEEeeeeccCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 999999999866 5888777777766666665553
No 10
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.50 E-value=3.9e-06 Score=75.74 Aligned_cols=127 Identities=17% Similarity=0.192 Sum_probs=85.0
Q ss_pred CHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCCC
Q 005722 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (681)
Q Consensus 215 ~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~p 294 (681)
|++++++.+++.+++++|+|++.||.++++..--.++... +..+-+.-.+| .+-| .....+.+++...+.|....+
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~--~~~~~~~~~l~-~~~~-~~~~~~~~~~~~~~~~~~~~~ 76 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVVAGW--GGDPRLSESLP-EDDP-LIGRALETGEPVSVPDIDERD 76 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEEEEE--SS-GCGHHCEE-TTSH-HHHHHHHHTS-EEESTCCC-T
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEEe--CCCccccccCC-CCcc-HHHHHHhhCCeEEeccccccc
Confidence 5799999999999999999999999999875433333332 22222222566 3333 334667777665565543210
Q ss_pred ceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCCCChh
Q 005722 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVPFP 374 (681)
Q Consensus 295 v~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~v~~~ 374 (681)
. .+.++.|.+||..+ ++++|+|..++..++.++..
T Consensus 77 ------------~--------------------~~~~s~~~vPl~~~-------------~~~~Gvl~~~~~~~~~~~~~ 111 (129)
T PF13492_consen 77 ------------F--------------------LGIRSLLVVPLRSR-------------DRVIGVLCLDSREPEEFSDE 111 (129)
T ss_dssp ------------T--------------------TTTCEEEEEEEEET-------------TEEEEEEEEEECTTCG-SHH
T ss_pred ------------C--------------------CCCCEEEEEEEeEC-------------CEEEEEEEEEECCCCCCCHH
Confidence 0 45688899999987 79999999988888888887
Q ss_pred HHHHHHHHHHHHHHHH
Q 005722 375 LRYACEFLIQVFGVQV 390 (681)
Q Consensus 375 ~R~a~e~l~q~~s~ql 390 (681)
.....+.++..++..|
T Consensus 112 d~~~l~~~a~~~a~al 127 (129)
T PF13492_consen 112 DLQLLESLANQLAIAL 127 (129)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7777776666666544
No 11
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=98.22 E-value=2.3e-05 Score=72.48 Aligned_cols=136 Identities=15% Similarity=0.153 Sum_probs=82.7
Q ss_pred CHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcC--CCC--CchHHHH-----HHHHcCCeE
Q 005722 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHY--PAT--DIPQASR-----FLIMKNKVR 285 (681)
Q Consensus 215 ~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhf--Pas--DIP~qaR-----~Ly~~n~vR 285 (681)
+++++++.+++.+.+++|+|...||-+|++..=..++-...+ ...++..+ |.. ..|...+ .++..++-.
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDP--SEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEPI 80 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSS--CTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-E
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCc--hhhhhhhcccCcccccccchhhhhHHHHHHhcCceE
Confidence 789999999999999999999999999877722222322222 22333222 111 1111110 014445444
Q ss_pred EeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeec
Q 005722 286 MICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHH 365 (681)
Q Consensus 286 ~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh 365 (681)
++. .+. + ...+ .......|+++-+++||+.+ |++||.|...+
T Consensus 81 ~~~-~~~-------------~---------~~~~--~~~~~~~~~~s~l~vPl~~~-------------~~~~Gvl~l~~ 122 (148)
T PF13185_consen 81 IIN-DDD-------------S---------SFPP--WELARHPGIRSILCVPLRSG-------------GEVIGVLSLYS 122 (148)
T ss_dssp EES-CCC-------------G---------GGST--THHHCCTT-SEEEEEEEEET-------------TEEEEEEEEEE
T ss_pred EEe-Ccc-------------c---------cccc--hhhhccccCCEEEEEEEeEC-------------CEEEEEEEEee
Confidence 444 100 0 0011 35688899999999999987 79999999998
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHH
Q 005722 366 TSPRFVPFPLRYACEFLIQVFGVQV 390 (681)
Q Consensus 366 ~spr~v~~~~R~a~e~l~q~~s~ql 390 (681)
..++..+.+.+..++.+++.++..|
T Consensus 123 ~~~~~f~~~~~~~l~~la~~~a~ai 147 (148)
T PF13185_consen 123 KEPNAFSEEDLELLEALADQIAIAI 147 (148)
T ss_dssp SSTT---HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHh
Confidence 8888888888877777766655443
No 12
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=98.21 E-value=2.7e-06 Score=94.93 Aligned_cols=73 Identities=23% Similarity=0.236 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcC-CCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDA-SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~-~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
.++++..+.++.++++++++|+++|. +|+|+++|+++++|+||+++|++|+++.+++++++.+.+...+..+.
T Consensus 126 ~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~ 199 (442)
T TIGR02040 126 WTLREMETRYRVVLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVR 199 (442)
T ss_pred HHHHHHHHHHHHHHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHH
Confidence 46777778999999999999999998 89999999999999999999999999999999999998888887765
No 13
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=98.13 E-value=0.00035 Score=80.50 Aligned_cols=226 Identities=15% Similarity=0.136 Sum_probs=129.3
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHH
Q 005722 200 LAAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLI 279 (681)
Q Consensus 200 l~~~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly 279 (681)
.+.++...+.. +.+++++++.+++.+.+++|+||..||-+++++.-.++ .+....-+..-..+|+... --....+
T Consensus 6 ~L~~is~~l~~--~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~-aa~g~~~~~~~~~~~~~~~--gi~g~v~ 80 (534)
T TIGR01817 6 ALYEISKILSA--PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLV-AAIGWSEEGFAPIRYRVGE--GAIGQIV 80 (534)
T ss_pred HHHHHHHHHhc--cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEE-EEeCCChhhcccccccCCc--cHHHHHH
Confidence 34455556655 56999999999999999999999999999888754433 3322211111113444332 2345667
Q ss_pred HcCCeEEeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeE
Q 005722 280 MKNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWG 359 (681)
Q Consensus 280 ~~n~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWG 359 (681)
..+..-+|.|+...|-.. + +. .+...|++|.|++||+.+ |+++|
T Consensus 81 ~~~~pvii~Dv~~d~~~~----------~-----------~~--~~~~~~~~S~l~VPL~~~-------------g~viG 124 (534)
T TIGR01817 81 ATGNSLVVPDVAAEPLFL----------D-----------RL--SLYDPGPVPFIGVPIKAD-------------SETIG 124 (534)
T ss_pred hcCCeEEecccccCchhh----------h-----------cc--ccccCCcceEEEEEEcCC-------------CEEEE
Confidence 778888888887432100 0 00 023467899999999966 89999
Q ss_pred EEEeecCC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-------c---CCccccccCC
Q 005722 360 LVVCHHTS-PRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLL-------R---DSPVGIVTQT 428 (681)
Q Consensus 360 Li~cHh~s-pr~v~~~~R~a~e~l~q~~s~ql~~~~el~~q~~e~~~~~~~~~l~~~l~-------~---~~~~~i~~~~ 428 (681)
.|..++.. ++....+.....+.++..++..|.... +..+.+++...+ +..+..-+. + .....++..+
T Consensus 125 vL~v~s~~~~~~ft~~d~~lL~~lA~~ia~aI~~~~-~~~~~~~~l~~~-~~~l~~~~~~~~~~~~~~~~~~~~~liG~s 202 (534)
T TIGR01817 125 VLAADRDFRSRERLEEEVRFLEMVANLIGQTVRLHR-LVAQRRERLIAE-AVQLSKQLRDKAPEIARRRSGKEDGIIGKS 202 (534)
T ss_pred EEEEEeccccccccHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH-HHHHHHHHhhhcccccccccCccCceEECC
Confidence 99999876 455555555556666666665553211 111111111111 111111111 1 1234577777
Q ss_pred hhhhhhccCCeEEEEECCeEEEeccCCCHHHHHHHHHHHHHh
Q 005722 429 PNVMDLVKCDGAALYYRGKLWLLGVTPTEEQIKDIAEWLLEY 470 (681)
Q Consensus 429 ~~ll~L~~adGaal~~~~~~~~~G~tP~~~~i~~l~~wl~~~ 470 (681)
+.+..+++--..+.-.+..+...|++=+-.+ .++.++...
T Consensus 203 ~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~--~lA~~ih~~ 242 (534)
T TIGR01817 203 PAMRQVVDQARVVARSNSTVLLRGESGTGKE--LIAKAIHYL 242 (534)
T ss_pred HHHHHHHHHHHHHhCcCCCEEEECCCCccHH--HHHHHHHHh
Confidence 7766665433333334556777787766432 334455443
No 14
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=98.05 E-value=1.2e-05 Score=66.14 Aligned_cols=67 Identities=18% Similarity=0.360 Sum_probs=58.7
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHc
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFL 677 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~ 677 (681)
+.+..+++.++++++++|.+|+++++|+++.+++|++..+++|+++.+++++.+...+...+..+..
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLE 69 (124)
T ss_pred hHHHHHHhhCCceEEEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHc
Confidence 3467799999999999999999999999999999999999999999998888887777666666554
No 15
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.02 E-value=1.5e-05 Score=95.11 Aligned_cols=74 Identities=19% Similarity=0.235 Sum_probs=65.1
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 603 IDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 603 ~~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
.+++++..+.++.++++++++|+++|.+|+|++||+++++++||+.+|++|+++.++++++....+.......+
T Consensus 147 ~~~l~~~~~~l~~il~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~ 220 (779)
T PRK11091 147 QIELEQQSSLLRSFLDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVF 220 (779)
T ss_pred HHHHHHHHHHHHHHHhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHH
Confidence 46677788889999999999999999999999999999999999999999999999999887776655555443
No 16
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.94 E-value=1e-05 Score=65.79 Aligned_cols=47 Identities=23% Similarity=0.300 Sum_probs=38.4
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccccccc
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA 661 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~ 661 (681)
+.++.+++++++||+++| +|+|+++|+++++++||+ ..|+.+..+++
T Consensus 1 e~~~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~~~~~ 47 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS---LEGEDIGQLFP 47 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS----HTCCCHHCTST
T ss_pred CHHHHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC---CCCCCHHHhCc
Confidence 357899999999999999 889999999999999999 66776654443
No 17
>PRK09776 putative diguanylate cyclase; Provisional
Probab=97.94 E-value=1.8e-05 Score=97.34 Aligned_cols=76 Identities=11% Similarity=0.125 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHcc
Q 005722 603 IDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLA 678 (681)
Q Consensus 603 ~~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~G 678 (681)
.+++++..++++.++|+++++|+.+|.+|+|++||+++++++||+.+|++|+++.+++++++.+.....+..+..|
T Consensus 275 ~~~l~~~e~r~~~l~e~~~~~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~ 350 (1092)
T PRK09776 275 RKHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSG 350 (1092)
T ss_pred HHHHHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcC
Confidence 3567778888999999999999999999999999999999999999999999999999999999887777776654
No 18
>PRK13560 hypothetical protein; Provisional
Probab=97.90 E-value=3.2e-05 Score=91.48 Aligned_cols=70 Identities=19% Similarity=0.279 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHH
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLS 673 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~ 673 (681)
++|++..+.++.++++++++|+++|.+|+|++||+++++++||+++|++|+++.++.++...+.......
T Consensus 197 ~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~ 266 (807)
T PRK13560 197 ERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADA 266 (807)
T ss_pred HHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHH
Confidence 4466667789999999999999999999999999999999999999999999999998777665544433
No 19
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=97.88 E-value=1.5e-05 Score=83.13 Aligned_cols=57 Identities=16% Similarity=0.301 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCC
Q 005722 608 IITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDS 664 (681)
Q Consensus 608 ~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~ 664 (681)
...++++.++++.+++|+++|.+|+|++||+++++++||+++|.+|+++.+++++++
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~ 59 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE 59 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH
Confidence 456788999999999999999999999999999999999999999999999887643
No 20
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=97.85 E-value=0.0021 Score=73.86 Aligned_cols=215 Identities=11% Similarity=0.043 Sum_probs=121.4
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHc
Q 005722 202 AKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMK 281 (681)
Q Consensus 202 ~~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~ 281 (681)
.++...|-+ +.+++++++.+++.+++.+++|.+-|+-++.+ ++...+....-....+..|+..+=|--.. ....
