Query psy8265
Match_columns 630
No_of_seqs 403 out of 1289
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 22:55:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8265.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8265hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3558|consensus 100.0 1.1E-46 2.4E-51 414.6 9.4 266 104-384 73-384 (768)
2 KOG3560|consensus 100.0 1.2E-45 2.6E-50 396.4 15.5 303 152-490 115-489 (712)
3 KOG3559|consensus 100.0 3.6E-34 7.8E-39 300.2 6.3 217 154-384 85-335 (598)
4 KOG3560|consensus 100.0 9E-31 2E-35 282.2 2.9 95 513-630 110-219 (712)
5 PF14598 PAS_11: PAS domain; P 99.9 5.7E-25 1.2E-29 198.7 12.7 106 276-381 2-111 (111)
6 KOG3561|consensus 99.9 8.6E-25 1.9E-29 249.6 5.2 255 109-378 52-477 (803)
7 KOG3753|consensus 99.7 1.3E-17 2.8E-22 188.3 10.5 210 171-386 196-446 (1114)
8 PF08447 PAS_3: PAS fold; Int 99.5 2.6E-13 5.6E-18 114.4 9.0 85 288-373 1-91 (91)
9 PF13426 PAS_9: PAS domain; PD 99.3 1.3E-11 2.7E-16 104.2 10.3 99 280-378 5-104 (104)
10 PRK09776 putative diguanylate 99.2 2E-11 4.3E-16 145.3 7.7 217 171-393 297-539 (1092)
11 PRK11359 cyclic-di-GMP phospho 99.1 3.7E-10 8.1E-15 130.0 15.0 209 171-384 26-256 (799)
12 TIGR02040 PpsR-CrtJ transcript 99.1 8.3E-11 1.8E-15 127.8 8.9 212 163-382 138-367 (442)
13 PF00989 PAS: PAS fold; Inter 99.1 5.5E-10 1.2E-14 95.8 11.3 99 278-376 13-113 (113)
14 PRK13560 hypothetical protein; 99.1 7.5E-10 1.6E-14 126.5 13.8 215 179-396 94-338 (807)
15 TIGR02040 PpsR-CrtJ transcript 99.1 2.9E-10 6.2E-15 123.6 9.8 206 166-381 4-245 (442)
16 PF08448 PAS_4: PAS fold; Int 99.0 2.6E-09 5.6E-14 91.2 10.6 101 279-380 8-109 (110)
17 PRK13560 hypothetical protein; 99.0 2E-09 4.3E-14 123.0 10.8 219 165-388 211-475 (807)
18 cd00130 PAS PAS domain; PAS mo 98.8 7.9E-08 1.7E-12 72.4 10.9 99 278-376 4-103 (103)
19 PRK13559 hypothetical protein; 98.6 1.2E-07 2.6E-12 99.5 9.9 102 284-385 64-166 (361)
20 PRK09776 putative diguanylate 98.6 5.7E-08 1.2E-12 116.0 7.3 116 278-393 295-413 (1092)
21 PRK13557 histidine kinase; Pro 98.6 1.6E-07 3.5E-12 102.3 9.9 98 284-381 51-149 (540)
22 TIGR00229 sensory_box PAS doma 98.6 5E-07 1.1E-11 71.7 10.0 102 280-381 17-119 (124)
23 PRK13558 bacterio-opsin activa 98.5 4.2E-07 9.1E-12 103.9 11.0 105 283-387 168-274 (665)
24 PRK10060 RNase II stability mo 98.4 7.6E-07 1.6E-11 102.8 10.7 130 277-412 122-256 (663)
25 TIGR02938 nifL_nitrog nitrogen 98.4 3.6E-07 7.7E-12 97.8 7.3 116 278-393 16-133 (494)
26 PRK11091 aerobic respiration c 98.4 7.1E-07 1.5E-11 103.9 10.1 109 278-386 167-277 (779)
27 TIGR02938 nifL_nitrog nitrogen 98.1 1.2E-06 2.5E-11 93.8 2.1 202 171-381 18-253 (494)
28 PRK11359 cyclic-di-GMP phospho 98.0 1.6E-05 3.4E-10 92.1 8.9 99 281-380 27-129 (799)
29 PF14598 PAS_11: PAS domain; P 97.4 0.00019 4.1E-09 65.1 4.7 41 172-217 7-48 (111)
30 TIGR02966 phoR_proteo phosphat 97.3 0.00046 1E-08 70.0 7.1 93 279-383 19-111 (333)
31 PRK11360 sensory histidine kin 97.3 0.0011 2.3E-08 72.8 10.3 100 279-381 275-376 (607)
32 KOG3558|consensus 97.3 0.00018 4E-09 82.1 3.6 59 534-603 127-185 (768)
33 PF13596 PAS_10: PAS domain; P 97.2 0.0043 9.2E-08 54.5 11.1 93 280-377 13-106 (106)
34 PRK11073 glnL nitrogen regulat 96.9 0.003 6.5E-08 65.8 8.6 96 279-380 20-115 (348)
35 KOG3561|consensus 96.8 0.00024 5.2E-09 83.4 -1.1 105 274-379 240-347 (803)
36 COG2202 AtoS FOG: PAS/PAC doma 96.4 0.024 5.2E-07 48.8 9.0 104 278-381 124-230 (232)
37 PF00989 PAS: PAS fold; Inter 95.9 0.0027 5.9E-08 54.1 0.9 40 171-215 15-54 (113)
38 PF12860 PAS_7: PAS fold 95.9 0.035 7.5E-07 49.4 8.0 95 279-382 8-113 (115)
39 smart00086 PAC Motif C-termina 95.6 0.086 1.9E-06 33.2 6.9 40 339-378 2-42 (43)
40 smart00091 PAS PAS domain. PAS 94.5 0.052 1.1E-06 37.5 3.7 51 280-330 15-65 (67)
41 KOG3559|consensus 94.0 0.036 7.9E-07 60.6 2.7 51 276-326 89-139 (598)
42 KOG0501|consensus 93.8 0.17 3.7E-06 57.8 7.8 92 284-379 38-136 (971)
43 PF13426 PAS_9: PAS domain; PD 93.7 0.028 6.1E-07 47.0 1.2 41 171-216 5-45 (104)
44 COG5002 VicK Signal transducti 92.8 0.3 6.5E-06 53.3 7.4 107 283-396 128-240 (459)
45 PRK11006 phoR phosphate regulo 92.2 0.25 5.4E-06 53.8 6.0 91 279-383 111-201 (430)
46 PF08447 PAS_3: PAS fold; Int 91.7 0.029 6.3E-07 46.9 -1.4 38 179-218 1-38 (91)
47 PRK10820 DNA-binding transcrip 91.4 0.35 7.5E-06 55.2 6.3 91 279-379 93-188 (520)
48 TIGR02373 photo_yellow photoac 90.3 0.94 2E-05 42.7 6.9 59 277-335 27-86 (124)
49 PF07310 PAS_5: PAS domain; I 89.4 1.2 2.6E-05 41.7 7.1 84 286-372 51-135 (137)
50 PRK11086 sensory histidine kin 89.2 1.4 3.1E-05 48.6 8.6 90 279-380 234-327 (542)
51 PF08446 PAS_2: PAS fold; Int 87.3 0.19 4E-06 45.8 0.1 47 156-214 11-61 (110)
52 PF08448 PAS_4: PAS fold; Int 87.2 0.19 4E-06 42.5 0.0 39 171-214 9-47 (110)
53 cd00130 PAS PAS domain; PAS mo 85.0 0.48 1E-05 34.9 1.3 41 171-216 6-46 (103)
