Query 020523
Match_columns 325
No_of_seqs 238 out of 1820
Neff 10.9
Searched_HMMs 46136
Date Fri Mar 29 03:04:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020523.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020523hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02040 PpsR-CrtJ transcript 99.9 1.6E-20 3.5E-25 167.7 19.7 202 15-324 130-342 (442)
2 PRK13560 hypothetical protein; 99.9 9.9E-20 2.1E-24 175.0 22.6 185 8-293 195-382 (807)
3 PRK09776 putative diguanylate 99.8 2.4E-20 5.3E-25 184.5 17.5 283 15-324 280-630 (1092)
4 TIGR02040 PpsR-CrtJ transcript 99.8 9.2E-20 2E-24 162.8 13.0 195 24-307 2-197 (442)
5 TIGR02938 nifL_nitrog nitrogen 99.8 6.1E-19 1.3E-23 160.1 14.8 181 18-298 4-184 (494)
6 PRK13560 hypothetical protein; 99.8 2.8E-18 6E-23 165.0 19.6 205 17-324 66-294 (807)
7 PRK11359 cyclic-di-GMP phospho 99.8 3.2E-17 7E-22 157.4 19.6 201 18-324 12-227 (799)
8 PF13426 PAS_9: PAS domain; PD 99.7 3.9E-16 8.4E-21 110.6 13.6 104 28-135 1-104 (104)
9 PF08448 PAS_4: PAS fold; Int 99.6 3.6E-15 7.7E-20 106.7 12.1 110 24-138 1-110 (110)
10 PF00989 PAS: PAS fold; Inter 99.6 1.1E-14 2.4E-19 104.7 13.3 112 18-133 1-113 (113)
11 PRK11091 aerobic respiration c 99.4 3.3E-12 7.2E-17 122.4 16.5 122 15-140 152-273 (779)
12 PRK13559 hypothetical protein; 99.4 6.7E-12 1.5E-16 109.5 15.2 125 15-140 40-164 (361)
13 PRK13557 histidine kinase; Pro 99.4 9.2E-12 2E-16 114.5 14.6 128 15-143 27-154 (540)
14 PF13426 PAS_9: PAS domain; PD 99.3 2E-12 4.3E-17 91.3 6.1 71 251-324 1-81 (104)
15 PF00989 PAS: PAS fold; Inter 99.3 1.7E-12 3.6E-17 93.2 5.8 81 241-324 1-92 (113)
16 PRK13558 bacterio-opsin activa 99.3 3.3E-10 7.2E-15 106.8 17.7 124 19-143 149-272 (665)
17 PRK10060 RNase II stability mo 99.2 3.6E-10 7.7E-15 106.0 14.5 123 16-143 109-233 (663)
18 TIGR00229 sensory_box PAS doma 99.2 8.6E-10 1.9E-14 78.2 12.6 118 18-140 3-121 (124)
19 PF08447 PAS_3: PAS fold; Int 99.2 3E-10 6.5E-15 78.1 9.5 86 43-130 1-91 (91)
20 PRK11359 cyclic-di-GMP phospho 99.0 2.4E-09 5.3E-14 103.3 13.2 120 17-140 135-255 (799)
21 PRK09776 putative diguanylate 99.0 6E-09 1.3E-13 103.9 14.5 127 8-140 401-528 (1092)
22 PRK13557 histidine kinase; Pro 99.0 9.2E-10 2E-14 101.3 7.3 84 241-324 30-123 (540)
23 cd00130 PAS PAS domain; PAS mo 99.0 4.5E-08 9.7E-13 66.1 13.8 103 27-133 1-103 (103)
24 PRK13559 hypothetical protein; 98.9 5E-09 1.1E-13 91.5 7.5 83 242-324 44-136 (361)
25 PF13596 PAS_10: PAS domain; P 98.9 2.2E-08 4.8E-13 70.9 8.9 106 20-134 1-106 (106)
26 PF08448 PAS_4: PAS fold; Int 98.9 3.5E-09 7.6E-14 75.4 4.7 75 247-324 1-84 (110)
27 PF12860 PAS_7: PAS fold 98.8 2.5E-08 5.4E-13 71.8 9.1 104 24-140 1-114 (115)
28 COG3829 RocR Transcriptional r 98.8 2.5E-08 5.5E-13 87.1 9.6 163 21-293 4-166 (560)
29 PRK11360 sensory histidine kin 98.8 1E-07 2.2E-12 88.9 13.8 121 16-143 260-381 (607)
30 PRK10060 RNase II stability mo 98.8 1.5E-08 3.2E-13 95.2 7.8 77 244-323 114-201 (663)
31 PF14598 PAS_11: PAS domain; P 98.8 4.2E-07 9.1E-12 64.5 12.8 102 32-136 6-109 (111)
32 KOG3558 Hypoxia-inducible fact 98.7 1.4E-07 3.1E-12 83.7 12.0 68 254-322 275-352 (768)
33 TIGR02966 phoR_proteo phosphat 98.7 1.1E-07 2.3E-12 81.9 11.1 108 15-139 3-110 (333)
34 PRK11073 glnL nitrogen regulat 98.7 1.5E-07 3.3E-12 81.7 10.9 111 18-139 7-117 (348)
35 KOG0501 K+-channel KCNQ [Inorg 98.7 2.1E-07 4.6E-12 81.2 10.2 123 16-139 12-139 (971)
36 COG3829 RocR Transcriptional r 98.6 1.6E-06 3.4E-11 76.2 15.0 112 15-139 114-225 (560)
37 PF08447 PAS_3: PAS fold; Int 98.6 3.4E-08 7.4E-13 67.7 3.3 58 266-324 1-73 (91)
38 PF13188 PAS_8: PAS domain; PD 98.5 1.3E-07 2.8E-12 60.1 4.4 45 242-293 2-46 (64)
39 PRK11091 aerobic respiration c 98.5 1.2E-07 2.7E-12 91.1 5.6 82 240-324 154-245 (779)
40 COG5002 VicK Signal transducti 98.5 2.7E-06 5.9E-11 70.2 12.0 114 15-139 108-221 (459)
41 PRK13558 bacterio-opsin activa 98.5 3.4E-07 7.4E-12 86.6 7.1 82 243-324 150-241 (665)
42 TIGR02938 nifL_nitrog nitrogen 98.4 2.4E-07 5.2E-12 84.2 5.0 80 241-323 4-93 (494)
43 TIGR02966 phoR_proteo phosphat 98.4 2.4E-07 5.2E-12 79.7 4.4 79 240-324 5-88 (333)
44 TIGR00229 sensory_box PAS doma 98.4 1.1E-06 2.3E-11 61.9 6.6 80 242-324 4-94 (124)
45 PRK11073 glnL nitrogen regulat 98.3 7.8E-07 1.7E-11 77.2 5.9 80 242-324 8-95 (348)
46 PF14598 PAS_11: PAS domain; P 98.3 1.1E-06 2.4E-11 62.3 4.6 61 263-323 11-83 (111)
47 PRK11006 phoR phosphate regulo 98.3 2.6E-06 5.6E-11 76.3 8.0 112 9-140 90-201 (430)
48 PRK10820 DNA-binding transcrip 98.3 6.2E-06 1.3E-10 75.1 10.4 109 15-137 77-189 (520)
49 PRK11388 DNA-binding transcrip 98.3 1.3E-05 2.9E-10 75.1 12.7 49 243-294 205-253 (638)
50 PF13188 PAS_8: PAS domain; PD 98.2 3.6E-06 7.9E-11 53.3 5.2 45 18-69 1-45 (64)
51 cd00130 PAS PAS domain; PAS mo 98.2 4.7E-06 1E-10 55.8 6.0 70 251-323 2-81 (103)
52 COG2202 AtoS FOG: PAS/PAC doma 98.0 0.00036 7.9E-09 54.1 14.3 117 17-138 111-230 (232)
53 COG5000 NtrY Signal transducti 97.9 6.7E-05 1.4E-09 66.8 8.7 113 15-139 367-480 (712)
54 PRK11086 sensory histidine kin 97.9 0.00013 2.7E-09 67.5 10.9 110 16-141 219-331 (542)
55 PRK11006 phoR phosphate regulo 97.8 1.2E-05 2.7E-10 71.9 3.2 51 242-295 99-149 (430)
56 PF12860 PAS_7: PAS fold 97.8 4.1E-05 8.9E-10 54.9 5.3 44 247-293 1-45 (115)
57 PRK10820 DNA-binding transcrip 97.8 1.4E-05 2.9E-10 72.9 3.2 52 242-296 81-132 (520)
58 KOG1229 3'5'-cyclic nucleotide 97.8 1.2E-05 2.7E-10 68.2 2.2 105 20-128 159-264 (775)
59 PF13596 PAS_10: PAS domain; P 97.6 4.8E-05 1E-09 53.6 3.0 59 243-305 1-59 (106)
60 KOG3559 Transcriptional regula 97.6 0.00068 1.5E-08 57.1 10.0 55 21-78 82-136 (598)
61 COG2202 AtoS FOG: PAS/PAC doma 97.6 0.0054 1.2E-07 47.3 14.7 77 243-322 114-203 (232)
62 PRK11388 DNA-binding transcrip 97.5 0.00086 1.9E-08 63.2 11.0 109 18-138 203-311 (638)
63 smart00091 PAS PAS domain. PAS 97.5 0.00027 5.8E-09 42.9 4.7 57 243-302 3-59 (67)
64 KOG0501 K+-channel KCNQ [Inorg 97.4 0.00015 3.2E-09 64.0 3.9 73 252-324 28-112 (971)
65 PRK09959 hybrid sensory histid 97.4 0.0055 1.2E-07 62.4 15.5 43 15-60 573-615 (1197)
66 PRK15053 dpiB sensor histidine 97.4 0.0013 2.8E-08 60.9 9.8 106 17-139 221-328 (545)
67 COG3290 CitA Signal transducti 97.3 0.0015 3.2E-08 57.9 9.1 109 16-139 213-323 (537)
68 PRK11360 sensory histidine kin 97.3 0.00036 7.9E-09 65.1 5.8 52 242-296 263-314 (607)
69 smart00091 PAS PAS domain. PAS 97.3 0.0013 2.7E-08 39.7 6.3 55 19-76 2-56 (67)
70 KOG3558 Hypoxia-inducible fact 97.3 0.00076 1.6E-08 60.9 6.6 95 34-131 280-374 (768)
71 TIGR02373 photo_yellow photoac 97.2 0.0011 2.5E-08 46.8 5.7 59 246-307 21-80 (124)
72 COG3852 NtrB Signal transducti 97.1 0.0051 1.1E-07 50.6 9.5 108 21-137 10-117 (363)
73 PRK15053 dpiB sensor histidine 97.1 0.0036 7.9E-08 57.9 9.5 52 242-296 223-276 (545)
74 COG3290 CitA Signal transducti 97.0 0.004 8.6E-08 55.3 8.2 53 243-298 217-271 (537)
75 COG2461 Uncharacterized conser 97.0 0.0036 7.8E-08 53.0 7.5 114 16-139 288-401 (409)
76 PF08670 MEKHLA: MEKHLA domain 96.9 0.051 1.1E-06 40.3 12.4 112 18-132 32-144 (148)
77 PF08670 MEKHLA: MEKHLA domain 96.9 0.0028 6.1E-08 46.8 5.5 79 243-322 33-121 (148)
78 TIGR02373 photo_yellow photoac 96.6 0.035 7.5E-07 39.4 9.1 67 21-90 19-86 (124)
79 KOG1229 3'5'-cyclic nucleotide 96.6 0.001 2.2E-08 56.9 1.6 52 243-297 159-210 (775)
80 KOG3561 Aryl-hydrocarbon recep 96.2 0.0023 5E-08 59.9 1.9 64 241-306 94-157 (803)
81 KOG3753 Circadian clock protei 96.2 0.015 3.3E-07 54.1 7.0 67 254-321 332-411 (1114)
82 KOG3560 Aryl-hydrocarbon recep 96.2 0.072 1.6E-06 47.2 10.5 59 22-83 115-173 (712)
83 COG3283 TyrR Transcriptional r 96.1 0.0085 1.8E-07 50.6 4.2 55 242-299 81-135 (511)
84 COG5002 VicK Signal transducti 95.9 0.014 3.1E-07 48.9 4.9 62 243-307 113-174 (459)
85 smart00086 PAC Motif C-termina 95.9 0.086 1.9E-06 27.6 7.0 40 96-136 4-43 (43)
86 PRK11086 sensory histidine kin 95.9 0.0099 2.1E-07 54.9 4.5 52 240-294 220-274 (542)
87 KOG3560 Aryl-hydrocarbon recep 95.7 0.049 1.1E-06 48.2 7.6 93 41-135 293-385 (712)
88 COG3283 TyrR Transcriptional r 95.7 0.048 1E-06 46.2 7.0 56 16-74 78-133 (511)
89 COG3852 NtrB Signal transducti 95.2 0.026 5.6E-07 46.6 3.9 49 245-296 11-59 (363)
90 PF07310 PAS_5: PAS domain; I 94.7 0.66 1.4E-05 34.2 10.1 86 41-130 51-136 (137)
91 PF08446 PAS_2: PAS fold; Int 94.5 0.046 9.9E-07 38.6 3.2 47 254-302 18-67 (110)
92 COG5000 NtrY Signal transducti 93.0 0.092 2E-06 47.6 3.2 48 243-293 372-419 (712)
93 KOG3561 Aryl-hydrocarbon recep 91.2 0.21 4.5E-06 47.4 3.4 58 18-78 95-152 (803)
94 PRK09959 hybrid sensory histid 89.9 0.43 9.3E-06 48.9 4.7 40 242-284 577-616 (1197)
95 COG3284 AcoR Transcriptional a 89.0 8 0.00017 35.9 11.3 41 250-293 231-272 (606)
96 KOG3559 Transcriptional regula 87.6 1.6 3.4E-05 37.7 5.6 85 30-117 227-311 (598)
97 PRK10841 hybrid sensory kinase 86.7 37 0.0008 34.1 15.5 42 15-58 331-372 (924)
98 PF08446 PAS_2: PAS fold; Int 84.9 1.3 2.9E-05 31.2 3.4 42 31-74 18-62 (110)
99 PF06785 UPF0242: Uncharacteri 75.5 1.5 3.2E-05 36.7 1.2 43 243-287 285-331 (401)
100 PRK10618 phosphotransfer inter 75.3 3.5 7.6E-05 40.8 3.9 39 240-280 342-380 (894)
101 PRK13719 conjugal transfer tra 73.1 4.9 0.00011 32.0 3.5 38 241-281 19-56 (217)
102 KOG3753 Circadian clock protei 70.0 14 0.0003 35.6 6.1 70 41-110 341-413 (1114)
103 PRK10618 phosphotransfer inter 68.0 13 0.00028 37.0 5.9 40 15-56 340-379 (894)
104 PF08348 PAS_6: YheO-like PAS 66.8 21 0.00045 25.5 5.3 45 92-139 68-112 (118)
105 PRK14538 putative bifunctional 66.3 11 0.00024 36.9 5.1 48 16-69 100-148 (838)
106 PRK14538 putative bifunctional 66.3 7.3 0.00016 38.1 3.8 46 243-293 104-149 (838)
107 COG3887 Predicted signaling pr 60.0 22 0.00048 32.9 5.4 39 15-56 72-110 (655)
108 PF06785 UPF0242: Uncharacteri 59.5 20 0.00044 30.3 4.7 88 20-115 285-378 (401)
109 PRK13719 conjugal transfer tra 58.1 24 0.00052 28.2 4.7 38 17-57 18-55 (217)
110 COG2461 Uncharacterized conser 57.5 16 0.00034 31.9 3.8 61 241-307 290-350 (409)
111 PRK10841 hybrid sensory kinase 43.7 32 0.00069 34.5 4.2 41 240-282 333-373 (924)
112 COG5388 Uncharacterized protei 43.3 1.6E+02 0.0035 23.1 7.7 106 23-134 53-160 (209)
113 COG3887 Predicted signaling pr 41.9 35 0.00076 31.7 3.7 48 240-293 74-121 (655)
114 PF07310 PAS_5: PAS domain; I 36.9 89 0.0019 22.8 4.7 42 263-307 50-91 (137)
115 COG4251 Bacteriophytochrome (l 29.5 33 0.00072 32.2 1.6 52 251-303 28-79 (750)
No 1
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.87 E-value=1.6e-20 Score=167.74 Aligned_cols=202 Identities=18% Similarity=0.134 Sum_probs=146.3
Q ss_pred hHHHHHHHHHhhCCCeEEEEcC-CCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020523 15 RYTLWVHEALDELPDSFTITDP-SISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~-~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (325)
..+.+++.+++.++++++++|. + |.++++|++++.++||+.++++|+++..++++.+...+...+......+....