T Consensus 7 ~eis~~L~~--s~d~~e~L~~vl~~l~~~l~~~~~~l~l~~~~---~l~~~as~gl~~~~~~~~~~~geGP~l~a-v~~~ 80 (509)
T PRK05022 7 LPIALDLSR--GLPHQDRFQRLLTTLRQVLPCDASALLRLDGD---QLVPLAIDGLSPDVLGRRFALEEHPRLEA-ILRA 80 (509)
T ss_pred HHHHHHHhc--CCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC---cEEEEEEcCCChHhhCCccCCCcchHHHH-HHhc
Confidence 344455655 67999999999999999999999999999753 33333333333334566787776553322 2232
Q ss_pred CCeEEeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEE
Q 005722 282 NKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLV 361 (681)
Q Consensus 282 n~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi 361 (681)
+++..|+|...-|.+ ++ |-.. ....++|++|.|++||.++ |+.+|.|
T Consensus 81 g~~v~v~~~~~~p~~----------~~------~~~~----~~~~~~gi~S~l~vPL~~~-------------~~~~GvL 127 (509)
T PRK05022 81 GDPVRFPADSELPDP----------YD------GLIP----GVQESLPVHDCMGLPLFVD-------------GRLIGAL 127 (509)
T ss_pred CCeEEEecCCCCCcc----------cc------cccc----cccccCCcceEEEEEEEEC-------------CEEEEEE
Confidence 444444444322211 10 0000 0234579999999999987 7999999
Q ss_pred EeecCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC-CccccccCChhhhhhccCCeE
Q 005722 362 VCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQTVLCDMLLRD-SPVGIVTQTPNVMDLVKCDGA 440 (681)
Q Consensus 362 ~cHh~spr~v~~~~R~a~e~l~q~~s~ql~~~~el~~q~~e~~~~~~~~~l~~~l~~~-~~~~i~~~~~~ll~L~~adGa 440 (681)
.+++..|...........+.++..++..|........ +++ ...+.+.....+..+. .+..++.+++.+.++++--..
T Consensus 128 ~l~~~~~~~f~~~~~~~l~~~a~~~a~Al~~a~~~~~-l~~-~~~~~~~~~~~~~~~~~~~~~iig~s~~~~~~~~~i~~ 205 (509)
T PRK05022 128 TLDALDPGQFDAFSDEELRALAALAAATLRNALLIEQ-LES-QAELPQDVAEFLRQEALKEGEMIGQSPAMQQLKKEIEV 205 (509)
T ss_pred EEeeCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH-HHHHHHHHHHHHhhhhccCCceeecCHHHHHHHHHHHH
Confidence 9998877666665555666677766666654322111 111 0011111111111111 345577777766554432222
Q ss_pred EEEECCeEEEeccCCCH
Q 005722 441 ALYYRGKLWLLGVTPTE 457 (681)
Q Consensus 441 al~~~~~~~~~G~tP~~ 457 (681)
+--.+..+...|++=+-
T Consensus 206 ~a~~~~pVlI~Ge~GtG 222 (509)
T PRK05022 206 VAASDLNVLILGETGVG 222 (509)
T ss_pred HhCCCCcEEEECCCCcc
Confidence 22335556667776663
No 21
>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=97.80 E-value=9.4e-06 Score=90.57 Aligned_cols=61 Identities=26% Similarity=0.251 Sum_probs=56.4
Q ss_pred HHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 616 LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 616 Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
|++.++|+|+++|.+|+|++||..+++++||+.+|++|+++.+++++++.+.+...+..+.
T Consensus 1 ~~~~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~ 61 (442)
T TIGR02040 1 LLATAADVTLLLDAEGVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEAL 61 (442)
T ss_pred CCcccCcEEEEECCCCcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHh
Confidence 4788999999999999999999999999999999999999999999999998888876654
No 22
>PRK13557 histidine kinase; Provisional
Probab=97.79 E-value=4.1e-05 Score=86.13 Aligned_cols=68 Identities=16% Similarity=0.197 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHhcCccEEEEcC---CCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHH
Q 005722 607 RIITNEMVRLIETAAVPILAVDA---SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSS 674 (681)
Q Consensus 607 ~~~~~el~~Lie~s~d~I~~vD~---~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~ 674 (681)
....+.+..++++++++|+++|. +|+|+|+|+++++++||+.+|++|+++.+++++++.......+..
T Consensus 26 ~~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~ 96 (540)
T PRK13557 26 DHRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRD 96 (540)
T ss_pred hhhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHH
Confidence 34467789999999999999995 899999999999999999999999999999987665544444433
No 23
>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=97.79 E-value=8.3e-05 Score=53.88 Aligned_cols=63 Identities=24% Similarity=0.391 Sum_probs=56.9
Q ss_pred HHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHH
Q 005722 613 MVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSA 675 (681)
Q Consensus 613 l~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~a 675 (681)
++.+++..+++++.+|.+|.+.++|..+.+++|++..+++|+.+.+++++.+...+...+..+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
T smart00091 3 LRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQRL 65 (67)
T ss_pred HHHHHhhCCceEEEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHHH
Confidence 467889999999999999999999999999999999999999999999999888777776654
No 24
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.79 E-value=0.0037 Score=74.36 Aligned_cols=211 Identities=9% Similarity=0.011 Sum_probs=115.5
Q ss_pred CCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeec--CCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecC
Q 005722 213 SGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECR--RPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDC 290 (681)
Q Consensus 213 ~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~--~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv 290 (681)
..+++++++.+++.+++++|+|++.|+-++++...-++.-+. ..+-....|...|... --+..-+..+...++.|.
T Consensus 197 ~~dl~ell~~I~~~i~~~~~a~~~~I~L~d~~~~~L~~~aa~g~~~~~~~~~~~~~~~~~--~l~g~V~~~~~p~lv~~~ 274 (686)
T PRK15429 197 RLDMDELVSEVAKEIHYYFDIDAISIVLRSHRKNKLNIYSTHYLDKQHPAHEQSEVDEAG--TLTERVFKSKEMLLINLH 274 (686)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCcEEEEEecccChhhcccccccCCccc--chHHHHHhcCceEEEECc
Confidence 568999999999999999999999999998886543332222 1222223333433322 123456667777777666
Q ss_pred CCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCC
Q 005722 291 LAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRF 370 (681)
Q Consensus 291 ~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~ 370 (681)
+..+ +.. ......+ +..-++++.+++|++.+ ++.=|.|..-++.++.
T Consensus 275 ~~d~------------~~~-------~~~~~~~-~~~~~~~s~l~vPL~~~-------------~~v~GvL~l~~~~~~~ 321 (686)
T PRK15429 275 ERDD------------LAP-------YERMLFD-TWGNQIQTLCLLPLMSG-------------DTMLGVLKLAQCEEKV 321 (686)
T ss_pred cCcc------------cch-------hhhhhhh-cccccceEEEEEeEEEC-------------CEEEEEEEEeeCCCCc
Confidence 5322 100 0000111 22335789999999976 7999999998877777
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhcc--CCccccccCChhhhhhccCCeEEEEECCe
Q 005722 371 VPFPLRYACEFLIQVFGVQVNKEVELSAQLREKHILRTQ-TVLCDMLLR--DSPVGIVTQTPNVMDLVKCDGAALYYRGK 447 (681)
Q Consensus 371 v~~~~R~a~e~l~q~~s~ql~~~~el~~q~~e~~~~~~~-~~l~~~l~~--~~~~~i~~~~~~ll~L~~adGaal~~~~~ 447 (681)
++.+....+..+++.++..|......+...+.++.+..+ ..+.+.+.. .....++..++.+..+++--..+.-.+..
T Consensus 322 F~~~dl~lL~~iA~~~A~Aie~a~~~~~~~~~~~~L~~e~~~lt~~L~~~n~~~~~liG~S~~~~~~~~~~~~~a~~~~p 401 (686)
T PRK15429 322 FTTTNLKLLRQIAERVAIAVDNALAYQEIHRLKERLVDENLALTEQLNNVDSEFGEIIGRSEAMYSVLKQVEMVAQSDST 401 (686)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhhHHHHHHHhhhhccccccceeecCHHHHHHHHHHHHHhCCCCC
Confidence 766555555555555555554322111111111111100 011111111 12334666777665554322222233456
Q ss_pred EEEeccCCCHH
Q 005722 448 LWLLGVTPTEE 458 (681)
Q Consensus 448 ~~~~G~tP~~~ 458 (681)
+...|++=+-.
T Consensus 402 VLI~GE~GTGK 412 (686)
T PRK15429 402 VLILGETGTGK 412 (686)
T ss_pred EEEECCCCcCH
Confidence 77778877744
No 25
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.73 E-value=3.8e-05 Score=85.25 Aligned_cols=61 Identities=18% Similarity=0.211 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDS 664 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~ 664 (681)
+++++..+.++.++++.+++|+++|.+|+|+++|+++++++||+.+|.+|+++.+++..++
T Consensus 91 ~~l~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~ 151 (430)
T PRK11006 91 RELGNLIKRFRSGAESLPDAVVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPE 151 (430)
T ss_pred HHHHHHHHHHHHHHHhCCCeEEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHH
Confidence 4466667789999999999999999999999999999999999999999999998876543
No 26
>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=97.73 E-value=6.8e-05 Score=58.31 Aligned_cols=57 Identities=21% Similarity=0.378 Sum_probs=50.8
Q ss_pred cCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 620 AAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 620 s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
++++|+++|.+|.+.++|.++++++|++.++++|+++.+++++.+...+...+..+.
T Consensus 1 ~~~~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (103)
T cd00130 1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL 57 (103)
T ss_pred CCceEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHH
Confidence 367999999999999999999999999999999999999999888877776666654
No 27
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.70 E-value=3.5e-05 Score=68.91 Aligned_cols=66 Identities=21% Similarity=0.286 Sum_probs=53.9
Q ss_pred HHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHccc
Q 005722 613 MVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLAI 679 (681)
Q Consensus 613 l~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~G~ 679 (681)
|+.++++.+.++.++|.+++|.++|+++++++++.+ ..+|+++.++-++.+.+.+...++.+..|+
T Consensus 1 L~~il~s~~~~i~~vD~~~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i~~~~~~~ 66 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRNLRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKIIEQVRSGK 66 (106)
T ss_dssp HHHHHHHSSSEEEEEETTSBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHHHHHHTTS
T ss_pred ChHHHhcCCCCEEEEcCCCeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHHHHHHcCC
Confidence 467999999999999999999999999999999885 458999999999988889999998887664
No 28
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=97.69 E-value=0.0017 Score=72.97 Aligned_cols=206 Identities=17% Similarity=0.155 Sum_probs=120.8
Q ss_pred CCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHH-HHHHcCC-eEEe-ecC
Q 005722 214 GNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASR-FLIMKNK-VRMI-CDC 290 (681)
Q Consensus 214 ~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR-~Ly~~n~-vR~I-~Dv 290 (681)
.+++.++..+++.+..+.|||+++++++|.+. .+..+.+.-..+.+|.+-+....|.+.- +.+..+. ++++ .|+
T Consensus 47 ~~~e~ll~~v~~~l~~~~~~~~~~ll~~d~~~---l~~~~~~gl~~~~~~~~~~~~~~~~~~l~~i~~~~~p~~~~~~d~ 123 (550)
T COG3604 47 LRLERLLAEVAKELHSLFGCDASALLRLDSKN---LIPLATDGLSKDHLGREQRFVVEGHPLLEQILKAGRPLVFHPADS 123 (550)
T ss_pred hhHHHHHHHHHHHHHHHhcCCeeEEEEecccc---cchhhhhcccccccccccccccCcchHHHHHHhCCCcEEEecCCc
Confidence 47999999999999999999999999999887 4444444444556666434444444432 2334343 4441 222
Q ss_pred CCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCC
Q 005722 291 LAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRF 370 (681)
Q Consensus 291 ~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~ 370 (681)
.. +++. | -++. -..||++.|+|.+||.++ +++||.+.--|+.|..
T Consensus 124 ~~------~~~~-----~----~l~~-------~~~~~~~~a~i~~PL~~~-------------~~~~G~Ltld~~~~~~ 168 (550)
T COG3604 124 LF------PDPY-----D----GLLP-------DTEGNKKHACIGVPLKSG-------------DKLIGALTLDHTEPDQ 168 (550)
T ss_pred cc------CCcc-----c----cccc-------CccCCcceeEEeeeeeeC-------------CeeeeeEEeeeecccc
Confidence 21 1111 1 0111 145678899999999987 8999999988887755
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHhhcc--CCccccccCChhhhhhccCCeEEEEECC
Q 005722 371 VPFPLRYACEFLIQVFGVQVNKEVELSAQLRE-K-HILRTQTVLCDMLLR--DSPVGIVTQTPNVMDLVKCDGAALYYRG 446 (681)
Q Consensus 371 v~~~~R~a~e~l~q~~s~ql~~~~el~~q~~e-~-~~~~~~~~l~~~l~~--~~~~~i~~~~~~ll~L~~adGaal~~~~ 446 (681)
..+..-....+|+...+...... .+.+++.. + +....+..+..-+.. -...+|+.+++.++.+++-=-++--.+-
T Consensus 169 f~~~~~~~lr~La~~a~la~~~~-~l~~~l~~~~~~l~~e~~~~~~~~~~~~~~~~~iIG~S~am~~ll~~i~~VA~Sd~ 247 (550)
T COG3604 169 FDEDLDEELRFLAALAALAVANA-LLHRELSSLKERLEEENLALEEQLSEVVLEVGGIIGRSPAMRQLLKEIEVVAKSDS 247 (550)
T ss_pred cchhHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhhhhccccchhcccccceecCHHHHHHHHHHHHHhcCCC
Confidence 54443344555655555444321 11111110 0 110101111111111 1245788899988888766555555566
Q ss_pred eEEEeccCCCHH
Q 005722 447 KLWLLGVTPTEE 458 (681)
Q Consensus 447 ~~~~~G~tP~~~ 458 (681)
.+...|+|-+-.