54 PRK11388 DNA-binding transcrip 82.8 2.9 6.4E-05 48.6 7.2 92 279-378 216-308 (638)
55 COG3829 RocR Transcriptional r 82.8 1.7 3.6E-05 50.1 4.9 93 279-380 130-223 (560)
56 PF08670 MEKHLA: MEKHLA domain 82.0 8.2 0.00018 37.5 8.7 87 283-370 50-139 (148)
57 TIGR00229 sensory_box PAS doma 75.8 1.6 3.4E-05 34.0 1.5 40 171-215 17-56 (124)
58 COG5000 NtrY Signal transducti 73.9 9.5 0.00021 44.7 7.5 92 282-380 386-478 (712)
59 PF08348 PAS_6: YheO-like PAS 70.9 14 0.0003 34.4 6.6 48 337-386 68-117 (118)
60 TIGR02966 phoR_proteo phosphat 70.8 1.9 4.1E-05 43.7 1.0 39 171-214 20-58 (333)
61 KOG1229|consensus 65.6 2.4 5.2E-05 47.5 0.6 68 282-349 173-241 (775)
62 smart00091 PAS PAS domain. PAS 65.0 3.2 6.9E-05 28.1 0.9 39 172-215 16-54 (67)
63 PRK13557 histidine kinase; Pro 64.4 3.4 7.3E-05 45.4 1.4 36 175-215 51-86 (540)
64 COG3290 CitA Signal transducti 64.2 10 0.00022 43.7 5.2 87 281-379 230-320 (537)
65 PF13596 PAS_10: PAS domain; P 64.2 4.3 9.3E-05 35.4 1.8 37 171-213 13-49 (106)
66 PRK15053 dpiB sensor histidine 64.1 17 0.00038 40.6 7.0 90 279-380 235-326 (545)
67 PRK11073 glnL nitrogen regulat 63.2 2.4 5.2E-05 44.2 0.0 39 171-214 21-59 (348)
68 PF08446 PAS_2: PAS fold; Int 63.0 4.8 0.0001 36.6 1.9 43 284-326 24-69 (110)
69 PRK10060 RNase II stability mo 58.2 3.9 8.5E-05 47.9 0.6 43 166-213 119-162 (663)
70 PF13188 PAS_8: PAS domain; PD 50.5 7.2 0.00016 30.8 0.8 28 281-312 16-43 (64)
71 KOG3753|consensus 48.3 12 0.00026 45.3 2.4 51 276-326 191-242 (1114)
72 TIGR02373 photo_yellow photoac 47.1 25 0.00055 33.3 3.9 41 172-217 31-71 (124)
73 PRK13559 hypothetical protein; 46.2 8.3 0.00018 40.6 0.7 34 176-214 65-98 (361)
74 PRK11091 aerobic respiration c 45.7 7.4 0.00016 46.0 0.3 46 164-214 161-207 (779)
75 PRK09959 hybrid sensory histid 42.6 90 0.0019 38.9 8.9 26 280-305 590-615 (1197)
76 PRK11006 phoR phosphate regulo 40.7 8.5 0.00019 41.9 -0.2 41 167-212 107-148 (430)
77 PF13188 PAS_8: PAS domain; PD 36.7 8 0.00017 30.5 -0.9 21 172-193 16-36 (64)
78 PRK10820 DNA-binding transcrip 34.1 12 0.00027 42.8 -0.3 39 171-214 94-132 (520)
79 PF12860 PAS_7: PAS fold 32.4 14 0.0003 32.7 -0.3 38 171-212 9-46 (115)
80 PRK11360 sensory histidine kin 27.1 28 0.0006 38.4 0.9 44 166-214 270-314 (607)
81 PRK13558 bacterio-opsin activa 24.5 39 0.00084 39.2 1.6 36 175-215 169-204 (665)
82 PF06531 DUF1108: Protein of u 23.7 32 0.00069 30.5 0.5 20 575-594 58-79 (86)
83 PRK11388 DNA-binding transcrip 23.0 26 0.00057 40.9 -0.2 37 171-212 217-253 (638)
No 1
>KOG3558|consensus
Probab=100.00 E-value=1.1e-46 Score=414.56 Aligned_cols=266 Identities=25% Similarity=0.337 Sum_probs=221.0
Q ss_pred CCCccCccccCcccccCccCCCCCC--cCCCCCCCcceeccccc-CCCCCCccceeeeeccCCCCCCCCCCccCCCCcEE
Q psy8265 104 QSHKLPSKSLNSKSLDGLSSNDSSP--VPSNHLVTPKVEDIKSE-SFNYSEVPRQTVLMWGSNPSRSPPASPILPNGHIN 180 (630)
Q Consensus 104 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~g~~s~~i~d~~~~-~f~~~d~l~Q~~L~~gfll~~~~~~~Vls~dGkIl 180 (630)
|..++.+.-|++-||-++..++.++ .+..|.-. .+++--+. --|.++-..|.+ |||.+ |++.||+|+
T Consensus 73 Plp~aisshLDkaSimRLtISyLRlrk~a~~g~~p-~~e~~~~~~e~~l~~~iLqsL--DGFVm-------~l~~dG~~l 142 (768)
T KOG3558|consen 73 PLPAAISSHLDKASIMRLTISYLRLRKFAGAGDPP-RAEGEPENLEQHLGDHILQSL--DGFVM-------ALTQDGDFL 142 (768)
T ss_pred CCcchhhhhhhhHHHHHHHHHHHHHHHHhhcCCcc-cccCCCcchhhhhhhhHHhhc--cceEE-------EEccCCCEE
Confidence 3555666789999999998777766 33333321 22222211 001134455666 89999 999999999
Q ss_pred eccccchhhcCCChhhhhhhccccCccccCCCCCCCCC--------Cc--c-----ccCCCCCCeEEeee----eee---
Q psy8265 181 YPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPK--------SY--Y-----QSYNENGPSERLDI----RGR--- 238 (630)
Q Consensus 181 YVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k--------~~--~-----c~ld~rSfF~RMk~----rGR--- 238 (630)
||||||++|||++|+| ++|.|||||+||+++.+ .- + ....+|+||+|||| |||
T Consensus 143 YiSEtVS~yLGLSQvE-----LTG~SvFDfiHP~DheE~~eqL~l~~~~p~~~es~~~~teRsFflRMKsTLT~RGRtln 217 (768)
T KOG3558|consen 143 YISETVSIYLGLSQVE-----LTGSSVFDFIHPCDHEEIAEQLGLRLTTPEVKESTDTSTERSFFLRMKSTLTKRGRTLN 217 (768)
T ss_pred EEechhHhhhCcccee-----eecchhhhccCccCHHHHHHHhccccCCCcccccccCccceeEEEEeeeeeccCCceee
Confidence 9999999999999999 49999999999997653 00 0 01126899999997 786
Q ss_pred -----EEEeeccccc----C----------CCCCeEEEEEEeeCCCCCCccccccceeeEEeeccCceeeeecccccccc
Q psy8265 239 -----IKILHGQNRK----L----------EEPPLALFAICTPFGPPSLLEIPHKEVMFKSKHKLDLSLVSMDQRGKMLL 299 (630)
Q Consensus 239 -----lKvLhg~~rk----s----------e~p~lcLVAIarPL~~ps~~Ei~l~s~~FiTRhslDGkftyVDprv~~LL 299 (630)
||++||+++. . ..|-+|||++|.+|++|+..|+++.+.+|++||++|++|+||++|+..++
T Consensus 218 lKSa~yKvlh~tgh~rv~~~~sh~s~~~g~~~Pl~~lV~~a~alp~ps~~EipL~~~~FvtRhs~DmkityCedRisdlm 297 (768)
T KOG3558|consen 218 LKSAGYKVLHCTGHLRVYNNPSHNSPLCGYKEPLLGLVALAEALPPPSYTEIPLDCHMFVTRHSLDMKITYCEDRISDLM 297 (768)
