Query 020287
Match_columns 328
No_of_seqs 226 out of 2363
Neff 10.8
Searched_HMMs 46136
Date Fri Mar 29 08:32:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09776 putative diguanylate 99.8 4.5E-20 9.7E-25 183.7 17.4 284 15-325 280-628 (1092)
2 PRK13560 hypothetical protein; 99.8 1.9E-19 4.1E-24 174.0 20.7 187 6-293 193-382 (807)
3 TIGR02040 PpsR-CrtJ transcript 99.8 2.9E-19 6.2E-24 160.6 18.4 201 15-325 130-340 (442)
4 TIGR02040 PpsR-CrtJ transcript 99.8 9.5E-19 2.1E-23 157.3 11.8 199 24-312 2-202 (442)
5 TIGR02938 nifL_nitrog nitrogen 99.8 3E-18 6.4E-23 156.5 11.5 179 18-296 4-182 (494)
6 PRK13560 hypothetical protein; 99.8 2.7E-17 5.9E-22 159.1 17.8 206 18-324 68-291 (807)
7 PRK11359 cyclic-di-GMP phospho 99.7 3.8E-16 8.3E-21 150.9 18.8 201 18-324 12-224 (799)
8 PF13426 PAS_9: PAS domain; PD 99.7 5.2E-16 1.1E-20 110.5 14.1 104 28-135 1-104 (104)
9 PF08448 PAS_4: PAS fold; Int 99.6 4E-15 8.7E-20 107.1 11.5 110 24-138 1-110 (110)
10 PF00989 PAS: PAS fold; Inter 99.6 2.4E-14 5.1E-19 103.5 13.5 112 18-133 1-113 (113)
11 PRK11091 aerobic respiration c 99.5 2.5E-13 5.4E-18 130.8 14.3 122 15-140 152-273 (779)
12 PRK13559 hypothetical protein; 99.5 1.4E-12 3.1E-17 114.4 15.6 124 15-139 40-163 (361)
13 PRK13557 histidine kinase; Pro 99.4 6.1E-12 1.3E-16 116.4 14.6 127 15-142 27-153 (540)
14 PRK13558 bacterio-opsin activa 99.3 8.6E-11 1.9E-15 111.4 14.9 124 19-143 149-272 (665)
15 PF00989 PAS: PAS fold; Inter 99.2 2.6E-11 5.7E-16 87.4 5.5 81 242-325 2-90 (113)
16 PF13426 PAS_9: PAS domain; PD 99.2 4.7E-11 1E-15 84.7 6.3 72 251-325 1-79 (104)
17 PRK10060 RNase II stability mo 99.2 4.3E-10 9.4E-15 106.0 14.4 136 16-156 109-252 (663)
18 TIGR00229 sensory_box PAS doma 99.2 8.3E-10 1.8E-14 78.7 12.3 118 18-140 3-121 (124)
19 PF08447 PAS_3: PAS fold; Int 99.1 1E-09 2.2E-14 75.9 9.6 86 43-130 1-91 (91)
20 PRK09776 putative diguanylate 99.1 1.7E-09 3.6E-14 108.5 14.3 133 7-144 526-662 (1092)
21 PRK11359 cyclic-di-GMP phospho 99.0 2.3E-09 4.9E-14 104.0 12.9 120 17-140 135-255 (799)
22 PF13596 PAS_10: PAS domain; P 99.0 6.7E-09 1.5E-13 74.0 10.2 106 20-134 1-106 (106)
23 cd00130 PAS PAS domain; PAS mo 98.9 6.5E-08 1.4E-12 65.6 13.9 102 28-133 2-103 (103)
24 PF12860 PAS_7: PAS fold 98.9 2.8E-08 6E-13 71.9 9.9 104 24-140 1-114 (115)
25 PRK13557 histidine kinase; Pro 98.8 1.2E-08 2.5E-13 94.6 7.9 84 242-325 31-121 (540)
26 PRK11360 sensory histidine kin 98.8 1.2E-07 2.7E-12 88.8 14.0 121 16-143 260-381 (607)
27 COG3829 RocR Transcriptional r 98.8 4.6E-08 1E-12 86.0 9.7 163 21-293 4-166 (560)
28 TIGR02966 phoR_proteo phosphat 98.7 8.9E-08 1.9E-12 82.8 10.7 108 15-139 3-110 (333)
29 PF08448 PAS_4: PAS fold; Int 98.7 1.4E-08 3.1E-13 72.5 4.5 65 247-314 1-65 (110)
30 PRK11073 glnL nitrogen regulat 98.7 1.3E-07 2.7E-12 82.7 10.2 111 18-139 7-117 (348)
31 KOG0501 K+-channel KCNQ [Inorg 98.7 1.5E-07 3.3E-12 82.6 10.1 122 17-139 13-139 (971)
32 PRK13559 hypothetical protein; 98.7 7.1E-08 1.5E-12 84.7 8.2 83 243-325 45-134 (361)
33 PRK10060 RNase II stability mo 98.7 2.9E-08 6.3E-13 93.8 5.7 80 243-325 113-200 (663)
34 PF14598 PAS_11: PAS domain; P 98.6 1.7E-06 3.7E-11 61.7 12.9 101 33-136 7-109 (111)
35 COG3829 RocR Transcriptional r 98.5 3.3E-06 7.2E-11 74.6 14.3 112 15-139 114-225 (560)
36 PF13188 PAS_8: PAS domain; PD 98.5 1.2E-07 2.6E-12 60.6 4.0 42 242-290 2-43 (64)
37 COG5002 VicK Signal transducti 98.5 2.1E-06 4.5E-11 71.3 11.8 114 15-139 108-221 (459)
38 PRK11006 phoR phosphate regulo 98.4 1.7E-06 3.8E-11 77.8 9.1 106 15-139 95-200 (430)
39 PRK10820 DNA-binding transcrip 98.3 4.8E-06 1E-10 76.2 10.6 109 15-137 77-189 (520)
40 TIGR02938 nifL_nitrog nitrogen 98.3 9.6E-07 2.1E-11 80.7 5.9 82 241-325 4-92 (494)
41 PF08447 PAS_3: PAS fold; Int 98.3 5E-07 1.1E-11 62.2 2.3 61 266-327 1-73 (91)
42 KOG3558 Hypoxia-inducible fact 98.3 2E-05 4.3E-10 71.0 12.6 70 254-324 275-351 (768)
43 PRK11091 aerobic respiration c 98.3 1.3E-06 2.9E-11 84.6 5.9 81 241-324 155-242 (779)
44 PRK11388 DNA-binding transcrip 98.3 1E-05 2.3E-10 76.3 11.7 49 243-294 205-253 (638)
45 TIGR02966 phoR_proteo phosphat 98.2 1.1E-06 2.5E-11 75.8 4.4 52 241-295 6-57 (333)
46 TIGR00229 sensory_box PAS doma 98.2 5.4E-06 1.2E-10 58.5 7.1 66 242-310 4-69 (124)
47 PRK13558 bacterio-opsin activa 98.2 3.7E-06 8E-11 80.1 7.6 83 243-325 150-239 (665)
48 PF13188 PAS_8: PAS domain; PD 98.2 4.5E-06 9.6E-11 53.2 5.4 42 18-66 1-42 (64)
49 PRK11073 glnL nitrogen regulat 98.1 4.8E-06 1E-10 72.7 6.0 77 243-324 9-92 (348)
50 PRK11086 sensory histidine kin 98.1 3.2E-05 6.9E-10 71.8 11.5 108 16-139 219-329 (542)
51 COG2202 AtoS FOG: PAS/PAC doma 98.1 0.00026 5.7E-09 55.2 14.5 118 17-139 111-231 (232)
52 PF14598 PAS_11: PAS domain; P 98.0 8.7E-06 1.9E-10 58.1 4.4 63 263-325 11-82 (111)
53 cd00130 PAS PAS domain; PAS mo 97.9 3.9E-05 8.5E-10 51.3 6.2 57 251-310 2-58 (103)
54 KOG1229 3'5'-cyclic nucleotide 97.8 9.8E-06 2.1E-10 69.1 2.2 104 21-128 160-264 (775)
55 smart00091 PAS PAS domain. PAS 97.8 6.3E-05 1.4E-09 46.0 5.0 60 243-305 3-62 (67)
56 PRK11006 phoR phosphate regulo 97.7 2.6E-05 5.7E-10 70.2 3.1 50 242-294 99-148 (430)
57 PF12860 PAS_7: PAS fold 97.7 2.3E-05 5.1E-10 56.5 2.1 43 247-292 1-44 (115)
58 PRK10820 DNA-binding transcrip 97.7 3E-05 6.5E-10 71.1 3.2 52 242-296 81-132 (520)
59 COG3290 CitA Signal transducti 97.6 0.0003 6.5E-09 62.5 8.9 110 15-139 212-323 (537)
60 PRK09959 hybrid sensory histid 97.6 0.00082 1.8E-08 68.6 13.2 43 15-60 573-615 (1197)
61 PRK11388 DNA-binding transcrip 97.6 0.00068 1.5E-08 64.2 11.4 108 19-138 204-311 (638)
62 COG5000 NtrY Signal transducti 97.6 0.00074 1.6E-08 60.7 10.5 113 15-139 367-480 (712)
63 PF13596 PAS_10: PAS domain; P 97.6 6.1E-05 1.3E-09 53.4 3.1 63 243-309 1-63 (106)
64 TIGR02373 photo_yellow photoac 97.6 0.00023 4.9E-09 50.5 5.7 64 246-312 21-85 (124)
65 COG2461 Uncharacterized conser 97.5 0.00049 1.1E-08 58.4 7.4 113 17-139 289-401 (409)
66 PRK15053 dpiB sensor histidine 97.4 0.0011 2.4E-08 61.7 10.5 106 17-139 221-328 (545)
67 PF08670 MEKHLA: MEKHLA domain 97.3 0.011 2.5E-07 43.9 12.2 111 19-132 33-144 (148)
68 KOG3559 Transcriptional regula 97.3 0.0035 7.5E-08 53.3 10.2 54 21-77 82-135 (598)
69 COG2202 AtoS FOG: PAS/PAC doma 97.2 0.015 3.2E-07 45.0 13.5 49 243-294 114-162 (232)
70 PF08670 MEKHLA: MEKHLA domain 97.2 0.00088 1.9E-08 49.7 5.7 81 243-324 33-120 (148)
71 KOG3558 Hypoxia-inducible fact 97.2 0.00067 1.4E-08 61.5 5.6 91 41-131 284-374 (768)
72 COG3852 NtrB Signal transducti 97.1 0.0048 1E-07 51.0 9.5 108 21-138 10-118 (363)
73 smart00091 PAS PAS domain. PAS 97.1 0.0027 5.9E-08 38.3 6.3 53 19-74 2-54 (67)
74 PRK15053 dpiB sensor histidine 97.0 0.0064 1.4E-07 56.6 10.5 50 243-295 224-275 (545)
75 KOG1229 3'5'-cyclic nucleotide 97.0 0.0004 8.8E-09 59.6 2.0 68 243-313 159-227 (775)
76 PRK11360 sensory histidine kin 96.9 0.0024 5.1E-08 60.0 7.0 51 243-296 264-314 (607)
77 COG3290 CitA Signal transducti 96.9 0.0043 9.4E-08 55.4 7.8 51 243-296 217-269 (537)
78 TIGR02373 photo_yellow photoac 96.7 0.024 5.3E-07 40.4 9.0 68 20-90 18-86 (124)
79 KOG0501 K+-channel KCNQ [Inorg 96.3 0.0039 8.5E-08 55.7 3.5 74 252-325 28-110 (971)
80 KOG3561 Aryl-hydrocarbon recep 96.2 0.0023 4.9E-08 60.3 1.6 57 246-305 100-156 (803)
81 COG3283 TyrR Transcriptional r 96.1 0.0086 1.9E-07 50.8 4.5 55 242-299 81-135 (511)
82 COG5002 VicK Signal transducti 96.1 0.0083 1.8E-07 50.6 4.1 59 242-303 112-170 (459)
83 PRK11086 sensory histidine kin 95.9 0.012 2.5E-07 54.8 4.9 51 241-294 221-274 (542)
84 smart00086 PAC Motif C-termina 95.9 0.087 1.9E-06 27.8 7.0 41 95-136 3-43 (43)
85 COG3283 TyrR Transcriptional r 95.8 0.028 6.2E-07 47.8 6.3 55 16-73 78-132 (511)
86 COG3852 NtrB Signal transducti 95.4 0.023 4.9E-07 47.2 4.3 65 245-314 11-75 (363)
87 KOG3560 Aryl-hydrocarbon recep 95.3 0.084 1.8E-06 47.1 7.4 93 41-135 293-385 (712)
88 PF07310 PAS_5: PAS domain; I 94.4 0.75 1.6E-05 34.1 9.9 86 41-130 51-136 (137)
89 COG5000 NtrY Signal transducti 91.8 0.17 3.7E-06 46.2 3.3 48 243-293 372-419 (712)
90 KOG3753 Circadian clock protei 91.7 1.1 2.3E-05 42.9 8.3 56 254-310 332-387 (1114)
91 PRK10841 hybrid sensory kinase 91.2 3.3 7.2E-05 41.5 11.9 42 15-58 331-372 (924)
92 PF08446 PAS_2: PAS fold; Int 91.0 0.19 4.1E-06 35.7 2.4 44 252-297 15-62 (110)
93 PRK09959 hybrid sensory histid 90.1 0.47 1E-05 48.9 5.2 39 243-284 578-616 (1197)
94 KOG3560 Aryl-hydrocarbon recep 89.1 0.43 9.3E-06 42.8 3.4 60 246-308 116-175 (712)
95 COG3284 AcoR Transcriptional a 88.9 11 0.00023 35.3 12.0 40 250-292 231-271 (606)
96 KOG3561 Aryl-hydrocarbon recep 86.2 0.5 1.1E-05 45.2 2.3 48 262-309 380-427 (803)
97 KOG3559 Transcriptional regula 84.5 2.8 6E-05 36.4 5.6 84 31-117 228-311 (598)
98 PF08446 PAS_2: PAS fold; Int 79.2 2.9 6.3E-05 29.6 3.5 41 31-73 18-61 (110)
99 KOG3753 Circadian clock protei 75.8 12 0.00025 36.3 7.1 80 31-111 332-414 (1114)
100 PRK13719 conjugal transfer tra 75.8 5.9 0.00013 31.7 4.6 38 17-57 18-55 (217)
101 PRK13719 conjugal transfer tra 73.0 5.5 0.00012 31.9 3.8 37 241-280 19-55 (217)
102 PRK10618 phosphotransfer inter 69.7 11 0.00024 37.6 5.9 40 15-56 340-379 (894)
103 PRK10618 phosphotransfer inter 65.8 7.7 0.00017 38.7 4.0 38 241-280 343-380 (894)
104 COG2461 Uncharacterized conser 65.5 11 0.00024 32.9 4.3 66 241-312 290-355 (409)
105 PF08348 PAS_6: YheO-like PAS 63.2 21 0.00045 25.6 4.8 45 92-139 68-112 (118)
106 PRK14538 putative bifunctional 61.3 11 0.00023 37.2 3.9 44 243-292 104-148 (838)
107 COG3887 Predicted signaling pr 59.6 25 0.00054 32.7 5.6 39 15-56 72-110 (655)
108 PRK14538 putative bifunctional 58.3 21 0.00046 35.2 5.4 46 17-68 101-147 (838)
109 PF11927 DUF3445: Protein of u 56.6 12 0.00026 30.9 3.0 56 243-298 98-153 (249)
110 COG5388 Uncharacterized protei 53.5 1.1E+02 0.0023 24.1 7.3 105 23-133 53-159 (209)
111 PF07310 PAS_5: PAS domain; I 52.5 24 0.00052 26.0 3.8 50 263-315 50-99 (137)
112 PF06785 UPF0242: Uncharacteri 50.4 34 0.00074 29.2 4.6 88 20-115 285-378 (401)
113 COG3887 Predicted signaling pr 47.4 28 0.00062 32.4 4.0 44 241-290 75-118 (655)
114 PF09884 DUF2111: Uncharacteri 46.1 71 0.0015 21.1 4.6 47 82-134 37-83 (84)
115 PF06785 UPF0242: Uncharacteri 45.5 5.8 0.00013 33.6 -0.5 39 252-292 298-336 (401)
116 PF02743 Cache_1: Cache domain 44.8 58 0.0013 21.1 4.5 29 107-136 13-41 (81)
117 PRK10841 hybrid sensory kinase 31.2 70 0.0015 32.3 4.4 39 241-281 334-372 (924)
118 PF12282 H_kinase_N: Signal tr 27.6 2.6E+02 0.0055 20.9 5.9 54 80-138 79-132 (145)
119 COG4251 Bacteriophytochrome (l 21.1 63 0.0014 30.6 1.8 33 262-294 38-70 (750)
No 1
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.84 E-value=4.5e-20 Score=183.74 Aligned_cols=284 Identities=14% Similarity=0.150 Sum_probs=176.8
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcC-CCee
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (328)
..+++++.++++++.+++++|.+ |+++++|+++++++||++++++|++...+.++++.......+......+ ..+.