T Consensus 248 tVLi~GETGtGK 259 (550)
T COG3604 248 TVLIRGETGTGK 259 (550)
T ss_pred eEEEecCCCccH
Confidence 677778887743
No 29
>PRK10060 RNase II stability modulator; Provisional
Probab=97.65 E-value=8.7e-05 Score=87.61 Aligned_cols=66 Identities=20% Similarity=0.330 Sum_probs=54.3
Q ss_pred HHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccc-cCCCHHHHHHHHHHH
Q 005722 610 TNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLV-AGDSVDVVKNMLSSA 675 (681)
Q Consensus 610 ~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv-~~~~~~~~~~~l~~a 675 (681)
...++.+++.++++|+++|.+|+|+++|+++++++||+.+|++|+++.+++ ++++.......+...
T Consensus 110 ~~~~~~v~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~ 176 (663)
T PRK10060 110 LSFAEQVVSEANSVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGF 176 (663)
T ss_pred HHHHHHHHhhCCceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHH
Confidence 345677999999999999999999999999999999999999999998776 444444444445443
No 30
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.61 E-value=6.9e-05 Score=86.08 Aligned_cols=60 Identities=20% Similarity=0.290 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHH
Q 005722 607 RIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVD 666 (681)
Q Consensus 607 ~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~ 666 (681)
+.-.++|.+++++.++||+++|.+|+|+++|+++++++|++.++++|+++.++++.....
T Consensus 76 e~e~~~L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~l~ 135 (520)
T PRK10820 76 EREHRALSALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFNFL 135 (520)
T ss_pred HHHHHHHHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcchHH
Confidence 344567899999999999999999999999999999999999999999999999876543
No 31
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.57 E-value=0.012 Score=69.36 Aligned_cols=135 Identities=16% Similarity=0.141 Sum_probs=84.8
Q ss_pred CCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCC-CCCchHHHHHHHH-cCCeEEeecC
Q 005722 213 SGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYP-ATDIPQASRFLIM-KNKVRMICDC 290 (681)
Q Consensus 213 ~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfP-asDIP~qaR~Ly~-~n~vR~I~Dv 290 (681)
..+.+++++.+++.+.+..+||.+-|+.++++..--+..+..... +...+..+. ...-| ..+.+-. .+..+.+.|.
T Consensus 300 ~~~~~~l~~~v~~~l~~~~~~~~awi~~~d~~~~~l~~~~~~g~~-~~~~~~~~~~~~~~p-~~~a~~~~~~~~~~~~~~ 377 (665)
T PRK13558 300 ATDREEIEAAVCDRVGAGGEYDGAWIGEYDPTSGTITVAEAAGGC-DGADGDVLDLAAAGP-AAAALQSVVAETEAVEST 377 (665)
T ss_pred cCCHHHHHHHHHHHHHhccCcceEEEeeecCCCCeEeeeecccCC-cccccccccccccCc-hHHHHHhccCceEEecCC
Confidence 458899999999999999999999999998877544343333221 112222211 11112 1112211 1333333332
Q ss_pred CCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCC
Q 005722 291 LAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRF 370 (681)
Q Consensus 291 ~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~ 370 (681)
+.. ++|... . | .|.+++||..+ |+.||+|+.+...|+.
T Consensus 378 ~~~-------------------------~~~~~~-~--~-~s~~~vPL~~~-------------g~~~GvL~v~~~~~~~ 415 (665)
T PRK13558 378 DVD-------------------------GVSGTV-D--G-SAVAAVPLVYR-------------ETTYGVLVVYTAEPDE 415 (665)
T ss_pred Ccc-------------------------cccccc-C--C-ceEEEEeEEEC-------------CEEEEEEEEeeCCCCC
Confidence 211 111110 0 1 19999999987 8999999999988999
Q ss_pred CChhHHHHHHHHHHHHHHHHH
Q 005722 371 VPFPLRYACEFLIQVFGVQVN 391 (681)
Q Consensus 371 v~~~~R~a~e~l~q~~s~ql~ 391 (681)
++.+.+...+.|+..++.-|+
T Consensus 416 f~~~e~~ll~~la~~ia~aI~ 436 (665)
T PRK13558 416 IDDRERVVLEALGRAVGAAIN 436 (665)
T ss_pred CCHHHHHHHHHHHHHHHHHHH
Confidence 999999988888887776663
No 32
>PRK13559 hypothetical protein; Provisional
Probab=97.55 E-value=0.00016 Score=77.81 Aligned_cols=68 Identities=13% Similarity=0.131 Sum_probs=55.8
Q ss_pred HHHHHHHHHHhcCccEEEEcC---CCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 609 ITNEMVRLIETAAVPILAVDA---SGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 609 ~~~el~~Lie~s~d~I~~vD~---~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
..+.++.+++.++++|+++|. +|+|++||+++++++||+.+|++|+++..+.++.+.......+..++
T Consensus 41 ~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~ 111 (361)
T PRK13559 41 SGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAI 111 (361)
T ss_pred hhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHh
Confidence 356678899999999999997 67899999999999999999999999988877665555444444443
No 33
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=97.49 E-value=0.003 Score=75.74 Aligned_cols=149 Identities=13% Similarity=0.059 Sum_probs=101.5
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcC
Q 005722 203 KAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKN 282 (681)
Q Consensus 203 ~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n 282 (681)
++...+.+ +.+++++++.+++.+++++|+|+..||-+|+|...-+++-+...+-+..-..+||-.. --....+..+
T Consensus 7 eIs~~L~s--~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~ge--Gi~G~Va~tg 82 (748)
T PRK11061 7 EIVEKVAS--APRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDE--GIVGLVGRLA 82 (748)
T ss_pred HHHHHHhc--cCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCc--chHHHHhccC
Confidence 34445555 5699999999999999999999999999999876655554433222222223454322 1224455556
Q ss_pred CeEEeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEE
Q 005722 283 KVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVV 362 (681)
Q Consensus 283 ~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~ 362 (681)
..-.|.|+...|-- ... + .+...+++|-|++||+.+ |++=|.|.
T Consensus 83 ~pV~V~Dv~~dprf---------------~~~----~----~~~~~~~~S~L~VPL~~~-------------geVIGVL~ 126 (748)
T PRK11061 83 EPINLADAQKHPSF---------------KYI----P----SVKEERFRAFLGVPIIYR-------------RQLLGVLV 126 (748)
T ss_pred ceEEECCcccCccc---------------ccC----c----cccCccceEEEEEEEeeC-------------CEEEEEEE
Confidence 66677888754310 000 0 112368999999999965 79999999
Q ss_pred eecCCCCCCChhHHHHHHHHHHHHHHHHH
Q 005722 363 CHHTSPRFVPFPLRYACEFLIQVFGVQVN 391 (681)
Q Consensus 363 cHh~spr~v~~~~R~a~e~l~q~~s~ql~ 391 (681)
+++..|+..+.+....++.|+..++..|.
T Consensus 127 v~~~~~~~Fs~~d~~lL~~LA~~aAiAL~ 155 (748)
T PRK11061 127 VQQRELRQFDESEESFLVTLATQLAAILS 155 (748)
T ss_pred EeeCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999988777777777777766553
No 34
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=97.46 E-value=0.00012 Score=78.30 Aligned_cols=54 Identities=20% Similarity=0.216 Sum_probs=49.8
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCC
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDS 664 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~ 664 (681)
.++..++++.+++|+++|.+|+|++||+++++++||+.++++|+++.++++...
T Consensus 7 ~~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~ 60 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS 60 (348)
T ss_pred chHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch
Confidence 356789999999999999999999999999999999999999999999987543
No 35
>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=97.27 E-value=0.0004 Score=76.74 Aligned_cols=56 Identities=20% Similarity=0.204 Sum_probs=49.8
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHH
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVD 666 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~ 666 (681)
+.++.+++.++++|+++|.+|++++||+++++++||++++++|++...+.++.+..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~ 59 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPP 59 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCH
Confidence 45789999999999999999999999999999999999999999877666555444
No 36
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=97.27 E-value=0.28 Score=58.54 Aligned_cols=203 Identities=13% Similarity=0.097 Sum_probs=111.1
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHH
Q 005722 201 AAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIM 280 (681)
Q Consensus 201 ~~~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~ 280 (681)
+.++-..+.+ ..+++++++.+-..++++.-+|||-|.-+|+.. +.|.-=....+-++. .| + ....+.
T Consensus 11 l~~is~~~~~--~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~-~~~~~~~~~~~~~~~---~~----~---~~~~~~ 77 (686)
T PRK15429 11 LFDITRTLLQ--QPDLASLCEALSQLVKRSALADNAAIVLWQAQT-QRASYYASREKGTPV---KY----E---DETVLA 77 (686)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHHHHhhcccceEEEEEEcCCC-Ceeeeeeccccccch---hc----c---chhhhc
Confidence 3334344444 459999999999999999999999999999876 555421111111110 00 0 122233
Q ss_pred cCCeEEeecCCCCCceeecCCCCCCCcccccccccCCCh--HHHHHHHhcCCeeEEEEEEEecCccccccccccccCcee
Q 005722 281 KNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHG--CHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLW 358 (681)
Q Consensus 281 ~n~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp--~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLW 358 (681)
.+++.++--.. +|+-+++..++-..| +...+...|| +-+.|||++. |+..
T Consensus 78 ~g~~g~vl~~~-------------~~l~~~~~~~~~~~~~l~~~~~~~~~~--~~lgvPl~~~-------------~~v~ 129 (686)
T PRK15429 78 HGPVRRILSRP-------------DTLHCSYEEFCETWPQLAAGGLYPKFG--HYCLMPLAAE-------------GHIF 129 (686)
T ss_pred cCcceEEeecC-------------ceEEEchHHhhhccHHHhhcccccCcc--ceEEeceeeC-------------CeeE
Confidence 34433333222 333222222221111 1111224554 4778999987 8999
Q ss_pred EEEEeecCCCCCCChhHHHHHHHHHHHHHHHHHHHH--HHHHH---HHHHHHHHHHHHHHHh----hccCCcccccc-CC
Q 005722 359 GLVVCHHTSPRFVPFPLRYACEFLIQVFGVQVNKEV--ELSAQ---LREKHILRTQTVLCDM----LLRDSPVGIVT-QT 428 (681)
Q Consensus 359 GLi~cHh~spr~v~~~~R~a~e~l~q~~s~ql~~~~--el~~q---~~e~~~~~~~~~l~~~----l~~~~~~~i~~-~~ 428 (681)
|-|.--.+.+...+.+......+|++.++..|+... +...+ ..+++... ...+.++ +...++..+.. -.
T Consensus 130 G~l~l~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~-~~~L~eIs~~l~s~~dl~ell~~I~ 208 (686)
T PRK15429 130 GGCEFIRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDN-FRILVAITNAVLSRLDMDELVSEVA 208 (686)
T ss_pred EEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH-HHHHHHHHHHHccCCCHHHHHHHHH
Confidence 999988887877888777777778887777775432 11111 11111111 1222222 22223333322 24
Q ss_pred hhhhhhccCCeEEEEEC
Q 005722 429 PNVMDLVKCDGAALYYR 445 (681)
Q Consensus 429 ~~ll~L~~adGaal~~~ 445 (681)
..+..+++||.+.|+.-
T Consensus 209 ~~i~~~~~a~~~~I~L~ 225 (686)
T PRK15429 209 KEIHYYFDIDAISIVLR 225 (686)
T ss_pred HHHHHHhCCCEEEEEEE
Confidence 56788999999877653
No 37
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=97.23 E-value=0.00035 Score=83.21 Aligned_cols=65 Identities=15% Similarity=0.207 Sum_probs=56.0
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHH
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSA 675 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~a 675 (681)
+.+...++.++++++++|.+|+|++||+++++++||+++|++|+++.++++++........+...