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 3456899999999999999998 7 99999999999999999999999998777777666655666666666665544
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (325)
.++. .++|...| .+.+.++.. ++. ..+++...|||+++++
T Consensus 207 ~~~~--~~~~~~~~-~~~~~~~~~--~~~-~~~l~~~~dit~~~~~---------------------------------- 246 (442)
T TIGR02040 207 VRIL--LRRSQKRL-LVVVSVFRQ--DGE-SLFLCQLSPAGATQPV---------------------------------- 246 (442)
T ss_pred eEEE--EcCCCeEE-EEEEEEEEe--CCc-eEEEEEEcccchhhhh----------------------------------
Confidence 4443 33444344 345666654 333 3567788899998773
Q ss_pred hhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCc
Q 020523 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (325)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (325)
+.... +.++.++++++++
T Consensus 247 ------------------------e~~~~--------------------------------------~~~~~l~e~~~d~ 264 (442)
T TIGR02040 247 ------------------------GDELS--------------------------------------ENLARLYHEAPDA 264 (442)
T ss_pred ------------------------hHHHH--------------------------------------HHHHHHHHhCCce
Confidence 00000 0155678899999
Q ss_pred eEEecCCCCCCCeEEEehhhHHhhCCC-cccccccccccccCCCCC--hHHHHHHHH-------hhccccCCCceeeEEe
Q 020523 254 FVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLNGVDTD--TTVLYQVSI-------AISPYPKKKSIYMEYV 323 (325)
Q Consensus 254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l~~~~~~--~~~~~~~~~-------e~~~~~kdG~~~~~~~ 323 (325)
|+++|. +|+|+++|++|++|+||+ .++++|+++..+.++... ......+.. +....++||+.+|+++
T Consensus 265 I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~ve~ 341 (442)
T TIGR02040 265 IVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRTLDRWLGRGGVDLRVLLSNVRRTGQVRLYATTLTGEFGAQTEVEI 341 (442)
T ss_pred EEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCCHHHHhCCCcccHHHHHHHHhhcCceEEEEEEEEcCCCCEEEEEE
Confidence 999998 579999999999999997 578999998776653322 222333332 3345689999999987
Q ss_pred e
Q 020523 324 R 324 (325)
Q Consensus 324 ~ 324 (325)
+
T Consensus 342 s 342 (442)
T TIGR02040 342 S 342 (442)
T ss_pred E
Confidence 6
No 2
>PRK13560 hypothetical protein; Provisional
Probab=99.85 E-value=9.9e-20 Score=174.98 Aligned_cols=185 Identities=15% Similarity=0.156 Sum_probs=145.1
Q ss_pred HHhhhhhhHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHH
Q 020523 8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR 87 (325)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~ 87 (325)
.++.+. ....+++.++++++++++++|.+ |.++++|++++.++||+.++++|+++..+.++.............+.
T Consensus 195 ae~~l~-~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~ 270 (807)
T PRK13560 195 AEERID-EALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFD 270 (807)
T ss_pred HHHHHH-HHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhc
Confidence 344444 56778999999999999999999 99999999999999999999999998887766544443334444555
Q ss_pred hCCCeEEEEEEEecCCCEEEEEEEE--EEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhh
Q 020523 88 EERPIEVNLLNYKKDGTPFWMLFKM--SLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRR 165 (325)
Q Consensus 88 ~~~~~~~e~~~~~~dg~~~~~~~~~--~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (325)
.+.....+..+.+++|..+|+.+.. .|+.+ .+|.+.+++++.+|||++|++
T Consensus 271 ~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~-~~g~~~g~~~~~~DITerk~~-------------------------- 323 (807)
T PRK13560 271 ADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDD-KENHCAGLVGAITDISGRRAA-------------------------- 323 (807)
T ss_pred cCCceEEEEEEEcCCCCEEEEEEEecceEEEc-CCCCEEEEEEEEEechHHHHH--------------------------
Confidence 5666677888889999999766554 55667 788999999999999999995
Q ss_pred hhcccchhhhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHh
Q 020523 166 EVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYI 245 (325)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 245 (325)
+..++.. +..++.
T Consensus 324 --------------------------------e~~L~~s-----------------------------------e~~l~~ 336 (807)
T PRK13560 324 --------------------------------ERELLEK-----------------------------------EDMLRA 336 (807)
T ss_pred --------------------------------HHHHHHH-----------------------------------HHHHHH
Confidence 2222222 122556
Q ss_pred hhhccCCceEEecCCCCCCCeEEE-ehhhHHhhCCCccccccccccccc
Q 020523 246 SLGRIKQSFVLIDPHLPDMPMVYA-SDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 246 ~~~~~~~~i~~~d~~~~dg~i~~~-N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
++++++.+++++|.+ |.++++ |+++++++||++++++|+++..+.
T Consensus 337 l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~~~~~~ 382 (807)
T PRK13560 337 IIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKPLPGMD 382 (807)
T ss_pred HHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCCccccC
Confidence 788899999999984 799987 567788999999999999876654
No 3
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.85 E-value=2.4e-20 Score=184.51 Aligned_cols=283 Identities=14% Similarity=0.148 Sum_probs=179.1
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (325)
..+.+++.+++.++.+++++|.+ |.++++|+++++++||+.++++|++...+.+|++.......+.....+. ..+.
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 46678999999999999999999 9999999999999999999999999888888877665555555544433 2456
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (325)
.+.+..+++|..+|+.++..++.+ .+|.+.+++++.+|||++|++|+++... +..++ .+.
T Consensus 357 ~e~~~~~~dG~~~~~~~~~~~~~~-~~g~~~~~i~~~~DITerk~~e~~l~~~----------~~~~~---------~~~ 416 (1092)
T PRK09776 357 MEKRYYRRDGEVVWALLAVSLVRD-TDGTPLYFIAQIEDINELKRTEQVNERL----------MERIT---------LAN 416 (1092)
T ss_pred eeeEEEcCCCCEEEEEEEEEEEEC-CCCCEeeehhhHHhhHHHHHHHHHHHHH----------HHHHH---------HHH
Confidence 778888999999999999999998 8899999999999999999984443211 01111 111
Q ss_pred hhhh--hccccccC------------CCCcccchhhhH-------HHHHHHHhhhhhhHhhh------hccceeecccee
Q 020523 174 DLDR--VLALDSDD------------TGLEIEDSCEAS-------DLEKRKAATAIDNILSV------LTHYSQLTGRLV 226 (325)
Q Consensus 174 ~~~~--~~~~~~~~------------~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~ 226 (325)
+..+ .+.++.+. .|++.++..... ..+.............. -.+.....| ..
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 1111 11111111 122221111000 00000000001100000 000111122 11
Q ss_pred e--------------------------eeecCCCCcccchhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCC
Q 020523 227 C--------------------------GKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (325)
Q Consensus 227 ~--------------------------~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~ 280 (325)
+ .++.....+....++++.++++++++++++|. +|+|+++|+++++++||+
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 HIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDM---AMKVTFMNPVAEKMTGWT 572 (1092)
T ss_pred EEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECC---CCeEEEEcHHHHHHhCCC
Confidence 1 01111112223345688899999999999998 479999999999999999
Q ss_pred cccccccccccccCCCC--ChHHHHHHHH------------hhccccCCCceeeEEee
Q 020523 281 RNEVVGQNCRFLNGVDT--DTTVLYQVSI------------AISPYPKKKSIYMEYVR 324 (325)
Q Consensus 281 ~~e~iG~~~~~l~~~~~--~~~~~~~~~~------------e~~~~~kdG~~~~~~~~ 324 (325)
.+|++|+++..+.++.+ .......+.. +....++||+.+|+.++
T Consensus 573 ~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~ 630 (1092)
T PRK09776 573 QEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVHYS 630 (1092)
T ss_pred HHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEEEE
Confidence 99999999877654321 1112222222 34456789999998764
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=99.82 E-value=9.2e-20 Score=162.84 Aligned_cols=195 Identities=14% Similarity=0.086 Sum_probs=138.5
Q ss_pred HhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC-CeEEEEEEEecC
Q 020523 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER-PIEVNLLNYKKD 102 (325)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~d 102 (325)
++.++++++++|.+ |.++++|++++.++||+.++++|+++..++++++.......+......+. .+..+.....++
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 57789999999999 99999999999999999999999999888887765555555545555443 344455555566
Q ss_pred CCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchhhhhhhcccc
Q 020523 103 GTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLALD 182 (325)
Q Consensus 103 g~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (325)
|..+|+.++..++.+ + .+++++.+|||++++.+++...
T Consensus 79 g~~~~~~~~~~~~~~---~--~~~~~i~rDi~~~~~~~~~l~~------------------------------------- 116 (442)
T TIGR02040 79 SFELPMRFILVRLGA---D--RGVLALGRDLRAVAELQQQLVA------------------------------------- 116 (442)
T ss_pred CCccCeEEEEEEeCC---C--CeEEEEecccHHHHHHHHHHHH-------------------------------------
Confidence 667777666666543 2 2567889999998874221100
Q ss_pred ccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEecCCCC
Q 020523 183 SDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPHLP 262 (325)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~~~ 262 (325)
....+++-... ++..+.+++.++++++++++++|..
T Consensus 117 ---------------------~~~~~e~~~~~---------------------l~~~e~r~~~l~e~~~~~i~~~d~~-- 152 (442)
T TIGR02040 117 ---------------------AQQAMERDYWT---------------------LREMETRYRVVLEVSSDAVLLVDMS-- 152 (442)
T ss_pred ---------------------HHHHHHHHHHH---------------------HHHHHHHHHHHHhhCCceEEEEECC--
Confidence 00000000000 0112334777899999999999973
Q ss_pred CCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020523 263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI 307 (325)
Q Consensus 263 dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~ 307 (325)
+|+|+++|+++++|+||++++++|+++..+++|+........+.+
T Consensus 153 ~g~i~~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~ 197 (442)
T TIGR02040 153 TGRIVEANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRN 197 (442)
T ss_pred CCEEEEEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHH
Confidence 489999999999999999999999999888877766555555543
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=99.80 E-value=6.1e-19 Score=160.10 Aligned_cols=181 Identities=22% Similarity=0.338 Sum_probs=146.2
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (325)
+.|+.+++.++.+++++|.+ +.++++|++++.++||++++++|++...+.++.........+.+.+..+..+..+..
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 47889999999999999999 999999999999999999999998866665555555556666666767777777777
Q ss_pred EEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchhhhhh
Q 020523 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDR 177 (325)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (325)
..+++|..+|+.....|+.+ .+|.+.+++++.+|||+++++
T Consensus 81 ~~~~~g~~~~~~~~~~~~~~-~~g~~~~~~~~~~DIt~~k~~-------------------------------------- 121 (494)
T TIGR02938 81 NRRKDGELYLAELTVAPVLN-EAGETTHFLGMHRDITELHRL-------------------------------------- 121 (494)
T ss_pred ccCCCccchhhheeeEEEEC-CCCCEEEEEEehhhhhHHHHH--------------------------------------
Confidence 78889999999999999998 889999999999999999984
Q ss_pred hccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEe
Q 020523 178 VLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLI 257 (325)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~ 257 (325)
+..++... ..++.++++++++++++
T Consensus 122 --------------------e~~l~~~~-----------------------------------~~~~~~~~~~~~~i~~~ 146 (494)
T TIGR02938 122 --------------------EQVVANQK-----------------------------------LLIESVVDAAPVAFVLL 146 (494)
T ss_pred --------------------HHHHHHHH-----------------------------------HHHHHHHhcccceEEEE
Confidence 11111111 12455788889999999
Q ss_pred cCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCC
Q 020523 258 DPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTD 298 (325)
Q Consensus 258 d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~ 298 (325)
|. +|.++++|++|++++|+...+..+..+..+.+++..
T Consensus 147 d~---~~~i~~~N~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 184 (494)
T TIGR02938 147 DP---TGRVILDNQEYKKLATDLRVKEPAHTVLDLLREAWR 184 (494)
T ss_pred cC---CCCEEEechhHHHhhchhhhhHHHHHHHHHhhHHhh
Confidence 97 479999999999999999888877766555544433
No 6
>PRK13560 hypothetical protein; Provisional
Probab=99.80 E-value=2.8e-18 Score=165.00 Aligned_cols=205 Identities=12% Similarity=0.041 Sum_probs=146.0
Q ss_pred HHHH-HHHHhhCCCeEEEEcCCCCCCC----EEEecHHHHHhcCCChhhhcCCC--CCcccCCCCChHHHH-------HH
Q 020523 17 TLWV-HEALDELPDSFTITDPSISGHP----IVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIM-------EI 82 (325)
Q Consensus 17 ~~~~-~~~~~~~~~~i~~~d~~~~~~~----i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~-------~~ 82 (325)
.+.+ +.+++++|.+++.++.+ +. +.+++++...++|+.+.++++.. +..+++|++...+.. .+
T Consensus 66 ~e~~~r~l~~~~p~~i~~~~~~---~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~ 142 (807)
T PRK13560 66 REQCERNLKANIPGGMFLFALD---GDGTFSFPSLLDANGELAAIAKHDLMADKGLLAMLIGGDDGDFFFANPFRSAETI 142 (807)
T ss_pred HHHHHHHHHhcCCceEEEEEEc---CccccccceeeccchhHHHhcCcccCCccchhhhhcCCCcchhhhhChhhHHHHH
Confidence 3444 99999999999998877 55 33477777788888777766533 344667776654432 22
Q ss_pred HHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhh
Q 020523 83 REAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGS 162 (325)
Q Consensus 83 ~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (325)
..++..+.....++++.++||+ |+.+...|.++ .+|.+ .+.|+..|||++|++
T Consensus 143 ~~~~~~~~~~~~e~r~~~~dg~--~~~~~~~~~~~-~~g~~-~~~g~~~DIT~rk~a----------------------- 195 (807)
T PRK13560 143 AMALQSDDWQEEEGHFRCGDGR--FIDCCLRFERH-AHADD-QVDGFAEDITERKRA----------------------- 195 (807)
T ss_pred HHHhccCcccceEEEEEeCCcc--EEEEEeeeeec-CCCce-EEEEEEEccchHHHH-----------------------
Confidence 2233344556678888888986 66677778877 66765 688999999999985
Q ss_pred hhhhhcccchhhhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhh
Q 020523 163 CRREVCSDSLLDLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSS 242 (325)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (325)
+..++.. ...
T Consensus 196 -----------------------------------e~~l~~~-----------------------------------~~~ 205 (807)
T PRK13560 196 -----------------------------------EERIDEA-----------------------------------LHF 205 (807)
T ss_pred -----------------------------------HHHHHHH-----------------------------------HHH
Confidence 1112221 122
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPY 312 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~ 312 (325)
|+.++++++++++++|. ||+|+++|+++++++||+++|++|+++.++.++............ +.+++
T Consensus 206 l~~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 282 (807)
T PRK13560 206 LQQLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMSIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQ 282 (807)
T ss_pred HHHHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCcchhcCCcchhHHHHHHHHHHhccCCceEEEEEEE
Confidence 56688999999999997 579999999999999999999999999998765544332121111 66778
Q ss_pred cCCCceeeEEee
Q 020523 313 PKKKSIYMEYVR 324 (325)
Q Consensus 313 ~kdG~~~~~~~~ 324 (325)
++||+.+|+++.
T Consensus 283 ~~dG~~~~~~~~ 294 (807)
T PRK13560 283 NKDGRTRPVDVI 294 (807)
T ss_pred cCCCCEEEEEEE
Confidence 899999987654
No 7
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.77 E-value=3.2e-17 Score=157.41 Aligned_cols=201 Identities=18% Similarity=0.248 Sum_probs=150.0
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCC----CeE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREER----PIE 93 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~~ 93 (325)
..+..+++.++.+++++|.+ |.++++|+++++++||++++++|+++..+.++.........+......+. .+.
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 35667899999999999999 99999999999999999999999998877776654433333443333332 234
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLL 173 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (325)
.+++..+++|..+|+.+...++.. .|. .+++++.+|||++++.