T ss_pred eeccceeEEEEeeeeeeccCCCCCCcccCccccchheeeeeccCCCCcccccccCCceeEEeeecceeEEEEchhHHHHh
Confidence 8999987652 1 13456999999999999999999999999999999999999999999999
Q ss_pred CCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe--CCCceEEEEEEEecC
Q psy8265 300 GYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK--NSKPDFVISTHRPLM 377 (630)
Q Consensus 300 GYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~--nGkpe~IVgt~rdIS 377 (630)
||+|+||+|+++|+|||+.|.+++++.|.+++.|||+++..|||+.|+|+|+|+|++++++++ |+.+++|||+|++|+
T Consensus 298 ~y~PeeLvGrS~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicVnYVlS 377 (768)
T KOG3558|consen 298 DYEPEELVGRSCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICVNYVLS 377 (768)
T ss_pred cCCHHHhhchhHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEEEeeec
Confidence 999999999999999999999999999999999999999999999999999999999999985 788899999999999
Q ss_pred chhhHHH
Q psy8265 378 EEEGRDL 384 (630)
Q Consensus 378 ErE~~E~ 384 (630)
+.|.+++
T Consensus 378 ~~e~~~~ 384 (768)
T KOG3558|consen 378 NIEEEDL 384 (768)
T ss_pred cccccCc
Confidence 9876654
No 2
>KOG3560|consensus
Probab=100.00 E-value=1.2e-45 Score=396.41 Aligned_cols=303 Identities=37% Similarity=0.582 Sum_probs=261.7
Q ss_pred ccceeeeeccCCCCCCCCCCccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC----------------
Q psy8265 152 VPRQTVLMWGSNPSRSPPASPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV---------------- 215 (630)
Q Consensus 152 ~l~Q~~L~~gfll~~~~~~~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l---------------- 215 (630)
.+.|.+ -||++ |++.||.|.|.|++|.+|||+.|.| +|-||+||+||-.+
T Consensus 115 ~lLqsL--nGF~l-------Vvt~eg~ifyAS~tIedYLGFhQSD-----V~HQsVYdlIHseDR~dfqrQLhwa~~ppq 180 (712)
T KOG3560|consen 115 LLLQSL--NGFAL-------VVTAEGEIFYASATIEDYLGFHQSD-----VMHQSVYDLIHSEDRQDFQRQLHWAMDPPQ 180 (712)
T ss_pred HHHHhc--CCeEE-------EEecCceEEEehhhHHhhhcccccc-----hhhhhHHHHhhhhhHHHHHHHHhhccCCch
Confidence 345555 58999 9999999999999999999999988 68999999999631
Q ss_pred --------------------------CCC-----------CccccCCCCCCeEEeeeeeeEEEeeccccc-----CCCCC
Q psy8265 216 --------------------------SPK-----------SYYQSYNENGPSERLDIRGRIKILHGQNRK-----LEEPP 253 (630)
Q Consensus 216 --------------------------s~k-----------~~~c~ld~rSfF~RMk~rGRlKvLhg~~rk-----se~p~ 253 (630)
+++ .|+|++|++|||+||+++||+|+|||+.+| ..+|+
T Consensus 181 ~~~s~q~~~e~~~~~~~~~~~~~d~~ppens~yleRcficR~RCLLDnTsGFLamdfqGklk~LhGqkkk~~~g~~lpP~ 260 (712)
T KOG3560|consen 181 VVFSQQPPLETGDDAILRAQEWGDGTPPENSAYLERCFICRFRCLLDNTSGFLAMDFQGKLKFLHGQKKKAPSGAMLPPR 260 (712)
T ss_pred hhccCCCccccccccceeeeccCccCCcccchHHhhhheeeEEEeecCCcceeeeecccceeeecCCcccCCCCccCCCc
Confidence 011 257999999999999999999999997654 35789
Q ss_pred eEEEEEEeeCCCCCCccccccceeeEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhc
Q psy8265 254 LALFAICTPFGPPSLLEIPHKEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKT 333 (630)
Q Consensus 254 lcLVAIarPL~~ps~~Ei~l~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkk 333 (630)
++|||||+|+.+|++.|++.+..+|.+||.+|+..+.+|.+++.+|||...||.|.+.|+|||.+|...++++|.+++++
T Consensus 261 LaLf~iatP~~pPS~lEi~~k~~i~rtKhklDfa~vs~Dak~k~~lgy~eaEL~~m~gY~lvH~~D~~y~Aeah~e~ikt 340 (712)
T KOG3560|consen 261 LALFCIATPFLPPSALEIKMKSAILRTKHKLDFALVSMDAKVKATLGYCEAELHGMPGYNLVHVEDKVYMAEAHSEGIKT 340 (712)
T ss_pred eeEEEEecCCCCchhhhhhhhhhhhhcccccccceeccchhhhhhhccchhhccCCCccceeehhhhhhhhHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeEEEEEecCCcEEEEEEEEEEEEeCCCceEEEEEEEecCchhhHHHHhhhc--ccccccccccCcccccccCCCC
Q psy8265 334 GASGMIAYRFQTNDGGWQWLQTSSRLVYKNSKPDFVISTHRPLMEEEGRDLLGKRT--MDFKVSYLDAGLNNSYFSDSDQ 411 (630)
Q Consensus 334 Gqs~s~eYRfrtKdGswVWVeTsa~li~~nGkpe~IVgt~rdISErE~~E~L~~r~--~elk~sf~d~gl~~~~~~~s~~ 411 (630)
|+++.+.||.++|+|+|.||+++++++++||+|++||+++|-++++|+.++|++|+ +.|+++..+++|..-.|.+.++
T Consensus 341 geSGmlvyR~qtk~grw~wvqssarllykngkPD~vi~thr~l~DeEgh~lL~Kr~~~~~f~~ttg~t~l~s~t~~~~~~ 420 (712)
T KOG3560|consen 341 GESGMLVYREQTKAGRWAWVQSSARLLYKNGKPDLVIDTHRGLGDEEGHRLLSKRSGVTGFRETTGPTKLLSWTFGKHSE 420 (712)
T ss_pred CCcceEEEEEeecCCcEEEeeccceeeeecCCCCEEEecCCCccchHHHHHHHhhccccccccccCcceeccccCCcchh
Confidence 99999999999999999999999999999999999999999999999999999998 7888888899999988877665
Q ss_pred CCCcccccCCCCCCCCCCCCCCCccchhhhhhhhHHHHHhhhhhhcccccCCCCCC--------CCCCCCCcccCCCh--
Q psy8265 412 LTPSHQTLAPSPGSAQSGSSSTTPQRVNRRYKTQLRDFLSTCRTKRKMSAQHAAPP--------PPTPAPPIEYLTPP-- 481 (630)
Q Consensus 412 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~-- 481 (630)
...-.+ . +| ++...+ ||++|+++|+++.+++.++ +|.|.++++|++++
T Consensus 421 ~~~~P~-~--~p-~~~~~p------------------~l~~m~s~r~l~~~~~~~T~~tspl~~~paPs~~~~~lk~~~~ 478 (712)