T Consensus 12 ~~~~~~le~~~~~i~~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~ 76 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHN 76 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhh
Confidence 34567889999999999999999999999999999999999999999999888776555444443
No 38
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=97.13 E-value=0.00088 Score=61.40 Aligned_cols=53 Identities=17% Similarity=0.304 Sum_probs=46.9
Q ss_pred EEEEcCCCceeeecHH-hHHhcCCChhhhhcCcccccccCCCHHH-HHHHHHHHH
Q 005722 624 ILAVDASGNVNGWNSK-AAELTGLTVDQAIGTALVDLVAGDSVDV-VKNMLSSAF 676 (681)
Q Consensus 624 I~~vD~~G~I~~~N~a-~~~l~G~~~~EliGk~l~~lv~~~~~~~-~~~~l~~al 676 (681)
+...+.||+|+++-.+ ...++||.++|++|+++.+++|++|... +.....+++
T Consensus 5 ~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~ 59 (111)
T PF14598_consen 5 TTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVL 59 (111)
T ss_dssp EEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHH
T ss_pred EEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHh
Confidence 3457899999999999 6999999999999999999999999996 888887775
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=97.11 E-value=0.00062 Score=77.20 Aligned_cols=55 Identities=27% Similarity=0.495 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccc
Q 005722 606 LRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLV 660 (681)
Q Consensus 606 l~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv 660 (681)
++.....++.+++.+.++|+++|.+|+++++|++++.++|++.++++||++.+++
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~ 166 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVV 166 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence 3445577899999999999999999999999999999999999999999999987
No 40
>PF12860 PAS_7: PAS fold
Probab=97.08 E-value=0.00031 Score=63.56 Aligned_cols=44 Identities=25% Similarity=0.468 Sum_probs=40.9
Q ss_pred HHhcCccEEEEcCCCceeeecHHhHHhcCCChhhh-hcCcccccc
Q 005722 617 IETAAVPILAVDASGNVNGWNSKAAELTGLTVDQA-IGTALVDLV 660 (681)
Q Consensus 617 ie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~El-iGk~l~~lv 660 (681)
||+.++||+++|.+|++++||+++.+|+|++++.+ .|.++.+++
T Consensus 1 Ld~l~~Gv~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~ 45 (115)
T PF12860_consen 1 LDSLPQGVAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLL 45 (115)
T ss_pred CCCcCceEEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHH
Confidence 47889999999999999999999999999999998 899988776
No 41
>PRK09776 putative diguanylate cyclase; Provisional
Probab=97.04 E-value=0.00076 Score=83.26 Aligned_cols=58 Identities=19% Similarity=0.297 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccccccc
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA 661 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~ 661 (681)
+++++..++++.++++++++|+.+|.+|+|+++|+++++++||+.+|++|+++.++++
T Consensus 529 ~~L~~~~~~l~~~l~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~ 586 (1092)
T PRK09776 529 EALFQEKERLHITLDSIGEAVVCTDMAMKVTFMNPVAEKMTGWTQEEALGVPLLTVLH 586 (1092)
T ss_pred HHHHHHHHHHHHHHhccccEEEEECCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHHcc
Confidence 4455666778899999999999999999999999999999999999999999887765
No 42
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.86 E-value=0.0016 Score=73.63 Aligned_cols=60 Identities=23% Similarity=0.369 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGD 663 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~ 663 (681)
+.++...+.++.++++.+++|+++|.+|+|+++|+++++++||++++++|+++.+++++.
T Consensus 255 ~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~ 314 (607)
T PRK11360 255 QALRETRSLNELILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPN 314 (607)
T ss_pred HHHHHHHHHHHHHHHhccCeEEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCc
Confidence 455666677888999999999999999999999999999999999999999999988754
No 43
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=96.74 E-value=0.0015 Score=55.87 Aligned_cols=43 Identities=16% Similarity=0.383 Sum_probs=36.2
Q ss_pred eeeecHHhHHhcCCChhhhhcCc----ccccccCCCHHHHHHHHHH-HH
Q 005722 633 VNGWNSKAAELTGLTVDQAIGTA----LVDLVAGDSVDVVKNMLSS-AF 676 (681)
Q Consensus 633 I~~~N~a~~~l~G~~~~EliGk~----l~~lv~~~~~~~~~~~l~~-al 676 (681)
|++||+.+.+++||+++++ |.. +..++||+|++.+.+.+.. ++
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~ 48 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAAL 48 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHH
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhh
Confidence 6899999999999999999 887 8899999999999999998 44
No 44
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=96.70 E-value=0.0032 Score=75.04 Aligned_cols=51 Identities=16% Similarity=0.321 Sum_probs=46.9
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccccccc
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA 661 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~ 661 (681)
+.+..+++.++++|+++|.+|+++++|+++++++||+.+|++|+++.++++
T Consensus 136 ~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~ 186 (799)
T PRK11359 136 RQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLN 186 (799)
T ss_pred HHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCChHHhcC
Confidence 445568999999999999999999999999999999999999999988775
No 45
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=96.70 E-value=0.002 Score=75.83 Aligned_cols=58 Identities=28% Similarity=0.335 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccC
Q 005722 605 ELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAG 662 (681)
Q Consensus 605 el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~ 662 (681)
++.....++..++++..+||+++|.+|+|+++|+++++++|++.++++|+++.++++.
T Consensus 197 ~~~~~~~~~~~il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~ 254 (638)
T PRK11388 197 ESNRHLNQLNALLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLTL 254 (638)
T ss_pred HHHHHHHHHHHHHhccCCcEEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhcc
Confidence 3344455677899999999999999999999999999999999999999999998853
No 46
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=96.65 E-value=0.0032 Score=71.21 Aligned_cols=61 Identities=20% Similarity=0.285 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCC---hhhhhcCcccccccCCC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLT---VDQAIGTALVDLVAGDS 664 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~---~~EliGk~l~~lv~~~~ 664 (681)
.|+..+.++++.++++.+++|+++|.+|+|++||+++++++|++ +++.+|+.+.++.+...
T Consensus 214 ~ei~~l~~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~~ 277 (542)
T PRK11086 214 YEISTLFEQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVSR 277 (542)
T ss_pred HHHHHHHHHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCchh
Confidence 56677788889999999999999999999999999999999875 45788998887776544
No 47
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=96.64 E-value=0.0027 Score=72.42 Aligned_cols=62 Identities=19% Similarity=0.345 Sum_probs=53.9
Q ss_pred hHHHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCCh--hhhhcCcccccccCC
Q 005722 602 KIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTV--DQAIGTALVDLVAGD 663 (681)
Q Consensus 602 ~~~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~--~EliGk~l~~lv~~~ 663 (681)
+.+++....++++.++++..+||+++|.+|+|+++|+++++++|++. ++++|+++.+++++.
T Consensus 213 e~~~~~~~~~~~~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~ 276 (545)
T PRK15053 213 EPKQIARVVRQQEALFSSVYEGLIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPA 276 (545)
T ss_pred CHHHHHHHHHHHHHHHHHhCceEEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCc
Confidence 34556666778899999999999999999999999999999999975 579999999888654
No 48
>PRK13560 hypothetical protein; Provisional
Probab=96.58 E-value=0.004 Score=73.74 Aligned_cols=59 Identities=24% Similarity=0.353 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeee-cHHhHHhcCCChhhhhcCcccccccC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGW-NSKAAELTGLTVDQAIGTALVDLVAG 662 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~-N~a~~~l~G~~~~EliGk~l~~lv~~ 662 (681)
++|++..+.++.++++++++|+.+|.+|+++++ |+++++++||+.+|++|+++.++.++
T Consensus 325 ~~L~~se~~l~~l~~~~~~~i~~~d~~g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~~~ 384 (807)
T PRK13560 325 RELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAERMLGWSAAEVMGKPLPGMDPE 384 (807)
T ss_pred HHHHHHHHHHHHHHHhCcccEEEEcCCCCEEEecCHHHHHHhCCCHHHHcCCCccccChh
Confidence 456666778899999999999999999999987 67888899999999999998776543
No 49
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.52 E-value=0.0071 Score=54.26 Aligned_cols=60 Identities=27% Similarity=0.412 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGD 663 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~ 663 (681)
+.++.....+..+++..+++++.+|.+|.+.+||+++++++|++..+.+|+...+.....
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~ 164 (232)
T COG2202 105 EALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPE 164 (232)
T ss_pred HHHHHHHHHHHHHHhhCCceEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecC
Confidence 334444455889999999999999999999999999999999998888888877665433
No 50
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.51 E-value=0.0051 Score=72.35 Aligned_cols=65 Identities=22% Similarity=0.185 Sum_probs=53.7
Q ss_pred HHHHHHHhcCccEEEEc---CCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 612 EMVRLIETAAVPILAVD---ASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 612 el~~Lie~s~d~I~~vD---~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
.++.+++.++++|+.+| .+|+|++||+++++++||+++|++|+++.++.++.+.......+..++
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~ 216 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAI 216 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHH
Confidence 34679999999999998 489999999999999999999999999998888776654444444443
No 51
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=96.39 E-value=0.0058 Score=65.97 Aligned_cols=67 Identities=13% Similarity=0.279 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHH
Q 005722 606 LRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNML 672 (681)
Q Consensus 606 l~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l 672 (681)
+..-.+.|..++-..+|||+++|..|+|..+|..+.+++|.+.++++|+++.+++.-++--.++.++
T Consensus 106 ~e~Er~kL~SvlayMtDGViATdRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL~ 172 (459)
T COG5002 106 TEQERRKLDSVLAYMTDGVIATDRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDLV 172 (459)
T ss_pred HHHHHHHHHHHHHHHcCceEeecCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHHH
Confidence 3344577889999999999999999999999999999999999999999999998766655555443
No 52
>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=96.38 E-value=0.0036 Score=69.13 Aligned_cols=66 Identities=14% Similarity=0.107 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHH
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVK 669 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~ 669 (681)
+++++....++.++++++++|+++|.+|+++++|+++++++|+...+..+..+.++++++......
T Consensus 123 ~~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 188 (494)
T TIGR02938 123 QVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWREALA 188 (494)
T ss_pred HHHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhhhhhh
Confidence 345556677889999999999999999999999999999999999999998888777766555443
No 53
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.24 E-value=0.0056 Score=66.45 Aligned_cols=56 Identities=29% Similarity=0.386 Sum_probs=52.2
Q ss_pred HHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHH
Q 005722 612 EMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDV 667 (681)
Q Consensus 612 el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~ 667 (681)
++.+|+++.++|++.+|..|.|...|+|+++++|.+++++.|+.+..|+...+..+
T Consensus 81 ~L~aLL~al~~pVlsvd~kg~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~~ 136 (511)
T COG3283 81 ALSALLEALPEPVLSVDMKGKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFLR 136 (511)
T ss_pred HHHHHHHhCCCceEEecccCceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHHH
Confidence 57899999999999999999999999999999999999999999999998776653
No 54
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=95.97 E-value=0.011 Score=67.19 Aligned_cols=65 Identities=23% Similarity=0.399 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChh--hhhcCcccccccC-CCHHHH
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVD--QAIGTALVDLVAG-DSVDVV 668 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~--EliGk~l~~lv~~-~~~~~~ 668 (681)
+|+.++.++..+++++..+||+++|..|.|+-+|.++.+|+|++.. +++|+++.++++| .+.+.+
T Consensus 208 ~EIa~l~~er~A~l~si~EGviAvd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~l~~v 275 (537)
T COG3290 208 EEIATLLEERQAMLQSIKEGVIAVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSDLPEV 275 (537)
T ss_pred HHHHHHHHHHHHHHHHhhceEEEECCCCeEeehhHHHHHHhcccCcCcccccccceEeeccccCcHHH
Confidence 8899999999999999999999999999999999999999999765 6999999999984 555555
No 55
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=95.17 E-value=0.035 Score=52.02 Aligned_cols=57 Identities=14% Similarity=0.314 Sum_probs=47.8
Q ss_pred HHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccc-ccccCCCHHHHHHHH
Q 005722 616 LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALV-DLVAGDSVDVVKNML 672 (681)
Q Consensus 616 Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~-~lv~~~~~~~~~~~l 672 (681)
-+|..|-||+-+|.+|+|+..|++-.++.|++++.++||++. |+.+=.....+..-+
T Consensus 21 elD~lpFGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF 78 (124)
T TIGR02373 21 QFDALPFGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRF 78 (124)
T ss_pred HhhcCCcceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHH
Confidence 488999999999999999999999999999999999999976 776655444343333
No 56
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=94.95 E-value=1.3 Score=52.65 Aligned_cols=151 Identities=12% Similarity=0.035 Sum_probs=85.5
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHH
Q 005722 201 AAKAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIM 280 (681)
Q Consensus 201 ~~~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~ 280 (681)
..+.+++|.+ +.+.+++++.+++.+.++++.++..+|-.++++ |........ +++. .+...|. +.|-. +.+-.