T Consensus 89 ~e~~~~~~dG~~~~v~~~~~~~~~--~g~-~~~~~~~~DiT~~~~~---------------------------------- 131 (799)
T PRK11359 89 RELQLEKKDGSKIWTRFALSKVSA--EGK-VYYLALVRDASVEMAQ---------------------------------- 131 (799)
T ss_pred eeeEEecCCcCEEEEEEEeeeecc--CCc-eEEEEEEeeccchhhh----------------------------------
Confidence 477788899999999999888853 455 4578889999998773
Q ss_pred hhhhhccccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCc
Q 020523 174 DLDRVLALDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQS 253 (325)
Q Consensus 174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~ 253 (325)
+...+ .+..++++++++
T Consensus 132 ------------------------~~~~~---------------------------------------~~~~~~~~~~~~ 148 (799)
T PRK11359 132 ------------------------KEQTR---------------------------------------QLIIAVDHLDRP 148 (799)
T ss_pred ------------------------HHHHH---------------------------------------HHHHHHhcCCCc
Confidence 00000 022356777899
Q ss_pred eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC-CCChHHHHHHHH----------hhccccCCCceeeEE
Q 020523 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV-DTDTTVLYQVSI----------AISPYPKKKSIYMEY 322 (325)
Q Consensus 254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~-~~~~~~~~~~~~----------e~~~~~kdG~~~~~~ 322 (325)
++++|. +|+++++|+++++++||+.++++|+++..+.++ .........+.. +++..+++|..+|+.
T Consensus 149 i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~ 225 (799)
T PRK11359 149 VIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIK 225 (799)
T ss_pred EEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEE
Confidence 999997 579999999999999999999999998877543 333333333332 556677999999986
Q ss_pred ee
Q 020523 323 VR 324 (325)
Q Consensus 323 ~~ 324 (325)
++
T Consensus 226 ~~ 227 (799)
T PRK11359 226 AS 227 (799)
T ss_pred ee
Confidence 53
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=3.9e-16 Score=110.55 Aligned_cols=104 Identities=27% Similarity=0.431 Sum_probs=94.8
Q ss_pred CCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEEE
Q 020523 28 PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFW 107 (325)
Q Consensus 28 ~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~ 107 (325)
|++++++|.+ |.++++|+++++++|+++++++|+++..++++.........+.+.+..+..+..+..+.+++|..+|
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 6899999999 9999999999999999999999999988888877778888889999988889999999999999999
Q ss_pred EEEEEEEeecCCCCceEEEEEEEeccCc
Q 020523 108 MLFKMSLVFGKEDGRATHFVAVQVPIVS 135 (325)
Q Consensus 108 ~~~~~~~~~~~~~g~~~~~~~~~~DITe 135 (325)
+.+++.|+.+ ++|.+.+++++++|||+
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=99.65 E-value=3.6e-15 Score=106.73 Aligned_cols=110 Identities=26% Similarity=0.452 Sum_probs=97.3
Q ss_pred HhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCC
Q 020523 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDG 103 (325)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg 103 (325)
|+++|++++++|.+ ++++++|+++.+++|++.++++|+++..++++.....+...+.+++.++.....+..... +|
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 68899999999999 999999999999999999999999988888887777778888888888877666555444 89
Q ss_pred CEEEEEEEEEEeecCCCCceEEEEEEEeccCcchh
Q 020523 104 TPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (325)
Q Consensus 104 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~ 138 (325)
...|+.+++.|+.+ .+|.+.+++++.+|||++|+
T Consensus 77 ~~~~~~~~~~Pi~~-~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 77 EERWFEVSISPIFD-EDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp CEEEEEEEEEEEEC-TTTCEEEEEEEEEEECCHHH
T ss_pred CcEEEEEEEEEeEc-CCCCEEEEEEEEEECchhhC
Confidence 99999999999999 89999999999999999975
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=99.63 E-value=1.1e-14 Score=104.68 Aligned_cols=112 Identities=23% Similarity=0.366 Sum_probs=94.0
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE-EEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE-VNL 96 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~e~ 96 (325)
++|+.++++++++++++|.+ |.++++|+++++++|++.++++|+++..++++++.......+...+..+.... ...
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 47889999999999999999 99999999999999999999999999888877765556677777777766543 334
Q ss_pred EEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEecc
Q 020523 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPI 133 (325)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (325)
....++|..+|+.++..|+.+ .+|.+.+++++++||
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 344469999999999999999 888899999999997
No 11
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.44 E-value=3.3e-12 Score=122.36 Aligned_cols=122 Identities=15% Similarity=0.193 Sum_probs=106.9
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
....+++.++++++++++++|.+ |.++++|+++++++|++.++++|+++..++++.............+..+.....
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 45667899999999999999999 999999999999999999999999988887766555555555666677777788
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+++
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 8899999999999999999873
No 12
>PRK13559 hypothetical protein; Provisional
Probab=99.41 E-value=6.7e-12 Score=109.47 Aligned_cols=125 Identities=38% Similarity=0.676 Sum_probs=105.3
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
.....+..+++.++.+++++|.+..++.++++|+++++++||+.++++|+++..+.++.........+...+..+..+..
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 34567888999999999999974222689999999999999999999999877666665555556666777777777777
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
+.....++|..+|+.++..|+.+ .+|.+.+++++.+|||++|+++
T Consensus 120 e~~~~~~dG~~~~~~~~~~~i~d-~~G~~~~~v~~~~DITerk~~e 164 (361)
T PRK13559 120 ELLNYRKDGEPFWNALHLGPVYG-EDGRLLYFFGSQWDVTDIRAVR 164 (361)
T ss_pred EEEEEcCCCCEEEEEEEEEEEEc-CCCCEEEeeeeeeehhcchhhH
Confidence 88888899999999999999998 8899999999999999999863
No 13
>PRK13557 histidine kinase; Provisional
Probab=99.38 E-value=9.2e-12 Score=114.51 Aligned_cols=128 Identities=37% Similarity=0.672 Sum_probs=110.0
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
....+|..+++.++.+++++|....+|+++|+|++|++++||+.++++|+++..+.++.+.......+...+..+..+..
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 45678999999999999999963223899999999999999999999999988888777766667777777777777777
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhcc
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~ 143 (325)
+....+++|..+|+.++..|+.+ .+|.+.+++++.+|||++++++++.
T Consensus 107 ~~~~~~~~G~~~~~~~~~~~i~~-~~g~~~~~~~~~~dit~~~~~e~~l 154 (540)
T PRK13557 107 EILNYRKDGSSFWNALFVSPVYN-DAGDLVYFFGSQLDVSRRRDAEDAL 154 (540)
T ss_pred EEEEEeCCCCEEEEEEEEEEeEC-CCCCEEEEEEEecChHHHHHHHHHH
Confidence 77888899999999999999998 8899999999999999999875443
No 14
>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=99.34 E-value=2e-12 Score=91.30 Aligned_cols=71 Identities=21% Similarity=0.351 Sum_probs=60.8
Q ss_pred CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020523 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM 320 (325)
Q Consensus 251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~ 320 (325)
|+|++++|. ||+|+++|++|++++||++++++|+++.+++++.........+.+ ++.+++++|+.+|
T Consensus 1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~ 77 (104)
T PF13426_consen 1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFW 77 (104)
T ss_dssp -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEE
T ss_pred CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEE
Confidence 589999998 479999999999999999999999999999988877777776666 7777889999999
Q ss_pred EEee
Q 020523 321 EYVR 324 (325)
Q Consensus 321 ~~~~ 324 (325)
+.++
T Consensus 78 ~~~~ 81 (104)
T PF13426_consen 78 VEVS 81 (104)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9876
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=99.34 E-value=1.7e-12 Score=93.24 Aligned_cols=81 Identities=19% Similarity=0.194 Sum_probs=64.6
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hh
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AI 309 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~ 309 (325)
++++.+++++++|++++|. +|+|+++|++++++|||++++++|+++.++.+++........+.+ +.
T Consensus 1 e~~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEV 77 (113)
T ss_dssp HHHHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEE
T ss_pred CHHHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEE
Confidence 3578899999999999997 589999999999999999999999999999887754444444443 33
Q ss_pred ccccCCCceeeEEee
Q 020523 310 SPYPKKKSIYMEYVR 324 (325)
Q Consensus 310 ~~~~kdG~~~~~~~~ 324 (325)
....++|+.+|+.++
T Consensus 78 ~~~~~~g~~~~~~~~ 92 (113)
T PF00989_consen 78 RFRLRDGRPRWVEVR 92 (113)
T ss_dssp EEEETTSCEEEEEEE
T ss_pred EEEecCCcEEEEEEE
Confidence 333469999998765
No 16
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.26 E-value=3.3e-10 Score=106.81 Aligned_cols=124 Identities=39% Similarity=0.703 Sum_probs=104.8
Q ss_pred HHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEE
Q 020523 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLN 98 (325)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (325)
.+..+++.++.++++.|....++.++++|+++++++||+.++++|+++..+.++.........+...+..+.....+...
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 45788999999999998522238999999999999999999999998877776666555556667777777778888888
Q ss_pred EecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhcc
Q 020523 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (325)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~ 143 (325)
.+++|..+|+.++..|+.+ .+|.+.+++++.+|||++|++++++
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 8999999999999999999974443
No 17
>PRK10060 RNase II stability modulator; Provisional
Probab=99.20 E-value=3.6e-10 Score=105.98 Aligned_cols=123 Identities=15% Similarity=0.182 Sum_probs=96.7
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCccc-CCCCChHHHHHHHHHHHhCCCeEE
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQ-GPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
...++..+++.++++++++|.+ |.++++|+++++++||+.++++|+++..++ ++.+.......+...+..+..+..
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 4457788999999999999999 999999999999999999999999975554 444444445566666777778888
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCC-ceEEEEEEEeccCcchhhhhcc
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDG-RATHFVAVQVPIVSRKHMRNSG 143 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g-~~~~~~~~~~DITe~k~~~~~~ 143 (325)
+....+++|..+|+.....+... .| ....++++.+|||+++++++++
T Consensus 186 e~~~~~~~G~~~~~~~~~~~~~~--~g~~~~~~i~~~~DITe~k~~e~~l 233 (663)
T PRK10060 186 ERWIKTRKGQRLFLFRNKFVHSG--SGKNEIFLICSGTDITEERRAQERL 233 (663)
T ss_pred EEEEEeCCCCEEEEEeeeEEEcC--CCCceEEEEEEEEechHHHHHHHHH
Confidence 88889999998887655444333 44 3456788899999999886654
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=99.18 E-value=8.6e-10 Score=78.20 Aligned_cols=118 Identities=21% Similarity=0.347 Sum_probs=91.5
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeEEEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIEVNL 96 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~ 96 (325)
..+..+++.++.+++++|.+ +.++++|+++..++|++..++.|.+...++++.........+...+..+ .......
T Consensus 3 ~~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEER 79 (124)
T ss_pred hHHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEe
Confidence 35678999999999999999 9999999999999999999999988776666655544444455555433 2233344
Q ss_pred EEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 97 LNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 97 ~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
.....+|...|+.+...|+.. +|...+++++..|||++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~dit~~~~~~ 121 (124)
T TIGR00229 80 RVRRKDGSEIWVEVSVSPIRT--NGGELGVVGIVRDITERKQAE 121 (124)
T ss_pred eeEcCCCCEEEEEEEEeehhh--CCCeeEEEEEeeehhHHHHHH
Confidence 445778999999988888863 677788999999999998863
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=99.17 E-value=3e-10 Score=78.10 Aligned_cols=86 Identities=26% Similarity=0.464 Sum_probs=71.7
Q ss_pred EEEecHHHHHhcCCChhhhcCCC----CCcccCCCCChHHHHHHHH-HHHhCCCeEEEEEEEecCCCEEEEEEEEEEeec
Q 020523 43 IVFASRGFLKMSGFSRAEIIGRN----GRMFQGPRTNRRTIMEIRE-AIREERPIEVNLLNYKKDGTPFWMLFKMSLVFG 117 (325)
Q Consensus 43 i~~~N~~~~~~~G~~~~e~~g~~----~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~ 117 (325)
++++|+.+++++||+++++ +.+ +..+++|++...+...+.. ....+..+..++++.+++|..+|+.+++.++.+
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 5799999999999999999 665 5667899999988888888 677777899999999999999999999999998
Q ss_pred CCCCceEEEEEEE
Q 020523 118 KEDGRATHFVAVQ 130 (325)
Q Consensus 118 ~~~g~~~~~~~~~ 130 (325)
++|.+..++|+.
T Consensus 80 -~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 -ENGKPIRIIGVI 91 (91)
T ss_dssp -TTS-EEEEEEEE
T ss_pred -CCCCEEEEEEEC
Confidence 899999998874
No 20
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.05 E-value=2.4e-09 Score=103.27 Aligned_cols=120 Identities=19% Similarity=0.307 Sum_probs=99.6
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccC-CCCChHHHHHHHHHHHhCCCeEEE
Q 020523 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQG-PRTNRRTIMEIREAIREERPIEVN 95 (325)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~e 95 (325)
...+..+++.++.+++++|.+ |.++++|+++++++||+.++++|.+...+++ +.........+...+..+..+..+
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 445667899999999999999 9999999999999999999999998765543 444444445555666666666677
Q ss_pred EEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
.+...++|..+|+.+...|+.+ .+|.+.+++++.+|||++++++
T Consensus 212 ~~~~~~dG~~~~~~~~~~~v~d-~~g~~~~~~~~~~DITerk~~e 255 (799)
T PRK11359 212 FLLLTRTGEKIWIKASISPVYD-VLAHLQNLVMTFSDITEERQIR 255 (799)
T ss_pred eEEeCCCCCEEEEEeeeeeeec-CCCceeEEEEEeehhhhHHHHH
Confidence 7788899999999999999998 7899999999999999999863
No 21
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.01 E-value=6e-09 Score=103.93 Aligned_cols=127 Identities=15% Similarity=0.137 Sum_probs=105.3
Q ss_pred HHhhhhhhHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCC-CCcccCCCCChHHHHHHHHHH
Q 020523 8 IEQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN-GRMFQGPRTNRRTIMEIREAI 86 (325)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~-~~~l~~~~~~~~~~~~~~~~~ 86 (325)
.++.+. +...+++.+++..+.+++.+|.+ +.++++|+++++++|++.++..+.. +...++|++.......+...+
T Consensus 401 ~e~~l~-~~~~~~~~~~~~~~~~i~~~d~~---~~~~~~n~~~~~l~G~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~ 476 (1092)
T PRK09776 401 TEQVNE-RLMERITLANEAGGIGIWEWDLK---PNIISWDKRMFELYEIPPHIKPTWQVWYACLHPEDRQRVEKEIRDAL 476 (1092)
T ss_pred HHHHHH-HHHHHHHHHHHhcCceEEEEecC---CCeEeeCHHHHHHhCCCcccCCCHHHHHHhcCHhHHHHHHHHHHHHH
Confidence 344444 56678889999999999999999 9999999999999999988744332 233456666666666777778
Q ss_pred HhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 87 REERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 87 ~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
.++..+..+++..+++| .+|+.....++.+ .+|.+.+++++.+|||++|+++
T Consensus 477 ~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d-~~G~~~~~ig~~~DITerk~~e 528 (1092)
T PRK09776 477 QGRSPFKLEFRIVVKDG-VRHIRALANRVLN-KDGEVERLLGINMDMTEVRQLN 528 (1092)
T ss_pred hcCCCeeEEEEEEcCCc-eEEEEEeeEEEEC-CCCCEEEEEeeeeehhHHHHHH
Confidence 88888889999999999 9999999999998 8999999999999999999973
No 22
>PRK13557 histidine kinase; Provisional
Probab=98.99 E-value=9.2e-10 Score=101.32 Aligned_cols=84 Identities=33% Similarity=0.671 Sum_probs=70.6
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS 310 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~ 310 (325)
..|+.++++++++++++|.+..||+|+|+|++|++++||+.+|++|+++.++.+|+........++. ++.