T Consensus 280 ~~e~r~~~l~e~~~~~i~~~d~d---G~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~ 356 (1092)
T PRK09776 280 ESETRFRNAMEYSAIGMALVGTE---GQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYS 356 (1092)
T ss_pred HHHHHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCcccee
Confidence 56678999999999999999999 9999999999999999999999998777766665554444444444333 3456
Q ss_pred EEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhh
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (328)
.+.+..+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|++++++ +... .....+.
T Consensus 357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l-----------------~~~~--~~~~~~~ 416 (1092)
T PRK09776 357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVN-----------------ERLM--ERITLAN 416 (1092)
T ss_pred eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHH-----------------HHHH--HHHHHHH
Confidence 788888999999999999999998 8899999999999999999984433 1111 1111111
Q ss_pred hhh--hhccccCCC------------CCCcccccccc-------chHHHHHHHhhhhhhhhhhc------cccccCCcee
Q 020287 174 DLD--RVLALDSDD------------TGLEIEDSCEA-------SDLEKRKAATAIDNILSVLT------HYSQLTGRLV 226 (328)
Q Consensus 174 ~~~--~~~~~d~~~------------~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~l~------~~~~~~~~~~ 226 (328)
+.. +.+.+|.+. .|++.++.... ...........+......-. +..+..| ..
T Consensus 417 ~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~ 495 (1092)
T PRK09776 417 EAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VR 495 (1092)
T ss_pred HhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eE
Confidence 111 122233222 33333331110 01111111111111110000 0111111 10
Q ss_pred ee--------------------------eeecCCCCccchhhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCC
Q 020287 227 CG--------------------------KRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (328)
Q Consensus 227 ~~--------------------------~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~ 280 (328)
.. ++.....+....+.++.++++++++|+++|.+ |+++++|+++++++||+
T Consensus 496 w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~ 572 (1092)
T PRK09776 496 HIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWT 572 (1092)
T ss_pred EEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCC
Confidence 00 00001111122245777899999999999999 99999999999999999
Q ss_pred cccccccCcccccCCC--CCHHHHHHHHhhhhcCcC---------cccccceeeec
Q 020287 281 RNEVVGQNCRFLNGVD--TDTTVLYQSSTDKGKHSN---------RASMHSTYLKL 325 (328)
Q Consensus 281 ~~e~iG~~~~~l~~~~--~~~~~~~~~~~~~~~~~~---------~~~~g~~~~~~ 325 (328)
.+|++|+++..+.++. ........+........+ ++++|..+|..
T Consensus 573 ~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~ 628 (1092)
T PRK09776 573 QEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVH 628 (1092)
T ss_pred HHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEE
Confidence 9999999987665422 222222334444333222 46788888753
No 2
>PRK13560 hypothetical protein; Provisional
Probab=99.84 E-value=1.9e-19 Score=174.00 Aligned_cols=187 Identities=14% Similarity=0.131 Sum_probs=147.7
Q ss_pred hhHHHhhhhhhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHH
Q 020287 6 GLIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREA 85 (328)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~ 85 (328)
+..++.+. ...++++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.++.............
T Consensus 193 k~ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~ 268 (807)
T PRK13560 193 KRAEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAK 268 (807)
T ss_pred HHHHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHH
Confidence 34455555 56678999999999999999999 999999999999999999999999988777655444333344455
Q ss_pred HHcCCCeeEEEEEEecCCCEEEEEEEE--EEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccc
Q 020287 86 IREERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSC 163 (328)
Q Consensus 86 ~~~~~~~~~e~~~~~~dg~~~~~~~~~--~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~ 163 (328)
+..+.....+..+.+++|..+|+.+.. .|+.+ .+|.+.+++++++|||++|+++ ..++..
T Consensus 269 ~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~e-----------------~~L~~s 330 (807)
T PRK13560 269 FDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAAE-----------------RELLEK 330 (807)
T ss_pred hccCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHHH-----------------HHHHHH
Confidence 556667778888899999999776654 45566 7889999999999999999982 222111
Q ss_pred cchhchhhhhhhhhhccccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhH
Q 020287 164 RREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSL 243 (328)
Q Consensus 164 ~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l 243 (328)
...+
T Consensus 331 ----------------------------------------------------------------------------e~~l 334 (807)
T PRK13560 331 ----------------------------------------------------------------------------EDML 334 (807)
T ss_pred ----------------------------------------------------------------------------HHHH
Confidence 1126
Q ss_pred HHHHhhccCceEEeCCCCCCCCEEEe-chhhHHhhCCCcccccccCccccc
Q 020287 244 YISLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGYDRNEVVGQNCRFLN 293 (328)
Q Consensus 244 ~~~~~~~~~~i~i~d~~~~dg~i~~~-N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (328)
+.++++++.+|+++|.+ |.++++ |+++++++||++++++|+++..+.
T Consensus 335 ~~l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~ 382 (807)
T PRK13560 335 RAIIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKPLPGMD 382 (807)
T ss_pred HHHHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCCccccC
Confidence 67889999999999998 999987 577788999999999999876553
No 3
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.83 E-value=2.9e-19 Score=160.64 Aligned_cols=201 Identities=16% Similarity=0.119 Sum_probs=141.0
Q ss_pred hhHHHHHHHHhcCCcEEEEEcC-CCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCee
Q 020287 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~-~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (328)
..+++++.+++.++++++++|. + |.++++|+++++++||++++++|++...+.++.+...+...+......+....
T Consensus 130 ~~e~r~~~l~e~~~~~i~~~d~~~---g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~ 206 (442)
T TIGR02040 130 EMETRYRVVLEVSSDAVLLVDMST---GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAAP 206 (442)
T ss_pred HHHHHHHHHHhhCCceEEEEECCC---CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCcc
Confidence 3457899999999999999997 7 99999999999999999999999987766666555545555556665665554
Q ss_pred EEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhh
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (328)
.+.. .++|...| .+.+.++.. .+. ..+++...|||++++++.+.
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~e~~~------------------------------ 250 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPVGDEL------------------------------ 250 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhhhHHH------------------------------
Confidence 4443 33443334 345555554 333 35667788999987761100
Q ss_pred hhhhhccccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHHHhhccCc
Q 020287 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (328)
Q Consensus 174 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (328)
++.+..++++++++
T Consensus 251 ------------------------------------------------------------------~~~~~~l~e~~~d~ 264 (442)
T TIGR02040 251 ------------------------------------------------------------------SENLARLYHEAPDA 264 (442)
T ss_pred ------------------------------------------------------------------HHHHHHHHHhCCce
Confidence 00166789999999
Q ss_pred eEEeCCCCCCCCEEEechhhHHhhCCC-cccccccCcccccCCCCCHHHHHHHHhhh-hcCc-------Ccccccceeee
Q 020287 254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLNGVDTDTTVLYQSSTDK-GKHS-------NRASMHSTYLK 324 (328)
Q Consensus 254 i~i~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l~~~~~~~~~~~~~~~~~-~~~~-------~~~~~g~~~~~ 324 (328)
|+++|.+ |+|+++|++|++++||+ .++++|+++..+.++... . ...+...+ ..+. .++++|+.+|.
T Consensus 265 I~v~D~~---G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~~~-~-~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~v 339 (442)
T TIGR02040 265 IVFSDAD---GTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRGGV-D-LRVLLSNVRRTGQVRLYATTLTGEFGAQTEV 339 (442)
T ss_pred EEEEcCC---CcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCCcc-c-HHHHHHHHhhcCceEEEEEEEEcCCCCEEEE
Confidence 9999998 99999999999999997 578999998766543321 1 12222222 2221 25789999887
Q ss_pred c
Q 020287 325 L 325 (328)
Q Consensus 325 ~ 325 (328)
.
T Consensus 340 e 340 (442)
T TIGR02040 340 E 340 (442)
T ss_pred E
Confidence 3
No 4
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.78 E-value=9.5e-19 Score=157.26 Aligned_cols=199 Identities=15% Similarity=0.082 Sum_probs=140.1
Q ss_pred HhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCC-CeeEEEEEEecC
Q 020287 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD 102 (328)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~d 102 (328)
+++++++++++|.+ |.++++|++++.++||+.++++|+++..+.++.........+.+....+. .+..+.....++
T Consensus 2 ~~~~~d~~~~~d~~---g~i~~~n~~~~~~~g~~~~el~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 78 (442)
T TIGR02040 2 LATAADVTLLLDAE---GVVREVAANPHHPSFEQLSEWEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPS 78 (442)
T ss_pred CcccCcEEEEECCC---CcEEEEEECCCcccccccccCCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCC
Confidence 57889999999999 99999999999999999999999998888776654444444445455443 344454445566
Q ss_pred CCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhhhhhhhcccc
Q 020287 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD 182 (328)
Q Consensus 103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 182 (328)
|..+|+.++..++.+ .+ +++++.+|||++++.+.++...
T Consensus 79 g~~~~~~~~~~~~~~--~~---~~~~i~rDi~~~~~~~~~l~~~------------------------------------ 117 (442)
T TIGR02040 79 SFELPMRFILVRLGA--DR---GVLALGRDLRAVAELQQQLVAA------------------------------------ 117 (442)
T ss_pred CCccCeEEEEEEeCC--CC---eEEEEecccHHHHHHHHHHHHH------------------------------------
Confidence 666777776666543 22 5678899999987751111000
Q ss_pred CCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHHHhhccCceEEeCC-CC
Q 020287 183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDP-HL 261 (328)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~-~~ 261 (328)
...+++-...+ +..++.+..++++++++|+++|. +
T Consensus 118 ----------------------~~~~e~~~~~l---------------------~~~e~r~~~l~e~~~~~i~~~d~~~- 153 (442)
T TIGR02040 118 ----------------------QQAMERDYWTL---------------------REMETRYRVVLEVSSDAVLLVDMST- 153 (442)
T ss_pred ----------------------HHHHHHHHHHH---------------------HHHHHHHHHHHhhCCceEEEEECCC-
Confidence 00000000000 00112377799999999999997 6
Q ss_pred CCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcC
Q 020287 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKH 312 (328)
Q Consensus 262 ~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~ 312 (328)
|+|+++|+++++++||+++|++|+++..+.+|.+.......+......+
T Consensus 154 --g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g 202 (442)
T TIGR02040 154 --GRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATG 202 (442)
T ss_pred --CEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999999999988888777666666666665544
No 5
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=99.76 E-value=3e-18 Score=156.48 Aligned_cols=179 Identities=22% Similarity=0.356 Sum_probs=146.9
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEE
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (328)
+.++.++++++.+++++|.+ ++++++|+++++++|+++++++|+....+..+.........+.+.+..+.++..+..
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80 (494)
T ss_pred HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence 56889999999999999999 999999999999999999999998766665555555556667777777778877877
Q ss_pred EEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhhhhhh
Q 020287 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (328)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (328)
..+++|..+|+.+...|+.+ .+|.+.+++++.+|||++|+++++ ++
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~e~~-----------------l~---------------- 126 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRLEQV-----------------VA---------------- 126 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHHHHH-----------------HH----------------
Confidence 78899999999999999998 789999999999999999987211 10
Q ss_pred hccccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHHHhhccCceEEe
Q 020287 178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI 257 (328)
Q Consensus 178 ~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~ 257 (328)
.. ...+..++++++++++++
T Consensus 127 -------------------------~~-----------------------------------~~~~~~~~~~~~~~i~~~ 146 (494)
T TIGR02938 127 -------------------------NQ-----------------------------------KLLIESVVDAAPVAFVLL 146 (494)
T ss_pred -------------------------HH-----------------------------------HHHHHHHHhcccceEEEE
Confidence 00 011566888999999999
Q ss_pred CCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCC
Q 020287 258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (328)
Q Consensus 258 d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (328)
|.+ |.++++|++|++++|+...+..+..+..+.++.
T Consensus 147 d~~---~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~ 182 (494)
T TIGR02938 147 DPT---GRVILDNQEYKKLATDLRVKEPAHTVLDLLREA 182 (494)
T ss_pred cCC---CCEEEechhHHHhhchhhhhHHHHHHHHHhhHH
Confidence 988 999999999999999998888777655444433
No 6
>PRK13560 hypothetical protein; Provisional
Probab=99.76 E-value=2.7e-17 Score=159.05 Aligned_cols=206 Identities=11% Similarity=0.049 Sum_probs=141.1
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCC--EEEechHHHHhhCCChhhhcCCC--CccccCCCCChhHHH-------HHHHHH
Q 020287 18 LWVHEALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM-------EIREAI 86 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~--i~~~N~~~~~~~g~~~~e~~g~~--~~~l~~~~~~~~~~~-------~~~~~~ 86 (328)
..++.+++++|.++++++.+ +++. +.+++++...++|+.+.++++.. ...+.+|++...+.. .+..++
T Consensus 68 ~~~r~l~~~~p~~i~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~ 146 (807)
T PRK13560 68 QCERNLKANIPGGMFLFALD-GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAETIAMAL 146 (807)
T ss_pred HHHHHHHhcCCceEEEEEEc-CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHHHHHHHh
Confidence 34499999999999998877 1233 33477777888888877766533 233444554433321 222233
Q ss_pred HcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccch
Q 020287 87 REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRRE 166 (328)
Q Consensus 87 ~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (328)
..+.....+.+++++||. |+.+...|..+ ++|.+ .+.+++.|||++|+++++ ++..
T Consensus 147 ~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~ae~~-----------------l~~~--- 202 (807)
T PRK13560 147 QSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRAEER-----------------IDEA--- 202 (807)
T ss_pred ccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHHHHH-----------------HHHH---
Confidence 344556678888889996 66677778877 66665 688999999999998222 2111
Q ss_pred hchhhhhhhhhhccccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHH
Q 020287 167 VCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYIS 246 (328)
Q Consensus 167 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 246 (328)
...++.+
T Consensus 203 -------------------------------------------------------------------------~~~l~~l 209 (807)
T PRK13560 203 -------------------------------------------------------------------------LHFLQQL 209 (807)
T ss_pred -------------------------------------------------------------------------HHHHHHH
Confidence 1126778
Q ss_pred HhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcC-------cCccccc
Q 020287 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKH-------SNRASMH 319 (328)
Q Consensus 247 ~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~-------~~~~~~g 319 (328)
++++|++|+++|.+ |+++++|+++++++||+++|++|+++.++.++.............+..+ ..+++||
T Consensus 210 ~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG 286 (807)
T PRK13560 210 LDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKDG 286 (807)
T ss_pred HhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCCC
Confidence 99999999999998 9999999999999999999999999988875544333322233333222 2346899
Q ss_pred ceeee
Q 020287 320 STYLK 324 (328)
Q Consensus 320 ~~~~~ 324 (328)
+.+|.