T Consensus 307 ~l~~~~~L~~--~~~~~~l~~~~~~~l~~~l~~~~g~l~l~~~~~-~~~~~~~~~-~~~~-~~~~~~~-~~~~~-~~~~~ 379 (679)
T TIGR02916 307 WLRFTQTLSE--ARSSDDLGERVIRALAQLVESPGGVLWLKSGND-GLYRPAARW-NQPL-AQAFEPS-DSAFC-QFLQE 379 (679)
T ss_pred HHHHHHHHhC--CCCCccHHHHHHHHHHHHhCCCCceEEEEcCCC-CEEeeehhc-CCCC-cccCCCC-CCHHH-HHHHh
Confidence 4566777777 568999999999999999999999999665443 544443321 1111 1212222 22211 12222
Q ss_pred cCCeEEeecCCCCCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEE
Q 005722 281 KNKVRMICDCLAPPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGL 360 (681)
Q Consensus 281 ~n~vR~I~Dv~~~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGL 360 (681)
.+++ .|.+... ..++. ..++ ..|.. .+..-++.+.+||..+ +++.|.
T Consensus 380 ~~~v---~~~~~~~--~~~~~--~~~~---------~~~~~----~~~~~~~~l~vPL~~~-------------~~~~G~ 426 (679)
T TIGR02916 380 SGWI---INLEEAR--SEPDH--YSGL---------VLPEW----LREIPNAWLIVPLISG-------------EELVGF 426 (679)
T ss_pred CCCc---ccchhhc--CCccc--cccc---------ccchh----hhcCCCceEEEEeccC-------------CEEEEE
Confidence 2322 1211110 00000 0000 01111 1222356889999976 799999
Q ss_pred EEeecC-CCCCCChhHHHHHHHHHHHHHHHHH
Q 005722 361 VVCHHT-SPRFVPFPLRYACEFLIQVFGVQVN 391 (681)
Q Consensus 361 i~cHh~-spr~v~~~~R~a~e~l~q~~s~ql~ 391 (681)
+++-+. .++.++.+.+...+.++..++..+.
T Consensus 427 l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~ 458 (679)
T TIGR02916 427 VVLARPRTAGEFNWEVRDLLKTAGRQAASYLA 458 (679)
T ss_pred EEEecCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 988766 4667788888877777776666554
No 57
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=94.84 E-value=0.036 Score=63.83 Aligned_cols=70 Identities=17% Similarity=0.295 Sum_probs=57.7
Q ss_pred hhHHHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHH
Q 005722 601 EKIDELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSA 675 (681)
Q Consensus 601 ~~~~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~a 675 (681)
++-+.+.+-.+-++.+++..+.|++.+|.+|+|.-+|+++|+|+|.+-.+++|+++..+- +.+++++..+
T Consensus 360 ~ak~~~e~rr~f~E~VLsgvtaGVi~~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~a-----p~~~~vf~~~ 429 (712)
T COG5000 360 RAKDALEQRRRFLEAVLSGLTAGVIGFDNRGCITTVNPSAEQILGKPFDQLLGQSLSAIA-----PELEEVFAEA 429 (712)
T ss_pred HHHHHHHHHHHHHHHHHhcCceeEEEEcCCCeeEeecchHHHHhcCChhHhhcchhhhhh-----hHHHHHHHHh
Confidence 334566677778899999999999999999999999999999999999999999987664 3344444444
No 58
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=94.47 E-value=0.023 Score=67.80 Aligned_cols=54 Identities=15% Similarity=0.241 Sum_probs=47.7
Q ss_pred HHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHH
Q 005722 616 LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVK 669 (681)
Q Consensus 616 Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~ 669 (681)
|+|++.--+|+|.-+|+|+||...++.++||..+|++|++|++++|+.+.+.+.
T Consensus 100 mLeAlDGF~fvV~cdG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~ 153 (803)
T KOG3561|consen 100 ILEALDGFLFVVNCDGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPR 153 (803)
T ss_pred HHHHhcCeEEEEecCceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCccc
Confidence 556666677889999999999999999999999999999999999999887543
No 59
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=93.19 E-value=0.07 Score=57.12 Aligned_cols=52 Identities=23% Similarity=0.287 Sum_probs=48.4
Q ss_pred HHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHH
Q 005722 615 RLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVD 666 (681)
Q Consensus 615 ~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~ 666 (681)
.++++...|++.+|.+|.|.|+|++++.+||.+..-+.|..+.++++..+..
T Consensus 11 ~~Ln~~~~pVl~vd~~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~gs~l 62 (363)
T COG3852 11 AILNNLINPVLLVDDELAIHYANPAAEQLLAVSARRLAGTRLSELLPFGSLL 62 (363)
T ss_pred hHHhccCCceEEEcCCCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCCcHH
Confidence 5889999999999999999999999999999999999999999999876654
No 60
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=92.17 E-value=0.26 Score=62.04 Aligned_cols=50 Identities=18% Similarity=0.071 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhc
Q 005722 604 DELRIITNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIG 653 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliG 653 (681)
.++++..+.++.++++.++||+++|.+|+|+++|+++++++|++..+..+
T Consensus 569 ~~l~~~~~~~~~i~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~~~~~~ 618 (1197)
T PRK09959 569 GDLENQISFRKALSDSLPNPTYVVNWQGNVISHNSAFEHYFTADYYKNAM 618 (1197)
T ss_pred HHHHHHHHHHHHHHhhCCCcEEEEcCCCcEEEehHHHHHHhCcccccccc
Confidence 45667777888999999999999999999999999999999987544333
No 61
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=91.69 E-value=0.17 Score=59.01 Aligned_cols=53 Identities=9% Similarity=0.162 Sum_probs=47.1
Q ss_pred EEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 624 ILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 624 I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
+..+.-|-+|+|+..++.++.||.++|||||+++++||..|.+.+.+-....+
T Consensus 277 vtRhs~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~ 329 (768)
T KOG3558|consen 277 VTRHSLDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLL 329 (768)
T ss_pred EEeeecceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHH
Confidence 44567889999999999999999999999999999999999998877766654
No 62
>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=91.27 E-value=0.22 Score=45.61 Aligned_cols=52 Identities=25% Similarity=0.440 Sum_probs=44.5
Q ss_pred cEEEEcC-CCceeeecHHhHHhcCCC---hhhhhcCcccccccCCCHHHHHHHHHH
Q 005722 623 PILAVDA-SGNVNGWNSKAAELTGLT---VDQAIGTALVDLVAGDSVDVVKNMLSS 674 (681)
Q Consensus 623 ~I~~vD~-~G~I~~~N~a~~~l~G~~---~~EliGk~l~~lv~~~~~~~~~~~l~~ 674 (681)
.++++|. +++|+.++..+++++|.+ +++++|+++.+++.++....+.+.+..
T Consensus 17 ~LLa~d~~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~~~~~ 72 (110)
T PF08446_consen 17 ALLALDPDDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLREALQS 72 (110)
T ss_dssp EEEEEETTTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHHHCTC
T ss_pred EEEEEECCCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHHhhhc
Confidence 5678885 689999999999999999 999999999999998888877766543
No 63
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=91.04 E-value=0.097 Score=57.89 Aligned_cols=51 Identities=18% Similarity=0.202 Sum_probs=45.7
Q ss_pred HHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccccccc
Q 005722 611 NEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVA 661 (681)
Q Consensus 611 ~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~ 661 (681)
+.+-+.++.-..+|-+.|.+-.|.|+|+|++.|+||-..|+|||+..|+-.
T Consensus 157 nalFaaLD~c~eAiEI~~ddhViQYVNpAfE~mmG~hkgEliGke~adlpk 207 (775)
T KOG1229|consen 157 NALFAALDECDEAIEICDDDHVIQYVNPAFENMMGCHKGELIGKEEADLPK 207 (775)
T ss_pred HHHHHHHhhhhhhheeccchhHHHHhcHHHHhhhcchhhhhcCCchhhccc
Confidence 455667788888999999999999999999999999999999999998754
No 64
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=90.19 E-value=15 Score=36.77 Aligned_cols=126 Identities=13% Similarity=0.168 Sum_probs=87.6
Q ss_pred CCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCC
Q 005722 214 GNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAP 293 (681)
Q Consensus 214 ~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~ 293 (681)
.++..+++.+++.+.+.||+ -|+|- +.-.|+|=+-.. -+. |-|.+ +.+..++.+..+++.+..+.+.+
T Consensus 52 ~~~~~~A~~~aeII~~~t~~-aVaIT-----Dr~~ILA~~G~g-~d~----~~~~~-is~~t~~~i~~gk~~~~~~~~~~ 119 (180)
T TIGR02851 52 GELGDFAKEYAESLYQSLGH-IVLIT-----DRDTVIAVAGVS-KKE----YLNKP-ISDELEDTMEERKTVILSDTKDG 119 (180)
T ss_pred cchHHHHHHHHHHHHHHhCC-EEEEE-----CCCcEEEEECCC-hhh----cCCCc-cCHHHHHHHHcCCEEEecCCccc
Confidence 36677788888889999999 88885 344667654322 223 33444 99999999999999888875422
Q ss_pred CceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCC--CC
Q 005722 294 PVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPR--FV 371 (681)
Q Consensus 294 pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr--~v 371 (681)
.++.... .+....+.+++||+.+ |+.=|.|.-. ...+ .+
T Consensus 120 ~i~c~~~-------------------------~~~~l~s~ii~Pl~~~-------------g~viGtLkly-~k~~~~~~ 160 (180)
T TIGR02851 120 PIEIIDG-------------------------QEFEYTSQVIAPIIAE-------------GDPIGAVIIF-SKEPGEKL 160 (180)
T ss_pred eeccccC-------------------------CCCCcceEEEEEEEEC-------------CeEEEEEEEE-ECCccCCC
Confidence 1222100 0112368899999987 6888866555 5555 77
Q ss_pred ChhHHHHHHHHHHHHHHHH
Q 005722 372 PFPLRYACEFLIQVFGVQV 390 (681)
Q Consensus 372 ~~~~R~a~e~l~q~~s~ql 390 (681)
+.-.+..++-+++.||.||
T Consensus 161 ~~~e~~la~glA~lLS~QL 179 (180)
T TIGR02851 161 GEVEQKAAETAAAFLGKQM 179 (180)
T ss_pred CHHHHHHHHHHHHHHHHhh
Confidence 7777888888999999887
No 65
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=89.70 E-value=0.25 Score=54.28 Aligned_cols=58 Identities=19% Similarity=0.271 Sum_probs=52.2
Q ss_pred HHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHH
Q 005722 616 LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLS 673 (681)
Q Consensus 616 Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~ 673 (681)
++++..--||++|++|.|.|++..+.--+|++.-|+-|..+.|++|+.|.+.+..+|.
T Consensus 84 lLqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~ 141 (598)
T KOG3559|consen 84 LLQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLT 141 (598)
T ss_pred HHHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHh
Confidence 5666666899999999999999999999999999999999999999999997776664
No 66
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=88.64 E-value=0.51 Score=55.15 Aligned_cols=63 Identities=11% Similarity=0.186 Sum_probs=54.3
Q ss_pred HHH-HHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHH
Q 005722 613 MVR-LIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSA 675 (681)
Q Consensus 613 l~~-Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~a 675 (681)
|.. ++++..--|++++.||.++|+...+...+|++.-|+.|.++.|++|+-|.+.+...|..-
T Consensus 120 l~~~iLqsLDGFVm~l~~dG~~lYiSEtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~ 183 (768)
T KOG3558|consen 120 LGDHILQSLDGFVMALTQDGDFLYISETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLR 183 (768)
T ss_pred hhhhHHhhccceEEEEccCCCEEEEechhHhhhCccceeeecchhhhccCccCHHHHHHHhccc
Confidence 444 455555568899999999999999999999999999999999999999999888877654
No 67
>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=86.09 E-value=1.7 Score=37.47 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=39.0
Q ss_pred ceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCch----HHHHHHHHh
Q 005722 81 GCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSS----GAAALQKAA 142 (681)
Q Consensus 81 G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~----~~~~l~~~l 142 (681)
-.++++|. +++|+.++.-+.++||.++++ ++|+++.+++.+. ....+...+
T Consensus 12 ~~i~~~d~-~g~I~~~N~a~~~l~g~~~~~----------~~g~~~~~~~~~~~~~~~~~~~~~~~ 66 (113)
T PF00989_consen 12 DGIFVIDE-DGRILYVNQAAEELLGYSREE----------LIGKSLFDLIHPEDRRELRERLRQAL 66 (113)
T ss_dssp SEEEEEET-TSBEEEECHHHHHHHSS-HHH----------HTTSBGGGGCSGGGHHHHHHHHHHHH
T ss_pred ceEEEEeC-cCeEEEECHHHHHHHccCHHH----------HcCCcHHHhcCchhhHHHHHHHHHHH
Confidence 45678885 689999999999999998754 6899999998876 444454444
No 68
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=85.65 E-value=1.8 Score=36.65 Aligned_cols=50 Identities=10% Similarity=0.216 Sum_probs=36.6
Q ss_pred EEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCch----HHHHHHHHhc
Q 005722 83 MIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSS----GAAALQKAAN 143 (681)
Q Consensus 83 LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~----~~~~l~~~l~ 143 (681)
++++|.+ ++|+.++.....++|+++++ ++|+++.+++.+. ..+.+.+++.