T KOG3560|consen 421 DGARPR-L--QP-SKNDPP------------------FLRPMPSGRCLQCPCVQGTFRTSPLSHPPAPSVSAYSLKDSRP 478 (712)
T ss_pred ccCCcc-c--CC-CCCCcc------------------hhccCCCCccccccccccccccCCCCCCCCCCccccccCCccc
Confidence 532100 1 11 111111 9999999999998777665 46667888999886
Q ss_pred --hhhhhccCC
Q psy8265 482 --DAVAAAYSN 490 (630)
Q Consensus 482 --~~~~~~~~~ 490 (630)
++.+.++++
T Consensus 479 ~~~~d~d~l~p 489 (712)
T KOG3560|consen 479 MRDVDEDQLHP 489 (712)
T ss_pred cccccccccCC
Confidence 445666655
No 3
>KOG3559|consensus
Probab=100.00 E-value=3.6e-34 Score=300.21 Aligned_cols=217 Identities=26% Similarity=0.345 Sum_probs=191.8
Q ss_pred ceeeeeccCCCCCCCCCCccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC----cccc-----C
Q psy8265 154 RQTVLMWGSNPSRSPPASPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS----YYQS-----Y 224 (630)
Q Consensus 154 ~Q~~L~~gfll~~~~~~~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~----~~c~-----l 224 (630)
.|++ |||++ |+..||||+||||+++.+||++|+| +.|.+|+||+||.+.++- -.|. .
T Consensus 85 LqtL--DGF~f-------vva~dGkimYISETaSvhLGLSQVE-----lTGNsi~eYIH~~D~demna~L~~h~H~qeye 150 (598)
T KOG3559|consen 85 LQTL--DGFIF-------VVAPDGKIMYISETASVHLGLSQVE-----LTGNSIYEYIHPQDHDEMNAVLTAHQHLQEYE 150 (598)
T ss_pred HHhh--cceEE-------EEeCCCCEEEEecceeeeecceeeE-----eecchhhhhhcccchHHHHHHHhhhhhhhhhh
Confidence 4555 99999 9999999999999999999999999 489999999999977651 1121 2
Q ss_pred CCCCCeEEeeee----------eeEEEeeccccc---------CCC----CCeEEEEEEeeCCCCCCccccccceeeEEe
Q psy8265 225 NENGPSERLDIR----------GRIKILHGQNRK---------LEE----PPLALFAICTPFGPPSLLEIPHKEVMFKSK 281 (630)
Q Consensus 225 d~rSfF~RMk~r----------GRlKvLhg~~rk---------se~----p~lcLVAIarPL~~ps~~Ei~l~s~~FiTR 281 (630)
-+|+||+||+|. +.+|++||.+.- +.. .+.+|||++.+++++.+.|+++.+++|+.|
T Consensus 151 IErsfflrmkCvlakrnaglt~sg~kvihcSgylKir~y~~~m~p~dscyqn~glvAvG~slP~saiteikl~sNmFmfr 230 (598)
T KOG3559|consen 151 IERSFFLRMKCVLAKRNAGLTCSGYKVIHCSGYLKIRQYELDMSPNDSCYQNVGLVAVGHSLPPSAITEIKLHSNMFMFR 230 (598)
T ss_pred hhhhhhhhhhhhheeccccccccCcceEeecCcceEEEEeeccCCccchhheeeeEEecCCCCcccceEEEeccceEEEE
Confidence 378999999882 347889987641 111 356899999999999999999999999999
Q ss_pred eccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEE
Q psy8265 282 HKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVY 361 (630)
Q Consensus 282 hslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~ 361 (630)
.++|++++|.|.++..++||++++|+++++|.+||..|...++.+|..++.+|+..+..|||+.|.|+|+|++..+.++.
T Consensus 231 aslDlkliF~D~rv~qltgYepqdliektLY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvqsyat~vH 310 (598)
T KOG3559|consen 231 ASLDLKLIFLDSRVHQLTGYEPQDLIEKTLYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQSYATFVH 310 (598)
T ss_pred eecceEEEeehhhHHHhhCCCchhhhhHHHHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEEEeeEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred e--CCCceEEEEEEEecCchhhHHH
Q psy8265 362 K--NSKPDFVISTHRPLMEEEGRDL 384 (630)
Q Consensus 362 ~--nGkpe~IVgt~rdISErE~~E~ 384 (630)
+ ..++.+|+.++.++++.|-+++
T Consensus 311 nSrSSR~~fivSvnyVls~~EyK~L 335 (598)
T KOG3559|consen 311 NSRSSRPHFIVSVNYVLSELEYKEL 335 (598)
T ss_pred ccccCCcceEEeeeeeeehhhhhhh
Confidence 5 5679999999999999987765
No 4
>KOG3560|consensus
Probab=99.96 E-value=9e-31 Score=282.21 Aligned_cols=95 Identities=37% Similarity=0.524 Sum_probs=85.1
Q ss_pred CCCCccccccccCCCCCCCccccCcccccccccccCCCCCeEEEeeeecccCCCCccCCCCCCccchhhhhhhccccCHH
Q psy8265 513 LPYENLFHQYRPYYPEYQPYTVSNGFSLPTYEVNKSNDCDKLYCHQTLTADQNSKGYSSPFESDIVHQSVYELVHSEDRE 592 (630)
Q Consensus 513 ~~~~n~~~q~~~~~~~~~~~~~~nGF~l~~~~~~~~~~~~~~y~~~~~~~~~~~~~ylg~hqsdv~hqsv~elih~edr~ 592 (630)
+.++++|+| ++|||+|++ +++|.|||+++ +|+||||||||||||||||||||+|||+
T Consensus 110 llege~lLq------------sLnGF~lVv-----t~eg~ifyAS~------tIedYLGFhQSDV~HQsVYdlIHseDR~ 166 (712)
T KOG3560|consen 110 LLEGELLLQ------------SLNGFALVV-----TAEGEIFYASA------TIEDYLGFHQSDVMHQSVYDLIHSEDRQ 166 (712)
T ss_pred ccchHHHHH------------hcCCeEEEE-----ecCceEEEehh------hHHhhhcccccchhhhhHHHHhhhhhHH
Confidence 667799999 999999997 79999999995 5899999999999999999999999999
Q ss_pred HHHHhhhccCCCCCCCCCCCc---------------cccCCCCCCCCccccCC
Q psy8265 593 ELQRQLMWNSFLPPESAGISL---------------QECFLQENSYLLERSFT 630 (630)
Q Consensus 593 ~f~~qlhw~~~~p~~~~~~~~---------------~~~~~~e~s~~l~r~f~ 630 (630)
|||||||||++||+...+... ++++|||||.||||||+
T Consensus 167 dfqrQLhwa~~ppq~~~s~q~~~e~~~~~~~~~~~~~d~~ppens~yleRcfi 219 (712)
T KOG3560|consen 167 DFQRQLHWAMDPPQVVFSQQPPLETGDDAILRAQEWGDGTPPENSAYLERCFI 219 (712)
T ss_pred HHHHHHhhccCCchhhccCCCccccccccceeeeccCccCCcccchHHhhhhe
Confidence 999999999999986544322 26789999999999996
No 5
>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=99.92 E-value=5.7e-25 Score=198.70 Aligned_cols=106 Identities=42% Similarity=0.692 Sum_probs=98.2