T Consensus 287 ~~~~~ 291 (807)
T PRK13560 287 RTRPV 291 (807)
T ss_pred CEEEE
Confidence 98864
No 7
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.72 E-value=3.8e-16 Score=150.91 Aligned_cols=201 Identities=18% Similarity=0.220 Sum_probs=149.0
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCC----Cee
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIE 93 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~ 93 (328)
..+..+++..+.+++++|.+ |.++++|+++++++||++++++|++...+.++.........+......+. .+.
T Consensus 12 ~~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (799)
T PRK11359 12 GIFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMS 88 (799)
T ss_pred hhHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccc
Confidence 34567889999999999999 99999999999999999999999987777666544333333333333322 234
Q ss_pred EEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhh
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (328)
.+++..+++|..+|+.+...|+.. +|. .+++++..|||++++.++..
T Consensus 89 ~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~~~~~------------------------------ 135 (799)
T PRK11359 89 RELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQKEQT------------------------------ 135 (799)
T ss_pred eeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhhHHHH------------------------------
Confidence 477788999999999998888753 455 45688889999887651100
Q ss_pred hhhhhccccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHHHhhccCc
Q 020287 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (328)
Q Consensus 174 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (328)
..+..++++++++
T Consensus 136 -------------------------------------------------------------------~~~~~~~~~~~~~ 148 (799)
T PRK11359 136 -------------------------------------------------------------------RQLIIAVDHLDRP 148 (799)
T ss_pred -------------------------------------------------------------------HHHHHHHhcCCCc
Confidence 0033467888999
Q ss_pred eEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccC-CCCCHHHHHHHHhhhhcCc-------Ccccccceeee
Q 020287 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG-VDTDTTVLYQSSTDKGKHS-------NRASMHSTYLK 324 (328)
Q Consensus 254 i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~-~~~~~~~~~~~~~~~~~~~-------~~~~~g~~~~~ 324 (328)
++++|.+ |+++++|+++++++||+.++++|+++..+.+ +.........+...+..+. ..+++|..+|.
T Consensus 149 i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~ 224 (799)
T PRK11359 149 VIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWI 224 (799)
T ss_pred EEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEE
Confidence 9999998 9999999999999999999999999876654 4455555555555544332 24578888875
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=99.71 E-value=5.2e-16 Score=110.48 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=94.8
Q ss_pred CcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEE
Q 020287 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (328)
Q Consensus 28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (328)
|++++++|.+ |.++++|+++++++|+++++++|+++..+.++.........+.+++..+..+..+..+..++|..+|
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 6799999999 9999999999999999999999999888888777778888899999988899999999999999999
Q ss_pred EEEEEEEeeeCCCCeEEEEEEEEecccc
Q 020287 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (328)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~DIte 135 (328)
+.+++.|+.+ ++|++.+++++++|||+
T Consensus 78 ~~~~~~~i~~-~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 78 VEVSASPIRD-EDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEEEEEE-TTSSEEEEEEEEEEEHH
T ss_pred EEEEEEEEEC-CCCCEEEEEEEEEECCC
Confidence 9999999999 89999999999999996
No 9
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=99.64 E-value=4e-15 Score=107.06 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=96.3
Q ss_pred HhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCC
Q 020287 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (328)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg 103 (328)
|++++++++++|.+ ++++++|+++.+++|++.++++|++...+.++.....+...+.+++.++.+...+..... +|
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 76 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG 76 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence 57899999999999 999999999999999999999999988887777666777778888888777666555444 89
Q ss_pred CEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccc
Q 020287 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (328)
Q Consensus 104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~ 138 (328)
...|+.+++.|+.+ .+|.+.+++++.+|||++|+
T Consensus 77 ~~~~~~~~~~Pi~~-~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 77 EERWFEVSISPIFD-EDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp CEEEEEEEEEEEEC-TTTCEEEEEEEEEEECCHHH
T ss_pred CcEEEEEEEEEeEc-CCCCEEEEEEEEEECchhhC
Confidence 99999999999998 89999999999999999985
No 10
>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=99.61 E-value=2.4e-14 Score=103.54 Aligned_cols=112 Identities=23% Similarity=0.363 Sum_probs=93.1
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE-EE
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV-NL 96 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-e~ 96 (328)
++++.++++++.+++++|.+ |+|+++|+++++++|+++++++|++...+.++.+.......+...+..+..... ..
T Consensus 1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV 77 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence 46889999999999999999 999999999999999999999999988877666544566677777776665443 44
Q ss_pred EEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecc
Q 020287 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (328)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (328)
....++|..+|+.+...|+.+ .++.+.+++++++||
T Consensus 78 ~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 78 RFRLRDGRPRWVEVRASPVRD-EDGQIIGILVIFRDI 113 (113)
T ss_dssp EEEETTSCEEEEEEEEEEEEE-TTEEEEEEEEEEEE-
T ss_pred EEEecCCcEEEEEEEEEEEEe-CCCCEEEEEEEEEeC
Confidence 444469999999999999999 888899999999997
No 11
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.51 E-value=2.5e-13 Score=130.80 Aligned_cols=122 Identities=15% Similarity=0.193 Sum_probs=106.1
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
+..++++.++++++++++++|.+ |+++++|+++++++|++.++++|++...+.++.............+..+.+...
T Consensus 152 ~~~~~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (779)
T PRK11091 152 QQSSLLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTY 228 (779)
T ss_pred HHHHHHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEE
Confidence 45567889999999999999999 999999999999999999999999887777665444455555566677778888
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e 140 (328)
+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+++
T Consensus 229 e~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e 273 (779)
T PRK11091 229 EQWLDYPDGRKACFELRKVPFYD-RVGKRHGLMGFGRDITERKRYQ 273 (779)
T ss_pred EEEEEcCCCCEEEEEEEeeeEEc-CCCCEEEEEEEEeehhHHHHHH
Confidence 88888899999999999999998 8899999999999999999983
No 12
>PRK13559 hypothetical protein; Provisional
Probab=99.48 E-value=1.4e-12 Score=114.38 Aligned_cols=124 Identities=37% Similarity=0.669 Sum_probs=105.8
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
.....++.++++++.+++++|.+.+++.++++|+++++++||+.++++|+++..+..+.........+...+..+..+..
T Consensus 40 ~~~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (361)
T PRK13559 40 ASGRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVV 119 (361)
T ss_pred hhhhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEE
Confidence 34567888999999999999985334789999999999999999999999877666555555556667777777888888
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
+.....++|..+|+.+...|+.+ .+|.+.+++++..|||++|++
T Consensus 120 e~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~ 163 (361)
T PRK13559 120 ELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAV 163 (361)
T ss_pred EEEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhh
Confidence 88888999999999999999998 789999999999999999987
No 13
>PRK13557 histidine kinase; Provisional
Probab=99.40 E-value=6.1e-12 Score=116.36 Aligned_cols=127 Identities=37% Similarity=0.688 Sum_probs=110.1
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
.....|..+++.++.+++++|.+..+|+++|+|++|++++||+.++++|+++..+.++.........+...+..+..+..
T Consensus 27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (540)
T PRK13557 27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIAT 106 (540)
T ss_pred hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceE
Confidence 44578999999999999999974334899999999999999999999999988777776666667777788888888888
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNS 142 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~ 142 (328)
+....+++|..+|+.+++.|+.+ .+|.+.+++++..|||++++++++
T Consensus 107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~ 153 (540)
T PRK13557 107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDA 153 (540)
T ss_pred EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHH
Confidence 88888899999999999999998 889999999999999999987543
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.28 E-value=8.6e-11 Score=111.39 Aligned_cols=124 Identities=39% Similarity=0.703 Sum_probs=105.9
Q ss_pred HHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEE
Q 020287 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (328)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (328)
.++.+++.++.++++.|...+++.++++|+++++++||++++++|++...+.++.........+...+..+.++..+.+.
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 228 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRN 228 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEE
Confidence 45678999999999998543448999999999999999999999998777766655555556667777778888889999
Q ss_pred EecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccccccc
Q 020287 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (328)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~ 143 (328)
.+++|..+|+.+...|+.+ .+|.+.+++++..|||++|++++++
T Consensus 229 ~~~dG~~~~~~~~~~pi~d-~~G~~~~~vgi~~DITerk~~E~~L 272 (665)
T PRK13558 229 YRKDGSTFWNQVDIAPIRD-EDGTVTHYVGFQTDVTERKEAELAL 272 (665)
T ss_pred ECCCCCEEEEEEEEEEEEC-CCCCEEEEEEEEEeCcHHHHHHHHH
Confidence 9999999999999999998 7999999999999999999986554
No 15
>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=99.20 E-value=2.6e-11 Score=87.42 Aligned_cols=81 Identities=15% Similarity=0.118 Sum_probs=65.6
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN------- 314 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~------- 314 (328)
.++.++++++++++++|.+ |+|+++|+++++++||+.++++|+++.++.++++.......+...+..+..
T Consensus 2 ~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (113)
T PF00989_consen 2 RYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVR 78 (113)
T ss_dssp HHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEE
T ss_pred HHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEE
Confidence 5788999999999999988 999999999999999999999999999998877665677777777665432
Q ss_pred c-ccccceeeec
Q 020287 315 R-ASMHSTYLKL 325 (328)
Q Consensus 315 ~-~~~g~~~~~~ 325 (328)
. .++|+.+|..
T Consensus 79 ~~~~~g~~~~~~ 90 (113)
T PF00989_consen 79 FRLRDGRPRWVE 90 (113)
T ss_dssp EEETTSCEEEEE
T ss_pred EEecCCcEEEEE
Confidence 1 2367776653
No 16
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.19 E-value=4.7e-11 Score=84.67 Aligned_cols=72 Identities=19% Similarity=0.302 Sum_probs=61.7
Q ss_pred cCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------cccccceee
Q 020287 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN-------RASMHSTYL 323 (328)
Q Consensus 251 ~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~~g~~~~ 323 (328)
|+|++++|++ |+|+++|++|++++||++++++|+++..+.++.........+.+++..+.. ++++|+.+|
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 6899999998 999999999999999999999999999999888888999999999886654 457898888
Q ss_pred ec
Q 020287 324 KL 325 (328)
Q Consensus 324 ~~ 325 (328)
..
T Consensus 78 ~~ 79 (104)
T PF13426_consen 78 VE 79 (104)
T ss_dssp EE
T ss_pred EE
Confidence 65
No 17
>PRK10060 RNase II stability modulator; Provisional
Probab=99.18 E-value=4.3e-10 Score=106.01 Aligned_cols=136 Identities=13% Similarity=0.155 Sum_probs=102.1
Q ss_pred hHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccC-CCCChhHHHHHHHHHHcCCCeeE
Q 020287 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
...+++.+++.++++|+++|.+ |+++++|+++++++||+.++++|+++..+.. +.........+...+..+..+..
T Consensus 109 ~~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (663)
T PRK10060 109 GLSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEV 185 (663)
T ss_pred HHHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEE
Confidence 3457788999999999999999 9999999999999999999999998755543 33333444556667777888888
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCC-eEEEEEEEEecccccccccccccc-cccc-----CCCccch
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDG-RATHFVAVQVPIVSRKHMRNSGMS-YSED-----GGGSRLR 156 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g-~~~~~~~~~~DIte~k~~e~~~~~-~~~~-----~~~~~~~ 156 (328)
+....+++|..+|+.....+ .. ..| ...+++++.+|||+++++++++.. ...| .||..+.
T Consensus 186 e~~~~~~~G~~~~~~~~~~~-~~-~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~ 252 (663)
T PRK10060 186 ERWIKTRKGQRLFLFRNKFV-HS-GSGKNEIFLICSGTDITEERRAQERLRILANTDSITGLPNRNAIQ 252 (663)
T ss_pred EEEEEeCCCCEEEEEeeeEE-Ec-CCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCCcCHHHHH
Confidence 99999999988887655433 33 344 345678889999999998766532 2333 2666554
No 18
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=99.17 E-value=8.3e-10 Score=78.69 Aligned_cols=118 Identities=21% Similarity=0.347 Sum_probs=90.2
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcC-CCeeEEE
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (328)
+.++.+++.++.+++++|.+ +.++++|+++++++|++..+++|.....+.++.........+...+..+ .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 45678899999999999999 9999999999999999999999987666555444444444444444423 2233444
Q ss_pred EEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccc
Q 020287 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (328)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e 140 (328)
.+...+|...|+.+...|+.. +|...+++++..|||++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~ 121 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAE 121 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHH
Confidence 455788999999988888763 677888999999999998873
No 19
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=99.10 E-value=1e-09 Score=75.86 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=70.1
Q ss_pred EEEechHHHHhhCCChhhhcCCC----CccccCCCCChhHHHHHHH-HHHcCCCeeEEEEEEecCCCEEEEEEEEEEeee
Q 020287 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (328)
Q Consensus 43 i~~~N~~~~~~~g~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~ 117 (328)
++++|+.+++++||+++++ +.. +..+.+|++...+...+.+ ....+..+..++++++++|..+|+.+...++.+
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d 79 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFD 79 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEET
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEEC
Confidence 5799999999999999998 655 5556778888888888888 677778899999999999999999999999998
Q ss_pred CCCCeEEEEEEEE
Q 020287 118 KEDGRATHFVAVQ 130 (328)
Q Consensus 118 ~~~g~~~~~~~~~ 130 (328)
++|.+..++|+.
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999988874
No 20
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.08 E-value=1.7e-09 Score=108.48 Aligned_cols=133 Identities=15% Similarity=0.186 Sum_probs=103.4
Q ss_pred hHHHhhhhhhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCC--CChhHHHHHHH
Q 020287 7 LIEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR--TNRRTIMEIRE 84 (328)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~--~~~~~~~~~~~ 84 (328)
..++.+. ...++++.++++++++++++|.+ |+++++|+++++++||+.++++|++...+.... ........+..
T Consensus 526 ~~e~~L~-~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~ 601 (1092)
T PRK09776 526 QLNEALF-QEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYS 601 (1092)
T ss_pred HHHHHHH-HHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHH
Confidence 3444444 55678899999999999999999 999999999999999999999999865544321 11122222444
Q ss_pred HHHcCCC--eeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccc
Q 020287 85 AIREERP--IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGM 144 (328)
Q Consensus 85 ~~~~~~~--~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~ 144 (328)
....... ...+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+.++++.