T Consensus 4 i~i~d~~-g~i~~~N~~~~~~~g~~~~~----------~~g~~~~~~~~~~~~~~~~~~~~~~~~ 57 (104)
T PF13426_consen 4 IFILDPD-GRILYVNPAFERLFGYSREE----------LIGKSISDFFPEEDRPEFEEQIERALE 57 (104)
T ss_dssp EEEEETT-SBEEEE-HHHHHHHTS-HHH----------HTTSBGGGGCSTTSCHHHHHHHHHHHH
T ss_pred EEEECCc-CcEEehhHHHHHHHCcCHHH----------HcCCCcccccCcccchhhHHHHHHHHh
Confidence 5678884 99999999999999998754 5899999998853 3345555554
No 69
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=85.04 E-value=0.94 Score=51.61 Aligned_cols=65 Identities=17% Similarity=0.189 Sum_probs=59.7
Q ss_pred HHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHH
Q 005722 612 EMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 612 el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al 676 (681)
|-+-++++..--++++..+|.|-|....++..+|+...++|-++++||||.||++-+++-|.-++
T Consensus 112 ege~lLqsLnGF~lVvt~eg~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa~ 176 (712)
T KOG3560|consen 112 EGELLLQSLNGFALVVTAEGEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWAM 176 (712)
T ss_pred chHHHHHhcCCeEEEEecCceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhcc
Confidence 34568889999999999999999999999999999999999999999999999999999887664
No 70
>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=82.24 E-value=3.5 Score=40.07 Aligned_cols=64 Identities=17% Similarity=0.058 Sum_probs=54.2
Q ss_pred HHHHHHhcCccEEEEcCC--CceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHc
Q 005722 613 MVRLIETAAVPILAVDAS--GNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFL 677 (681)
Q Consensus 613 l~~Lie~s~d~I~~vD~~--G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~ 677 (681)
.+.|.+ +|++|+.-|.+ =.++|.|+++-+|++++-+|++|-+...-..+..+..-.++|.++.+
T Consensus 34 ~~~L~~-ap~ailsh~~~~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~ 99 (148)
T PF08670_consen 34 AKALWH-APFAILSHGTKADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQ 99 (148)
T ss_pred HHHHHc-CCCEEEEcCCCCCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHH
Confidence 334455 99999998754 59999999999999999999999999977788888888888888863
No 71
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=77.87 E-value=1.7 Score=52.49 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=35.3
Q ss_pred ceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCc
Q 005722 81 GCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTS 132 (681)
Q Consensus 81 G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~ 132 (681)
|||+||.-+ |+|+.||||+..+||..+++ ++|+.|-+++.+
T Consensus 106 GF~fvV~cd-G~IvyVSeSVT~~L~y~QsD----------L~~qSly~ilhp 146 (803)
T KOG3561|consen 106 GFLFVVNCD-GRIVYVSESVTSVLGYLQSD----------LMGQSLYDILHP 146 (803)
T ss_pred CeEEEEecC-ceEEEEecchHHhhCcCHHH----------HhcchHHHhcCc
Confidence 999999987 99999999999999998876 477777777644
No 72
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=76.81 E-value=3.7 Score=50.79 Aligned_cols=44 Identities=23% Similarity=0.184 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHhcCccEEEEc-CCCceeeecHHhHHhcCCC
Q 005722 604 DELRIITNEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGLT 647 (681)
Q Consensus 604 ~el~~~~~el~~Lie~s~d~I~~vD-~~G~I~~~N~a~~~l~G~~ 647 (681)
+++++.....+.++++.|+||+++| .+|+|+.+|+++++++|..
T Consensus 336 ~~L~~~~~l~~~Ii~~lp~Gilv~D~~~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 336 HELRILRALNEEIVSNLPLGLLVYDFESNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHHHHHHHHHhCCceEEEEECCCCeEEEEhHHHHHHhCcc
Confidence 5677777888999999999999999 7899999999999999974
No 73
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=73.49 E-value=2.3e+02 Score=34.77 Aligned_cols=132 Identities=10% Similarity=0.045 Sum_probs=72.6
Q ss_pred CHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHHHHHcCCeEEeecCCCCC
Q 005722 215 NISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRFLIMKNKVRMICDCLAPP 294 (681)
Q Consensus 215 ~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~Ly~~n~vR~I~Dv~~~p 294 (681)
..+..++.+.+.+.+++|.|++.++-|+.++...+... -|.. |..+.+...+.+-..-. .. ..
T Consensus 293 ~~~~~~~~~l~~i~~~~~~~~~~~~l~~~~~~~~~~~~---------~~~~-~~~~~~~~~~~~~~~~~------~~-~~ 355 (828)
T PRK13837 293 ELEASIEAALGILAKFFDADSAALALVDVGGRARIWTF---------PGLT-PDPVWPDRLRALASTVK------AA-ER 355 (828)
T ss_pred hhHHHHHHHHHHHHHHhCCCeeEEEEEcCCCCeeeccC---------CccC-CCCCchHHHHHHHHHHh------cc-CC
Confidence 35689999999999999999999999988765433221 1211 23334433333211100 00 00
Q ss_pred ceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCC-CCh
Q 005722 295 VKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRF-VPF 373 (681)
Q Consensus 295 v~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~-v~~ 373 (681)
..+.. .+...+....++...+....+.+|+... +++.|++.+....+.. +..
T Consensus 356 ~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~g~l~~~~~~~~~~~~~ 408 (828)
T PRK13837 356 DVVFV--------------DRNGPVRKRSCLTRRGPALWACLAFKSG-------------DRIVALLGLGRQRYGLRPPA 408 (828)
T ss_pred ceEEe--------------ecccchhhhcccccCCcceEEEEEeccC-------------CceEEEEEecccccCCCCCh
Confidence 00000 0111222333444567888899999876 8999999987765332 223
Q ss_pred hHHHHHHHHHHHHHHHH
Q 005722 374 PLRYACEFLIQVFGVQV 390 (681)
Q Consensus 374 ~~R~a~e~l~q~~s~ql 390 (681)
......+.++..++..+
T Consensus 409 ~~~~~l~~~~~~~~~~~ 425 (828)
T PRK13837 409 GELQLLELALDCLAHAI 425 (828)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 33344444444444433
No 74
>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=73.32 E-value=3.1 Score=35.67 Aligned_cols=51 Identities=20% Similarity=0.344 Sum_probs=37.7
Q ss_pred eEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchHH----HHHHHHhc
Q 005722 82 CMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGA----AALQKAAN 143 (681)
Q Consensus 82 ~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~----~~l~~~l~ 143 (681)
+++++|.+ ++|+.+.....+++|.++++ ++|+++.+++++... ..+++++.
T Consensus 7 ~i~v~D~~-~~i~~~N~~~~~~~~~~~~~----------~~G~~~~~~~~~~~~~~~~~~~~~~~~ 61 (110)
T PF08448_consen 7 GIFVIDPD-GRIVYANQAAAELFGVSPEE----------LIGRSLFDLLPPEDREEFQAALRRALA 61 (110)
T ss_dssp EEEEEETT-SBEEEE-HHHHHHHTSTHHH----------HTTSBHHHHSCCGCHHHHHHHHHHHHH
T ss_pred eeEEECCC-CEEEEEHHHHHHHhCCCHHH----------HhhccchhccccchhhhhHHHHHHhhc
Confidence 45667884 89999999999999998754 689999999987543 34444444
No 75
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=72.99 E-value=6.5 Score=43.68 Aligned_cols=68 Identities=19% Similarity=0.143 Sum_probs=60.8
Q ss_pred HHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHccc
Q 005722 610 TNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFLAI 679 (681)
Q Consensus 610 ~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~G~ 679 (681)
.+++.+++++.|.-|-.+|.++++.|.|.. +++|-.++.. +|+++...=+|.+.+.+...+..+..|.
T Consensus 289 ~~e~naif~~lP~Ditfvdk~diV~ffs~~-~rif~rt~sv-iGr~v~~chpPksv~iv~ki~~~fksG~ 356 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKNDIVRFFSGG-ERIFPRTPSV-IGRRVQLCHPPKSVHIVEKILKDFKSGE 356 (409)
T ss_pred HHHHHHHHhhCCCceEEecccceEEecCCc-ceecccChHh-hCCcccCCCCCchHHHHHHHHHHhhcCC
Confidence 367889999999888889999999999998 9999887665 9999998989999999999999987764
No 76
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=67.57 E-value=10 Score=33.45 Aligned_cols=48 Identities=19% Similarity=0.348 Sum_probs=32.4
Q ss_pred eEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchHHHHHHHH
Q 005722 82 CMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKA 141 (681)
Q Consensus 82 ~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~~~l~~~ 141 (681)
.++++|.+ ++|..++.++..++++.+. .+|+++.++..+.....+.+.
T Consensus 11 ~i~~vD~~-~~I~~~n~~a~~~f~~~~~-----------~iGr~l~~~~~~~~~~~l~~~ 58 (106)
T PF13596_consen 11 GIIFVDRN-LRIRYFNPAAARLFNLSPS-----------DIGRPLFDIHPPLSYPNLKKI 58 (106)
T ss_dssp EEEEEETT-SBEEEE-SCGC-SS---GG-----------GTTSBCCCSS-HHHHHHHHHH
T ss_pred CEEEEcCC-CeEEEeChhHhhhcCCChH-----------HCCCCHHHcCCccchHHHHHH
Confidence 46788985 8899999999999998764 479999999877555555443
No 77
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=67.10 E-value=1.3e+02 Score=30.85 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=29.9
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCC
Q 005722 203 KAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEH 246 (681)
Q Consensus 203 ~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~ 246 (681)
++.-+|-. +.+++++++.+...+++..+.|-|-+--|++++.
T Consensus 82 ~l~l~LL~--a~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~ 123 (225)
T PF04340_consen 82 RLVLALLA--ARSLQELLQALDDGLREDFDVDAVRLRLFDDDAA 123 (225)
T ss_dssp HHHHHHHC----SHHHHHHHHHHHHHHTS--SEEEEEEE-SS--
T ss_pred HHHHHHhc--CCCHHHHHHHHHHHHHHhcCCCeEEEEeeccccc
Confidence 34445555 5699999999999999999999999999997665
No 78
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=64.63 E-value=6.6 Score=43.60 Aligned_cols=51 Identities=14% Similarity=0.089 Sum_probs=43.8
Q ss_pred cEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHH
Q 005722 623 PILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLS 673 (681)
Q Consensus 623 ~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~ 673 (681)
-+|....|=.++|...++.+|+||++.+++||.++.+|+.-|...+..+=.