T Consensus 30 ~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (540)
T PRK13557 30 DIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEIL 109 (540)
T ss_pred HHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEE
Confidence 3477889999999999998655799999999999999999999999999999888777666655554 455
Q ss_pred cccCCCceeeEEee
Q 020523 311 PYPKKKSIYMEYVR 324 (325)
Q Consensus 311 ~~~kdG~~~~~~~~ 324 (325)
.+++||+.+|+.++
T Consensus 110 ~~~~~G~~~~~~~~ 123 (540)
T PRK13557 110 NYRKDGSSFWNALF 123 (540)
T ss_pred EEeCCCCEEEEEEE
Confidence 67899999998654
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=98.97 E-value=4.5e-08 Score=66.06 Aligned_cols=103 Identities=21% Similarity=0.404 Sum_probs=82.9
Q ss_pred CCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEE
Q 020523 27 LPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPF 106 (325)
Q Consensus 27 ~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~ 106 (325)
++.+++++|.+ +.++++|++++.++|++..++.|.....++++.+.......+......+.....+......+|...
T Consensus 1 ~~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (103)
T cd00130 1 LPDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVI 77 (103)
T ss_pred CCceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEE
Confidence 35788999999 999999999999999999999998877777776665555555555555555666777777889999
Q ss_pred EEEEEEEEeecCCCCceEEEEEEEecc
Q 020523 107 WMLFKMSLVFGKEDGRATHFVAVQVPI 133 (325)
Q Consensus 107 ~~~~~~~~~~~~~~g~~~~~~~~~~DI 133 (325)
|+.+...++.+ ..|...+++++..||
T Consensus 78 ~~~~~~~~~~~-~~~~~~~~~~~~~di 103 (103)
T cd00130 78 WVLVSLTPIRD-EGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEEEEEEEec-CCCCEEEEEEEEecC
Confidence 99999999887 677888888888875
No 24
>PRK13559 hypothetical protein; Provisional
Probab=98.88 E-value=5e-09 Score=91.46 Aligned_cols=83 Identities=35% Similarity=0.679 Sum_probs=67.5
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhcc
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISP 311 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~ 311 (325)
.+..++++++++++++|.+..+|+|+++|++|++++||+.++++|+++.++.++.........+.. +...
T Consensus 44 ~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~ 123 (361)
T PRK13559 44 LFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLN 123 (361)
T ss_pred HHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEE
Confidence 467789999999999998655789999999999999999999999999888776665554444443 4555
Q ss_pred ccCCCceeeEEee
Q 020523 312 YPKKKSIYMEYVR 324 (325)
Q Consensus 312 ~~kdG~~~~~~~~ 324 (325)
+++||+.+|+.++
T Consensus 124 ~~~dG~~~~~~~~ 136 (361)
T PRK13559 124 YRKDGEPFWNALH 136 (361)
T ss_pred EcCCCCEEEEEEE
Confidence 7899999998764
No 25
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=98.86 E-value=2.2e-08 Score=70.85 Aligned_cols=106 Identities=21% Similarity=0.272 Sum_probs=71.5
Q ss_pred HHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEE
Q 020523 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNY 99 (325)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 99 (325)
+..++++++.++.++|.+ +.+.++|+++.++++..+.+ +|+++..+.++.....+...+ +.+..+.....+...
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~~~-iGr~l~~~~~~~~~~~l~~~i-~~~~~~~~~~~~~~~- 74 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSPSD-IGRPLFDIHPPLSYPNLKKII-EQVRSGKEEEFEIVI- 74 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---GGG-TTSBCCCSS-HHHHHHHHHHH-HHHHTTSBSEEEEEE-
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCChHH-CCCCHHHcCCccchHHHHHHH-HHHHcCCCceEEEEe-
Confidence 357899999999999999 99999999999999977544 799988876554333333333 334444443333332
Q ss_pred ecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccC
Q 020523 100 KKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (325)
Q Consensus 100 ~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT 134 (325)
..+| .|+.+.+.|+++ ++|...|++.++.|||
T Consensus 75 ~~~~--~~~~~~~~P~~~-~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 75 PNGG--RWYLVRYRPYRD-EDGEYAGAVITFQDIT 106 (106)
T ss_dssp EETT--EEEEEEEEEEE--TTS-EEEEEEEEEE-G
T ss_pred cCCC--EEEEEEEEEEEC-CCCCEEEEEEEEEecC
Confidence 2344 466789999998 8999999999999997
No 26
>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=98.85 E-value=3.5e-09 Score=75.36 Aligned_cols=75 Identities=20% Similarity=0.158 Sum_probs=59.3
Q ss_pred hhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH---------hhccccCCCc
Q 020523 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI---------AISPYPKKKS 317 (325)
Q Consensus 247 ~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~---------e~~~~~kdG~ 317 (325)
|++++++++++|. ||+|+++|+++++++|+++++++|+++.+++++.........+.+ .......+|.
T Consensus 1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (110)
T PF08448_consen 1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLRDGE 77 (110)
T ss_dssp HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECTTSC
T ss_pred CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEeecCC
Confidence 5778999999998 579999999999999999999999999999888766666666666 1111223788
Q ss_pred eeeEEee
Q 020523 318 IYMEYVR 324 (325)
Q Consensus 318 ~~~~~~~ 324 (325)
.+|..++
T Consensus 78 ~~~~~~~ 84 (110)
T PF08448_consen 78 ERWFEVS 84 (110)
T ss_dssp EEEEEEE
T ss_pred cEEEEEE
Confidence 8887765
No 27
>PF12860 PAS_7: PAS fold
Probab=98.85 E-value=2.5e-08 Score=71.76 Aligned_cols=104 Identities=20% Similarity=0.342 Sum_probs=70.9
Q ss_pred HhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhh-cCCCCCccc---------CCCCChHHHHHHHHHHHhCCCeE
Q 020523 24 LDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEI-IGRNGRMFQ---------GPRTNRRTIMEIREAIREERPIE 93 (325)
Q Consensus 24 ~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~-~g~~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~ 93 (325)
+++++.|++++|.+ ++++++|+.|.+++|++.+.+ .|.++..++ .+.+...................
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 999999999999999999888 677754432 11222222222222233333333
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
.+ ....+|+ |+.+...|..+ | |++.+..|||+++++|
T Consensus 78 ~~--~~~~dgr--~l~~~~~~~~~---G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 78 FE--LRLPDGR--WLEVRAQPLPD---G---GFVLTFTDVTERRRAE 114 (115)
T ss_pred eE--EECCCCE--EEEEEeEECCC---C---CEEEEEEeCCHHHHhc
Confidence 33 3346665 66778888854 4 5788899999999863
No 28
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.82 E-value=2.5e-08 Score=87.10 Aligned_cols=163 Identities=20% Similarity=0.191 Sum_probs=117.6
Q ss_pred HHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020523 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (325)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (325)
..+++.+.+++.+++.. ..+..+|..+..+++-....++|++...+.++....... .+...........
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 34889999999999998 899999999999999999999999877766554433221 1122222222222
Q ss_pred cCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhccCCcccCCCCchhhHHHhhhhhhhhcccchhhhhhhcc
Q 020523 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSGMSYSEDGGGSRLREIVFGSCRREVCSDSLLDLDRVLA 180 (325)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (325)
+ ....+.+...|+. +.+.+.|++.++.|+++....
T Consensus 73 ~--~~~~~~~~~~~~~--~~~~~~g~~~~~~~~~e~~~~----------------------------------------- 107 (560)
T COG3829 73 K--VKRIVVVGKTPVD--EQGRVVGVLEVFLDISEALEL----------------------------------------- 107 (560)
T ss_pred c--ceeEEEcCCceee--cCCceeeeehhhhhhHHHHHH-----------------------------------------
Confidence 2 2333434455554 588999999999999996552
Q ss_pred ccccCCCCcccchhhhHHHHHHHHhhhhhhHhhhhccceeeccceeeeeecCCCCcccchhhhHhhhhccCCceEEecCC
Q 020523 181 LDSDDTGLEIEDSCEASDLEKRKAATAIDNILSVLTHYSQLTGRLVCGKRCSLPGMGFISSSLYISLGRIKQSFVLIDPH 260 (325)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~i~~~d~~ 260 (325)
.+..+... ...|..+++.+.++++++|.+
T Consensus 108 ----------------~~~~l~~~-----------------------------------~~~l~~il~~~~~~l~vvD~~ 136 (560)
T COG3829 108 ----------------IEENLRQL-----------------------------------RQRLEAILDSIDDGLLVVDED 136 (560)
T ss_pred ----------------HHHHHHHH-----------------------------------HHHHHHHHhhccCceEEEcCC
Confidence 11111111 122566888889999999984
Q ss_pred CCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020523 261 LPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 261 ~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
|.++++|+++.+++|++.++++|+++.++.
T Consensus 137 ---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~ 166 (560)
T COG3829 137 ---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVV 166 (560)
T ss_pred ---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHH
Confidence 799999999999999999999999998886
No 29
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.79 E-value=1e-07 Score=88.94 Aligned_cols=121 Identities=14% Similarity=0.181 Sum_probs=95.1
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCC-eEE
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERP-IEV 94 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~ 94 (325)
....+..+++.++++++++|.+ +.++++|+++++++|+++++++|+++..++++.. .....+...+..+.. ...
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 4456788999999999999999 9999999999999999999999998877766432 223344444544433 334
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhhcc
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRNSG 143 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~~~ 143 (325)
+......+|... +.++..|+.+ .+|.+.+++++++|||+++++++++
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 555666677666 8899999998 8999999999999999999875443
No 30
>PRK10060 RNase II stability modulator; Provisional
Probab=98.79 E-value=1.5e-08 Score=95.24 Aligned_cols=77 Identities=12% Similarity=0.040 Sum_probs=58.9
Q ss_pred HhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccC-CCCChHHHHHHHH----------hhccc
Q 020523 244 YISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG-VDTDTTVLYQVSI----------AISPY 312 (325)
Q Consensus 244 ~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~-~~~~~~~~~~~~~----------e~~~~ 312 (325)
+.++++++++|+++|. ||+|+++|+++++++||+.++++|+++.+++. |.........+.. |++.+
T Consensus 114 ~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~ 190 (663)
T PRK10060 114 EQVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIK 190 (663)
T ss_pred HHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEE
Confidence 3467888999999998 47999999999999999999999999877654 4333222222222 66778
Q ss_pred cCCCceeeEEe
Q 020523 313 PKKKSIYMEYV 323 (325)
Q Consensus 313 ~kdG~~~~~~~ 323 (325)
+++|+.+|+..
T Consensus 191 ~~~G~~~~~~~ 201 (663)
T PRK10060 191 TRKGQRLFLFR 201 (663)
T ss_pred eCCCCEEEEEe
Confidence 89999888753
No 31
>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=98.76 E-value=4.2e-07 Score=64.49 Aligned_cols=102 Identities=17% Similarity=0.261 Sum_probs=83.4
Q ss_pred EEEcCCCCCCCEEEecHH-HHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 020523 32 TITDPSISGHPIVFASRG-FLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (325)
Q Consensus 32 ~~~d~~~~~~~i~~~N~~-~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (325)
...+.+ |+++++.+. ...++||.+++++|+++..+++|+|... +.......+..|.....-++...++|..+|+.
T Consensus 6 trhs~d---gki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvq 82 (111)
T PF14598_consen 6 TRHSLD---GKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQ 82 (111)
T ss_dssp EEEETT---SBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEE
T ss_pred EEECCC---cEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEE
Confidence 345677 999999999 6999999999999999999999999886 77778888888887666789999999999999
Q ss_pred EEEEEeecCCCCceEEEEEEEeccCcc
Q 020523 110 FKMSLVFGKEDGRATHFVAVQVPIVSR 136 (325)
Q Consensus 110 ~~~~~~~~~~~g~~~~~~~~~~DITe~ 136 (325)
....++.++.++++..++++..=|++.
T Consensus 83 t~~~~~~n~~~~~~~~Iv~~n~vlse~ 109 (111)
T PF14598_consen 83 TKATLFYNPWTSKPEFIVCTNTVLSEE 109 (111)
T ss_dssp EEEEEEEETTTTCEEEEEEEEEEESCE
T ss_pred EEEEEEECCCCCCccEEEEEEEEeccC
Confidence 999999864566777777766655553
No 32
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=98.75 E-value=1.4e-07 Score=83.74 Aligned_cols=68 Identities=19% Similarity=0.221 Sum_probs=54.8
Q ss_pred eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceeeEE
Q 020523 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYMEY 322 (325)
Q Consensus 254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~~~ 322 (325)
.|+.-... |.+|+|+.+.+.++.||+++||+|+++.+|+++.+-..+...... .+++..|.|...|++
T Consensus 275 ~FvtRhs~-DmkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQ 352 (768)
T KOG3558|consen 275 MFVTRHSL-DMKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQ 352 (768)
T ss_pred eeEEeeec-ceeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEE
Confidence 45554443 789999999999999999999999999999988876655444433 777778999999986
No 33
>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=1.1e-07 Score=81.85 Aligned_cols=108 Identities=13% Similarity=0.093 Sum_probs=81.9
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
+..+.++.+++.++++++++|.+ |.++++|+++++++|+++++.+|+++..+..+. .+...+..+.. ..
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~-------~~~~~l~~~~~-~~ 71 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHP-------EFVEYLAAGRF-SE 71 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCH-------HHHHHHHhccc-CC
Confidence 44567899999999999999999 999999999999999999999998876665432 22333333222 22
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
......++|...|+.+...|+.+ . . .+++.+|||++++.
T Consensus 72 ~~~~~~~~~~~~~~~~~~~p~~~-~--~---~~~~~~dit~~~~~ 110 (333)
T TIGR02966 72 PLELPSPINSERVLEIRIAPYGE-E--Q---KLLVARDVTRLRRL 110 (333)
T ss_pred CeEeecCCCCceEEEEEEEEcCC-C--c---eEEEEeCchHHHHH
Confidence 23344577888899999999875 2 2 67788999998876
No 34
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.70 E-value=1.5e-07 Score=81.69 Aligned_cols=111 Identities=14% Similarity=0.133 Sum_probs=84.3
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (325)
..+..++++++++++++|.+ +.++++|+++++++|++..+++|.++..++++... ....+...+..+........
T Consensus 7 ~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 81 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSL--NIELMRESLQAGQGFTDNEV 81 (348)
T ss_pred chHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchh--hHHHHHHHHHcCCcccccce
Confidence 35688999999999999999 99999999999999999999999998777654321 12334445555544333333
Q ss_pred EEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
....+|..+|+.++..|+.. .+++..++|+|++++.
T Consensus 82 ~~~~~g~~~~~~~~~~~~~~------~~~~~~~~dit~~~~~ 117 (348)
T PRK11073 82 TLVIDGRSHILSLTAQRLPE------GMILLEMAPMDNQRRL 117 (348)
T ss_pred EEEECCceEEEEEEEEEccC------ceeEEEEechhHHHHH
Confidence 44569999999999999853 2456778999998876
No 35
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.66 E-value=2.1e-07 Score=81.23 Aligned_cols=123 Identities=26% Similarity=0.519 Sum_probs=95.5
Q ss_pred HHHHHHHHHhhCC--C-eEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCC--CCcccCCCCChHHHHHHHHHHHhCC
Q 020523 16 YTLWVHEALDELP--D-SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRN--GRMFQGPRTNRRTIMEIREAIREER 90 (325)
Q Consensus 16 ~~~~~~~~~~~~~--~-~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~--~~~l~~~~~~~~~~~~~~~~~~~~~ 90 (325)
++-+++.++..+. + .+++.+.+.-|..++|+|.+||++.||.+.+++.++ +....+..........+++.+..-.
T Consensus 12 QNTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~ 91 (971)
T KOG0501|consen 12 QNTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYE 91 (971)
T ss_pred chhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhh
Confidence 4445666665444 3 333444433336689999999999999999999987 4445555555555677777787777
Q ss_pred CeEEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 91 PIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 91 ~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
.-++|+....++..++|+.+.+.|+++ +.+.++.+++.+.|||..|+-
T Consensus 92 ~~qfEillyKKN~TPvW~~vqiAPIrN-e~d~VVLfLctFkDIT~~KQP 139 (971)
T KOG0501|consen 92 TNQFEILLYKKNRTPVWLLVQIAPIRN-EKDKVVLFLCTFKDITALKQP 139 (971)
T ss_pred hcceeeEeeecCCCceEEEEEeecccC-CCceEEEEEeecccchhhcCC
Confidence 778898899999999999999999999 999999999999999999874
No 36
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=98.64 E-value=1.6e-06 Score=76.19 Aligned_cols=112 Identities=17% Similarity=0.371 Sum_probs=84.0
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
.....|..+++.+.+++.++|.+ |.++++|+++..++|++.++++|++..+++..... .....++..+.+...