T Consensus 602 ~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~-~~g~~~g~v~~~~DITe~k~~e~~L~ 662 (1092)
T PRK09776 602 CLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLST-LDGENIGSVLVIQDVTESRKMLRQLS 662 (1092)
T ss_pred HHhcCCCccccceEEEEeCCCcEEEEEEEeeeeec-CCCCEEEEEEEEEecchHHHHHHHHH
Confidence 4444333 44566778899999999999999998 89999999999999999999977663
No 21
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.04 E-value=2.3e-09 Score=104.05 Aligned_cols=120 Identities=19% Similarity=0.307 Sum_probs=99.7
Q ss_pred HHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccC-CCCChhHHHHHHHHHHcCCCeeEE
Q 020287 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEVN 95 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~e 95 (328)
...+..+++.++.+++++|.+ |.++++|+++++++|++.++++|++...+.+ +.........+...+..+..+..+
T Consensus 135 ~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 211 (799)
T PRK11359 135 TRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDE 211 (799)
T ss_pred HHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcce
Confidence 345667899999999999999 9999999999999999999999998665543 334444445556666666667778
Q ss_pred EEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccc
Q 020287 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (328)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e 140 (328)
.+...++|..+|+.+...|+.+ .+|.+.+++++.+|||++++++
T Consensus 212 ~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e 255 (799)
T PRK11359 212 FLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIR 255 (799)
T ss_pred eEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHH
Confidence 8888899999999999999998 7899999999999999999873
No 22
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.99 E-value=6.7e-09 Score=73.95 Aligned_cols=106 Identities=21% Similarity=0.306 Sum_probs=72.6
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEE
Q 020287 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (328)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (328)
++.++++++.++.++|.+ +++.+.|+++.++|+..+.+ +|++...+.++.... ....+.+.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~-~l~~~i~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYP-NLKKIIEQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHH-HHHHHHHHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchH-HHHHHHHHHHcCCCceEEEEe-
Confidence 467899999999999999 99999999999999987654 899987776542222 233344555556554444333
Q ss_pred ecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccc
Q 020287 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (328)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt 134 (328)
..+|. |+.+.+.|+.+ ++|...|++.++.|||
T Consensus 75 ~~~~~--~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGGR--WYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETTE--EEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCCE--EEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 34444 77889999998 8999999999999997
No 23
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.95 E-value=6.5e-08 Score=65.55 Aligned_cols=102 Identities=21% Similarity=0.395 Sum_probs=81.2
Q ss_pred CcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEE
Q 020287 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (328)
Q Consensus 28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (328)
+.+++++|.+ +.+.++|+.++.++|++..+++|.....+.++.........+......+.....+..+...+|...|
T Consensus 2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (103)
T cd00130 2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIW 78 (103)
T ss_pred CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEE
Confidence 5688999999 9999999999999999999999988666665555555555555555555566677777778899999
Q ss_pred EEEEEEEeeeCCCCeEEEEEEEEecc
Q 020287 108 MLFKMSLVFGKEDGRATHFVAVQVPI 133 (328)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (328)
+.+...++.. ..+...+++++..||
T Consensus 79 ~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 79 VLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEec-CCCCEEEEEEEEecC
Confidence 9999999887 677888888888775
No 24
>PF12860 PAS_7: PAS fold
Probab=98.86 E-value=2.8e-08 Score=71.91 Aligned_cols=104 Identities=21% Similarity=0.357 Sum_probs=70.8
Q ss_pred HhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhh-cCCCCcccc---------CCCCChhHHHHHHHHHHcCCCee
Q 020287 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (328)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (328)
+++++.|++++|.+ ++++++|+.|.++++++.+.+ .|.+...+. .+.....................
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLARLRRRQPRS 77 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhcCCCce
Confidence 47899999999999 999999999999999999887 677644332 11111222222222333333333
Q ss_pred EEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccc
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e 140 (328)
.+ ....||. |+.+...|.. +| |++.+..|||+++++|
T Consensus 78 ~~--~~~~dgr--~l~~~~~~~~---~G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 78 FE--LRLPDGR--WLEVRAQPLP---DG---GFVLTFTDVTERRRAE 114 (115)
T ss_pred eE--EECCCCE--EEEEEeEECC---CC---CEEEEEEeCCHHHHhc
Confidence 33 3456776 7778888875 45 5678899999999874
No 25
>PRK13557 histidine kinase; Provisional
Probab=98.81 E-value=1.2e-08 Score=94.58 Aligned_cols=84 Identities=29% Similarity=0.625 Sum_probs=71.8
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN------- 314 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~------- 314 (328)
.+..++++++++|+++|.+..||+|+|+|++|++++||+.+|++|+++..+.+|+........++..+..+..
T Consensus 31 ~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (540)
T PRK13557 31 IFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEILN 110 (540)
T ss_pred HHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEE
Confidence 4778999999999999976566999999999999999999999999999999888888888888877765532
Q ss_pred cccccceeeec
Q 020287 315 RASMHSTYLKL 325 (328)
Q Consensus 315 ~~~~g~~~~~~ 325 (328)
++++|+.+|..
T Consensus 111 ~~~~G~~~~~~ 121 (540)
T PRK13557 111 YRKDGSSFWNA 121 (540)
T ss_pred EeCCCCEEEEE
Confidence 46799998863
No 26
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.78 E-value=1.2e-07 Score=88.84 Aligned_cols=121 Identities=14% Similarity=0.166 Sum_probs=94.8
Q ss_pred hHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCe-eE
Q 020287 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI-EV 94 (328)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~ 94 (328)
....++.+++.++++++++|.+ +.++++|+++++++|+++++++|++...+.++.. .....+.+.+..+... ..
T Consensus 260 ~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 334 (607)
T PRK11360 260 TRSLNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPNT--PFASPLLDTLEHGTEHVDL 334 (607)
T ss_pred HHHHHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCch--hHHHHHHHHHhcCCCccce
Confidence 3356778999999999999999 9999999999999999999999998777665432 2333445555554443 34
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~ 143 (328)
++.....+|... +.++..|+.+ .+|.+.++++++.|||+++++++++
T Consensus 335 ~~~~~~~~~~~~-~~~~~~~i~~-~~g~~~~~i~~~~Dite~~~~e~~l 381 (607)
T PRK11360 335 EISFPGRDRTIE-LSVSTSLLHN-THGEMIGALVIFSDLTERKRLQRRV 381 (607)
T ss_pred EEEEEcCCCcEE-EEEEEeeEEc-CCCCEEEEEEEEeechHHHHHHHHH
Confidence 556666777665 8889999998 8999999999999999999984443
No 27
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.77 E-value=4.6e-08 Score=85.98 Aligned_cols=163 Identities=20% Similarity=0.179 Sum_probs=116.7
Q ss_pred HHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEe
Q 020287 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (328)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (328)
..+++..++++++++.. ..+..+|..+..+++-....++|++..++.++....... .+...........
T Consensus 4 ~~~l~~~~~~~~vi~~~---~~~~~~~~~a~~~~~~~~~~~i~~~~~~i~~~~~~~~v~--------~~~~~~~~~~~~~ 72 (560)
T COG3829 4 EGILKSILDGPVVIDKN---TGIDVANALALAKRQKNAEAVIGRPLREILETLGMERVE--------QSRDKELTERLKL 72 (560)
T ss_pred hhhhhhcccceEEEEcC---CceeeechHHHHhhhcceEEEecccceeeccccCcceee--------ccCccceeeeeec
Confidence 34788999999999998 899999999999999988889999877766544333221 1222222222222
Q ss_pred cCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccccccccccccccCCCccchhhhhccccchhchhhhhhhhhhcc
Q 020287 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180 (328)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (328)
+ ....+.+...|+. +.+.++|++.++.|+++....
T Consensus 73 ~--~~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~----------------------------------------- 107 (560)
T COG3829 73 K--VKRIVVVGKTPVD--EQGRVVGVLEVFLDISEALEL----------------------------------------- 107 (560)
T ss_pred c--ceeEEEcCCceee--cCCceeeeehhhhhhHHHHHH-----------------------------------------
Confidence 2 2333333444554 488999999999999985543
Q ss_pred ccCCCCCCccccccccchHHHHHHHhhhhhhhhhhccccccCCceeeeeeecCCCCccchhhHHHHHhhccCceEEeCCC
Q 020287 181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH 260 (328)
Q Consensus 181 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~i~d~~ 260 (328)
.... .. .....|..+++.+.++++++|..
T Consensus 108 -----------------~~~~--l~--------------------------------~~~~~l~~il~~~~~~l~vvD~~ 136 (560)
T COG3829 108 -----------------IEEN--LR--------------------------------QLRQRLEAILDSIDDGLLVVDED 136 (560)
T ss_pred -----------------HHHH--HH--------------------------------HHHHHHHHHHhhccCceEEEcCC
Confidence 0000 00 00112677899999999999999
Q ss_pred CCCCCEEEechhhHHhhCCCcccccccCccccc
Q 020287 261 LPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (328)
Q Consensus 261 ~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (328)
|.++++|+++.+++|++.++++|+++.++.
T Consensus 137 ---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~ 166 (560)
T COG3829 137 ---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVV 166 (560)
T ss_pred ---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence 999999999999999999999999987775
No 28
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=98.74 E-value=8.9e-08 Score=82.82 Aligned_cols=108 Identities=13% Similarity=0.085 Sum_probs=81.9
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
+..+.++.++++++.+++++|.+ |.++++|+++++++|+++++.+|++...+..+ . .+...+..+.. ..
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~---~----~~~~~l~~~~~-~~ 71 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRH---P----EFVEYLAAGRF-SE 71 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccC---H----HHHHHHHhccc-CC
Confidence 34567899999999999999999 99999999999999999999999886655432 1 22333333222 22
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
......++|...|+.+...|+.+ . + ++.+..|||++++.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~-~-~----~~~~~~dit~~~~~ 110 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE-E-Q----KLLVARDVTRLRRL 110 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC-C-c----eEEEEeCchHHHHH
Confidence 34445578888899999999875 2 2 56788999999886
No 29
>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=98.72 E-value=1.4e-08 Score=72.53 Aligned_cols=65 Identities=20% Similarity=0.209 Sum_probs=57.9
Q ss_pred HhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC
Q 020287 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN 314 (328)
Q Consensus 247 ~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 314 (328)
++++|++|+++|.+ ++|+++|+++++++|+++++++|+++.++.++...+.....+.+++..+.+
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEP 65 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSE
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCce
Confidence 57899999999999 999999999999999999999999999988887888888889888887653
No 30
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.69 E-value=1.3e-07 Score=82.66 Aligned_cols=111 Identities=14% Similarity=0.159 Sum_probs=84.1
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEE
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (328)
..+..++++++++++++|.+ +.++++|+++++++|++.++++|.+...+.+... .....+...+..+..+.....
T Consensus 7 ~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 81 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEV 81 (348)
T ss_pred chHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccce
Confidence 45688999999999999999 9999999999999999999999998776654332 122334455555554443334
Q ss_pred EEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
....+|..+|+.++..|+.. + +++..++|+|++++.
T Consensus 82 ~~~~~g~~~~~~~~~~~~~~---~---~~~~~~~dit~~~~~ 117 (348)
T PRK11073 82 TLVIDGRSHILSLTAQRLPE---G---MILLEMAPMDNQRRL 117 (348)
T ss_pred EEEECCceEEEEEEEEEccC---c---eeEEEEechhHHHHH
Confidence 44569999999999888753 2 356678999998876
No 31
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.68 E-value=1.5e-07 Score=82.55 Aligned_cols=122 Identities=26% Similarity=0.528 Sum_probs=97.3
Q ss_pred HHHHHHHHhcCC--c-EEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCC--CccccCCCCChhHHHHHHHHHHcCCC
Q 020287 17 TLWVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREERP 91 (328)
Q Consensus 17 ~~~~~~~~~~~~--~-~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~~ 91 (328)
+.+++.++..+. + .+++.+.+.-|..|+|+|+.||++.||.+.|++.++ +.++.....+..-...+.+.+...+.
T Consensus 13 NTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~ 92 (971)
T KOG0501|consen 13 NTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYET 92 (971)
T ss_pred hhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhh
Confidence 456666766554 2 344444433346789999999999999999999887 45566666666667777888877777
Q ss_pred eeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
-.+|.....++.+++|+.+.+.|+++ +.+.++-+++.+.|||..|+-
T Consensus 93 ~qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 93 NQFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred cceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence 77888889999999999999999999 899999999999999999875
No 32
>PRK13559 hypothetical protein; Provisional
Probab=98.67 E-value=7.1e-08 Score=84.67 Aligned_cols=83 Identities=33% Similarity=0.610 Sum_probs=68.6
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------c
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN-------R 315 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~ 315 (328)
+..++++++++|+++|...++|.++++|++|++++||+.++++|+++..+.++.........+...+..+.. +
T Consensus 45 ~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 124 (361)
T PRK13559 45 FEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNY 124 (361)
T ss_pred HHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEE
Confidence 677899999999999986455899999999999999999999999998888777777777777777665432 4
Q ss_pred ccccceeeec
Q 020287 316 ASMHSTYLKL 325 (328)
Q Consensus 316 ~~~g~~~~~~ 325 (328)
+++|+.+|..
T Consensus 125 ~~dG~~~~~~ 134 (361)
T PRK13559 125 RKDGEPFWNA 134 (361)
T ss_pred cCCCCEEEEE
Confidence 6789888853
No 33
>PRK10060 RNase II stability modulator; Provisional
Probab=98.66 E-value=2.9e-08 Score=93.80 Aligned_cols=80 Identities=10% Similarity=0.031 Sum_probs=62.2
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCccccc-CCCCCHHHHHHHHhhhhcCc-------C
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN-GVDTDTTVLYQSSTDKGKHS-------N 314 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~-~~~~~~~~~~~~~~~~~~~~-------~ 314 (328)
+..+++++++||+++|.+ |+|+++|+++++++||+.+|++|+++..+. +|.+.......+...+..+. .
T Consensus 113 ~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 189 (663)
T PRK10060 113 AEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWI 189 (663)
T ss_pred HHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEE
Confidence 455788899999999999 999999999999999999999999986654 45444455555666555443 2
Q ss_pred cccccceeeec
Q 020287 315 RASMHSTYLKL 325 (328)
Q Consensus 315 ~~~~g~~~~~~ 325 (328)
++++|..+|.+
T Consensus 190 ~~~~G~~~~~~ 200 (663)
T PRK10060 190 KTRKGQRLFLF 200 (663)
T ss_pred EeCCCCEEEEE
Confidence 46789888754
No 34
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.64 E-value=1.7e-06 Score=61.71 Aligned_cols=101 Identities=16% Similarity=0.255 Sum_probs=81.6
Q ss_pred EEcCCCCCCCEEEechH-HHHhhCCChhhhcCCCCccccCCCCChh-HHHHHHHHHHcCCCeeEEEEEEecCCCEEEEEE
Q 020287 33 ITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWMLF 110 (328)
Q Consensus 33 ~~d~~~~~~~i~~~N~~-~~~~~g~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~ 110 (328)
..+.+ |+++++..+ ...++||.+++++|+.+..+.++++... +...+...+..|.....-+++..++|..+|+..
T Consensus 7 rhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt 83 (111)
T PF14598_consen 7 RHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT 83 (111)
T ss_dssp EEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred EECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence 45666 999999999 6999999999999999999998888875 666778888888887778999999999999999
Q ss_pred EEEEeeeCCCCeEEEEEEEEeccccc
Q 020287 111 KMSLVFGKEDGRATHFVAVQVPIVSR 136 (328)
Q Consensus 111 ~~~~~~~~~~g~~~~~~~~~~DIte~ 136 (328)
...+..++..+++..++++..=|++.
T Consensus 84 ~~~~~~n~~~~~~~~Iv~~n~vlse~ 109 (111)
T PF14598_consen 84 KATLFYNPWTSKPEFIVCTNTVLSEE 109 (111)
T ss_dssp EEEEEEETTTTCEEEEEEEEEEESCE
T ss_pred EEEEEECCCCCCccEEEEEEEEeccC
Confidence 99888863466777777766655543
No 35
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.53 E-value=3.3e-06 Score=74.61 Aligned_cols=112 Identities=17% Similarity=0.349 Sum_probs=85.3
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
...+.++.+++.+.+++.++|.. |.++++|.++..++|++.++++|++...+..... .....+++..+.+...