T Consensus 227 FmfraslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~ 277 (598)
T KOG3559|consen 227 FMFRASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHH 277 (598)
T ss_pred EEEEeecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHH
Confidence 567778889999999999999999999999999999999888775554433
No 79
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=62.77 E-value=8.7 Score=46.42 Aligned_cols=54 Identities=17% Similarity=0.246 Sum_probs=46.8
Q ss_pred EEEEc--CCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHHHHHHc
Q 005722 624 ILAVD--ASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNMLSSAFL 677 (681)
Q Consensus 624 I~~vD--~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l~~al~ 677 (681)
||++- ..+.|.-+..++..++||-+.++||+++..+||++|+..+...-..+++
T Consensus 332 iFtT~HTptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q 387 (1114)
T KOG3753|consen 332 IFTTTHTPTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQ 387 (1114)
T ss_pred eeEeccCCcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHH
Confidence 66654 6788999999999999999999999999999999999987777666653
No 80
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=59.99 E-value=1.9e+02 Score=28.75 Aligned_cols=114 Identities=20% Similarity=0.194 Sum_probs=75.2
Q ss_pred HHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHH---HHHHHHcCCeEEeecCCC
Q 005722 216 ISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQA---SRFLIMKNKVRMICDCLA 292 (681)
Q Consensus 216 l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~q---aR~Ly~~n~vR~I~Dv~~ 292 (681)
+..+-++.+---..+..+|=|=.|.++ +++.| +.||-|. -+=.+||-- ...--.+|++-.|.||++
T Consensus 34 ianlan~sall~~~l~~~nW~GFYl~~---~~~Lv-------LgPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~ 102 (163)
T COG1956 34 IANLANASALLKERLPDVNWVGFYLLE---GDELV-------LGPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHA 102 (163)
T ss_pred HHHHHHHHHHHHhhccCCceEEEEEec---CCeEE-------EecccCC-cceEEeccCcchhHHHHhcCCeEEeccccc
Confidence 444444444444445559999999998 66666 5689997 333477721 233456789999999997
Q ss_pred CCceeecCCCCCCCcccccccccCCChHHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEeecCCCCCCC
Q 005722 293 PPVKVIQDKKLDQPLSLCGSTLRAPHGCHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCHHTSPRFVP 372 (681)
Q Consensus 293 ~pv~lv~~~~~~~pldLs~s~LRsvsp~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cHh~spr~v~ 372 (681)
-|=-|--++ -++|-+++||+.+ |++-|.|=.-..+|-+.+
T Consensus 103 ~~ghiaCD~---------------------------as~SEIVvPi~~~-------------g~~iGvlDiDS~~~~~Fd 142 (163)
T COG1956 103 FPGHIACDA---------------------------ASNSEIVVPIFKD-------------GKLIGVLDIDSPTPGRFD 142 (163)
T ss_pred CCCcccccc---------------------------ccCceEEEEEEEC-------------CEEEEEEecCCCCcccCC
Confidence 542221111 2578899999987 899999998888876666
Q ss_pred hhHHHHHH
Q 005722 373 FPLRYACE 380 (681)
Q Consensus 373 ~~~R~a~e 380 (681)
.+-+.-.+
T Consensus 143 ~~D~~~Le 150 (163)
T COG1956 143 EEDEAGLE 150 (163)
T ss_pred HHHHHHHH
Confidence 55443333
No 81
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=57.12 E-value=20 Score=44.60 Aligned_cols=50 Identities=14% Similarity=0.066 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCccEEEEc-CCCceeeecHHhHHhcCCChhh
Q 005722 601 EKIDELRIITNEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGLTVDQ 650 (681)
Q Consensus 601 ~~~~el~~~~~el~~Lie~s~d~I~~vD-~~G~I~~~N~a~~~l~G~~~~E 650 (681)
+...++.+.....+.+++++|++|+++| .+|.+.+.|..+..++|+...+
T Consensus 324 ~~~~~L~e~e~~~r~iv~~~p~gi~i~~~~~g~~~~~N~~a~~~~~l~~~~ 374 (924)
T PRK10841 324 SNALRLEEHEQFNRKIVASAPVGICILRTSDGTNILSNELAHNYLNMLTHE 374 (924)
T ss_pred HHHHHHHHHHHHHHHHHHhCCccEEEEEcCCCcEEEehHHHHHHhccCChh
Confidence 3445677777788999999999999997 7999999999999999985443
No 82
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=45.12 E-value=27 Score=36.08 Aligned_cols=46 Identities=11% Similarity=0.024 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCccc
Q 005722 610 TNEMVRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALV 657 (681)
Q Consensus 610 ~~el~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~ 657 (681)
.+.+..+++.++-|+++-|.+|.+.+.|.++.++++-.-. .|..|.
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~g~fi~~N~~F~~~f~~~~~--s~~~~~ 63 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNESGKFIFYNTLFLKEFLGQLQ--SKEWWF 63 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCCCCeeecchHHHHHHHhcCC--cchhhh
Confidence 3468889999999999999999999999999999976544 455553
No 83
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=43.40 E-value=1.2e+02 Score=33.35 Aligned_cols=91 Identities=10% Similarity=0.128 Sum_probs=57.9
Q ss_pred EEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCc--hHHHHHHHHhccCCCccCCceeeeccCC
Q 005722 83 MIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTS--SGAAALQKAANFGEVNLLNPILIHCKTS 160 (681)
Q Consensus 83 LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~--~~~~~l~~~l~~~~~~~~~p~~~~~~~~ 160 (681)
.|.+|. ++.|.++-.-++.+||.+.. .+.|+++.++|+. .....+++....+.....+.+.+.....
T Consensus 20 Vl~vd~-~~~i~yaN~aAe~~~~~Sa~----------~L~~~~l~~l~~~gs~ll~ll~q~~~~~~~~~~~~v~l~~~g~ 88 (363)
T COG3852 20 VLLVDD-ELAIHYANPAAEQLLAVSAR----------RLAGTRLSELLPFGSLLLSLLDQVLERGQPVTEYEVTLVILGR 88 (363)
T ss_pred eEEEcC-CCcEEecCHHHHHHHHHHHH----------HHhcCChHHHcCCCcHHHHHHHHHHHhcCCcccceeeeeecCc
Confidence 456777 57799999999999998653 2578899888764 4456666655433332223344431222
Q ss_pred CceEEEEEEee---CCeEEEEeccCCC
Q 005722 161 GKPFYAILHRI---DVGLVIDLEPVNP 184 (681)
Q Consensus 161 ~~~f~~~~Hr~---~~~lviElEp~~~ 184 (681)
.+.+++.+-+. +|.+++||-|...
T Consensus 89 ~~~v~~~v~~v~~~~G~vlle~~~~~~ 115 (363)
T COG3852 89 SHIVDLTVAPVPEEPGSVLLEFHPRDM 115 (363)
T ss_pred cceEEEEEeeccCCCCeEEEEechhHH
Confidence 34566555543 6789999999854
No 84
>PRK10490 sensor protein KdpD; Provisional
Probab=41.35 E-value=8.1e+02 Score=30.63 Aligned_cols=39 Identities=3% Similarity=-0.136 Sum_probs=29.3
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHhhCCCEEEEEEecCC
Q 005722 203 KAISRLQSLPSGNISLLCDVLVNEVSDLTGYDRVMVYKFHED 244 (681)
Q Consensus 203 ~~i~rl~~~~~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D 244 (681)
++..+|.. +.+.+++++.+.+.++++++++-+ +|-.+++
T Consensus 517 els~~L~~--a~~~~~i~~~~~~~l~~~~~~~~~-l~l~~~~ 555 (895)
T PRK10490 517 EMSKALAV--GLSPEDIAATSEHFLASTFQARSQ-LLLPDDN 555 (895)
T ss_pred HHHHHHHh--CCCHHHHHHHHHHHHHHhhCCCEE-EEEEcCC
Confidence 34556666 568999999999999999997654 5555543
No 85
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=34.90 E-value=24 Score=42.89 Aligned_cols=50 Identities=20% Similarity=0.185 Sum_probs=44.9
Q ss_pred cEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHHHHH
Q 005722 623 PILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVKNML 672 (681)
Q Consensus 623 ~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~~~l 672 (681)
.+++-+.+|+|+|+..-++-++||+.+-+.|.++.|++++.|+......+
T Consensus 194 ~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~vF~sft 243 (1114)
T KOG3753|consen 194 VVAVSFLDGRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGVFYSFT 243 (1114)
T ss_pred EEEEeccCCcEEEeechhhhhccCchhhhccchhhhhcchhhhhhhhhcc
Confidence 56777899999999999999999999999999999999999998665544
No 86
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=34.60 E-value=1.9e+02 Score=30.56 Aligned_cols=41 Identities=12% Similarity=0.263 Sum_probs=32.7
Q ss_pred eEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCch
Q 005722 82 CMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSS 133 (681)
Q Consensus 82 ~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~ 133 (681)
.++++|.+ ++|+.+...+.+++|.++.. .+|+++.+++...
T Consensus 19 gi~~~d~~-~~i~~~N~a~~~~~g~~~~~----------~~g~~~~~~~~~~ 59 (348)
T PRK11073 19 SILLLDDD-LAIHYANPAAQQLLAQSSRK----------LFGTPLPELLSYF 59 (348)
T ss_pred eEEEECCC-CeEeeEcHHHHHHhCCCHHH----------HcCCCHHHHcCcc
Confidence 45667874 89999999999999987643 4788988888653
No 87
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=33.63 E-value=49 Score=27.81 Aligned_cols=24 Identities=33% Similarity=0.670 Sum_probs=18.3
Q ss_pred EEEECCeEEEeccCCCHHHHHHHH
Q 005722 441 ALYYRGKLWLLGVTPTEEQIKDIA 464 (681)
Q Consensus 441 al~~~~~~~~~G~tP~~~~i~~l~ 464 (681)
+++.+|++...|..|+.+++..++
T Consensus 52 alvIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 52 ALVINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EEEETTEEEEESS--HHHHHHHHH
T ss_pred EEEECCEEEEEecCCCHHHHHHHh
Confidence 568899999999999998877654
No 88
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=31.67 E-value=26 Score=42.43 Aligned_cols=27 Identities=41% Similarity=0.645 Sum_probs=21.6
Q ss_pred HhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCchHHHHH
Q 005722 229 DLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIPQASRF 277 (681)
Q Consensus 229 ~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP~qaR~ 277 (681)
.|||++||+| |||||| |.+|--+.-|+
T Consensus 614 NLTgAnRVII--fDPdWN--------------------PStD~QAreRa 640 (923)
T KOG0387|consen 614 NLTGANRVII--FDPDWN--------------------PSTDNQARERA 640 (923)
T ss_pred ccccCceEEE--ECCCCC--------------------CccchHHHHHH
Confidence 6899999999 588887 78887665554
No 89
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=29.53 E-value=75 Score=37.35 Aligned_cols=64 Identities=11% Similarity=0.156 Sum_probs=46.3
Q ss_pred HHHHHHhcC--ccEEEEc----CCCceeeecHHhHHhcCCChhhhhcCccc------ccccCCCHHHHHHHHHHHH
Q 005722 613 MVRLIETAA--VPILAVD----ASGNVNGWNSKAAELTGLTVDQAIGTALV------DLVAGDSVDVVKNMLSSAF 676 (681)
Q Consensus 613 l~~Lie~s~--d~I~~vD----~~G~I~~~N~a~~~l~G~~~~EliGk~l~------~lv~~~~~~~~~~~l~~al 676 (681)
++.+|..+. |.-|+.. .|.-|+|+|..++.|.||...|++-|+.. |+-..+..+++++.++..-
T Consensus 16 LENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~ 91 (971)
T KOG0501|consen 16 LENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYE 91 (971)
T ss_pred HHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhh
Confidence 445555554 5444433 36789999999999999999999999843 5555666777777777653
No 90
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=28.99 E-value=37 Score=30.93 Aligned_cols=52 Identities=23% Similarity=0.402 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHHhhCCCEEEEEEecCCCCeEEEEeecCCCCCCcCCCcCCCCCch
Q 005722 213 SGNISLLCDVLVNEVSDLTGYDRVMVYKFHEDEHGEVVAECRRPDLEPYLGFHYPATDIP 272 (681)
Q Consensus 213 ~~~l~~l~~~~v~evr~ltg~DRVmiYrF~~D~~GeVVAEs~~~~l~s~LGlhfPasDIP 272 (681)
..+....++..++.+++.++.|-|.|- |-+|.+++=+ ++ ..+|.+|...|+.
T Consensus 19 ~~~~~~~lq~~~~~~~~~~~~~~i~v~----D~~g~~l~~s-~~---~~iG~~~~~~~~~ 70 (116)
T PF14827_consen 19 QGDPEAELQALLEQLRKESDIDYIVVT----DRDGIVLAHS-DP---ERIGDRYSDEDVR 70 (116)
T ss_dssp TTGHHSCCCCHHHHHHHHCT-SEEEEE----CTTSBECE-S-SC---CCTTSB-SSCCHC
T ss_pred cCCccHHHHHHHHHHHhhcCCeEEEEE----cCCCCEEEcC-Ch---HHcCCcccCCChh
Confidence 346665568899999999999988874 8899999987 43 3589999876644
No 91
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=27.92 E-value=34 Score=29.38 Aligned_cols=19 Identities=32% Similarity=0.282 Sum_probs=15.7
Q ss_pred cCCchhhhHHhhhccccCC
Q 005722 541 HPRSSFKAFLEVVKQRSLP 559 (681)
Q Consensus 541 ~PR~SFe~w~E~v~~~s~p 559 (681)
.+++||+.|+..|.|+...
T Consensus 37 Lk~~sfk~WRkRv~gr~tK 55 (73)
T PF10985_consen 37 LKPSSFKLWRKRVSGRKTK 55 (73)
T ss_pred cChhHHHHHHHHHhcCCCc
Confidence 3558999999999998754
No 92
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=25.95 E-value=42 Score=39.17 Aligned_cols=56 Identities=13% Similarity=0.170 Sum_probs=49.8
Q ss_pred HHHHHhcCccEEEEcCCCceeeecHHhHHhcCCChhhhhcCcccccccCCCHHHHH
Q 005722 614 VRLIETAAVPILAVDASGNVNGWNSKAAELTGLTVDQAIGTALVDLVAGDSVDVVK 669 (681)
Q Consensus 614 ~~Lie~s~d~I~~vD~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv~~~~~~~~~ 669 (681)
+.+++...++++++|....|..+|..+..+++-....++|+++.++++....+++.
T Consensus 4 ~~~l~~~~~~~~vi~~~~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~ 59 (560)
T COG3829 4 EGILKSILDGPVVIDKNTGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE 59 (560)
T ss_pred hhhhhhcccceEEEEcCCceeeechHHHHhhhcceEEEecccceeeccccCcceee
Confidence 34899999999999999999999999999999999999999999988776666544
No 93
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=25.08 E-value=87 Score=38.75 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHhcCccEEEEc-CCCceeeecHHhHHhcCCChhhhhcCcccccc
Q 005722 608 IITNEMVRLIETAAVPILAVD-ASGNVNGWNSKAAELTGLTVDQAIGTALVDLV 660 (681)
Q Consensus 608 ~~~~el~~Lie~s~d~I~~vD-~~G~I~~~N~a~~~l~G~~~~EliGk~l~~lv 660 (681)
.+.+.....+...|-||+++| .+|.|.-.|+.+.+++| .+ ++|+++.++.