T Consensus 114 ~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~----s~~l~vl~~~kp~~~ 186 (560)
T COG3829 114 QLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED----STLLEVLRTGKPIRD 186 (560)
T ss_pred HHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC----ceehhhhhcCCccee
Confidence 45678999999999999999999 99999999999999999999999987666411110 123455666666555
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
....+..+. . .++..|++. +|.+.|.+++..|+++...+
T Consensus 187 ~~~~~~~~~--~--i~~~~pv~~--~g~l~G~v~~~~~~~~l~~l 225 (560)
T COG3829 187 VVQTYNGNK--I--IVNVAPVYA--DGQLIGVVGISKDVSELERL 225 (560)
T ss_pred eeeeecCCc--e--eEeeccEec--CCcEEEEEEeecchHHHHHH
Confidence 443332222 1 356677774 78999999999999998876
No 37
>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=98.60 E-value=3.4e-08 Score=67.72 Aligned_cols=58 Identities=22% Similarity=0.228 Sum_probs=46.2
Q ss_pred eEEEehhhHHhhCCCcccccccc----cccccCCCCChHHHHHHHH-----------hhccccCCCceeeEEee
Q 020523 266 MVYASDAFLKLTGYDRNEVVGQN----CRFLNGVDTDTTVLYQVSI-----------AISPYPKKKSIYMEYVR 324 (325)
Q Consensus 266 i~~~N~a~~~~~Gy~~~e~iG~~----~~~l~~~~~~~~~~~~~~~-----------e~~~~~kdG~~~~~~~~ 324 (325)
|+|+|+++++|+||+++++ |.. +..+++|++...+.+.+.+ +++.+++||+.+|++.+
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 7778899988877665555 88889999999999864
No 38
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.54 E-value=1.3e-07 Score=60.08 Aligned_cols=45 Identities=22% Similarity=0.362 Sum_probs=36.4
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
+++.+++++++||+++| . ++|+++|+++++|+||+ ..|+.+..++
T Consensus 2 ~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~~~~ 46 (64)
T PF13188_consen 2 RYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIGQLF 46 (64)
T ss_dssp HHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHHCTS
T ss_pred HHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHHHhC
Confidence 57889999999999999 5 49999999999999998 6666665444
No 39
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.51 E-value=1.2e-07 Score=91.13 Aligned_cols=82 Identities=15% Similarity=-0.013 Sum_probs=66.8
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hh
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AI 309 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~ 309 (325)
...++.++++++++|+++|. +|+|+++|+++++++||+.++++|+++.++++++........... +.
T Consensus 154 ~~~l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~ 230 (779)
T PRK11091 154 SSLLRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQ 230 (779)
T ss_pred HHHHHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEE
Confidence 45588899999999999998 579999999999999999999999999999877655544433332 55
Q ss_pred ccccCCCceeeEEee
Q 020523 310 SPYPKKKSIYMEYVR 324 (325)
Q Consensus 310 ~~~~kdG~~~~~~~~ 324 (325)
+..++||+.+|+.++
T Consensus 231 ~~~~~~G~~~~~~~~ 245 (779)
T PRK11091 231 WLDYPDGRKACFELR 245 (779)
T ss_pred EEEcCCCCEEEEEEE
Confidence 567789999988764
No 40
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=98.50 E-value=2.7e-06 Score=70.22 Aligned_cols=114 Identities=15% Similarity=0.242 Sum_probs=89.2
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
....++.+++..+.+|+...|.. |.++.+|..+.+++|.+.++++|+++..+..-.+.-. +...+....+...
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 34567899999999999999999 9999999999999999999999999766654433322 2333344333333
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
+. ...++.+.+.+..+.+.. +.|-+.|++.+.+|+|++.+.
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 236777778888888888 899999999999999999875
No 41
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.46 E-value=3.4e-07 Score=86.56 Aligned_cols=82 Identities=34% Similarity=0.629 Sum_probs=67.0
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPY 312 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~ 312 (325)
+..+++.++.++++.|...++|.|+++|+++++++||++++++|+++..+.++.........+.. +++.+
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 35678899999999986545789999999999999999999999999888877766555444433 66778
Q ss_pred cCCCceeeEEee
Q 020523 313 PKKKSIYMEYVR 324 (325)
Q Consensus 313 ~kdG~~~~~~~~ 324 (325)
++||+.+|+.++
T Consensus 230 ~~dG~~~~~~~~ 241 (665)
T PRK13558 230 RKDGSTFWNQVD 241 (665)
T ss_pred CCCCCEEEEEEE
Confidence 899999998754
No 42
>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=98.43 E-value=2.4e-07 Score=84.22 Aligned_cols=80 Identities=21% Similarity=0.375 Sum_probs=64.0
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhc
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AIS 310 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~ 310 (325)
+.++.++++++++++++|.+ |+++++|+++++++||++++++|++...+.++.........+.+ ++.
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 45788999999999999984 79999999999999999999999987777666555544444433 455
Q ss_pred cccCCCceeeEEe
Q 020523 311 PYPKKKSIYMEYV 323 (325)
Q Consensus 311 ~~~kdG~~~~~~~ 323 (325)
..+++|+.+|+.+
T Consensus 81 ~~~~~g~~~~~~~ 93 (494)
T TIGR02938 81 NRRKDGELYLAEL 93 (494)
T ss_pred ccCCCccchhhhe
Confidence 5778999888654
No 43
>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=98.41 E-value=2.4e-07 Score=79.70 Aligned_cols=79 Identities=14% Similarity=0.106 Sum_probs=60.8
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----hhccccC
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----AISPYPK 314 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----e~~~~~k 314 (325)
.+.|+.+++++++|++++|.+ |+|+++|++|++++||++++++|+++..+..+.. ....+.. .+....+
T Consensus 5 ~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~---~~~~l~~~~~~~~~~~~~~ 78 (333)
T TIGR02966 5 LSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPE---FVEYLAAGRFSEPLELPSP 78 (333)
T ss_pred HHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHH---HHHHHHhcccCCCeEeecC
Confidence 456888999999999999984 7999999999999999999999999988875432 2222222 3444456
Q ss_pred CCceeeEEee
Q 020523 315 KKSIYMEYVR 324 (325)
Q Consensus 315 dG~~~~~~~~ 324 (325)
+|..+|+.++
T Consensus 79 ~~~~~~~~~~ 88 (333)
T TIGR02966 79 INSERVLEIR 88 (333)
T ss_pred CCCceEEEEE
Confidence 7777777654
No 44
>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=98.39 E-value=1.1e-06 Score=61.90 Aligned_cols=80 Identities=19% Similarity=0.199 Sum_probs=60.4
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----------hhc
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----------AIS 310 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----------e~~ 310 (325)
.++.++++++.+++++|.+ |.++++|+++++++|++..+++|+++..+.++.........+.. ++.
T Consensus 4 ~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (124)
T TIGR00229 4 RYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERR 80 (124)
T ss_pred HHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEee
Confidence 4677889999999999984 79999999999999999999999998887766655444333322 222
Q ss_pred cccCCCceeeEEee
Q 020523 311 PYPKKKSIYMEYVR 324 (325)
Q Consensus 311 ~~~kdG~~~~~~~~ 324 (325)
...++|..+|+.++
T Consensus 81 ~~~~~~~~~~~~~~ 94 (124)
T TIGR00229 81 VRRKDGSEIWVEVS 94 (124)
T ss_pred eEcCCCCEEEEEEE
Confidence 23678888777543
No 45
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.34 E-value=7.8e-07 Score=77.22 Aligned_cols=80 Identities=14% Similarity=0.086 Sum_probs=59.8
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh-HHH-HHHHH------hhcccc
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT-TVL-YQVSI------AISPYP 313 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~-~~~-~~~~~------e~~~~~ 313 (325)
.+..+++++++|++++|. ||+|+++|+++++++||+.++++|+++.++.++.... ... ..+.. +.....
T Consensus 8 ~~~~il~~~~~gi~~~d~---~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (348)
T PRK11073 8 DAGQILNSLINSILLLDD---DLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLNIELMRESLQAGQGFTDNEVTLV 84 (348)
T ss_pred hHHHHHhcCcCeEEEECC---CCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchhhHHHHHHHHHcCCcccccceEEE
Confidence 467899999999999997 4799999999999999999999999998887543211 111 11211 122245
Q ss_pred CCCceeeEEee
Q 020523 314 KKKSIYMEYVR 324 (325)
Q Consensus 314 kdG~~~~~~~~ 324 (325)
+||+.+|+.++
T Consensus 85 ~~g~~~~~~~~ 95 (348)
T PRK11073 85 IDGRSHILSLT 95 (348)
T ss_pred ECCceEEEEEE
Confidence 79999998765
No 46
>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=98.29 E-value=1.1e-06 Score=62.32 Aligned_cols=61 Identities=16% Similarity=0.072 Sum_probs=49.7
Q ss_pred CCCeEEEehh-hHHhhCCCcccccccccccccCCCCChH-HHHHHHH----------hhccccCCCceeeEEe
Q 020523 263 DMPMVYASDA-FLKLTGYDRNEVVGQNCRFLNGVDTDTT-VLYQVSI----------AISPYPKKKSIYMEYV 323 (325)
Q Consensus 263 dg~i~~~N~a-~~~~~Gy~~~e~iG~~~~~l~~~~~~~~-~~~~~~~----------e~~~~~kdG~~~~~~~ 323 (325)
||+|+++-+. ...++||.++|++|+++.++++|++... ..+..++ -+++..|+|..+|+.-
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt 83 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQT 83 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEE
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEE
Confidence 7999999999 5999999999999999999999999886 4444443 5677789999888853
No 47
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=98.29 E-value=2.6e-06 Score=76.27 Aligned_cols=112 Identities=13% Similarity=0.151 Sum_probs=75.4
Q ss_pred HhhhhhhHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHh
Q 020523 9 EQSFNNRYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIRE 88 (325)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~ 88 (325)
++.+. ....+++.++++++++++++|.+ |.++++|+++++++||+.+++.|+++..+..+. ... ..+..
T Consensus 90 ~~~l~-~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~---~~~----~~~~~ 158 (430)
T PRK11006 90 RRELG-NLIKRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYP---EFT----QYLKT 158 (430)
T ss_pred HHHHH-HHHHHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCCcHHHHhcCH---HHH----HHHHh
Confidence 33343 46678999999999999999999 999999999999999999999999876654332 111 11222
Q ss_pred CCCeEEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhh
Q 020523 89 ERPIEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMR 140 (325)
Q Consensus 89 ~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~ 140 (325)
... .........++. ++.+...|..+ + +.+.+.+|||++++++
T Consensus 159 ~~~-~~~~~~~~~~~~--~~~~~~~~~~~---~---~~~~~~~dit~~~~~e 201 (430)
T PRK11006 159 RDF-SRPLTLVLNNGR--HLEIRVMPYTE---G---QLLMVARDVTQMHQLE 201 (430)
T ss_pred ccc-CCCeEEEcCCCC--EEEEEEEEcCC---C---cEEEEEehhhHHHHHH
Confidence 111 111222234444 45556666643 3 2567789999998863
No 48
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=98.28 E-value=6.2e-06 Score=75.07 Aligned_cols=109 Identities=14% Similarity=0.137 Sum_probs=78.5
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
+....+..+++++++||+++|.+ |.++++|+++++++|++.++++|+++..+++... +...+..+.....
T Consensus 77 ~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~-------l~~~le~~~~~~~ 146 (520)
T PRK10820 77 REHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-------FLRWLESEPQDSH 146 (520)
T ss_pred HHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcch-------HHHHHHcCCCccc
Confidence 34567899999999999999999 9999999999999999999999999887765432 2233444433111
Q ss_pred EEEEEecCCCEEEEEEEEEEee--cCCCCc--eEEEEEEEeccCcch
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVF--GKEDGR--ATHFVAVQVPIVSRK 137 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~--~~~~g~--~~~~~~~~~DITe~k 137 (325)
. .....+|..++ +...|+. + ++|. ..|.+.+++|+++..
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 5667776 4 4554 379999999998754
No 49
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=98.27 E-value=1.3e-05 Score=75.13 Aligned_cols=49 Identities=14% Similarity=0.131 Sum_probs=43.2
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccC
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNG 294 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~ 294 (325)
+..+++++++||+++|. +|+|+++|+++++++|++.++++|+++.++++
T Consensus 205 ~~~il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~ 253 (638)
T PRK11388 205 LNALLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRAITELLT 253 (638)
T ss_pred HHHHHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCcHHHHhc
Confidence 34467788999999998 47999999999999999999999999988774
No 50
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.21 E-value=3.6e-06 Score=53.30 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=36.9
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcc
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF 69 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l 69 (325)
++++.+++++|.+++++| + ++++++|+++++++||+ ..|.....+
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~~~~~~ 45 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGEDIGQL 45 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCCCHHCT
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCCCHHHh
Confidence 368899999999999999 9 89999999999999998 556654333
No 51
>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=98.19 E-value=4.7e-06 Score=55.78 Aligned_cols=70 Identities=20% Similarity=0.264 Sum_probs=53.3
Q ss_pred CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH----------hhccccCCCceee
Q 020523 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI----------AISPYPKKKSIYM 320 (325)
Q Consensus 251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~~ 320 (325)
+++++++|. +|.++++|+++++++|++..+++|+++..+.++.........+.. ++....++|...|
T Consensus 2 ~~~i~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (103)
T cd00130 2 PDGVIVLDL---DGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIW 78 (103)
T ss_pred CceEEEECC---CCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEE
Confidence 578888887 479999999999999999999999998888877766544443333 4444556787777
Q ss_pred EEe
Q 020523 321 EYV 323 (325)
Q Consensus 321 ~~~ 323 (325)
+.+
T Consensus 79 ~~~ 81 (103)
T cd00130 79 VLV 81 (103)
T ss_pred EEE
Confidence 654
No 52
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=98.00 E-value=0.00036 Score=54.13 Aligned_cols=117 Identities=25% Similarity=0.378 Sum_probs=84.1
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChH-HHHHHHHHH-HhCCCeEE
Q 020523 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRR-TIMEIREAI-REERPIEV 94 (325)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~-~~~~~~~~~-~~~~~~~~ 94 (325)
..++..+++..+.+++.+|.+ +.+.++|+++..++|++..+..+.....+........ ......... ........
T Consensus 111 ~~~~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 187 (232)
T COG2202 111 EERLRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEI 187 (232)
T ss_pred HHHHHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcce
Confidence 344889999999999999999 9999999999999999988777776554433322211 111222222 22234566
Q ss_pred EEEEEecCCCE-EEEEEEEEEeecCCCCceEEEEEEEeccCcchh
Q 020523 95 NLLNYKKDGTP-FWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (325)
Q Consensus 95 e~~~~~~dg~~-~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~ 138 (325)
+.....++|.. .+......+... .|.+..+.....|+++++.
T Consensus 188 ~~~~~~~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~d~~~~~~ 230 (232)
T COG2202 188 EYRVRRKDGERVRWILSRISPVRD--DGEIVGVVGIARDITERKQ 230 (232)
T ss_pred EEEEEecCCCEEEEEEeeeeEecC--CCceEEEEEEEechHHHhh
Confidence 77778889985 777777777653 6888888899999998876
No 53
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=97.90 E-value=6.7e-05 Score=66.79 Aligned_cols=113 Identities=11% Similarity=0.024 Sum_probs=77.3
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhC-CCeE
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREE-RPIE 93 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~ 93 (325)
+..++++.+++....|++.+|.+ |.+..+|++++.|+|.+-.++.|.+.+.+.+. +...+...-..+ ....
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 35667889999999999999999 99999999999999999999999886544321 122222211111 2223
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
.+.. ....|+...+.+....... + .-.+++.++.|||+...+
T Consensus 439 ~ev~-~~r~g~~rtl~Vq~t~~~~-d--~~~gyVvt~DDITdLV~A 480 (712)
T COG5000 439 VEVK-LAREGEERTLNVQATREPE-D--NGNGYVVTFDDITDLVIA 480 (712)
T ss_pred ceee-cccCCCceeeeeeeeeccc-c--cCCceEEEecchHHHHHH
Confidence 3333 3345555566666655543 2 224788999999999886
No 54
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=97.87 E-value=0.00013 Score=67.46 Aligned_cols=110 Identities=10% Similarity=0.140 Sum_probs=75.6
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCCh---hhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR---AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI 92 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~---~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 92 (325)
....++.++++++++++++|.+ |+++++|+++++++|++. .+.+|.....+.++ ..+...+..+...