T Consensus 114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~----~s~~l~vl~~~kp~~~ 186 (560)
T COG3829 114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGE----DSTLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccC----CceehhhhhcCCccee
Confidence 55678999999999999999999 9999999999999999999999998655541111 1233566677777665
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
.......+.. ..+..|+.. +|.+.|.+.+..|+++.+..
T Consensus 187 ~~~~~~~~~~----i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l 225 (560)
T COG3829 187 VVQTYNGNKI----IVNVAPVYA--DGQLIGVVGISKDVSELERL 225 (560)
T ss_pred eeeeecCCce----eEeeccEec--CCcEEEEEEeecchHHHHHH
Confidence 4433332222 456677775 78999999999999998877
No 36
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.52 E-value=1.2e-07 Score=60.56 Aligned_cols=42 Identities=21% Similarity=0.401 Sum_probs=35.4
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcc
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR 290 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~ 290 (328)
.++.+++++|+||+++| . ++|+++|+++++++||+ ..|+.+.
T Consensus 2 ~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~ 43 (64)
T PF13188_consen 2 RYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIG 43 (64)
T ss_dssp HHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred HHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHH
Confidence 47889999999999999 8 89999999999999998 6666654
No 37
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.51 E-value=2.1e-06 Score=71.27 Aligned_cols=114 Identities=15% Similarity=0.242 Sum_probs=87.7
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
.-..++..++.++.+|++.+|.. |.++.+|..+.+++|.+.++++|++...+....+.-. +.+.+....+...
T Consensus 108 ~Er~kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~----~~dL~e~~~s~ll 180 (459)
T COG5002 108 QERRKLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYT----FEDLVEKNDSLLL 180 (459)
T ss_pred HHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee----HHHHHhcCCcEEE
Confidence 34467888999999999999999 9999999999999999999999998666554433322 2333333333333
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
+. ...++.+.+.+....+.. +.|-+.|++.+..|+|++.+.
T Consensus 181 d~---~~~~E~~~lrv~Fs~i~r-EsGfisGlIaVlhDvTEqek~ 221 (459)
T COG5002 181 DS---SDEEEGYVLRVNFSVIQR-ESGFISGLIAVLHDVTEQEKV 221 (459)
T ss_pred ee---cCCCccEEEEEEEEEEee-cccccceeEEEEecccHHHHH
Confidence 32 226677777788888887 899999999999999999887
No 38
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.37 E-value=1.7e-06 Score=77.78 Aligned_cols=106 Identities=13% Similarity=0.158 Sum_probs=72.9
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
...++++.++++++++++++|.+ |+++++|+++++++|++.++.+|++...+.... ... ..+... ....
T Consensus 95 ~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~----~~~~~~-~~~~ 163 (430)
T PRK11006 95 NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFT----QYLKTR-DFSR 163 (430)
T ss_pred HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHH----HHHHhc-ccCC
Confidence 45678899999999999999999 999999999999999999999999865554321 111 111111 1112
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
.......+|. ++.+...|..+ + ..+.+.+|||++++.
T Consensus 164 ~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~ 200 (430)
T PRK11006 164 PLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQL 200 (430)
T ss_pred CeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHH
Confidence 2223344454 55566666543 2 245678999999887
No 39
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.32 E-value=4.8e-06 Score=76.21 Aligned_cols=109 Identities=14% Similarity=0.137 Sum_probs=78.0
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
+....+..+++++++|++++|.+ |+|+++|++++++||++.++++|++...+.+... +.+.+..+.....
T Consensus 77 ~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~ 146 (520)
T PRK10820 77 REHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccc
Confidence 34467889999999999999999 9999999999999999999999999777765432 2233444443111
Q ss_pred EEEEEecCCCEEEEEEEEEEee--eCCCCe--EEEEEEEEecccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRK 137 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~--~~~~g~--~~~~~~~~~DIte~k 137 (328)
. .....+|..++ +...|+. + ++|. ..|.+.+++|+++..
T Consensus 147 ~-~~v~~~g~~~~--v~~~PI~~~d-~~g~~~~~GaVivlrd~~~l~ 189 (520)
T PRK10820 147 N-EHVVINGQDFL--MEITPVYLQD-ENDQHVLVGAVVMLRSTARMG 189 (520)
T ss_pred e-EEEEECCEEEE--EEEEeeeecC-CCCceeEEEEEEEeccHHHHH
Confidence 1 12234565544 5567776 4 4444 379999999998753
No 40
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=98.31 E-value=9.6e-07 Score=80.74 Aligned_cols=82 Identities=22% Similarity=0.346 Sum_probs=66.8
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC------
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN------ 314 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~------ 314 (328)
+.+..+++++++++++.|.+ |+++++|+++++++||++++++|++...+.++.........+...+..+.+
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80 (494)
T ss_pred HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceee
Confidence 34788999999999999999 999999999999999999999999887777766666667777666554432
Q ss_pred -cccccceeeec
Q 020287 315 -RASMHSTYLKL 325 (328)
Q Consensus 315 -~~~~g~~~~~~ 325 (328)
++++|..+|..
T Consensus 81 ~~~~~g~~~~~~ 92 (494)
T TIGR02938 81 NRRKDGELYLAE 92 (494)
T ss_pred ccCCCccchhhh
Confidence 45788888743
No 41
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=98.26 E-value=5e-07 Score=62.21 Aligned_cols=61 Identities=18% Similarity=0.141 Sum_probs=47.0
Q ss_pred EEEechhhHHhhCCCcccccccC----cccccCCCCCHHHHHHHHh-hhhcCcC-------cccccceeeeccC
Q 020287 266 MVYASDAFLKLTGYDRNEVVGQN----CRFLNGVDTDTTVLYQSST-DKGKHSN-------RASMHSTYLKLQE 327 (328)
Q Consensus 266 i~~~N~a~~~~~Gy~~~e~iG~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~-------~~~~g~~~~~~~~ 327 (328)
|+|+|+++++++||+++++ |.. +..++||++.+.+...+.. +...+.. ++++|+..|....
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~ 73 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVR 73 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEE
Confidence 6899999999999999999 766 7788999999999999999 5555532 5689999997643
No 42
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.26 E-value=2e-05 Score=70.97 Aligned_cols=70 Identities=19% Similarity=0.180 Sum_probs=55.7
Q ss_pred eEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcCc-------ccccceeee
Q 020287 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR-------ASMHSTYLK 324 (328)
Q Consensus 254 i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-------~~~g~~~~~ 324 (328)
++++--. -|.+|+|+.+.+.+++||+++||+|+.+.+++|+.+-..+.....+.+.+|..+ .|.|..-|.
T Consensus 275 ~FvtRhs-~DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWl 351 (768)
T KOG3558|consen 275 MFVTRHS-LDMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWL 351 (768)
T ss_pred eeEEeee-cceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEE
Confidence 4544322 348999999999999999999999999999999988877777777878877542 356777774
No 43
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.26 E-value=1.3e-06 Score=84.60 Aligned_cols=81 Identities=11% Similarity=-0.013 Sum_probs=64.7
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC------
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN------ 314 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~------ 314 (328)
..+..++++++++|+++|.+ |+|+++|+++++++||+.++++|+++.++.+++...............+.+
T Consensus 155 ~~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 231 (779)
T PRK11091 155 SLLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQW 231 (779)
T ss_pred HHHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence 34778999999999999999 999999999999999999999999999888776655555555555544432
Q ss_pred -cccccceeee
Q 020287 315 -RASMHSTYLK 324 (328)
Q Consensus 315 -~~~~g~~~~~ 324 (328)
..++|..+|.
T Consensus 232 ~~~~~G~~~~~ 242 (779)
T PRK11091 232 LDYPDGRKACF 242 (779)
T ss_pred EEcCCCCEEEE
Confidence 3467877664
No 44
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.25 E-value=1e-05 Score=76.32 Aligned_cols=49 Identities=14% Similarity=0.133 Sum_probs=44.0
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~ 294 (328)
+..+++++++||+++|.+ |+|+++|+++++++|++.++++|+++..+..
T Consensus 205 ~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~ 253 (638)
T PRK11388 205 LNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLT 253 (638)
T ss_pred HHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence 445788889999999999 9999999999999999999999999877763
No 45
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=98.23 E-value=1.1e-06 Score=75.85 Aligned_cols=52 Identities=17% Similarity=0.193 Sum_probs=47.9
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCC
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV 295 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~ 295 (328)
+.+..+++++++||+++|.+ |.++++|+++++++||++++++|+++..+.++
T Consensus 6 ~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~ 57 (333)
T TIGR02966 6 SRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRH 57 (333)
T ss_pred HHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccC
Confidence 45888999999999999999 99999999999999999999999998887654
No 46
>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=98.22 E-value=5.4e-06 Score=58.45 Aligned_cols=66 Identities=18% Similarity=0.233 Sum_probs=54.8
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhh
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKG 310 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~ 310 (328)
.+..++++++.+++++|.+ +.++++|+++++++|++..+++|+++..+.++.........+...+.
T Consensus 4 ~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (124)
T TIGR00229 4 RYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLE 69 (124)
T ss_pred HHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHc
Confidence 3677889999999999998 99999999999999999999999998887776665555555555544
No 47
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.21 E-value=3.7e-06 Score=80.05 Aligned_cols=83 Identities=31% Similarity=0.539 Sum_probs=67.8
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------c
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN-------R 315 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~ 315 (328)
+..+++.++.+|+++|...++|.++|+|+++++++||++++++|+++..+.++.........+...+..+.+ +
T Consensus 150 ~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 229 (665)
T PRK13558 150 KERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNY 229 (665)
T ss_pred HHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEE
Confidence 456788999999999865556999999999999999999999999998888777777777777776654432 4
Q ss_pred ccccceeeec
Q 020287 316 ASMHSTYLKL 325 (328)
Q Consensus 316 ~~~g~~~~~~ 325 (328)
+++|+.+|..
T Consensus 230 ~~dG~~~~~~ 239 (665)
T PRK13558 230 RKDGSTFWNQ 239 (665)
T ss_pred CCCCCEEEEE
Confidence 6899988863
No 48
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.19 E-value=4.5e-06 Score=53.20 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.4
Q ss_pred HHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCC
Q 020287 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG 66 (328)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~ 66 (328)
++++.++++++.|++++| + ++++++|+++++++||+ ..|...
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~ 42 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDI 42 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCH
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCH
Confidence 468899999999999999 8 89999999999999998 555554
No 49
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.12 E-value=4.8e-06 Score=72.69 Aligned_cols=77 Identities=13% Similarity=0.045 Sum_probs=58.3
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC-------c
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN-------R 315 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~ 315 (328)
+..+++++++|++++|.+ |+|+++|+++++++||+.++++|+++.++.++.. .....+...+..+.. .
T Consensus 9 ~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~ 83 (348)
T PRK11073 9 AGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFS--LNIELMRESLQAGQGFTDNEVTL 83 (348)
T ss_pred HHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcch--hhHHHHHHHHHcCCcccccceEE
Confidence 678999999999999999 9999999999999999999999999988875432 122333334333321 3
Q ss_pred ccccceeee
Q 020287 316 ASMHSTYLK 324 (328)
Q Consensus 316 ~~~g~~~~~ 324 (328)
.++|..+|.
T Consensus 84 ~~~g~~~~~ 92 (348)
T PRK11073 84 VIDGRSHIL 92 (348)
T ss_pred EECCceEEE
Confidence 457877774
No 50
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=98.11 E-value=3.2e-05 Score=71.79 Aligned_cols=108 Identities=10% Similarity=0.142 Sum_probs=76.0
Q ss_pred hHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCCh---hhhcCCCCccccCCCCChhHHHHHHHHHHcCCCe
Q 020287 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (328)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (328)
..+.++.+++++++|++++|.+ |+++++|+++++++|++. .+.+|.....+.+. ..+...+..+.+.
T Consensus 219 l~~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~ 288 (542)
T PRK11086 219 LFEQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPV-------SRLKEVLRTGTPR 288 (542)
T ss_pred HHHHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCc-------hhHHHHHhcCCCc
Confidence 4456788999999999999999 999999999999998753 34555554333321 1233445555443
Q ss_pred eEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
.... ...+|. ++.+...|+.+ +|.+.|++.+++|+|+.++.
T Consensus 289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l 329 (542)
T PRK11086 289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQL 329 (542)
T ss_pred cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHH
Confidence 3221 122444 44566778886 78999999999999999877
No 51
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.06 E-value=0.00026 Score=55.23 Aligned_cols=118 Identities=25% Similarity=0.405 Sum_probs=83.8
Q ss_pred HHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHH--HcCCCeeE
Q 020287 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAI--REERPIEV 94 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~--~~~~~~~~ 94 (328)
..++..+++..+.+++..|.+ +.+.++|+.+..++|++..+..+.....+................. ........
T Consensus 111 ~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 187 (232)
T COG2202 111 EERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEI 187 (232)
T ss_pred HHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcce
Confidence 344888999999999999998 9999999999999999987777766444433222211011112222 22334667
Q ss_pred EEEEEecCCCE-EEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~-~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
+.....++|.. .+......+... .|.+..+.....|++++++.
T Consensus 188 ~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 188 EYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred EEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhhc
Confidence 77888899986 777666666543 68888888999999988764
No 52
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=98.01 E-value=8.7e-06 Score=58.10 Aligned_cols=63 Identities=17% Similarity=0.113 Sum_probs=51.8
Q ss_pred CCCEEEechh-hHHhhCCCcccccccCcccccCCCCCHH-HHHHHHhhhhcCcC-------cccccceeeec
Q 020287 263 DMPMVYASDA-FLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQSSTDKGKHSN-------RASMHSTYLKL 325 (328)
Q Consensus 263 dg~i~~~N~a-~~~~~Gy~~~e~iG~~~~~l~~~~~~~~-~~~~~~~~~~~~~~-------~~~~g~~~~~~ 325 (328)
||+|+++.+. ...++||.++|++|+++..++||++... ..+..++.+.+|.. ..|+|...|..
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq 82 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ 82 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence 3999999999 6999999999999999999999999886 77778888877754 24788777754
No 53
>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=97.90 E-value=3.9e-05 Score=51.33 Aligned_cols=57 Identities=18% Similarity=0.229 Sum_probs=47.8
Q ss_pred cCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhh
Q 020287 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKG 310 (328)
Q Consensus 251 ~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~ 310 (328)
+++++++|.+ +.++++|+++++++|++..+++|+++..+.++.........+.....
T Consensus 2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 (103)
T cd00130 2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLS 58 (103)
T ss_pred CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHh
Confidence 5788999988 99999999999999999999999998888877776666665555543
No 54
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=97.81 E-value=9.8e-06 Score=69.12 Aligned_cols=104 Identities=23% Similarity=0.374 Sum_probs=85.5
Q ss_pred HHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCC-CChhHHHHHHHHHHcCCCeeEEEEEE
Q 020287 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLLNY 99 (328)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (328)
-.+++....+|-+.|.+ ..+.|+|++|+.|.|+.+.+++|+...++...+ ....+++.+..++..|..+.++...+
T Consensus 160 FaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~aR 236 (775)
T KOG1229|consen 160 FAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEAR 236 (775)
T ss_pred HHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHHh
Confidence 34678888899999998 899999999999999999999999987776543 34557788889999999999988888
Q ss_pred ecCCCEEEEEEEEEEeeeCCCCeEEEEEE
Q 020287 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVA 128 (328)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~ 128 (328)
++.|...-..+.++|+.. ..|++..++.