Q ss_pred eeeEEeeccCceeeeeccc-cccccCCChhhhccCcccceeccccHHH-HHHHHHHHHhcCCceeeEEEEEecCCcEEEE
Q psy8265 276 VMFKSKHKLDLSLVSMDQR-GKMLLGYSDTELANMGGYDLVHYDDLAY-VASAHQELLKTGASGMIAYRFQTNDGGWQWL 353 (630)
Q Consensus 276 ~~FiTRhslDGkftyVDpr-v~~LLGYspEELlG~S~ydlIHPDDl~~-V~eah~~lLkkGqs~s~eYRfrtKdGswVWV 353 (630)
.+|++||++||+|++||++ +..++||.++||+|+++|+|+||+|+.. +.++|++++++|+..+..|||+.|+|+||||
T Consensus 2 ~~F~trhs~dgki~~~d~~~v~~~lgy~~~eLvG~s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwv 81 (111)
T PF14598_consen 2 EEFTTRHSLDGKITYVDSRAVSSLLGYLPEELVGRSIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWV 81 (111)
T ss_dssp -EEEEEEETTSBEEEEETTHHHHHHSS-HHHHTTSBGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEE
T ss_pred ceEEEEECCCcEEEEEcCccChhhcCCCcHHHcCCchHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEE
Confidence 5899999999999999999 6999999999999999999999999997 9999999999999988999999999999999
Q ss_pred EEEEEEEEe--CCCceEEEEEEEecCchhh
Q psy8265 354 QTSSRLVYK--NSKPDFVISTHRPLMEEEG 381 (630)
Q Consensus 354 eTsa~li~~--nGkpe~IVgt~rdISErE~ 381 (630)
+++++++++ ++++++|||+|++|+|.|+
T Consensus 82 qt~~~~~~n~~~~~~~~Iv~~n~vlse~e~ 111 (111)
T PF14598_consen 82 QTKATLFYNPWTSKPEFIVCTNTVLSEEEA 111 (111)
T ss_dssp EEEEEEEEETTTTCEEEEEEEEEEESCEB-
T ss_pred EEEEEEEECCCCCCccEEEEEEEEeccCCC
Confidence 999999985 7899999999999999874
No 6
>KOG3561|consensus
Probab=99.90 E-value=8.6e-25 Score=249.64 Aligned_cols=255 Identities=17% Similarity=0.211 Sum_probs=189.5
Q ss_pred CccccCcccccCccCCCCCCcCCCC---CCCcceecccccCCCCCCccceeeee--ccCCCCCCCCCCccCCCCcEEecc
Q psy8265 109 PSKSLNSKSLDGLSSNDSSPVPSNH---LVTPKVEDIKSESFNYSEVPRQTVLM--WGSNPSRSPPASPILPNGHINYPS 183 (630)
Q Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~g---~~s~~i~d~~~~~f~~~d~l~Q~~L~--~gfll~~~~~~~Vls~dGkIlYVS 183 (630)
.+++.++..|..-.-.. +...+| .+..+..|||+.++. +|+|.+++|+ |||+| |++-||+|||||
T Consensus 52 ~~RK~DK~tVLr~aV~~--lr~~k~~~~~~~~~~~d~KpSflS-~~eL~~LmLeAlDGF~f-------vV~cdG~IvyVS 121 (803)
T KOG3561|consen 52 LSRKPDKLTVLRMAVDH--LRLIKEQESENSSIDQDYKPSFLS-NDELTHLILEALDGFLF-------VVNCDGRIVYVS 121 (803)
T ss_pred cccCchHHHHHHHHHHH--HHHHhhhhcccccccccccccccc-hHHHHHHHHHHhcCeEE-------EEecCceEEEEe
Confidence 45677777776522111 112444 344455555555555 9999999999 99999 888889999999
Q ss_pred ccchhhcCCChhhhhhhccccCccccCCCCCCCCC------------Cccc-----------------------------
Q psy8265 184 QEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPK------------SYYQ----------------------------- 222 (630)
Q Consensus 184 EnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k------------~~~c----------------------------- 222 (630)
|||+.+|||.|+| |+|+|||+|+||.+..+ .|.|
T Consensus 122 eSVT~~L~y~QsD-----L~~qSly~ilhp~d~~~~~~ql~~r~~e~~f~~r~l~~~~~~~~~E~~~~~~~~~~~~~~~~ 196 (803)
T KOG3561|consen 122 ESVTSVLGYLQSD-----LMGQSLYDILHPLDNDKPREQLSPRSNEHTFNCRLLDGKTGPPPEEAVKFYGNFQCFTNSQP 196 (803)
T ss_pred cchHHhhCcCHHH-----HhcchHHHhcCccccCcccccccccccccccchhhhccCCCCchHHhhhhhhhcccccccCc
Confidence 9999999999999 58999999999952211 1111
Q ss_pred ----------------------------------------------cCCCCCCeEEeee----------------eee--
Q psy8265 223 ----------------------------------------------SYNENGPSERLDI----------------RGR-- 238 (630)
Q Consensus 223 ----------------------------------------------~ld~rSfF~RMk~----------------rGR-- 238 (630)
...+++|+|||.+ +|+
T Consensus 197 ~s~e~~~~~i~~~~~~~~~~~~~~~~~r~~~p~~~~~~~~id~~~~~~aRrsfe~r~r~~~~r~~p~~gy~~~~~~g~~~ 276 (803)
T KOG3561|consen 197 KSIEGFQSTICRQRRKAEGDRVCFGVSRLTTPQLIGEMCIIDTRLCEGARRSFECRMRFCDHRAPPIIGYEPFEVLGTSR 276 (803)
T ss_pred cccccccccceeeccccccCccccccccccchhhccceeccccccccccccchhhhhhhccccCCccccccceeeccccc
Confidence 1115678787753 121
Q ss_pred ------------EEEeeccccc-C---------------------C--------CCCeEEEEEEeeCC------CCCCcc
Q psy8265 239 ------------IKILHGQNRK-L---------------------E--------EPPLALFAICTPFG------PPSLLE 270 (630)
Q Consensus 239 ------------lKvLhg~~rk-s---------------------e--------~p~lcLVAIarPL~------~ps~~E 270 (630)
+.++||++.. + . ....|||++++-.. .|...|
T Consensus 277 ~~~~~~~~~~~~y~~~h~~g~~~s~~~~c~~~~~t~~~q~~~~~~d~~i~~~~~~s~p~~v~~~~~~vs~~~~~~p~~~~ 356 (803)
T KOG3561|consen 277 NYDYYHKDDLPNYRVIHCTGYIKSAGPSCKYRFLTKGQQWIWLPQDDYISYHQWNSKPCLVAIGRLVVSYAEVRVPSRAD 356 (803)
T ss_pred cccccccCcccceEEEeeeeeEeccCCcceeccccccccccccCccccccccccCCCcceeEecccccchhhccCccccc
Confidence 4466665431 0 0 12238888877432 233333
Q ss_pred cc----------ccceeeEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhc-CCceee
Q psy8265 271 IP----------HKEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKT-GASGMI 339 (630)
Q Consensus 271 i~----------l~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkk-Gqs~s~ 339 (630)
.. .....|.+||..||+|+++|.++..++||.+.|++|++++.+.|++|..++...++.+... ++....