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 3455688999999999999999 999999999999998753 34555554433322 1223344444433
Q ss_pred EEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhhhh
Q 020523 93 EVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHMRN 141 (325)
Q Consensus 93 ~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~~~ 141 (325)
.... ...+|. ++.+...|+.+ +|.+.|++.+++|+|+.+++++
T Consensus 289 ~~~~--~~~~g~--~~~~~~~pi~~--~g~~~g~v~~~rDite~~~l~~ 331 (542)
T PRK11086 289 RDEE--ININGR--LLLTNTVPVRV--NGEIIGAIATFRDKTEVRQLAQ 331 (542)
T ss_pred cceE--EEECCE--EEEEEEEEEeE--CCEEEEEEEEEEEchHHHHHHH
Confidence 2211 122443 34566788886 7889999999999999887633
No 55
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.82 E-value=1.2e-05 Score=71.89 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=45.8
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCC
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGV 295 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~ 295 (325)
.++.+++++++|++++|. +|+|+++|+++++++||+.++++|+++..+..+
T Consensus 99 ~~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~ 149 (430)
T PRK11006 99 RFRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRY 149 (430)
T ss_pred HHHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCCcHHHHhcC
Confidence 477789999999999997 579999999999999999999999998877653
No 56
>PF12860 PAS_7: PAS fold
Probab=97.82 E-value=4.1e-05 Score=54.87 Aligned_cols=44 Identities=25% Similarity=0.349 Sum_probs=38.5
Q ss_pred hhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccc-ccccccccc
Q 020523 247 LGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV-VGQNCRFLN 293 (325)
Q Consensus 247 ~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~-iG~~~~~l~ 293 (325)
+++++.||+++|. ||+++++|++|.+|+|++++.+ .|.++..+.
T Consensus 1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~ 45 (115)
T PF12860_consen 1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPGASFRDLL 45 (115)
T ss_pred CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHH
Confidence 4678999999998 4799999999999999999888 788876653
No 57
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.81 E-value=1.4e-05 Score=72.87 Aligned_cols=52 Identities=17% Similarity=0.094 Sum_probs=47.2
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (325)
.+..+++++++||+++|.+ |+|+++|++++++||++.++++|+++.++++..
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 4777899999999999985 799999999999999999999999999988643
No 58
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=97.78 E-value=1.2e-05 Score=68.17 Aligned_cols=105 Identities=23% Similarity=0.377 Sum_probs=85.3
Q ss_pred HHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCC-CChHHHHHHHHHHHhCCCeEEEEEE
Q 020523 20 VHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPR-TNRRTIMEIREAIREERPIEVNLLN 98 (325)
Q Consensus 20 ~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~e~~~ 98 (325)
+..+++....++-+.|.+ ..+.|+|++|+.|+|+...+++|++..++...+ ....+...+..+++.|..+.++...
T Consensus 159 lFaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~a 235 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEA 235 (775)
T ss_pred HHHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHH
Confidence 346788888899999998 999999999999999999999999987765433 2445677888999999999988777
Q ss_pred EecCCCEEEEEEEEEEeecCCCCceEEEEE
Q 020523 99 YKKDGTPFWMLFKMSLVFGKEDGRATHFVA 128 (325)
Q Consensus 99 ~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~ 128 (325)
+++.|......+.+.|+-+ ..|.+..++.
T Consensus 236 RRksgdS~dqh~~itP~~g-qggkirhfvs 264 (775)
T KOG1229|consen 236 RRKSGDSCDQHFIITPFAG-QGGKIRHFVS 264 (775)
T ss_pred hhccCCcccceEEEeeecC-CCCceeeehh
Confidence 7888877777778889987 6777776653
No 59
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.62 E-value=4.8e-05 Score=53.64 Aligned_cols=59 Identities=12% Similarity=0.121 Sum_probs=41.8
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHH
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQV 305 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~ 305 (325)
|..++++++.+++++|.+ ++|.++|+++.++|+..+ ..+|+++..++++...+.+...+
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~~-~~iGr~l~~~~~~~~~~~l~~~i 59 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLSP-SDIGRPLFDIHPPLSYPNLKKII 59 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS---G-GGTTSBCCCSS-HHHHHHHHHHH
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCCh-HHCCCCHHHcCCccchHHHHHHH
Confidence 456889999999999985 699999999999999775 55799999998774444443333
No 60
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=97.62 E-value=0.00068 Score=57.11 Aligned_cols=55 Identities=18% Similarity=0.264 Sum_probs=46.1
Q ss_pred HHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHH
Q 020523 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78 (325)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~ 78 (325)
..+++.+.--+++++++ |.+.|++....-.+|++.-|+.|-.+.+.+++.|...+
T Consensus 82 shlLqtLDGF~fvva~d---GkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~dem 136 (598)
T KOG3559|consen 82 SHLLQTLDGFIFVVAPD---GKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEM 136 (598)
T ss_pred HhHHHhhcceEEEEeCC---CCEEEEecceeeeecceeeEeecchhhhhhcccchHHH
Confidence 45566666678899999 99999999999999999999999988888888766543
No 61
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.57 E-value=0.0054 Score=47.35 Aligned_cols=77 Identities=18% Similarity=0.160 Sum_probs=53.2
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh----HHHHHHHH--------hhc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT----TVLYQVSI--------AIS 310 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~----~~~~~~~~--------e~~ 310 (325)
+..++++++++++++|. +|.+.++|+++++++||+..+..+.....+....... ........ ++.
T Consensus 114 ~~~~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (232)
T COG2202 114 LRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYR 190 (232)
T ss_pred HHHHHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcceEEE
Confidence 34467778899999997 4799999999999999998888888776655433332 11111111 555
Q ss_pred cccCCCce-eeEE
Q 020523 311 PYPKKKSI-YMEY 322 (325)
Q Consensus 311 ~~~kdG~~-~~~~ 322 (325)
...++|.. .|..
T Consensus 191 ~~~~~g~~~~~~~ 203 (232)
T COG2202 191 VRRKDGERVRWIL 203 (232)
T ss_pred EEecCCCEEEEEE
Confidence 56688875 5553
No 62
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=97.54 E-value=0.00086 Score=63.15 Aligned_cols=109 Identities=12% Similarity=0.217 Sum_probs=75.5
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (325)
..+..+++.++++++++|.+ |.++++|+++++++|++.++++|+++..+++.. ..+..++..+........
T Consensus 203 ~~~~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~------~~l~~vl~~~~~~~~~~~ 273 (638)
T PRK11388 203 NQLNALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGRAITELLTLP------AVLQQAIKQAHPLKHVEV 273 (638)
T ss_pred HHHHHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCCcHHHHhccc------hHHHHHHhcCCceeeEEE
Confidence 34456889999999999999 999999999999999999999999877665321 122344555544332222
Q ss_pred EEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchh
Q 020523 98 NYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKH 138 (325)
Q Consensus 98 ~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~ 138 (325)
....+|..+++.+...|+.+ ..|. +++.+..|++..+.
T Consensus 274 ~l~~~g~~~~~~v~~~Pi~~-~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 274 TFESQGQFIDAVITLKPIIE-GQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred EEecCCceEEEEEEEEeecc-cCce--EEEEEehhhHHHHH
Confidence 23345666678888899865 4443 35555677776543
No 63
>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=97.46 E-value=0.00027 Score=42.85 Aligned_cols=57 Identities=23% Similarity=0.311 Sum_probs=46.3
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHH
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVL 302 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~ 302 (325)
++.+++.+++++++++.. +.+.++|+.+.+++|++..++.|+.+..+.++.......
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQ 59 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHH
Confidence 455777888999999974 699999999999999999999999887777666554433
No 64
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=97.42 E-value=0.00015 Score=64.03 Aligned_cols=73 Identities=36% Similarity=0.620 Sum_probs=57.2
Q ss_pred CceEEecCCCCCCCeEEEehhhHHhhCCCccccccccc--ccccCCCCChHHHHHHHH----------hhccccCCCcee
Q 020523 252 QSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNC--RFLNGVDTDTTVLYQVSI----------AISPYPKKKSIY 319 (325)
Q Consensus 252 ~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~--~~l~~~~~~~~~~~~~~~----------e~~~~~kdG~~~ 319 (325)
..+++.+++-.|.+|+|.|++||++.||.+.|++.+++ .++.....+....+.+++ |+..++|+.++.
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 45666666667889999999999999999999999965 445555555555566555 888899999999
Q ss_pred eEEee
Q 020523 320 MEYVR 324 (325)
Q Consensus 320 ~~~~~ 324 (325)
|..+.
T Consensus 108 W~~vq 112 (971)
T KOG0501|consen 108 WLLVQ 112 (971)
T ss_pred EEEEE
Confidence 98764
No 65
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.40 E-value=0.0055 Score=62.35 Aligned_cols=43 Identities=9% Similarity=0.063 Sum_probs=38.0
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhh
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAE 60 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e 60 (325)
....+++.+++.++.+++++|.+ |.++++|++++.++|++...
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 45567889999999999999999 99999999999999986433
No 66
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.36 E-value=0.0013 Score=60.88 Aligned_cols=106 Identities=14% Similarity=0.108 Sum_probs=73.0
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCCh--hhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEE
Q 020523 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR--AEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEV 94 (325)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~--~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (325)
...+..+++.+++|++++|.+ |.++++|+++++++|++. ++++|++...++++... . ...... .....
T Consensus 221 ~~~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~---~---~~~~~~-~~~~~ 290 (545)
T PRK15053 221 VRQQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADF---F---TEQIDE-KRQDV 290 (545)
T ss_pred HHHHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchh---h---hhhcCC-cccce
Confidence 345678999999999999999 999999999999999965 46889887666543211 0 111111 11111
Q ss_pred EEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 95 NLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 95 e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
. ...+| ..+.+...|+.. .|.+.|.+.+++|+|+.+..
T Consensus 291 ~---~~~~~--~~~~~~~~~i~~--~~~~~G~v~~~~d~te~~~l 328 (545)
T PRK15053 291 V---ANFNG--LSVIANREAIRS--GDDLLGAIISFRSKDEISTL 328 (545)
T ss_pred E---EEECC--EEEEEEeeeEEE--CCeEEEEEEEEEchHHHHHH
Confidence 1 12234 234467778875 66778999999999998765
No 67
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=97.33 E-value=0.0015 Score=57.91 Aligned_cols=109 Identities=13% Similarity=0.171 Sum_probs=80.4
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChh--hhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeE
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRA--EIIGRNGRMFQGPRTNRRTIMEIREAIREERPIE 93 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~--e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 93 (325)
.......+++++..|++.+|+. |.+..+|.++++|+|+... +.+|++...+++|+.. +...+..+.+..
T Consensus 213 l~~er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~------l~~vl~~~~~~~ 283 (537)
T COG3290 213 LLEERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD------LPEVLETGKPQH 283 (537)
T ss_pred HHHHHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC------cHHHHhcCCccc
Confidence 4445678899999999999999 9999999999999999765 6889988888776321 112234444333
Q ss_pred EEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
.+. ..-+|. ++.+...|+.- +|++.|++.+++|-|+-++.
T Consensus 284 ~~e--~~~ng~--~~i~nr~pI~~--~~~~~GaI~tFRdktei~~L 323 (537)
T COG3290 284 DEE--IRINGR--LLVANRVPIRS--GGQIVGAIITFRDKTEIKKL 323 (537)
T ss_pred chh--hhcCCe--EEEEEeccEEE--CCEEeEEEEEEecHHHHHHH
Confidence 222 122343 45577888885 89999999999999998875
No 68
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=97.33 E-value=0.00036 Score=65.14 Aligned_cols=52 Identities=23% Similarity=0.215 Sum_probs=46.5
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (325)
.+..++++++++++++|. +|.++++|+++++++||++++++|+++..++++.
T Consensus 263 ~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~ 314 (607)
T PRK11360 263 LNELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKPYSELFPPN 314 (607)
T ss_pred HHHHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCc
Confidence 456788999999999997 4799999999999999999999999999888654
No 69
>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=97.29 E-value=0.0013 Score=39.67 Aligned_cols=55 Identities=24% Similarity=0.412 Sum_probs=45.5
Q ss_pred HHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCCh
Q 020523 19 WVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNR 76 (325)
Q Consensus 19 ~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~ 76 (325)
++..+++.++.++++++.. +.+.++|+.+..++|++..++.|.....+.++.+..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (67)
T smart00091 2 RLRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRE 56 (67)
T ss_pred hHHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHH
Confidence 3567888999999999999 999999999999999999888887766665555443
No 70
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=97.26 E-value=0.00076 Score=60.86 Aligned_cols=95 Identities=11% Similarity=0.252 Sum_probs=79.6
Q ss_pred EcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEE
Q 020523 34 TDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMS 113 (325)
Q Consensus 34 ~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~ 113 (325)
.+.+ .+|.|+.+.+..++||.+++++|+++..+++..|...+.......+..|.....-++...+.|..+|+...+.
T Consensus 280 hs~D---mkityCedRisdlm~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqAT 356 (768)
T KOG3558|consen 280 HSLD---MKITYCEDRISDLMDYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQAT 356 (768)
T ss_pred eecc---eeEEEEchhHHHHhcCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeE
Confidence 3455 7899999999999999999999999999999999888888888999999888888888999999999999998
Q ss_pred EeecCCCCceEEEEEEEe
Q 020523 114 LVFGKEDGRATHFVAVQV 131 (325)
Q Consensus 114 ~~~~~~~g~~~~~~~~~~ 131 (325)
.+.+..+++...++++.-
T Consensus 357 Vi~~tkn~q~q~IicVnY 374 (768)
T KOG3558|consen 357 VIYNTKNPQEQNIICVNY 374 (768)
T ss_pred EEecCCCCCcceEEEEEe
Confidence 887623344444555443
No 71
>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=97.21 E-value=0.0011 Score=46.75 Aligned_cols=59 Identities=14% Similarity=0.072 Sum_probs=48.3
Q ss_pred hhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccc-cccCCCCChHHHHHHHH
Q 020523 246 SLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCR-FLNGVDTDTTVLYQVSI 307 (325)
Q Consensus 246 ~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~-~l~~~~~~~~~~~~~~~ 307 (325)
-++..|-|++-.|.+ |+|+..|.+-..+.|++++.++|+++. ++.|=...+.+..++.+
T Consensus 21 elD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~ 80 (124)
T TIGR02373 21 QFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFME 80 (124)
T ss_pred HhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHh
Confidence 367778999999984 899999999999999999999999974 55554556667777765
No 72
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=97.13 E-value=0.0051 Score=50.59 Aligned_cols=108 Identities=12% Similarity=0.105 Sum_probs=78.9
Q ss_pred HHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020523 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (325)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (325)
..++++++..++++|.+ +.+.|+|++++.+||.+...+.|.++..+++.. ......+.+....+......-....
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g--s~ll~ll~q~~~~~~~~~~~~v~l~ 84 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGTRLSELLPFG--SLLLSLLDQVLERGQPVTEYEVTLV 84 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC--cHHHHHHHHHHHhcCCcccceeeee
Confidence 46889999999999999 999999999999999999999999887776543 2345556666666655432222223
Q ss_pred cCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcch
Q 020523 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRK 137 (325)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k 137 (325)
.+|....+...+.|+.. ..|.+ +..+..+....
T Consensus 85 ~~g~~~~v~~~v~~v~~-~~G~v---lle~~~~~~~~ 117 (363)
T COG3852 85 ILGRSHIVDLTVAPVPE-EPGSV---LLEFHPRDMQR 117 (363)
T ss_pred ecCccceEEEEEeeccC-CCCeE---EEEechhHHHh
Confidence 68888899999999976 56643 44445444444
No 73
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=97.06 E-value=0.0036 Score=57.92 Aligned_cols=52 Identities=10% Similarity=0.115 Sum_probs=44.3
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCc--ccccccccccccCCC
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR--NEVVGQNCRFLNGVD 296 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~--~e~iG~~~~~l~~~~ 296 (325)
.+..+++++++|++++|. +|+|+++|+++++++|++. ++++|+++.++.++.