T Consensus 237 RksgdS~dqh~~itP~~g-qggkirhfvs 264 (775)
T KOG1229|consen 237 RKSGDSCDQHFIITPFAG-QGGKIRHFVS 264 (775)
T ss_pred hccCCcccceEEEeeecC-CCCceeeehh
Confidence 888877766777889887 6677666643
No 55
>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=97.76 E-value=6.3e-05 Score=46.03 Aligned_cols=60 Identities=22% Similarity=0.268 Sum_probs=48.7
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHH
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQS 305 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~ 305 (328)
+..+++.++.++++++.. +.+.++|+.+.+++|++..++.|+.+..+.++.+.......+
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEAL 62 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHH
Confidence 456778889999999988 999999999999999999999998877777666654444433
No 56
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.69 E-value=2.6e-05 Score=70.20 Aligned_cols=50 Identities=18% Similarity=0.165 Sum_probs=45.9
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccC
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~ 294 (328)
.++.+++++|+||+++|.+ |+|+++|+++++++||+.++++|+++..+..
T Consensus 99 ~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~ 148 (430)
T PRK11006 99 RFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLR 148 (430)
T ss_pred HHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhc
Confidence 3777999999999999998 9999999999999999999999999877654
No 57
>PF12860 PAS_7: PAS fold
Probab=97.68 E-value=2.3e-05 Score=56.48 Aligned_cols=43 Identities=23% Similarity=0.347 Sum_probs=38.7
Q ss_pred HhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccc-cccCcccc
Q 020287 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV-VGQNCRFL 292 (328)
Q Consensus 247 ~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~-iG~~~~~l 292 (328)
+++++.||++.|.+ ++++++|++|.+++|++++.+ .|.++..+
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l 44 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGASFRDL 44 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCCCHHHH
Confidence 46789999999999 999999999999999999988 78887555
No 58
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.67 E-value=3e-05 Score=71.06 Aligned_cols=52 Identities=17% Similarity=0.094 Sum_probs=47.8
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCC
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (328)
.+..+++++++||+++|.+ |+|+++|+++++++|++.++++|+++..+.++.
T Consensus 81 ~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~ 132 (520)
T PRK10820 81 ALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGF 132 (520)
T ss_pred HHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcc
Confidence 4778999999999999999 999999999999999999999999998887543
No 59
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.64 E-value=0.0003 Score=62.50 Aligned_cols=110 Identities=13% Similarity=0.154 Sum_probs=82.2
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChh--hhcCCCCccccCCCCChhHHHHHHHHHHcCCCe
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (328)
++-....++++++.+|++.+|.. |.+..+|.++++|+|+... +.+|++..++.+|+..- .+.+..+.+.
T Consensus 212 ~l~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~l------~~vl~~~~~~ 282 (537)
T COG3290 212 TLLEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSDL------PEVLETGKPQ 282 (537)
T ss_pred HHHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccCc------HHHHhcCCcc
Confidence 34455678899999999999999 9999999999999999765 68898877777653221 2223444443
Q ss_pred eEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
..+. ...+|. ++.+...|+.. .+++.|++.+++|-|+.++.
T Consensus 283 ~~~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L 323 (537)
T COG3290 283 HDEE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKL 323 (537)
T ss_pred cchh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHH
Confidence 3322 123444 56677889986 89999999999999999887
No 60
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.63 E-value=0.00082 Score=68.64 Aligned_cols=43 Identities=9% Similarity=0.063 Sum_probs=37.5
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhh
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e 60 (328)
....+++.++++++.+++++|.+ |+++++|+++++++|.+...
T Consensus 573 ~~~~~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~ 615 (1197)
T PRK09959 573 NQISFRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYK 615 (1197)
T ss_pred HHHHHHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCccccc
Confidence 34467788999999999999999 99999999999999986433
No 61
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.60 E-value=0.00068 Score=64.17 Aligned_cols=108 Identities=12% Similarity=0.228 Sum_probs=75.4
Q ss_pred HHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEE
Q 020287 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (328)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (328)
.+..+++..+++++++|.+ |+|+++|+++++++|++.++++|++...+++.. ..+..++..+.........
T Consensus 204 ~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~~ 274 (638)
T PRK11388 204 QLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEVT 274 (638)
T ss_pred HHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEEE
Confidence 4456899999999999999 999999999999999999999999876665321 1233455555544432222
Q ss_pred EecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccc
Q 020287 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (328)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~ 138 (328)
...+|..+++.+.+.|+.+ ..|. +++.+..+++..++
T Consensus 275 l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 275 FESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 3345666778888889865 3443 34555677776443
No 62
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.59 E-value=0.00074 Score=60.75 Aligned_cols=113 Identities=12% Similarity=0.032 Sum_probs=75.6
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCC-ee
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IE 93 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~ 93 (328)
+..++++.+++.+..|++..|.+ |.+.-+|+++++|+|.+-.+++|.+...+.|. +...+...-..+.. ..
T Consensus 367 ~rr~f~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~ap~-----~~~vf~~~~a~~~~~~~ 438 (712)
T COG5000 367 QRRRFLEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIAPE-----LEEVFAEAGAAARTDKR 438 (712)
T ss_pred HHHHHHHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhhhH-----HHHHHHHhhhhcCCCcc
Confidence 34567888999999999999999 99999999999999999999999885443221 11222222222222 22
Q ss_pred EEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
.+..+ ...|+...+.+..+.... + .-.+++.++.|||+...+
T Consensus 439 ~ev~~-~r~g~~rtl~Vq~t~~~~-d--~~~gyVvt~DDITdLV~A 480 (712)
T COG5000 439 VEVKL-AREGEERTLNVQATREPE-D--NGNGYVVTFDDITDLVIA 480 (712)
T ss_pred ceeec-ccCCCceeeeeeeeeccc-c--cCCceEEEecchHHHHHH
Confidence 23333 345556666666555443 2 223688899999998877
No 63
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.58 E-value=6.1e-05 Score=53.39 Aligned_cols=63 Identities=11% Similarity=0.088 Sum_probs=44.0
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhh
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDK 309 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~ 309 (328)
|..++++++.+++++|.+ ++|.+.|+++.++++..+ ..+|+++..+.++...+.....+....
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i~~~~ 63 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKIIEQVR 63 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHHHHHH
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHHHHHH
Confidence 456899999999999999 999999999999999875 458999999876544444444443333
No 64
>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=97.57 E-value=0.00023 Score=50.50 Aligned_cols=64 Identities=13% Similarity=0.052 Sum_probs=54.0
Q ss_pred HHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcc-cccCCCCCHHHHHHHHhhhhcC
Q 020287 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR-FLNGVDTDTTVLYQSSTDKGKH 312 (328)
Q Consensus 246 ~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~-~l~~~~~~~~~~~~~~~~~~~~ 312 (328)
-++..|-|++-.|.+ |+|+..|.+-.++.|++++.++|+++. ++.+-...+.+...+.+...++
T Consensus 21 elD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g 85 (124)
T TIGR02373 21 QFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASG 85 (124)
T ss_pred HhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcC
Confidence 467789999999999 999999999999999999999999974 5544446777888888876665
No 65
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=97.47 E-value=0.00049 Score=58.36 Aligned_cols=113 Identities=16% Similarity=0.163 Sum_probs=89.7
Q ss_pred HHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEE
Q 020287 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNL 96 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 96 (328)
.+.+++++++.|.-+-.+|.+ +.+.|.|+. .++|..++.. +|+.... .+|.........+.+.+.+|..-..++
T Consensus 289 ~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~sv-iGr~v~~-chpPksv~iv~ki~~~fksG~kd~~ef 362 (409)
T COG2461 289 LEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPSV-IGRRVQL-CHPPKSVHIVEKILKDFKSGEKDFAEF 362 (409)
T ss_pred HHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChHh-hCCcccC-CCCCchHHHHHHHHHHhhcCCcchHHH
Confidence 357889999999889999999 999999988 8888777764 7887653 445555667778888888888777776
Q ss_pred EEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
+. ... ...+.++..++.+ ++|...|.+-+.+|||..+..
T Consensus 363 w~-~~~--~~~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l 401 (409)
T COG2461 363 WI-NMG--DKFIHIRYFAVKD-EEGEYLGTLEVVQDITRIKEL 401 (409)
T ss_pred hc-cCC--CceEEEEEEEEEc-CCCceeeeehhhhhhHHHHhc
Confidence 63 222 2356788899999 899999999999999999876
No 66
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.45 E-value=0.0011 Score=61.67 Aligned_cols=106 Identities=14% Similarity=0.097 Sum_probs=72.7
Q ss_pred HHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCCh--hhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeE
Q 020287 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (328)
...++.+++.+++|++++|.+ |+++++|+++++++|++. ++++|++...+.++... . ..... ......
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~---~---~~~~~-~~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF---F---TEQID-EKRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh---h---hhhcC-Ccccce
Confidence 345677999999999999999 999999999999999965 46888886655433211 1 11111 111111
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
. ...+|. .+.+...|+.. .+.+.|.+.+++|+|+.++.
T Consensus 291 ~---~~~~~~--~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l 328 (545)
T PRK15053 291 V---ANFNGL--SVIANREAIRS--GDDLLGAIISFRSKDEISTL 328 (545)
T ss_pred E---EEECCE--EEEEEeeeEEE--CCeEEEEEEEEEchHHHHHH
Confidence 1 122443 34466778776 67788999999999998776
No 67
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=97.31 E-value=0.011 Score=43.91 Aligned_cols=111 Identities=11% Similarity=0.114 Sum_probs=75.2
Q ss_pred HHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEE
Q 020287 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (328)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (328)
.++.+++ .|.+|+--+.. ++-.++|.|.++.+|++++-+++++.+.+.-..+.........+.++...|-.....-..
T Consensus 33 ~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~GiR 110 (148)
T PF08670_consen 33 LAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIR 110 (148)
T ss_pred HHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeEE
Confidence 3444444 88888776654 446799999999999999999999998665544444444455555666666443334444
Q ss_pred EecCCCEEEEE-EEEEEeeeCCCCeEEEEEEEEec
Q 020287 99 YKKDGTPFWML-FKMSLVFGKEDGRATHFVAVQVP 132 (328)
Q Consensus 99 ~~~dg~~~~~~-~~~~~~~~~~~g~~~~~~~~~~D 132 (328)
+.+.|+.+++. ..+-.+.+ ++|...|.-.++.+
T Consensus 111 iss~Grrf~ie~a~vW~l~D-~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 111 ISSTGRRFRIERATVWNLID-EDGNYCGQAAMFSN 144 (148)
T ss_pred EcCCCCeEEEeceEEEEEEc-CCCCEEEEEEEEee
Confidence 67888888764 34556677 78887776655544
No 68
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.27 E-value=0.0035 Score=53.28 Aligned_cols=54 Identities=19% Similarity=0.273 Sum_probs=43.0
Q ss_pred HHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChh
Q 020287 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR 77 (328)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~ 77 (328)
..+++.+.--|++++++ |.|.|++..+.-.+|++.-|+.|-...+.+++.+...
T Consensus 82 shlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~de 135 (598)
T KOG3559|consen 82 SHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDE 135 (598)
T ss_pred HhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHH
Confidence 34566666667889999 9999999999999999999999988666666655444
No 69
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.24 E-value=0.015 Score=45.02 Aligned_cols=49 Identities=24% Similarity=0.276 Sum_probs=41.8
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~ 294 (328)
+..++++++++++++|.+ +.++++|+++++++||+..+.+++....+..
T Consensus 114 ~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~ 162 (232)
T COG2202 114 LRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIH 162 (232)
T ss_pred HHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEe
Confidence 455788889999999998 9999999999999999988888887655544
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=97.24 E-value=0.00088 Score=49.75 Aligned_cols=81 Identities=16% Similarity=0.071 Sum_probs=58.2
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCc-------Cc
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHS-------NR 315 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~-------~~ 315 (328)
+...+-+.|.+|+..+.. +|..++|.|.++.+|++|+.+|++|.+-+--..+....+....+.++..+|- ..
T Consensus 33 ~~~~L~~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRi 111 (148)
T PF08670_consen 33 LAKALWHAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRI 111 (148)
T ss_pred HHHHHHcCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeEEE
Confidence 344455588888887776 7789999999999999999999999986655555555555555655555442 23
Q ss_pred ccccceeee
Q 020287 316 ASMHSTYLK 324 (328)
Q Consensus 316 ~~~g~~~~~ 324 (328)
.+.|..|+.
T Consensus 112 ss~Grrf~i 120 (148)
T PF08670_consen 112 SSTGRRFRI 120 (148)
T ss_pred cCCCCeEEE
Confidence 567877754
No 71
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.19 E-value=0.00067 Score=61.52 Aligned_cols=91 Identities=11% Similarity=0.269 Sum_probs=76.0
Q ss_pred CCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCC
Q 020287 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (328)
Q Consensus 41 ~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (328)
.+|.||.+.+..++||++++++|+..-++++..+...+-....+.+..|....+.+++..++|...|+...++.+.+-.+
T Consensus 284 mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn 363 (768)
T KOG3558|consen 284 MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKN 363 (768)
T ss_pred eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCC
Confidence 78999999999999999999999999888888888888888889999999999999999999999999998888775123
Q ss_pred CeEEEEEEEEe
Q 020287 121 GRATHFVAVQV 131 (328)
Q Consensus 121 g~~~~~~~~~~ 131 (328)
.+...++++..
T Consensus 364 ~q~q~IicVnY 374 (768)
T KOG3558|consen 364 PQEQNIICVNY 374 (768)
T ss_pred CCcceEEEEEe
Confidence 33344444433
No 72
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=97.15 E-value=0.0048 Score=51.05 Aligned_cols=108 Identities=12% Similarity=0.102 Sum_probs=78.9
Q ss_pred HHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCee-EEEEEE
Q 020287 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNLLNY 99 (328)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~~~~ 99 (328)
..+++++..+++++|.+ +.|.|+|++++.+|+.+...+.|.....+.+.. .....-+.+....+.++. .+..+.
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~ 84 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV 84 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee
Confidence 46899999999999999 999999999999999999999998877766543 234445555666665544 333333
Q ss_pred ecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccc
Q 020287 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (328)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~ 138 (328)
.+|....+..++.|+.. ..|.++ ..+..+....+
T Consensus 85 -~~g~~~~v~~~v~~v~~-~~G~vl---le~~~~~~~~r 118 (363)
T COG3852 85 -ILGRSHIVDLTVAPVPE-EPGSVL---LEFHPRDMQRR 118 (363)
T ss_pred -ecCccceEEEEEeeccC-CCCeEE---EEechhHHHhH
Confidence 78999999999999986 566443 44444444433
No 73
>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=97.08 E-value=0.0027 Score=38.27 Aligned_cols=53 Identities=25% Similarity=0.423 Sum_probs=43.2
Q ss_pred HHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCC
Q 020287 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74 (328)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~ 74 (328)
+++.+++..+.++++++.. +.+.++|+.+..++|++..++.+.....+.++..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 54 (67)
T smart00091 2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPED 54 (67)
T ss_pred hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCccc
Confidence 3566788899999999998 9999999999999999998888876554444433
No 74
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.00 E-value=0.0064 Score=56.62 Aligned_cols=50 Identities=12% Similarity=0.157 Sum_probs=44.0
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCc--ccccccCcccccCC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGV 295 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~--~e~iG~~~~~l~~~ 295 (328)
+..+++++++||+++|.+ |+|+++|+++++++|++. ++++|+++..+.++
T Consensus 224 ~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~ 275 (545)
T PRK15053 224 QEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRP 275 (545)
T ss_pred HHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCC
Confidence 566889999999999999 999999999999999975 47999998777654
No 75
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.97 E-value=0.0004 Score=59.59 Aligned_cols=68 Identities=21% Similarity=0.304 Sum_probs=55.3
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCC-CCHHHHHHHHhhhhcCc
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD-TDTTVLYQSSTDKGKHS 313 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~-~~~~~~~~~~~~~~~~~ 313 (328)
+..+++...++|-|+|.+ ..|.|||+||+.|+||-..|++|+...++...+ .+....+.+...+++|.