T Consensus 357 ~~~~~~~~~~~~~~~~~~~sr~~~~g~~~~~dqr~~~i~~~~~~~~~g~ss~~s~h~~d~~~~~~s~~~~~~~s~~~~~~ 436 (803)
T KOG3561|consen 357 MSIEGPRQQPSSPQSSEFISRSSSDGSFTFVDQRASAILGYQPQELLGRSSYESSHPADSSPLSESLKQVQALSEQRSTL 436 (803)
T ss_pred CccccccccccCcccchhhcccCcCCceeccccccccccccCchhhcCcccccccCccccchhhchHHHHHHhccccccc
Confidence 22 2567788999999999999999999999999999999999999999999999999988764 345678
Q ss_pred EEEEEecCCcEEEEEEEEEEEEe--CCCceEEEEEEEecCc
Q psy8265 340 AYRFQTNDGGWQWLQTSSRLVYK--NSKPDFVISTHRPLME 378 (630)
Q Consensus 340 eYRfrtKdGswVWVeTsa~li~~--nGkpe~IVgt~rdISE 378 (630)
.||++.++|.|+|..+.+..+.+ +.+.++|+|++..+.+
T Consensus 437 ~yr~~~~n~~~~~~~~~~~~~~n~~s~~~~~~~~~ns~~~~ 477 (803)
T KOG3561|consen 437 LYRFRSKNGSSIPNKSSAYLFSNPGSDEVEYIVCTNSNVPT 477 (803)
T ss_pred ccccccCCCCccccccccccccCCCccccceeeeccccccc
Confidence 99999999999999999988754 5678999999999985
No 7
>KOG3753|consensus
Probab=99.72 E-value=1.3e-17 Score=188.26 Aligned_cols=210 Identities=20% Similarity=0.218 Sum_probs=157.6
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCC-------C----C-cccc---------CCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSP-------K----S-YYQS---------YNENGP 229 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~-------k----~-~~c~---------ld~rSf 229 (630)
+|...||+|||+||.++.+||+..+ +|.|..+.||+||++-. + . .+|. ...++|
T Consensus 196 ~vS~~dG~iLyis~q~a~ilg~krD-----v~s~a~FvdflapqD~~vF~sfta~~~lp~ws~~s~~ds~~~~c~~~ks~ 270 (1114)
T KOG3753|consen 196 AVSFLDGRILYISEQAALILGCKRD-----VLSSAKFVDFLAPQDVGVFYSFTARYKLPLWSMGSSADSFTQECAEEKSF 270 (1114)
T ss_pred EEeccCCcEEEeechhhhhccCchh-----hhccchhhhhcchhhhhhhhhccccccCccccccccccchhhhhhhhcce
Confidence 5779999999999999999999643 37899999999997321 0 0 0121 235678
Q ss_pred eEEeeeee-e-----EEE-----eecccc--cC-CCCCeEEEEEEeeCCC-CCCccccccceeeEEeeccCceeeeeccc
Q psy8265 230 SERLDIRG-R-----IKI-----LHGQNR--KL-EEPPLALFAICTPFGP-PSLLEIPHKEVMFKSKHKLDLSLVSMDQR 294 (630)
Q Consensus 230 F~RMk~rG-R-----lKv-----Lhg~~r--ks-e~p~lcLVAIarPL~~-ps~~Ei~l~s~~FiTRhslDGkftyVDpr 294 (630)
|||+-.+- + +.. ..+..+ .+ +....||+.++| |.. -...+|+.+..+|++||+..+.|..||.+
T Consensus 271 fcRisgr~~~~~~~~y~PFRl~pyl~ev~~~~~~~s~~ccLllaer-ihSgYeAPrIps~KriFtT~HTptClf~hVDea 349 (1114)
T KOG3753|consen 271 FCRISGRKDRENEIRYHPFRLTPYLVEVRDQQGAESQPCCLLLAER-IHSGYEAPRIPSNKRIFTTTHTPTCLFQHVDEA 349 (1114)
T ss_pred eeeeecccCCcCccccCcccccceeEEeccccccCcCcceeehhhh-hhcccccCcCCcccceeEeccCCcceeeecchh
Confidence 88864311 1 110 111111 11 233346666565 432 12336666777999999999999999999
Q ss_pred cccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcC-Cc--eeeEEEEEecCCcEEEEEEEEEEEEe--CCCceEE
Q psy8265 295 GKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTG-AS--GMIAYRFQTNDGGWQWLQTSSRLVYK--NSKPDFV 369 (630)
Q Consensus 295 v~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkG-qs--~s~eYRfrtKdGswVWVeTsa~li~~--nGkpe~I 369 (630)
+..+|||.|+||+|+++..|+|++|+..+.+.|+.+++.| +. ....+||+..||.||-+++.|..+.+ ..|.++|
T Consensus 350 AVp~LGyLPqDLIG~sil~f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTeWSsFVNPWSRKieFV 429 (1114)
T KOG3753|consen 350 AVPLLGYLPQDLIGTSILAFVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTEWSSFVNPWSRKIEFV 429 (1114)
T ss_pred hhhhhccCchhhhccchhhhhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEechhhhccChhhhheeee
Confidence 9999999999999999999999999999999999999875 44 35789999999999999999998765 7899999
Q ss_pred EEEEEecCchhhHHHHh
Q psy8265 370 ISTHRPLMEEEGRDLLG 386 (630)
Q Consensus 370 Vgt~rdISErE~~E~L~ 386 (630)
|+-|++-+-...++.+.