T Consensus 99 ~~~~~~~~~l~~~p~gi~~~~~~~~~i~W~N~~~~~~~~--~~-~~g~~i~~~~ 149 (838)
T PRK14538 99 HVSQIGEEVLNELPIGIVLIDISSKEIQWLNPYANFILK--NP-EINTPLAQIN 149 (838)
T ss_pred HHhHHHHHHHHhCCceEEEEeCCCCEEEEECHHHHHHhC--cc-ccCCcHHHhc
Confidence 445566778999999999999 79999999999999988 23 8999998754
No 94
>PF12860 PAS_7: PAS fold
Probab=24.94 E-value=2.6e+02 Score=24.66 Aligned_cols=40 Identities=20% Similarity=0.355 Sum_probs=28.7
Q ss_pred CceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhc
Q 005722 80 FGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLF 130 (681)
Q Consensus 80 ~G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~ 130 (681)
+|+ +++|++ ++++.+-....+++|++++.+ ..|.++.+++
T Consensus 6 ~Gv-~v~D~~-~rl~~~N~~~~~l~~~~~~~~---------~~G~~~~~l~ 45 (115)
T PF12860_consen 6 QGV-AVFDSD-GRLVFWNQRFRELFGLPPEML---------RPGASFRDLL 45 (115)
T ss_pred ceE-EEEcCC-CeEEeEcHHHHHHhCCCHHHh---------cCCCCHHHHH
Confidence 444 567774 889999999999999987643 2466655554
No 95
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=24.65 E-value=48 Score=31.45 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=21.1
Q ss_pred CCCCCceEEEEecCCceEEEEccChhhh
Q 005722 76 LIQPFGCMIAVDEQNFTVLGYSENAPEM 103 (681)
Q Consensus 76 ~IQp~G~LLa~d~~~~~I~~~SeN~~~~ 103 (681)
-|||||+.+.++..+-=.+|+||=+..+
T Consensus 15 gI~~yGAFV~l~~g~tGLVHISEIa~~f 42 (129)
T COG1098 15 GITPYGAFVELEGGKTGLVHISEIADGF 42 (129)
T ss_pred eeEecceEEEecCCCcceEEehHhhhhh
Confidence 5999999999998544478999743333
No 96
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=24.32 E-value=94 Score=36.21 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=39.2
Q ss_pred CCCC-CceEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchHHHHHHHHh
Q 005722 76 LIQP-FGCMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAAALQKAA 142 (681)
Q Consensus 76 ~IQp-~G~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~~~l~~~l 142 (681)
+.|. .|++|||..+ +.|-.+|+|++++||+--.+ ++-+++-+++-.+--+.+++-|
T Consensus 116 lLqsLnGF~lVvt~e-g~ifyAS~tIedYLGFhQSD----------V~HQsVYdlIHseDR~dfqrQL 172 (712)
T KOG3560|consen 116 LLQSLNGFALVVTAE-GEIFYASATIEDYLGFHQSD----------VMHQSVYDLIHSEDRQDFQRQL 172 (712)
T ss_pred HHHhcCCeEEEEecC-ceEEEehhhHHhhhcccccc----------hhhhhHHHHhhhhhHHHHHHHH
Confidence 3555 6999999775 78999999999999985433 3555666665555445555544
No 97
>PRK10234 DNA-binding transcriptional activator GutM; Provisional
Probab=23.91 E-value=66 Score=30.20 Aligned_cols=55 Identities=27% Similarity=0.237 Sum_probs=37.6
Q ss_pred hcCccEEEEcCCCceeeecHHhHHhcCC-------ChhhhhcCcccccccCCCH---HHHHHHHHHHHc
Q 005722 619 TAAVPILAVDASGNVNGWNSKAAELTGL-------TVDQAIGTALVDLVAGDSV---DVVKNMLSSAFL 677 (681)
Q Consensus 619 ~s~d~I~~vD~~G~I~~~N~a~~~l~G~-------~~~EliGk~l~~lv~~~~~---~~~~~~l~~al~ 677 (681)
.....++++|.+|+|+.. ..|-|+ +.+++.|+++.++-++.-. ..+++++..|+.
T Consensus 51 ~g~IvllaiD~~~~I~d~----~~M~G~TVFARfk~~~~~~G~~i~~l~~~~~~~~~~~~q~Al~~A~~ 115 (118)
T PRK10234 51 PRVVVALALDEQQRVVDT----LFMKGLTVFARPQKIPALTGLHLGDLQPDVIFPHDPLSQNALSLALK 115 (118)
T ss_pred CCeEEEEEECCCCcEEee----EEEccEEEEecccchhhhcCCcHHHcCHHhhccCCHHHHHHHHHHhc
Confidence 344567899999999864 455555 3478999999877652221 256777777764
No 98
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=23.82 E-value=5.1e+02 Score=29.13 Aligned_cols=40 Identities=25% Similarity=0.310 Sum_probs=32.3
Q ss_pred eEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCc
Q 005722 82 CMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTS 132 (681)
Q Consensus 82 ~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~ 132 (681)
+++++|.+ ++|+.++..+..++|..+++ .+|+++.+++.+
T Consensus 274 ~i~~~d~~-g~i~~~N~~~~~l~g~~~~~----------~~g~~~~~~~~~ 313 (607)
T PRK11360 274 GVIAIDRQ-GKITTMNPAAEVITGLQRHE----------LVGKPYSELFPP 313 (607)
T ss_pred eEEEEcCC-CCEEEECHHHHHHhCCChHH----------hcCCcHHHHcCC
Confidence 35678874 78999999999999998754 478888888874
No 99
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=23.47 E-value=2.3e+02 Score=28.94 Aligned_cols=79 Identities=14% Similarity=0.203 Sum_probs=50.1
Q ss_pred hhhhhccCCeEEEEECCeEEEe-ccCCC--HHHHHHHHHHHHHhcCCCe-eeeeccccccCCCCccc---cccccccEEE
Q 005722 430 NVMDLVKCDGAALYYRGKLWLL-GVTPT--EEQIKDIAEWLLEYHRGST-GLSTDSLVEAGYPGALA---LGDAVCGIAA 502 (681)
Q Consensus 430 ~ll~L~~adGaal~~~~~~~~~-G~tP~--~~~i~~l~~wl~~~~~~~~-~~~td~L~~~~~p~a~~---~~~~~~G~la 502 (681)
.|+.--.|.+++||++|++..- |...+ ..... .|++....+.. ++-.| +. -||+-.+ +++-..|+++
T Consensus 87 ~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g---~i~~~~~~~~~~~yL~n-l~--lyPGr~Ef~~lP~ntq~Vlv 160 (195)
T PF11152_consen 87 ALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPG---PICQRAMESGKLIYLVN-LK--LYPGRVEFDYLPENTQSVLV 160 (195)
T ss_pred HHHhhCCceEEEEEECCEEEEEeeccCCCCCcchH---HHHHHHHhcCCceeccc-cc--cCCCchhhhhcCCCCcEEEE
Confidence 4777789999999999998764 65442 33333 34443332222 22222 22 3777765 4567889999
Q ss_pred EEeCCCcEEEEe
Q 005722 503 VKITSKDFLFWF 514 (681)
Q Consensus 503 v~i~~~~~l~wF 514 (681)
.|+..+.+++.+
T Consensus 161 qP~g~~G~lvlg 172 (195)
T PF11152_consen 161 QPLGQNGVLVLG 172 (195)
T ss_pred EEcCCCeEEEEe
Confidence 999888777653
No 100
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=23.34 E-value=5.6e+02 Score=23.17 Aligned_cols=32 Identities=6% Similarity=0.073 Sum_probs=24.7
Q ss_pred HHHHHHHhcCCeeEEEEEEEecCccccccccccccCceeEEEEee
Q 005722 320 CHARYMENMGSIASLVMSVTINEAEDELDNDQEQGRKLWGLVVCH 364 (681)
Q Consensus 320 ~H~qYL~NMGV~ASlsvsIiv~~~~~~~~~~~~~~~kLWGLi~cH 364 (681)
--.+..+.+|+++.+++|+--. +|.. |+|...
T Consensus 89 ~~~~~a~~~Gl~~G~~~p~~~~------------~g~~-~~~s~~ 120 (149)
T PF03472_consen 89 RFFDEARDFGLRSGVSVPLHGP------------DGRF-GALSFA 120 (149)
T ss_dssp HHHHHHHHTTTSEEEEEEEEEC------------CGCE-EEEEEE
T ss_pred HHHHHHHHcCCCceEEEEeEcC------------CCCE-EEEEEE
Confidence 4566678999999999999854 2666 888663
No 101
>PF06923 GutM: Glucitol operon activator protein (GutM); InterPro: IPR009693 This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system, which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes [].
Probab=22.03 E-value=36 Score=31.36 Aligned_cols=38 Identities=21% Similarity=0.377 Sum_probs=29.9
Q ss_pred hcCccEEEEcCCCceeeecHHhHHhcCC-------ChhhhhcCcccccc
Q 005722 619 TAAVPILAVDASGNVNGWNSKAAELTGL-------TVDQAIGTALVDLV 660 (681)
Q Consensus 619 ~s~d~I~~vD~~G~I~~~N~a~~~l~G~-------~~~EliGk~l~~lv 660 (681)
.....++++|.+|+|+.. +.|-|. +.+++.|+++.++-
T Consensus 50 ~g~Ivlla~D~~~~I~~~----~~M~G~TVFArFk~~~~l~G~~l~~i~ 94 (109)
T PF06923_consen 50 PGVIVLLAVDEDGRIVDA----EIMKGITVFARFKPLPELEGKNLDEID 94 (109)
T ss_pred CCeEEEEEECCCCcEEEE----EEEeceEEEEeeEehHhhCCCCHHHhC
Confidence 445578999999999874 666676 45889999998876
No 102
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=21.03 E-value=78 Score=28.79 Aligned_cols=37 Identities=8% Similarity=0.156 Sum_probs=29.7
Q ss_pred CceEEEEccC-hhhhhCCCCCCCCCccccchhccCCchhhhcCchHHH
Q 005722 90 NFTVLGYSEN-APEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSGAA 136 (681)
Q Consensus 90 ~~~I~~~SeN-~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~~~ 136 (681)
+++|+.+..+ +..+||..|++ ++|+.+-+++-+.-..
T Consensus 11 dgki~~~d~~~v~~~lgy~~~e----------LvG~s~y~~~H~~D~~ 48 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEE----------LVGRSIYDFVHPDDLQ 48 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHH----------HTTSBGGGGBSCCTHH
T ss_pred CcEEEEEcCccChhhcCCCcHH----------HcCCchHHhCCHhhhh
Confidence 6899999999 79999998865 6899998888765444
No 103
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=20.94 E-value=56 Score=28.00 Aligned_cols=18 Identities=33% Similarity=0.333 Sum_probs=15.1
Q ss_pred CCchhhhHHhhhccccCC
Q 005722 542 PRSSFKAFLEVVKQRSLP 559 (681)
Q Consensus 542 PR~SFe~w~E~v~~~s~p 559 (681)
+.+||+.|+..|.|+...
T Consensus 39 k~~Sfk~WRkRV~gr~tK 56 (72)
T TIGR03643 39 KPSSFKLWRKRVSGRKTK 56 (72)
T ss_pred ChhHHHHHHHHHhcCCCc
Confidence 458999999999998653
No 104
>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=20.76 E-value=1.5e+02 Score=23.09 Aligned_cols=42 Identities=17% Similarity=0.263 Sum_probs=29.9
Q ss_pred eEEEEecCCceEEEEccChhhhhCCCCCCCCCccccchhccCCchhhhcCchH
Q 005722 82 CMIAVDEQNFTVLGYSENAPEMLDLAPHAVPNIEQQDALTLGIDVRTLFTSSG 134 (681)
Q Consensus 82 ~LLa~d~~~~~I~~~SeN~~~~Lg~~~~~~~~~~~~~~~~lG~~l~~~~~~~~ 134 (681)
.++++|.+ ++|+.++..+.+++|.++.. ++|..+..++.+..
T Consensus 15 ~~~~~d~~-~~i~~~n~~~~~~~g~~~~~----------~~~~~~~~~~~~~~ 56 (124)
T TIGR00229 15 AIIVIDLE-GNILYVNPAFEEIFGYSAEE----------LIGRNVLELIPEED 56 (124)
T ss_pred eEEEEcCC-CcEEEEchHHHHHhCCChHH----------hcCcchhhhcChhh
Confidence 35567764 77999999999999987643 35777666665443
Done!