T Consensus 159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgk 227 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGK 227 (775)
T ss_pred HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCc
Confidence 556777788999999988 999999999999999999999999988886544 34556666777776653
No 76
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.92 E-value=0.0024 Score=60.03 Aligned_cols=51 Identities=24% Similarity=0.234 Sum_probs=46.3
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (328)
+..++++++++++++|.+ |.++++|+++++++||++++++|+++..+.++.
T Consensus 264 ~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~ 314 (607)
T PRK11360 264 NELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGKPYSELFPPN 314 (607)
T ss_pred HHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCCcHHHHcCCc
Confidence 566889999999999998 999999999999999999999999998887644
No 77
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=96.89 E-value=0.0043 Score=55.40 Aligned_cols=51 Identities=20% Similarity=0.207 Sum_probs=45.3
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcc--cccccCcccccCCC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN--EVVGQNCRFLNGVD 296 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~--e~iG~~~~~l~~~~ 296 (328)
...+++++.+||+.+|.. |.|..+|.++++|+|+... +.+|+++.++..|+
T Consensus 217 r~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~ 269 (537)
T COG3290 217 RQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPD 269 (537)
T ss_pred HHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccc
Confidence 455889999999999999 9999999999999999765 79999998888764
No 78
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=96.72 E-value=0.024 Score=40.38 Aligned_cols=68 Identities=18% Similarity=0.088 Sum_probs=54.7
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCC-ccccCCCCChhHHHHHHHHHHcCC
Q 020287 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNG-RMFQGPRTNRRTIMEIREAIREER 90 (328)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~-~~l~~~~~~~~~~~~~~~~~~~~~ 90 (328)
-..-++.+|-|++-+|.+ |.|+..|.+-..+.|++++.++|++. .++-|-...+.+...+.+....|.
T Consensus 18 s~eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 18 GDAQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred CHhHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 345689999999999999 99999999999999999999999984 445454555567777777665554
No 79
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=96.30 E-value=0.0039 Score=55.74 Aligned_cols=74 Identities=30% Similarity=0.520 Sum_probs=56.1
Q ss_pred CceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCc--ccccCCCCCHHHHHHHHhhhhcCcC-------ccccccee
Q 020287 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQSSTDKGKHSN-------RASMHSTY 322 (328)
Q Consensus 252 ~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~--~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~~g~~~ 322 (328)
-.+++.+++.-|..|+|+|+.||++.||.+.|++.+++ .+..+...+....++++..+...+. +.|..+..
T Consensus 28 tsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TPv 107 (971)
T KOG0501|consen 28 TSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTPV 107 (971)
T ss_pred cceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCce
Confidence 34666777778899999999999999999999999875 4444455677788888888876542 45566666
Q ss_pred eec
Q 020287 323 LKL 325 (328)
Q Consensus 323 ~~~ 325 (328)
|-+
T Consensus 108 W~~ 110 (971)
T KOG0501|consen 108 WLL 110 (971)
T ss_pred EEE
Confidence 654
No 80
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=96.18 E-value=0.0023 Score=60.27 Aligned_cols=57 Identities=16% Similarity=0.187 Sum_probs=47.8
Q ss_pred HHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHH
Q 020287 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQS 305 (328)
Q Consensus 246 ~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~ 305 (328)
+++++...++++..+ |+|+||.++...++||..+|++|+++..+.||.+....++.+
T Consensus 100 mLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql 156 (803)
T KOG3561|consen 100 ILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQL 156 (803)
T ss_pred HHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcccccc
Confidence 566666666777777 999999999999999999999999999999988866665544
No 81
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.11 E-value=0.0086 Score=50.82 Aligned_cols=55 Identities=16% Similarity=0.088 Sum_probs=48.9
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCH
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT 299 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~ 299 (328)
.+...++++|+.++-+|.. |.+..+|+|+++++|.+.+++.|.+...+....+.+
T Consensus 81 ~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~nf~ 135 (511)
T COG3283 81 ALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFNFL 135 (511)
T ss_pred HHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCCHH
Confidence 3677899999999999999 999999999999999999999999988887655543
No 82
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=96.05 E-value=0.0083 Score=50.56 Aligned_cols=59 Identities=15% Similarity=0.208 Sum_probs=51.3
Q ss_pred hHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHH
Q 020287 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY 303 (328)
Q Consensus 242 ~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~ 303 (328)
+|..++.-+.+||+-+|.. |+|+.+|..+.+++|.+.++++|+++.++..-.+...+.+
T Consensus 112 kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~d 170 (459)
T COG5002 112 KLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFED 170 (459)
T ss_pred HHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHH
Confidence 4777888889999999999 9999999999999999999999999988877666554444
No 83
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=95.89 E-value=0.012 Score=54.75 Aligned_cols=51 Identities=16% Similarity=0.227 Sum_probs=42.2
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCC---cccccccCcccccC
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNG 294 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~ 294 (328)
+.+..+++++++||+++|.+ |+|+++|+++++++|++ +.+.+|+.+..+..
T Consensus 221 ~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~ 274 (542)
T PRK11086 221 EQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMP 274 (542)
T ss_pred HHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCC
Confidence 34677899999999999999 99999999999999875 35677877665543
No 84
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=95.87 E-value=0.087 Score=27.76 Aligned_cols=41 Identities=29% Similarity=0.448 Sum_probs=32.6
Q ss_pred EEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccc
Q 020287 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (328)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~ 136 (328)
++.....+|...|+.....++.+ ..+.+.+++++..|||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence 34456678888898888888887 678888899999999863
No 85
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=95.84 E-value=0.028 Score=47.80 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=47.7
Q ss_pred hHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCC
Q 020287 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR 73 (328)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~ 73 (328)
....+.+++++++++++.+|.. |.+..+|++++.++|.+++.+.|.....+.+..
T Consensus 78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~ 132 (511)
T COG3283 78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGF 132 (511)
T ss_pred HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcC
Confidence 3346788999999999999999 999999999999999999999998866665443
No 86
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=95.43 E-value=0.023 Score=47.21 Aligned_cols=65 Identities=15% Similarity=0.162 Sum_probs=52.6
Q ss_pred HHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcC
Q 020287 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSN 314 (328)
Q Consensus 245 ~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 314 (328)
.++++++..++++|.+ +.|.|+|++++.+||-+..-+.|..+..|.... .....-+.+...++.+
T Consensus 11 ~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~ 75 (363)
T COG3852 11 AILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQP 75 (363)
T ss_pred hHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCC
Confidence 5788999999999999 999999999999999999999999998887533 3445555566555544
No 87
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=95.26 E-value=0.084 Score=47.05 Aligned_cols=93 Identities=14% Similarity=0.162 Sum_probs=74.8
Q ss_pred CCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCC
Q 020287 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (328)
Q Consensus 41 ~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (328)
+..+.+......++||...|+.|.....+.+.++..-......+.+.+|.+....++..+++|++.|+..+...++. +
T Consensus 293 fa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarllyk--n 370 (712)
T KOG3560|consen 293 FALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLYK--N 370 (712)
T ss_pred cceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeeee--c
Confidence 56777888899999999999998876667766666556677788889999888888999999999999988877775 7
Q ss_pred CeEEEEEEEEecccc
Q 020287 121 GRATHFVAVQVPIVS 135 (328)
Q Consensus 121 g~~~~~~~~~~DIte 135 (328)
|+.-.++.+.+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 777777766655554
No 88
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=94.43 E-value=0.75 Score=34.08 Aligned_cols=86 Identities=13% Similarity=0.156 Sum_probs=67.7
Q ss_pred CCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCC
Q 020287 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (328)
Q Consensus 41 ~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (328)
.++..+-...++++|+ ++.|+...++..+.....+...+..++....+..........+|....++.-..|+.+ +.
T Consensus 51 ~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~-~~ 126 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRS-DG 126 (137)
T ss_pred eEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCC-CC
Confidence 4566788899999998 4678888877777766666677777877777877777777788888888888999988 67
Q ss_pred CeEEEEEEEE
Q 020287 121 GRATHFVAVQ 130 (328)
Q Consensus 121 g~~~~~~~~~ 130 (328)
|.+..++|..
T Consensus 127 ~~v~rilG~~ 136 (137)
T PF07310_consen 127 GTVDRILGAL 136 (137)
T ss_pred CCccEEEEec
Confidence 8888777754
No 89
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=91.76 E-value=0.17 Score=46.23 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=43.1
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCccccc
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (328)
+...++..+.|++..|.+ |++.-+|++.++|+|.+.++++|++.+.+.
T Consensus 372 ~E~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~~lsa~a 419 (712)
T COG5000 372 LEAVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQSLSAIA 419 (712)
T ss_pred HHHHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcchhhhhh
Confidence 455788899999999999 999999999999999999999999976654
No 90
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=91.70 E-value=1.1 Score=42.86 Aligned_cols=56 Identities=11% Similarity=0.119 Sum_probs=42.7
Q ss_pred eEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhh
Q 020287 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKG 310 (328)
Q Consensus 254 i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~ 310 (328)
||++--. +.+.|..|..++.-++||-+.++||+.+..++|+.+.....+.-...++
T Consensus 332 iFtT~HT-ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q 387 (1114)
T KOG3753|consen 332 IFTTTHT-PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQ 387 (1114)
T ss_pred eeEeccC-CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHH
Confidence 4554322 4488889999999999999999999999999999887665554444443
No 91
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=91.19 E-value=3.3 Score=41.46 Aligned_cols=42 Identities=7% Similarity=0.025 Sum_probs=34.6
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCCh
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~ 58 (328)
...++.+.+++.+|.++++++.. +|.+++.|+.+..++|+..
T Consensus 331 e~e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~ 372 (924)
T PRK10841 331 EHEQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLT 372 (924)
T ss_pred HHHHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCC
Confidence 45567889999999999999743 3999999999999887643
No 92
>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=91.01 E-value=0.19 Score=35.66 Aligned_cols=44 Identities=27% Similarity=0.477 Sum_probs=34.8
Q ss_pred Cce-EEeCCCCCCCCEEEechhhHHhhCCC---cccccccCcccccCCCC
Q 020287 252 QSF-VLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNGVDT 297 (328)
Q Consensus 252 ~~i-~i~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~~~~ 297 (328)
-|+ +.+|.. |++|+.++....+++|.+ +++++|+++..+.++..
T Consensus 15 hG~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~ 62 (110)
T PF08446_consen 15 HGALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES 62 (110)
T ss_dssp TSEEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred CEEEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence 344 445543 489999999999999999 99999999998886554
No 93
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=90.11 E-value=0.47 Score=48.92 Aligned_cols=39 Identities=8% Similarity=-0.039 Sum_probs=34.0
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccc
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV 284 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~ 284 (328)
++.++++++.+|+++|.+ |+|+++|+++++++|++..+.
T Consensus 578 ~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~ 616 (1197)
T PRK09959 578 RKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKN 616 (1197)
T ss_pred HHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCcccccc
Confidence 456789999999999999 999999999999999875443
No 94
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=89.06 E-value=0.43 Score=42.79 Aligned_cols=60 Identities=15% Similarity=0.151 Sum_probs=52.5
Q ss_pred HHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhh
Q 020287 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTD 308 (328)
Q Consensus 246 ~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~ 308 (328)
.+.+....++++..+ |.|.|+....+..+|+-..+++-+++.+|+|.+++.++-+.+.-+
T Consensus 116 lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLhwa 175 (712)
T KOG3560|consen 116 LLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLHWA 175 (712)
T ss_pred HHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHhhc
Confidence 566666777888888 999999999999999999999999999999999988888777655
No 95
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=88.86 E-value=11 Score=35.27 Aligned_cols=40 Identities=18% Similarity=0.250 Sum_probs=32.2
Q ss_pred ccCceEEeCCCCCCCCEEEechhhHHhhCCC-cccccccCcccc
Q 020287 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFL 292 (328)
Q Consensus 250 ~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l 292 (328)
.+++.+++|.+ ++++..|++...+++.+ ..-++|.+...+
T Consensus 231 ~~~~~lavd~~---grvl~at~aA~~~La~~~~~~l~g~p~~~~ 271 (606)
T COG3284 231 QSEALLAVDQD---GRVLGATRAARQLLALTDRQRLIGQPVEDF 271 (606)
T ss_pred ccceeeeecCc---chhhhccHHHHHhhccchhhHhhcCCcccc
Confidence 46778889988 99999999999999987 555677765444
No 96
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=86.19 E-value=0.5 Score=45.18 Aligned_cols=48 Identities=10% Similarity=0.163 Sum_probs=41.2
Q ss_pred CCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhh
Q 020287 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDK 309 (328)
Q Consensus 262 ~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~ 309 (328)
.||.++++-.....+.||...++.|+++..+.|+++.......+....
T Consensus 380 ~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~s~h~~d~~~~~~s~~~~~ 427 (803)
T KOG3561|consen 380 SDGSFTFVDQRASAILGYQPQELLGRSSYESSHPADSSPLSESLKQVQ 427 (803)
T ss_pred cCCceeccccccccccccCchhhcCcccccccCccccchhhchHHHHH
Confidence 559999999999999999999999999988888888777776665553
No 97
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=84.50 E-value=2.8 Score=36.38 Aligned_cols=84 Identities=8% Similarity=0.062 Sum_probs=56.4
Q ss_pred EEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEecCCCEEEEEE
Q 020287 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLF 110 (328)
Q Consensus 31 i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~ 110 (328)
++....+ ..+++......+++||.+.+++++..-..+...+...+.......+..|....--+++..+.|.+.|+.-
T Consensus 228 mfraslD---lkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvqs 304 (598)
T KOG3559|consen 228 MFRASLD---LKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQS 304 (598)
T ss_pred EEEeecc---eEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEEE
Confidence 4455566 7899999999999999999999998554444444333333333444555544444556678888888876
Q ss_pred EEEEeee
Q 020287 111 KMSLVFG 117 (328)
Q Consensus 111 ~~~~~~~ 117 (328)
..+.+.+
T Consensus 305 yat~vHn 311 (598)
T KOG3559|consen 305 YATFVHN 311 (598)
T ss_pred eeEEEec
Confidence 6665554
No 98
>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=79.19 E-value=2.9 Score=29.58 Aligned_cols=41 Identities=27% Similarity=0.395 Sum_probs=32.7
Q ss_pred EEEEcCCCCCCCEEEechHHHHhhCCC---hhhhcCCCCccccCCC
Q 020287 31 FTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPR 73 (328)
Q Consensus 31 i~~~d~~~~~~~i~~~N~~~~~~~g~~---~~e~~g~~~~~l~~~~ 73 (328)
++++|.+ +++|+.++.+...++|.+ .++++|++...+....
T Consensus 18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~ 61 (110)
T PF08446_consen 18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAE 61 (110)
T ss_dssp EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCC
T ss_pred EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHH
Confidence 4556553 489999999999999999 9999999988776544
No 99
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=75.81 E-value=12 Score=36.32 Aligned_cols=80 Identities=10% Similarity=0.145 Sum_probs=58.6
Q ss_pred EEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCC-C--eeEEEEEEecCCCEEE
Q 020287 31 FTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-P--IEVNLLNYKKDGTPFW 107 (328)
Q Consensus 31 i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~--~~~e~~~~~~dg~~~~ 107 (328)
++.+... +++.+..|..++..++||-+.++||+.+..+.++.+...+.+...+.+..+. + ....+++...+|..+.