T Consensus 430 vGRHrVrt~PlneDVFa 446 (1114)
T KOG3753|consen 430 VGRHRVRTGPLNEDVFA 446 (1114)
T ss_pred eeeceeeccCccccccc
Confidence 99999987655444433
No 8
>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=99.46 E-value=2.6e-13 Score=114.41 Aligned_cols=85 Identities=27% Similarity=0.467 Sum_probs=73.4
Q ss_pred eeeeccccccccCCChhhhccCc----ccceeccccHHHHHHHHHH-HHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe
Q psy8265 288 LVSMDQRGKMLLGYSDTELANMG----GYDLVHYDDLAYVASAHQE-LLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK 362 (630)
Q Consensus 288 ftyVDprv~~LLGYspEELlG~S----~ydlIHPDDl~~V~eah~~-lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~ 362 (630)
++|+|+++.+++||.++|+ +.. |.+++||||++.+.+.+.+ .+.++.....+||+++++|+++|++.++.++++
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 666 9999999999999999999 677788899999999999999999999999985
Q ss_pred -CCCceEEEEEE
Q psy8265 363 -NSKPDFVISTH 373 (630)
Q Consensus 363 -nGkpe~IVgt~ 373 (630)
+|++..++|++
T Consensus 80 ~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 80 ENGKPIRIIGVI 91 (91)
T ss_dssp TTS-EEEEEEEE
T ss_pred CCCCEEEEEEEC
Confidence 89999999985
No 9
>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=99.31 E-value=1.3e-11 Score=104.20 Aligned_cols=99 Identities=20% Similarity=0.229 Sum_probs=87.8
Q ss_pred EeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEE
Q psy8265 280 SKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRL 359 (630)
Q Consensus 280 TRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~l 359 (630)
...+.||+|+++|+++..++||.++|++|+++.+++++++.....+.+.+.+++|.....+.++++++|+.+|++.++.+
T Consensus 5 ~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~ 84 (104)
T PF13426_consen 5 FILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFWVEVSASP 84 (104)
T ss_dssp EEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEEEEEEEEE
T ss_pred EEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEEEEEEEEE
Confidence 34577999999999999999999999999999999998887777788888888787778899999999999999999999
Q ss_pred EEe-CCCceEEEEEEEecCc
Q psy8265 360 VYK-NSKPDFVISTHRPLME 378 (630)
Q Consensus 360 i~~-nGkpe~IVgt~rdISE 378 (630)
+.+ +|+..+++++.+||||
T Consensus 85 i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 85 IRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEETTSSEEEEEEEEEEEHH
T ss_pred EECCCCCEEEEEEEEEECCC
Confidence 987 7888999999999986
No 10
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.20 E-value=2e-11 Score=145.30 Aligned_cols=217 Identities=14% Similarity=0.093 Sum_probs=152.2
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC---ccccCC-C-C--CCeEEe-eeeeeEEEe
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS---YYQSYN-E-N--GPSERL-DIRGRIKIL 242 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~---~~c~ld-~-r--SfF~RM-k~rGRlKvL 242 (630)
.+++.+|+|+|++++..+++||+.+|+ +|.++.+++||.+.... +..... . . .+-.|+ ...|...++
T Consensus 297 ~~~d~dG~i~~~N~~~~~l~G~~~~el-----~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~ 371 (1092)
T PRK09776 297 ALVGTEGQWLQVNKALCQFLGYSQEEL-----RGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYYRRDGEVVWA 371 (1092)
T ss_pred EEEcCCCcEEehhHHHHHHhCCCHHHH-----ccCCceeccCcchhHhHHHHHHHHHcCCccceeeeeEEEcCCCCEEEE
Confidence 467999999999999999999999994 89999999999754321 000111 1 0 111121 233443332
Q ss_pred ecccc---cCCCCCeEEEEEEeeCCCCCCccccc------------cceeeEEeeccCceeeeeccccccccCCChhhhc
Q psy8265 243 HGQNR---KLEEPPLALFAICTPFGPPSLLEIPH------------KEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELA 307 (630)
Q Consensus 243 hg~~r---kse~p~lcLVAIarPL~~ps~~Ei~l------------~s~~FiTRhslDGkftyVDprv~~LLGYspEELl 307 (630)
..... .......+++++.+.+......|..+ .....+...+.++.++++|+++..++||.+++..
T Consensus 372 ~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G~~~~~~~ 451 (1092)
T PRK09776 372 LLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYEIPPHIKP 451 (1092)
T ss_pred EEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhCCCcccCC
Confidence 21111 11122335666666665433222111 1223455668899999999999999999998865
Q ss_pred cC-cccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe-CCCceEEEEEEEecCchh-hHHH
Q psy8265 308 NM-GGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK-NSKPDFVISTHRPLMEEE-GRDL 384 (630)
Q Consensus 308 G~-S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~-nGkpe~IVgt~rdISErE-~~E~ 384 (630)
+. .|.+++||+|.+.+...+.+.+..+.....+||++++|| ++|+...+.++.+ +|++..++++.+|||+++ .++.
T Consensus 452 ~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~ 530 (1092)
T PRK09776 452 TWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEA 530 (1092)
T ss_pred CHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHH
Confidence 53 478899999999999988888888888889999999999 9999999988876 789999999999999976 4555
Q ss_pred Hhhhccccc
Q psy8265 385 LGKRTMDFK 393 (630)
Q Consensus 385 L~~r~~elk 393 (630)
|++.++++.
T Consensus 531 L~~~~~~l~ 539 (1092)
T PRK09776 531 LFQEKERLH 539 (1092)
T ss_pred HHHHHHHHH
Confidence 665555443
No 11
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=99.15 E-value=3.7e-10 Score=130.03 Aligned_cols=209 Identities=16% Similarity=0.078 Sum_probs=141.9
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC---ccccCC--CC--CCe---EEe-eeeeeE
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS---YYQSYN--EN--GPS---ERL-DIRGRI 239 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~---~~c~ld--~r--SfF---~RM-k~rGRl 239 (630)
.+++.+|+|+|+++...+++||+.+|+ +|+++.++.|+...... ...... .. ..+ +++ ...|..
T Consensus 26 ~~~d~~g~i~~~N~~~~~l~G~s~eel-----iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~ 100 (799)
T PRK11359 26 VLINENDEVLFFNPAAEKLWGYKREEV-----IGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSK 100 (799)
T ss_pred EEEcCCCeEEEEcHHHHHHhCCCHHHH-----cCCCHHHhcCccccccchHHHhhhhccCCccccccceeeEEecCCcCE
Confidence 467899999999999999999999994 89999999988644321 000000 00 111 111 223443
Q ss_pred EEeeccccc-CCCCCeEEEEEEeeCCCCCCcccc--------ccceeeEEeeccCceeeeeccccccccCCChhhhccCc
Q psy8265 240 KILHGQNRK-LEEPPLALFAICTPFGPPSLLEIP--------HKEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMG 310 (630)
Q Consensus 240 KvLhg~~rk-se~p~lcLVAIarPL~~ps~~Ei~--------l~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S 310 (630)
.++...... ........+++.+.+......+.. ......+...+.+|+++++|+++..++||.++|++|+.
T Consensus 101 ~~v~~~~~~~~~~g~~~~~~~~~DiT~~~~~~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~G~~~~e~~g~~ 180 (799)
T PRK11359 101 IWTRFALSKVSAEGKVYYLALVRDASVEMAQKEQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQ 180 (799)
T ss_pred EEEEEEeeeeccCCceEEEEEEeeccchhhhHHHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhhCCCHHHHCCCC
Confidence 332211111 112233556777777543211110 11233455668899999999999999999999999999
Q ss_pred ccceec-cccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe-CCCceEEEEEEEecCchhhHHH
Q psy8265 311 GYDLVH-YDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK-NSKPDFVISTHRPLMEEEGRDL 384 (630)
Q Consensus 311 ~ydlIH-PDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~-nGkpe~IVgt~rdISErE~~E~ 384 (630)
+.++++ +++.......+...+..+.....++|+++++|.++|+.....++.+ +|.+.+++++.+|||+++..+.