T Consensus 223 ~~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~ 276 (545)
T PRK15053 223 QQEALFSSVYEGLIAVDP---HGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPA 276 (545)
T ss_pred HHHHHHHHhCceEEEECC---CCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCc
Confidence 356688999999999998 4799999999999999975 479999988877543
No 74
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=96.98 E-value=0.004 Score=55.32 Aligned_cols=53 Identities=21% Similarity=0.238 Sum_probs=46.2
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcc--cccccccccccCCCCC
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN--EVVGQNCRFLNGVDTD 298 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~--e~iG~~~~~l~~~~~~ 298 (325)
...+++++.+|++.+|.. |.|+.+|.++++|+|+... +.+|+++.++.+|+.+
T Consensus 217 r~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~ 271 (537)
T COG3290 217 RQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSD 271 (537)
T ss_pred HHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccccceEeeccccC
Confidence 456788999999999986 6999999999999999765 7999999999987543
No 75
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.97 E-value=0.0036 Score=53.00 Aligned_cols=114 Identities=17% Similarity=0.189 Sum_probs=85.7
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEE
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVN 95 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e 95 (325)
+.+.+..+++..|.-+..+|.+ +.+.+.|+. .++|-.++. ++|++...- +|.........+.+...+|..-..+
T Consensus 288 ~~~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~s-viGr~v~~c-hpPksv~iv~ki~~~fksG~kd~~e 361 (409)
T COG2461 288 SLEELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTPS-VIGRRVQLC-HPPKSVHIVEKILKDFKSGEKDFAE 361 (409)
T ss_pred eHHHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccChH-hhCCcccCC-CCCchHHHHHHHHHHhhcCCcchHH
Confidence 3457889999999888889999 999999998 777776655 468886644 4444455566677777777665555
Q ss_pred EEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
+.. . .| ...+.++..++++ ++|...|.+.+.+|||..+..
T Consensus 362 fw~-~-~~-~~~i~i~Y~av~d-e~ge~~g~le~~qdi~~i~~l 401 (409)
T COG2461 362 FWI-N-MG-DKFIHIRYFAVKD-EEGEYLGTLEVVQDITRIKEL 401 (409)
T ss_pred Hhc-c-CC-CceEEEEEEEEEc-CCCceeeeehhhhhhHHHHhc
Confidence 542 1 22 2356788999999 899999999999999998875
No 76
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=96.92 E-value=0.051 Score=40.27 Aligned_cols=112 Identities=11% Similarity=0.105 Sum_probs=72.8
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEE
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLL 97 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~ 97 (325)
..++.++. .|.+|+-.+.+ .+=.++|.|.++.++++++-+++++.|...-..+.........+.++...|-.....-.
T Consensus 32 ~~~~~L~~-ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~Gi 109 (148)
T PF08670_consen 32 ELAKALWH-APFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGI 109 (148)
T ss_pred HHHHHHHc-CCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeE
Confidence 34555555 88888877665 22468999999999999999999999876655555444445556666666644333333
Q ss_pred EEecCCCEEEEE-EEEEEeecCCCCceEEEEEEEec
Q 020523 98 NYKKDGTPFWML-FKMSLVFGKEDGRATHFVAVQVP 132 (325)
Q Consensus 98 ~~~~dg~~~~~~-~~~~~~~~~~~g~~~~~~~~~~D 132 (325)
-+.+.|+.+++. ..+--+.+ ++|...|.-..+.+
T Consensus 110 Riss~Grrf~ie~a~vW~l~D-~~g~~~GqAa~F~~ 144 (148)
T PF08670_consen 110 RISSTGRRFRIERATVWNLID-EDGNYCGQAAMFSN 144 (148)
T ss_pred EEcCCCCeEEEeceEEEEEEc-CCCCEEEEEEEEee
Confidence 356778777664 23344555 67776665444443
No 77
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=96.88 E-value=0.0028 Score=46.83 Aligned_cols=79 Identities=16% Similarity=0.094 Sum_probs=55.3
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH-----hhc-----cc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI-----AIS-----PY 312 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~-----e~~-----~~ 312 (325)
+...+-+.|.+|+.-+.. +|-.++|+|.++.+||+|+-+|++|.+.+--..+..+......+.+ -.. ..
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 444555588888888766 4778999999999999999999999987765555544444333333 111 13
Q ss_pred cCCCceeeEE
Q 020523 313 PKKKSIYMEY 322 (325)
Q Consensus 313 ~kdG~~~~~~ 322 (325)
.+.|..++++
T Consensus 112 ss~Grrf~ie 121 (148)
T PF08670_consen 112 SSTGRRFRIE 121 (148)
T ss_pred cCCCCeEEEe
Confidence 4788877654
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=96.62 E-value=0.035 Score=39.39 Aligned_cols=67 Identities=18% Similarity=0.076 Sum_probs=54.4
Q ss_pred HHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCC-cccCCCCChHHHHHHHHHHHhCC
Q 020523 21 HEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGR-MFQGPRTNRRTIMEIREAIREER 90 (325)
Q Consensus 21 ~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~-~l~~~~~~~~~~~~~~~~~~~~~ 90 (325)
..-++..|.|++-+|.+ |.++..|.+=..+.|++++.++|++.. ++.|......+...+.+....+.
T Consensus 19 ~eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 19 DAQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred HhHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 35589999999999999 999999999999999999999999844 44455555667777777665554
No 79
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.59 E-value=0.001 Score=56.94 Aligned_cols=52 Identities=23% Similarity=0.420 Sum_probs=44.4
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCC
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDT 297 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~ 297 (325)
+..+++....+|-++|. |..|.|||++|+.|+||-+.|++|+...++...+.
T Consensus 159 lFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGke~adlpkkdk 210 (775)
T KOG1229|consen 159 LFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDK 210 (775)
T ss_pred HHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCCchhhcccccc
Confidence 55677788889999987 46899999999999999999999999988875543
No 80
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=96.24 E-value=0.0023 Score=59.90 Aligned_cols=64 Identities=19% Similarity=0.211 Sum_probs=48.7
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHH
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVS 306 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~ 306 (325)
..|..++=.+.||++++-.. ||+|+||+.+.+.++||..+|++|+++.++++|.+....+..+-
T Consensus 94 ~eL~~LmLeAlDGF~fvV~c--dG~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~~~ql~ 157 (803)
T KOG3561|consen 94 DELTHLILEALDGFLFVVNC--DGRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKPREQLS 157 (803)
T ss_pred HHHHHHHHHHhcCeEEEEec--CceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCccccccc
Confidence 34554444445666555443 69999999999999999999999999999998887766655544
No 81
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=96.23 E-value=0.015 Score=54.15 Aligned_cols=67 Identities=13% Similarity=0.113 Sum_probs=49.9
Q ss_pred eEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHH---HHH----------hhccccCCCceee
Q 020523 254 FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQ---VSI----------AISPYPKKKSIYM 320 (325)
Q Consensus 254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~---~~~----------e~~~~~kdG~~~~ 320 (325)
||++-.. +.+.|..|..++..++||-+.++||+++..++++++.....+. +.+ .+++..++|.++-
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 5555443 5788999999999999999999999999888888776544332 222 5566678888764
Q ss_pred E
Q 020523 321 E 321 (325)
Q Consensus 321 ~ 321 (325)
+
T Consensus 411 l 411 (1114)
T KOG3753|consen 411 L 411 (1114)
T ss_pred E
Confidence 4
No 82
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=96.18 E-value=0.072 Score=47.18 Aligned_cols=59 Identities=12% Similarity=0.147 Sum_probs=49.5
Q ss_pred HHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHH
Q 020523 22 EALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIR 83 (325)
Q Consensus 22 ~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~ 83 (325)
-++..++--++++..+ |.|.|++......+|+...+++-.++.++++.+|...+...+.
T Consensus 115 ~lLqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQsVYdlIHseDR~dfqrQLh 173 (712)
T KOG3560|consen 115 LLLQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQSVYDLIHSEDRQDFQRQLH 173 (712)
T ss_pred HHHHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhhHHHHhhhhhHHHHHHHHh
Confidence 3456666667888899 9999999999999999999999999999999888777655443
No 83
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=96.05 E-value=0.0085 Score=50.57 Aligned_cols=55 Identities=16% Similarity=0.088 Sum_probs=47.8
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCCh
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDT 299 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~ 299 (325)
.|..++++++++++-+|.. |.+..+|+|++++||.+.+++.|+....++....-.
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 3777899999999999985 799999999999999999999999988877554433
No 84
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=95.93 E-value=0.014 Score=48.91 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=51.8
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI 307 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~ 307 (325)
|..++--+.+|++-+|.. |+|+.+|..+.+|+|.+.++++|+++.++..-.+.-.+.+.+.+
T Consensus 113 L~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~~~dL~e~ 174 (459)
T COG5002 113 LDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRSILELLKIEDTYTFEDLVEK 174 (459)
T ss_pred HHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhcccHHHHhCCccceeHHHHHhc
Confidence 455555667999999986 79999999999999999999999999999877776666655544
No 85
>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=95.91 E-value=0.086 Score=27.63 Aligned_cols=40 Identities=30% Similarity=0.452 Sum_probs=32.5
Q ss_pred EEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcc
Q 020523 96 LLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSR 136 (325)
Q Consensus 96 ~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~ 136 (325)
+.....+|...|+.....++.+ ..+.+.++++...|||++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 4 YRLRRKDGSYIWVLVSASPIRD-EDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEecCCCEEEEEEEeEEEEC-CCCCEEEEEEEEEeccCC
Confidence 3456678888899888888887 778888999999999863
No 86
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=95.90 E-value=0.0099 Score=54.95 Aligned_cols=52 Identities=15% Similarity=0.199 Sum_probs=42.7
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCC---cccccccccccccC
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNG 294 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~ 294 (325)
...++.+++++++||+++|. +|+|+++|+++++++|++ ..+.+|+.+..+.+
T Consensus 220 ~~~~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~ 274 (542)
T PRK11086 220 FEQRQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMP 274 (542)
T ss_pred HHHHHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCC
Confidence 34567889999999999998 479999999999999875 35677887766654
No 87
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=95.74 E-value=0.049 Score=48.19 Aligned_cols=93 Identities=14% Similarity=0.162 Sum_probs=75.7
Q ss_pred CCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 020523 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (325)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (325)
+..+.+......++||...|+.|.+...+++-+|..-......+.+++|.+.-.-++..+++|++.|+..++..++. +
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 55677788888999999999999888888887776555666778888888877888889999999999988888874 7
Q ss_pred CceEEEEEEEeccCc
Q 020523 121 GRATHFVAVQVPIVS 135 (325)
Q Consensus 121 g~~~~~~~~~~DITe 135 (325)
|.+-.++...+-.++
T Consensus 371 gkPD~vi~thr~l~D 385 (712)
T KOG3560|consen 371 GKPDLVIDTHRGLGD 385 (712)
T ss_pred CCCCEEEecCCCccc
Confidence 887777766665555
No 88
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=95.67 E-value=0.048 Score=46.22 Aligned_cols=56 Identities=14% Similarity=0.158 Sum_probs=49.7
Q ss_pred HHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCC
Q 020523 16 YTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRT 74 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~ 74 (325)
....+..++++++++++-+|.. |.+..+|++++.++|.+.+.+.|.+...+++...
T Consensus 78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~~~~~l~~~~n 133 (511)
T COG3283 78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGHTAAQLINGFN 133 (511)
T ss_pred HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCccHHHhcCcCC
Confidence 4456789999999999999999 9999999999999999999999998777765543
No 89
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=95.20 E-value=0.026 Score=46.60 Aligned_cols=49 Identities=18% Similarity=0.259 Sum_probs=43.7
Q ss_pred hhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCC
Q 020523 245 ISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVD 296 (325)
Q Consensus 245 ~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~ 296 (325)
.+++++..+++++|. +|.|.|+|++++.+||-|..-+.|..+..+++..
T Consensus 11 ~~Ln~~~~pVl~vd~---~~~i~yaN~aAe~~~~~Sa~~L~~~~l~~l~~~g 59 (363)
T COG3852 11 AILNNLINPVLLVDD---ELAIHYANPAAEQLLAVSARRLAGTRLSELLPFG 59 (363)
T ss_pred hHHhccCCceEEEcC---CCcEEecCHHHHHHHHHHHHHHhcCChHHHcCCC
Confidence 478888999999998 4799999999999999999999999999888543
No 90
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=94.72 E-value=0.66 Score=34.21 Aligned_cols=86 Identities=13% Similarity=0.156 Sum_probs=68.6
Q ss_pred CCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEEEEEEEeecCCC
Q 020523 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWMLFKMSLVFGKED 120 (325)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~~~~~~~~~~~~ 120 (325)
.++..+-...+.++|+ ++.|+++..++.+.....+...+..++....+..........+|....+..-.-|+.+ .+
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 4456789999999997 5779988888888777777778888888877777777777788888888888999988 67
Q ss_pred CceEEEEEEE
Q 020523 121 GRATHFVAVQ 130 (325)
Q Consensus 121 g~~~~~~~~~ 130 (325)
|.+..++|..
T Consensus 127 ~~v~rilG~~ 136 (137)
T PF07310_consen 127 GTVDRILGAL 136 (137)
T ss_pred CCccEEEEec
Confidence 7787777754
No 91
>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=94.47 E-value=0.046 Score=38.61 Aligned_cols=47 Identities=26% Similarity=0.458 Sum_probs=37.3
Q ss_pred eEEecCCCCCCCeEEEehhhHHhhCCC---cccccccccccccCCCCChHHH
Q 020523 254 FVLIDPHLPDMPMVYASDAFLKLTGYD---RNEVVGQNCRFLNGVDTDTTVL 302 (325)
Q Consensus 254 i~~~d~~~~dg~i~~~N~a~~~~~Gy~---~~e~iG~~~~~l~~~~~~~~~~ 302 (325)
++++|.. |++|+.++....+++|.+ +++++|+++..++++.....+.
T Consensus 18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~ 67 (110)
T PF08446_consen 18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLR 67 (110)
T ss_dssp EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHH
T ss_pred EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHH
Confidence 3456664 689999999999999999 9999999999999766544333
No 92
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=93.03 E-value=0.092 Score=47.62 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=42.2
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
+...++.+..|++.+|.+ |+|.-+|+++++|+|.+-++++|+++..+.
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 445788889999999985 799999999999999999999999977665
No 93
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=91.18 E-value=0.21 Score=47.40 Aligned_cols=58 Identities=17% Similarity=0.289 Sum_probs=48.1
Q ss_pred HHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHH
Q 020523 18 LWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRT 78 (325)
Q Consensus 18 ~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~ 78 (325)
++-..+++++.--++++..+ |+|+||+.+...++||..++++|.++..+.+|++....
T Consensus 95 eL~~LmLeAlDGF~fvV~cd---G~IvyVSeSVT~~L~y~QsDL~~qSly~ilhp~d~~~~ 152 (803)
T KOG3561|consen 95 ELTHLILEALDGFLFVVNCD---GRIVYVSESVTSVLGYLQSDLMGQSLYDILHPLDNDKP 152 (803)
T ss_pred HHHHHHHHHhcCeEEEEecC---ceEEEEecchHHhhCcCHHHHhcchHHHhcCccccCcc
Confidence 34456677777677899999 99999999999999999999999998888887765443
No 94
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=89.88 E-value=0.43 Score=48.93 Aligned_cols=40 Identities=8% Similarity=-0.064 Sum_probs=34.0
Q ss_pred hhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccc
Q 020523 242 SLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEV 284 (325)
Q Consensus 242 ~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~ 284 (325)
.++.++++++++|+++|. +|+|+++|+++++++|++....
T Consensus 577 ~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~~~~ 616 (1197)
T PRK09959 577 FRKALSDSLPNPTYVVNW---QGNVISHNSAFEHYFTADYYKN 616 (1197)
T ss_pred HHHHHHhhCCCcEEEEcC---CCcEEEehHHHHHHhCcccccc
Confidence 356788999999999998 4799999999999999875433
No 95
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=88.99 E-value=8 Score=35.85 Aligned_cols=41 Identities=20% Similarity=0.254 Sum_probs=32.3
Q ss_pred cCCceEEecCCCCCCCeEEEehhhHHhhCCC-ccccccccccccc
Q 020523 250 IKQSFVLIDPHLPDMPMVYASDAFLKLTGYD-RNEVVGQNCRFLN 293 (325)
Q Consensus 250 ~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~-~~e~iG~~~~~l~ 293 (325)
.+.+.+++|. ||+|+.+|+++..+++.+ ..-++|++...+.