T Consensus 332 iFtT~HT-ptClf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ 410 (1114)
T KOG3753|consen 332 IFTTTHT-PTCLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVR 410 (1114)
T ss_pred eeEeccC-CcceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEE
Confidence 4444433 4577888999999999999999999998878777777777777677776553 3 2246777888998776
Q ss_pred EEEE
Q 020287 108 MLFK 111 (328)
Q Consensus 108 ~~~~ 111 (328)
+...
T Consensus 411 ldTe 414 (1114)
T KOG3753|consen 411 LDTE 414 (1114)
T ss_pred Eech
Confidence 5543
No 100
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=75.78 E-value=5.9 Score=31.70 Aligned_cols=38 Identities=18% Similarity=0.085 Sum_probs=33.5
Q ss_pred HHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCCC
Q 020287 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFS 57 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~~ 57 (328)
.+-+..+++..+.|+++-+.+ |.+++.|.+|.+.|...
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhc
Confidence 346778999999999999999 99999999999988643
No 101
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=73.00 E-value=5.5 Score=31.89 Aligned_cols=37 Identities=14% Similarity=0.057 Sum_probs=32.3
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCC
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~ 280 (328)
+.+..++...+.+++|-+.+ |.+++.|.+|.+.++-+
T Consensus 19 ~~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhc
Confidence 34777889999999999988 99999999999998744
No 102
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=69.72 E-value=11 Score=37.64 Aligned_cols=40 Identities=13% Similarity=0.075 Sum_probs=34.1
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCC
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~ 56 (328)
......+.+++.+|.|++++|.. +++++.+|+++.+++|.
T Consensus 340 ~~~~l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~ 379 (894)
T PRK10618 340 ILRALNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPH 379 (894)
T ss_pred HHHHHHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCc
Confidence 45567889999999999999943 28999999999999875
No 103
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=65.78 E-value=7.7 Score=38.69 Aligned_cols=38 Identities=8% Similarity=-0.095 Sum_probs=32.3
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCC
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~ 280 (328)
...+.+++++|+|++++|.. +++++++|+++.+++|+.
T Consensus 343 ~l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 343 ALNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCcc
Confidence 34667899999999999943 289999999999999874
No 104
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=65.49 E-value=11 Score=32.86 Aligned_cols=66 Identities=9% Similarity=0.119 Sum_probs=51.2
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcC
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKH 312 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~ 312 (328)
+.+..++...|--|.-+|.+ +++-|.|+. .++|-.++. ++|+++.. +||.........+.+..+.|
T Consensus 290 ~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~~-chpPksv~iv~ki~~~fksG 355 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQL-CHPPKSVHIVEKILKDFKSG 355 (409)
T ss_pred HHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCcccC-CCCCchHHHHHHHHHHhhcC
Confidence 45888899999777778888 899999998 888877664 58998764 45555577777887777766
No 105
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=63.17 E-value=21 Score=25.65 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=34.7
Q ss_pred eeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecccccccc
Q 020287 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (328)
Q Consensus 92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~~ 139 (328)
....+....++|+ .+..+...+++ ++|+++|++++-.|+|....+
T Consensus 68 ~~~nY~~~~~~Gk--~lrSsT~~Ird-~~g~~iG~LCIN~D~s~~~~~ 112 (118)
T PF08348_consen 68 YIINYKTKTKDGK--ILRSSTFFIRD-ENGKLIGALCINFDISALEQA 112 (118)
T ss_pred ccccccccCCCCC--EEEEEEEEEEC-CCCCEEEEEEEEeccHHHHHH
Confidence 3344555677886 45667778888 889999999999999988766
No 106
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=61.32 E-value=11 Score=37.22 Aligned_cols=44 Identities=11% Similarity=0.018 Sum_probs=37.1
Q ss_pred HHHHHhhccCceEEeC-CCCCCCCEEEechhhHHhhCCCcccccccCcccc
Q 020287 243 LYISLGRIKQSFVLID-PHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL 292 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d-~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l 292 (328)
...++...|-|++++| .+ |.|.+.|+.|.+++| .+ ++|+++..+
T Consensus 104 ~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 104 GEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 5567888999999999 57 999999999999988 33 899988764
No 107
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=59.64 E-value=25 Score=32.74 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=33.7
Q ss_pred hhHHHHHHHHhcCCcEEEEEcCCCCCCCEEEechHHHHhhCC
Q 020287 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (328)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~g~ 56 (328)
+....++.++.++|.|+++.+.+ +.+.|+||-...+|+-
T Consensus 72 ~~~~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~~ 110 (655)
T COG3887 72 QAEKSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFNK 110 (655)
T ss_pred HHHHHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcCh
Confidence 45556788999999999999988 9999999999888753
No 108
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=58.33 E-value=21 Score=35.24 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=37.0
Q ss_pred HHHHHHHHhcCCcEEEEEc-CCCCCCCEEEechHHHHhhCCChhhhcCCCCcc
Q 020287 17 TLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRM 68 (328)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d-~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~ 68 (328)
..-.+.++...|.|++++| .+ |.+.|+|+.|..++| .. ++|.+...
T Consensus 101 ~~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~ 147 (838)
T PRK14538 101 SQIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQ 147 (838)
T ss_pred hHHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHH
Confidence 3445668899999999999 67 999999999999987 22 78887554
No 109
>PF11927 DUF3445: Protein of unknown function (DUF3445); InterPro: IPR021848 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 264 to 418 amino acids in length. This protein has a conserved RLP sequence motif. This protein has two completely conserved R residues that may be functionally important.
Probab=56.57 E-value=12 Score=30.93 Aligned_cols=56 Identities=13% Similarity=0.114 Sum_probs=42.9
Q ss_pred HHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccccCCCCC
Q 020287 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298 (328)
Q Consensus 243 l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~ 298 (328)
|..+-..+++-++|...+..+|.+...--+.|==.|+++.+-+|+++..++.|-..
T Consensus 98 L~~~~~~vqEDl~il~~~~~~~~~~L~A~~~cfP~~W~l~~K~G~~l~~IH~PVP~ 153 (249)
T PF11927_consen 98 LEILGRLVQEDLCILLRDEEDGEYRLRAGVVCFPAGWSLSEKIGKPLAAIHGPVPG 153 (249)
T ss_pred HHHHHHhChhcEEEEeecCCCCcEEEeheeeecCCCCCHHHHcCCcHHHhcCCccc
Confidence 55566667777777665545578888877888888999999999999998876543
No 110
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.46 E-value=1.1e+02 Score=24.12 Aligned_cols=105 Identities=16% Similarity=0.204 Sum_probs=66.5
Q ss_pred HHhcCCcEEEEEcCCCCCCC--EEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHHcCCCeeEEEEEEe
Q 020287 23 ALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (328)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~~~--i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (328)
+...+++.+++ ..+.. |. +..+-...|.+||- |+-|.....+..+.+.......+..+.....++-.......
T Consensus 53 l~slL~d~FiL-~~~~~-G~~~FRLAGTriC~LfGR---ELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s 127 (209)
T COG5388 53 LKSLLPDVFIL-ERDGR-GKLPFRLAGTRICDLFGR---ELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRS 127 (209)
T ss_pred HHhhcCceEEE-eccCC-CCceEEecccchhhhhch---hhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhh
Confidence 45566665444 33311 33 34456667888775 56777766666666665555555556666666666555666
Q ss_pred cCCCEEEEEEEEEEeeeCCCCeEEEEEEEEecc
Q 020287 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (328)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (328)
..|...-+++-..|+.. ..|+...++|...-+
T Consensus 128 ~~G~sl~fEmLl~PL~~-~~g~~~R~LGais~~ 159 (209)
T COG5388 128 HGGRSLGFEMLLAPLQG-ASGETDRFLGAISPI 159 (209)
T ss_pred ccCcccceeeeeecccC-CCCCccchhhhcccc
Confidence 77777788888999987 677756666665544
No 111
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=52.53 E-value=24 Score=26.02 Aligned_cols=50 Identities=14% Similarity=0.102 Sum_probs=40.9
Q ss_pred CCCEEEechhhHHhhCCCcccccccCcccccCCCCCHHHHHHHHhhhhcCcCc
Q 020287 263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQSSTDKGKHSNR 315 (328)
Q Consensus 263 dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 315 (328)
+.++-.+=...++++|+ |+.|+++.++..+.........+..++....+.
T Consensus 50 ~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~ 99 (137)
T PF07310_consen 50 DFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPV 99 (137)
T ss_pred ceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceE
Confidence 35667888999999997 578999999988888888888888888777664
No 112
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=50.42 E-value=34 Score=29.20 Aligned_cols=88 Identities=14% Similarity=0.307 Sum_probs=53.9
Q ss_pred HHHHHhcCC----cEEEEEcCCCCCCCEEEechHHHHhhCCChhhhcCCCCccccCCCCChhHHHHHHHHHH--cCCCee
Q 020287 20 VHEALDELP----DSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR--EERPIE 93 (328)
Q Consensus 20 ~~~~~~~~~----~~i~~~d~~~~~~~i~~~N~~~~~~~g~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~ 93 (328)
.++++|++. .+++|..+. +.+.+|+|.-+..++||+.++++......+. .....+...+. ......
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV~------eGl~qW~~dL~~~s~~E~~ 356 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIVQ------EGLAQWETDLQLLSRQERS 356 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHHH------hhHHHHHHHHHhhhhhhhh
Confidence 455555543 345666654 3788999999999999999998765332221 11222222222 223345
Q ss_pred EEEEEEecCCCEEEEEEEEEEe
Q 020287 94 VNLLNYKKDGTPFWMLFKMSLV 115 (328)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~ 115 (328)
+...+.+++|....+......+
T Consensus 357 grlviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 357 GRLVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred ceEEEEecCCCceeeEEEEeec
Confidence 6677788888887776665554
No 113
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=47.45 E-value=28 Score=32.40 Aligned_cols=44 Identities=14% Similarity=0.194 Sum_probs=34.9
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcc
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR 290 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~ 290 (328)
..+..++.++|-||++.|.+ +.+.++||-...+|+ ++.+|....
T Consensus 75 ~~~~~al~nmPiGii~~~e~---~~veW~Npf~~~if~---~~~~~~~~~ 118 (655)
T COG3887 75 KSLEEALTNMPIGIILFNET---NKVEWVNPFASKIFN---KNEIGESLS 118 (655)
T ss_pred HHHHHHHHhCCceEEEEcCC---CceEEecHHHHHhcC---hhhhhhhHH
Confidence 34677899999999999988 999999999999986 334454333
No 114
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=46.08 E-value=71 Score=21.14 Aligned_cols=47 Identities=15% Similarity=0.151 Sum_probs=30.2
Q ss_pred HHHHHHcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccc
Q 020287 82 IREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (328)
Q Consensus 82 ~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt 134 (328)
+.+++..+... +.....|...-+-+.+.|+.+ .+|++++.+++. |+|
T Consensus 37 Le~vl~~g~v~----r~~P~~G~Y~G~PViV~PI~~-~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 37 LEEVLETGKVI----RVTPIEGPYKGVPVIVAPIKD-EDGEVIAAIGVV-DLT 83 (84)
T ss_pred HHHHHHcCCEE----EeccCCcccCCeeEEEEEEEc-CCCCEEEEEEEE-Ecc
Confidence 34455555422 223445655556677899998 779999999876 544
No 115
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=45.49 E-value=5.8 Score=33.56 Aligned_cols=39 Identities=15% Similarity=0.409 Sum_probs=29.7
Q ss_pred CceEEeCCCCCCCCEEEechhhHHhhCCCcccccccCcccc
Q 020287 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFL 292 (328)
Q Consensus 252 ~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l 292 (328)
.++++..+. +.+.+|+|.-+..++||+.++++..-...+
T Consensus 298 gmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~dIV 336 (401)
T PF06785_consen 298 GMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSDIV 336 (401)
T ss_pred ceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchHHH
Confidence 445666654 488999999999999999999886543333
No 116
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=44.85 E-value=58 Score=21.07 Aligned_cols=29 Identities=10% Similarity=0.255 Sum_probs=21.9
Q ss_pred EEEEEEEEeeeCCCCeEEEEEEEEeccccc
Q 020287 107 WMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (328)
Q Consensus 107 ~~~~~~~~~~~~~~g~~~~~~~~~~DIte~ 136 (328)
++.....|+.+ .+|++.|++++-.++...
T Consensus 13 ~vi~~s~pi~~-~~g~~~Gvv~~di~l~~l 41 (81)
T PF02743_consen 13 PVITISVPIYD-DDGKIIGVVGIDISLDQL 41 (81)
T ss_dssp EEEEEEEEEEE-TTTEEEEEEEEEEEHHHH
T ss_pred EEEEEEEEEEC-CCCCEEEEEEEEecccee
Confidence 55566789998 799999998876665544
No 117
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=31.18 E-value=70 Score=32.34 Aligned_cols=39 Identities=3% Similarity=-0.070 Sum_probs=32.1
Q ss_pred hhHHHHHhhccCceEEeCCCCCCCCEEEechhhHHhhCCCc
Q 020287 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR 281 (328)
Q Consensus 241 ~~l~~~~~~~~~~i~i~d~~~~dg~i~~~N~a~~~~~Gy~~ 281 (328)
+..+.+++++|.|+++++.. ||.+++.|+.+..++|+..
T Consensus 334 ~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~ 372 (924)
T PRK10841 334 QFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLT 372 (924)
T ss_pred HHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCC
Confidence 34667889999999998743 4999999999999998743
No 118
>PF12282 H_kinase_N: Signal transduction histidine kinase; InterPro: IPR022066 This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with PF07568 from PFAM, PF08448 from PFAM, PF02518 from PFAM. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this. ; PDB: 2YKH_B 2YKF_A.
Probab=27.58 E-value=2.6e+02 Score=20.92 Aligned_cols=54 Identities=9% Similarity=0.081 Sum_probs=23.5
Q ss_pred HHHHHHHHcCCCeeEEEEEEecCCCEEEEEEEEEEeeeCCCCeEEEEEEEEeccccccc
Q 020287 80 MEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (328)
Q Consensus 80 ~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIte~k~ 138 (328)
..+.+++.+|......- ........+...+.|+++ +|++++++..-.++...+.
T Consensus 79 p~v~~a~~tg~~~~~~~---~~~~~~~~v~~~~~PI~~--~~~vIaVl~~~~~~~~~~~ 132 (145)
T PF12282_consen 79 PAVDRALETGRPVRGGR---AVWQGGVPVRQEVVPIRR--NGRVIAVLIRETNLSASRT 132 (145)
T ss_dssp HHHHHHHH---------------------EEEEEEEEE--TTEEEEEEEEE--GGGS--
T ss_pred HHHHHHHHhCCceecCC---ccccCCceeEEEEEEEEE--CCEEEEEEEEEcccccccC
Confidence 34556666665544321 111222367788999998 6798888876656655544
No 119
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=21.06 E-value=63 Score=30.61 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=29.3
Q ss_pred CCCCEEEechhhHHhhCCCcccccccCcccccC
Q 020287 262 PDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (328)
Q Consensus 262 ~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~ 294 (328)
+|+.|+.++..+..++|..++++.|+++..+..
T Consensus 38 ~~~~Vlq~S~N~~~~LG~~~e~l~~~tl~~vl~ 70 (750)
T COG4251 38 ADLMVLQASENCANILGREPEDLLGRTLGAVLT 70 (750)
T ss_pred CCchhhhhhhhHHHHhCCChhhhhcCCHHHhcc
Confidence 359999999999999999999999999877654
Done!