T Consensus 231 ~~~~~lavd~---~grvl~at~aA~~~La~~~~~~l~g~p~~~~~ 272 (606)
T COG3284 231 QSEALLAVDQ---DGRVLGATRAARQLLALTDRQRLIGQPVEDFL 272 (606)
T ss_pred ccceeeeecC---cchhhhccHHHHHhhccchhhHhhcCCccccc
Confidence 3577888887 579999999999999987 5566677666554
No 96
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=87.62 E-value=1.6 Score=37.65 Aligned_cols=85 Identities=8% Similarity=0.051 Sum_probs=59.4
Q ss_pred eEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEecCCCEEEEE
Q 020523 30 SFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYKKDGTPFWML 109 (325)
Q Consensus 30 ~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dg~~~~~~ 109 (325)
-++....+ ..+++.......++||.+.+++++.+...++..|...+...-.-.+..|..-.--+++..+.|.++|+.
T Consensus 227 FmfraslD---lkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvq 303 (598)
T KOG3559|consen 227 FMFRASLD---LKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQ 303 (598)
T ss_pred EEEEeecc---eEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEE
Confidence 34555666 789999999999999999999999876666665554444443444455554443455667788888887
Q ss_pred EEEEEeec
Q 020523 110 FKMSLVFG 117 (325)
Q Consensus 110 ~~~~~~~~ 117 (325)
-....+.+
T Consensus 304 syat~vHn 311 (598)
T KOG3559|consen 304 SYATFVHN 311 (598)
T ss_pred EeeEEEec
Confidence 66666654
No 97
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=86.70 E-value=37 Score=34.08 Aligned_cols=42 Identities=7% Similarity=0.025 Sum_probs=34.7
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCCh
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFSR 58 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~ 58 (325)
..+++++.+++.+|.++++++.. ++.++..|+.+..++|+..
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 45667889999999999999743 3999999999999887643
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=84.88 E-value=1.3 Score=31.17 Aligned_cols=42 Identities=26% Similarity=0.397 Sum_probs=33.7
Q ss_pred EEEEcCCCCCCCEEEecHHHHHhcCCC---hhhhcCCCCCcccCCCC
Q 020523 31 FTITDPSISGHPIVFASRGFLKMSGFS---RAEIIGRNGRMFQGPRT 74 (325)
Q Consensus 31 i~~~d~~~~~~~i~~~N~~~~~~~G~~---~~e~~g~~~~~l~~~~~ 74 (325)
++++|.+ +++++.++.....++|.+ .++++|+++..++++..
T Consensus 18 LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~ 62 (110)
T PF08446_consen 18 LLALDPD--DLRIVQASENIAELLGIPPELPEELLGRPLSELLGAES 62 (110)
T ss_dssp EEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCC
T ss_pred EEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHH
Confidence 3456553 489999999999999999 99999999888876553
No 99
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=75.52 E-value=1.5 Score=36.70 Aligned_cols=43 Identities=14% Similarity=0.381 Sum_probs=30.8
Q ss_pred hHhhhhccC---Cc-eEEecCCCCCCCeEEEehhhHHhhCCCccccccc
Q 020523 243 LYISLGRIK---QS-FVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQ 287 (325)
Q Consensus 243 l~~~~~~~~---~~-i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~ 287 (325)
.+.++++.. .| ++|-.+. +.+.+|+|.-+..++||+.++++..
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~ 331 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKD 331 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhc
Confidence 445555443 34 4444443 6799999999999999999998744
No 100
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=75.29 E-value=3.5 Score=40.77 Aligned_cols=39 Identities=8% Similarity=-0.094 Sum_probs=34.1
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCC
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYD 280 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~ 280 (325)
...++.+++++|+|+++.|.. +|+|+++|+++++++|+.
T Consensus 342 ~~l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 342 RALNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCcc
Confidence 445778899999999999975 589999999999999874
No 101
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=73.06 E-value=4.9 Score=31.99 Aligned_cols=38 Identities=13% Similarity=0.043 Sum_probs=31.7
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCc
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDR 281 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~ 281 (325)
+++..++...+.+++|-+. +|.+++.|.+|.+.|+-+-
T Consensus 19 ~~~~~~i~~~~~P~CiR~~---~g~fi~~N~~F~~~f~~~~ 56 (217)
T PRK13719 19 ESLTAFIDDYSYPACIRNE---SGKFIFYNTLFLKEFLGQL 56 (217)
T ss_pred HHHHHHHHcCCCCeEEECC---CCCeeecchHHHHHHHhcC
Confidence 3566788888999999997 4899999999999887543
No 102
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=69.96 E-value=14 Score=35.63 Aligned_cols=70 Identities=9% Similarity=0.115 Sum_probs=53.9
Q ss_pred CCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCe---EEEEEEEecCCCEEEEEE
Q 020523 41 HPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPI---EVNLLNYKKDGTPFWMLF 110 (325)
Q Consensus 41 ~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~~e~~~~~~dg~~~~~~~ 110 (325)
+.+..+..++..++||-+.++||+++..++++.|..........++..+... .-.+++...+|..+.+..
T Consensus 341 Clf~hVDeaAVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldT 413 (1114)
T KOG3753|consen 341 CLFQHVDEAAVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDT 413 (1114)
T ss_pred ceeeecchhhhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEec
Confidence 5677889999999999999999999988889988887777777777665332 234566677887765554
No 103
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=67.95 E-value=13 Score=36.99 Aligned_cols=40 Identities=13% Similarity=0.075 Sum_probs=34.5
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCC
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~ 56 (325)
....+.+.+++.+|.|++++|.. ++.++.+|+++..++|+
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 45668899999999999999943 38999999999999875
No 104
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=66.79 E-value=21 Score=25.54 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=35.1
Q ss_pred eEEEEEEEecCCCEEEEEEEEEEeecCCCCceEEEEEEEeccCcchhh
Q 020523 92 IEVNLLNYKKDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIVSRKHM 139 (325)
Q Consensus 92 ~~~e~~~~~~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DITe~k~~ 139 (325)
....+....++|+ .+..+...+++ ++|.+.|++++-.|+|....+
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 3344555677885 45677788898 899999999999999998765
No 105
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=66.33 E-value=11 Score=36.88 Aligned_cols=48 Identities=19% Similarity=0.101 Sum_probs=38.3
Q ss_pred HHHHHHHHHhhCCCeEEEEc-CCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcc
Q 020523 16 YTLWVHEALDELPDSFTITD-PSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMF 69 (325)
Q Consensus 16 ~~~~~~~~~~~~~~~i~~~d-~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l 69 (325)
...--..++..+|.|+.++| .+ |.+.|.|+.|..++| .. ++|.++..+
T Consensus 100 ~~~~~~~~l~~~p~gi~~~~~~~---~~i~W~N~~~~~~~~--~~-~~g~~i~~~ 148 (838)
T PRK14538 100 VSQIGEEVLNELPIGIVLIDISS---KEIQWLNPYANFILK--NP-EINTPLAQI 148 (838)
T ss_pred HhHHHHHHHHhCCceEEEEeCCC---CEEEEECHHHHHHhC--cc-ccCCcHHHh
Confidence 33445678999999999999 68 999999999999987 22 788876643
No 106
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=66.28 E-value=7.3 Score=38.10 Aligned_cols=46 Identities=13% Similarity=0.026 Sum_probs=37.5
Q ss_pred hHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020523 243 LYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 243 l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
-..++...|-|++++|.. +|.|+++|+.|.+++| .+ ++|+++..+.
T Consensus 104 ~~~~l~~~p~gi~~~~~~--~~~i~W~N~~~~~~~~--~~-~~g~~i~~~~ 149 (838)
T PRK14538 104 GEEVLNELPIGIVLIDIS--SKEIQWLNPYANFILK--NP-EINTPLAQIN 149 (838)
T ss_pred HHHHHHhCCceEEEEeCC--CCEEEEECHHHHHHhC--cc-ccCCcHHHhc
Confidence 456788889999999953 4799999999999988 23 8999888754
No 107
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=60.04 E-value=22 Score=32.88 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=34.0
Q ss_pred hHHHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCC
Q 020523 15 RYTLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGF 56 (325)
Q Consensus 15 ~~~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~ 56 (325)
+.+..+..++.++|.|+.+++.+ +.+.|+||-...+|+-
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 9999999999998863
No 108
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=59.47 E-value=20 Score=30.31 Aligned_cols=88 Identities=13% Similarity=0.286 Sum_probs=54.8
Q ss_pred HHHHHhhC----CCeEEEEcCCCCCCCEEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHH--hCCCeE
Q 020523 20 VHEALDEL----PDSFTITDPSISGHPIVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIR--EERPIE 93 (325)
Q Consensus 20 ~~~~~~~~----~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~--~~~~~~ 93 (325)
.++++|+. ..++++..+. +.+.+++|.-+..++||+.++.+..... ++ ......|...+. ......
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl~~~~d-IV-----~eGl~qW~~dL~~~s~~E~~ 356 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFLKDFSD-IV-----QEGLAQWETDLQLLSRQERS 356 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHHhcchH-HH-----HhhHHHHHHHHHhhhhhhhh
Confidence 44555543 3456677666 4778999999999999999887653221 11 111233333332 223345
Q ss_pred EEEEEEecCCCEEEEEEEEEEe
Q 020523 94 VNLLNYKKDGTPFWMLFKMSLV 115 (325)
Q Consensus 94 ~e~~~~~~dg~~~~~~~~~~~~ 115 (325)
..+.+.++.|...++.+....+
T Consensus 357 grlviKTK~~g~ipf~ycL~ii 378 (401)
T PF06785_consen 357 GRLVIKTKNGGNIPFYYCLGII 378 (401)
T ss_pred ceEEEEecCCCceeeEEEEeec
Confidence 6677788899888877766665
No 109
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=58.07 E-value=24 Score=28.18 Aligned_cols=38 Identities=18% Similarity=0.085 Sum_probs=33.6
Q ss_pred HHHHHHHHhhCCCeEEEEcCCCCCCCEEEecHHHHHhcCCC
Q 020523 17 TLWVHEALDELPDSFTITDPSISGHPIVFASRGFLKMSGFS 57 (325)
Q Consensus 17 ~~~~~~~~~~~~~~i~~~d~~~~~~~i~~~N~~~~~~~G~~ 57 (325)
.+.+..+++..+.++.+-+.+ |.+++.|.+|.+.|...
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 346777899999999999999 99999999999998754
No 110
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=57.48 E-value=16 Score=31.85 Aligned_cols=61 Identities=8% Similarity=0.145 Sum_probs=48.0
Q ss_pred hhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020523 241 SSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI 307 (325)
Q Consensus 241 ~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~ 307 (325)
..++.++...|.-|-.+|.+ +++-|.|+. .++|-.++ .++|++... ++|......+..+.+
T Consensus 290 ~e~naif~~lP~Ditfvdk~---diV~ffs~~-~rif~rt~-sviGr~v~~-chpPksv~iv~ki~~ 350 (409)
T COG2461 290 EELNAIFKHLPVDITFVDKN---DIVRFFSGG-ERIFPRTP-SVIGRRVQL-CHPPKSVHIVEKILK 350 (409)
T ss_pred HHHHHHHhhCCCceEEeccc---ceEEecCCc-ceecccCh-HhhCCcccC-CCCCchHHHHHHHHH
Confidence 56889999999888888875 589999998 88887776 567998874 556667777777766
No 111
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=43.71 E-value=32 Score=34.53 Aligned_cols=41 Identities=2% Similarity=-0.055 Sum_probs=34.7
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCcc
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRN 282 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~ 282 (325)
+..++.+++++|.|+++.+.. ||.+++.|+.+..++|+...
T Consensus 333 e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~~ 373 (924)
T PRK10841 333 EQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLTH 373 (924)
T ss_pred HHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCCh
Confidence 445778899999999999874 79999999999999987543
No 112
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.28 E-value=1.6e+02 Score=23.07 Aligned_cols=106 Identities=16% Similarity=0.198 Sum_probs=66.2
Q ss_pred HHhhCCCeEEEEcCCCCCCC--EEEecHHHHHhcCCChhhhcCCCCCcccCCCCChHHHHHHHHHHHhCCCeEEEEEEEe
Q 020523 23 ALDELPDSFTITDPSISGHP--IVFASRGFLKMSGFSRAEIIGRNGRMFQGPRTNRRTIMEIREAIREERPIEVNLLNYK 100 (325)
Q Consensus 23 ~~~~~~~~i~~~d~~~~~~~--i~~~N~~~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 100 (325)
+-..+++.++ +..+.+ |. +..+-...|.+|| .|+-|.....+..+.+.......+..+.....+.-.......
T Consensus 53 l~slL~d~Fi-L~~~~~-G~~~FRLAGTriC~LfG---RELr~~~F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s 127 (209)
T COG5388 53 LKSLLPDVFI-LERDGR-GKLPFRLAGTRICDLFG---RELRGRDFLSLWAEADRLELKRAADGVRKRRTPVLVTADGRS 127 (209)
T ss_pred HHhhcCceEE-EeccCC-CCceEEecccchhhhhc---hhhcCCchhHhccccchHHHHHHHHHHhhccCceEEecchhh
Confidence 3445555443 333311 33 3457777888888 477788766666666665555555555555555555555556
Q ss_pred cCCCEEEEEEEEEEeecCCCCceEEEEEEEeccC
Q 020523 101 KDGTPFWMLFKMSLVFGKEDGRATHFVAVQVPIV 134 (325)
Q Consensus 101 ~dg~~~~~~~~~~~~~~~~~g~~~~~~~~~~DIT 134 (325)
..|...-+++-..|+.. ..|+...++|...-+.
T Consensus 128 ~~G~sl~fEmLl~PL~~-~~g~~~R~LGais~~~ 160 (209)
T COG5388 128 HGGRSLGFEMLLAPLQG-ASGETDRFLGAISPIA 160 (209)
T ss_pred ccCcccceeeeeecccC-CCCCccchhhhccccc
Confidence 67777778888899987 7777566666655543
No 113
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=41.87 E-value=35 Score=31.70 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=36.0
Q ss_pred hhhhHhhhhccCCceEEecCCCCCCCeEEEehhhHHhhCCCccccccccccccc
Q 020523 240 SSSLYISLGRIKQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLN 293 (325)
Q Consensus 240 ~~~l~~~~~~~~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~ 293 (325)
+..+..++.++|.||++.+. ++.+.++||-+..+|+- +.+|+...+++
T Consensus 74 ~~~~~~al~nmPiGii~~~e---~~~veW~Npf~~~if~~---~~~~~~~~~~~ 121 (655)
T COG3887 74 EKSLEEALTNMPIGIILFNE---TNKVEWVNPFASKIFNK---NEIGESLSELI 121 (655)
T ss_pred HHHHHHHHHhCCceEEEEcC---CCceEEecHHHHHhcCh---hhhhhhHHHHh
Confidence 34577889999999999995 47999999999998863 34444444433
No 114
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=36.88 E-value=89 Score=22.85 Aligned_cols=42 Identities=17% Similarity=0.161 Sum_probs=33.3
Q ss_pred CCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHHHHHH
Q 020523 263 DMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLYQVSI 307 (325)
Q Consensus 263 dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~~~~~ 307 (325)
+.++-.+=...++++|+ |+.|+++.++..+.......+.+..
T Consensus 50 ~~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~ 91 (137)
T PF07310_consen 50 DFRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRA 91 (137)
T ss_pred ceEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHH
Confidence 45677788889999998 7789999999888877766665555
No 115
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=29.47 E-value=33 Score=32.16 Aligned_cols=52 Identities=12% Similarity=0.196 Sum_probs=38.5
Q ss_pred CCceEEecCCCCCCCeEEEehhhHHhhCCCcccccccccccccCCCCChHHHH
Q 020523 251 KQSFVLIDPHLPDMPMVYASDAFLKLTGYDRNEVVGQNCRFLNGVDTDTTVLY 303 (325)
Q Consensus 251 ~~~i~~~d~~~~dg~i~~~N~a~~~~~Gy~~~e~iG~~~~~l~~~~~~~~~~~ 303 (325)
|-|.+++-.. .|+.|+.++..+..++|..+++++|+++..+.....-+....
T Consensus 28 PHG~Llvl~~-~~~~Vlq~S~N~~~~LG~~~e~l~~~tl~~vl~~~qv~~l~~ 79 (750)
T COG4251 28 PHGALLVLDE-ADLMVLQASENCANILGREPEDLLGRTLGAVLTSEQVPPLQS 79 (750)
T ss_pred CceeEEEeec-CCchhhhhhhhHHHHhCCChhhhhcCCHHHhcchhhccHHHH
Confidence 3444443322 378999999999999999999999999988876554444433
Done!