T Consensus 181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~ 256 (799)
T PRK11359 181 PDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQ 256 (799)
T ss_pred hHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHH
Confidence 988876 4455555555666666566667789999999999999999888875 6788899999999999875443
No 12
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=99.15 E-value=8.3e-11 Score=127.77 Aligned_cols=212 Identities=11% Similarity=0.006 Sum_probs=130.3
Q ss_pred CCCCCCCC-CccCC-CCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC---ccccC-CCCCCeEEee-e
Q psy8265 163 NPSRSPPA-SPILP-NGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS---YYQSY-NENGPSERLD-I 235 (630)
Q Consensus 163 ll~~~~~~-~Vls~-dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~---~~c~l-d~rSfF~RMk-~ 235 (630)
++..++++ .+++. +|+|+|+++...+++||+.+|| +|+++.+++||...... +.... .....-.++. .
T Consensus 138 l~e~~~~~i~~~d~~~g~i~~~N~a~~~l~G~~~~el-----~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~~~~ 212 (442)
T TIGR02040 138 VLEVSSDAVLLVDMSTGRIVEANSAAAALLGGVGQSL-----VGRAFPQEFEGRRREELMLTLRNVRATGSAAPVRILLR 212 (442)
T ss_pred HHhhCCceEEEEECCCCEEEEEcHHHHHHhCcCHHHH-----cCCCHHHhCCHHHHHHHHHHHHHHHhcCCCcceEEEEc
Confidence 44445554 34565 8999999999999999999994 89999999988543210 00000 0111111111 1
Q ss_pred eeeEE-EeecccccCCCCCeEEEEEEeeCCCCCCcccc---------ccceeeEEeeccCceeeeeccccccccCCC-hh
Q psy8265 236 RGRIK-ILHGQNRKLEEPPLALFAICTPFGPPSLLEIP---------HKEVMFKSKHKLDLSLVSMDQRGKMLLGYS-DT 304 (630)
Q Consensus 236 rGRlK-vLhg~~rkse~p~lcLVAIarPL~~ps~~Ei~---------l~s~~FiTRhslDGkftyVDprv~~LLGYs-pE 304 (630)
.|... .+....... .....+++..+++......|.. .....-+...+.+|+|+++|+++..++||. .+
T Consensus 213 ~~~~~~~~~~~~~~~-~~~~~~l~~~~dit~~~~~e~~~~~~~~~l~e~~~d~I~v~D~~G~I~~~N~a~~~l~G~~~~~ 291 (442)
T TIGR02040 213 RSQKRLLVVVSVFRQ-DGESLFLCQLSPAGATQPVGDELSENLARLYHEAPDAIVFSDADGTIRGANEAFLELTDSSSLE 291 (442)
T ss_pred CCCeEEEEEEEEEEe-CCceEEEEEEcccchhhhhhHHHHHHHHHHHHhCCceEEEEcCCCcEEehhHHHHHHhCCCChH
Confidence 11111 111110010 1122344444555443222110 112334455688999999999999999997 57
Q ss_pred hhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEeCCCceEEEEEEEecCchhhH
Q psy8265 305 ELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYKNSKPDFVISTHRPLMEEEGR 382 (630)
Q Consensus 305 ELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~nGkpe~IVgt~rdISErE~~ 382 (630)
+++|+++.++++++... .......+...|.....+.++++++|..+||+.++.++.+. ....++++.+|||+++..
T Consensus 292 ~l~G~~~~~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~ve~s~~~i~~~-~~~~~~~v~rDITeR~~~ 367 (442)
T TIGR02040 292 AVRGRTLDRWLGRGGVD-LRVLLSNVRRTGQVRLYATTLTGEFGAQTEVEISAAWVDQG-ERPLIVLVIRDISRRLTM 367 (442)
T ss_pred HHcCCCHHHHhCCCccc-HHHHHHHHhhcCceEEEEEEEEcCCCCEEEEEEEEEEeccC-CceEEEEEEecchhhccC
Confidence 89999998888754322 22223444445665667888999999999999999987543 335788999999998754
No 13
>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=99.13 E-value=5.5e-10 Score=95.76 Aligned_cols=99 Identities=23% Similarity=0.311 Sum_probs=84.1
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCc-eeeEEEEEecCCcEEEEEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGAS-GMIAYRFQTNDGGWQWLQTS 356 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs-~s~eYRfrtKdGswVWVeTs 356 (630)
.+...+.+|+|+++|+++..++||.++|++|+++++++|++|.....+.+.+.+..++. .....++..++|+.+|++..
T Consensus 13 ~i~~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~ 92 (113)
T PF00989_consen 13 GIFVIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRDGRPRWVEVR 92 (113)
T ss_dssp EEEEEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETTSCEEEEEEE
T ss_pred eEEEEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecCCcEEEEEEE
Confidence 34445689999999999999999999999999999999999888888888888877765 45667777789999999999
Q ss_pred EEEEEe-CCCceEEEEEEEec
Q psy8265 357 SRLVYK-NSKPDFVISTHRPL 376 (630)
Q Consensus 357 a~li~~-nGkpe~IVgt~rdI 376 (630)
+.++.+ ++++.+++++.+||
T Consensus 93 ~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 93 ASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp EEEEEETTEEEEEEEEEEEE-
T ss_pred EEEEEeCCCCEEEEEEEEEeC
Confidence 999987 56678999999987
No 14
>PRK13560 hypothetical protein; Provisional
Probab=99.09 E-value=7.5e-10 Score=126.47 Aligned_cols=215 Identities=8% Similarity=-0.056 Sum_probs=142.8
Q ss_pred EEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCCc----cc------cC---CCCCCeEEeee-eeeEEEeec
Q psy8265 179 INYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKSY----YQ------SY---NENGPSERLDI-RGRIKILHG 244 (630)
Q Consensus 179 IlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~~----~c------~l---d~rSfF~RMk~-rGRlKvLhg 244 (630)
+.|+|+....++|+...|++. -...+..++||.+...-+ .+ .+ .-..+-.|+.+ .|+|-...+
T Consensus 94 ~~~~~~~~~~l~~~~~~~~~~---~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~~dg~~~~~~~ 170 (807)
T PRK13560 94 FPSLLDANGELAAIAKHDLMA---DKGLLAMLIGGDDGDFFFANPFRSAETIAMALQSDDWQEEEGHFRCGDGRFIDCCL 170 (807)
T ss_pred cceeeccchhHHHhcCcccCC---ccchhhhhcCCCcchhhhhChhhHHHHHHHHhccCcccceEEEEEeCCccEEEEEe
Confidence 334888888999988888521 123466789998654311 00 01 11223344443 355433322
Q ss_pred ccccCCCCCeEEEEEEeeCCCCCCcccc------------ccceeeEEeeccCceeeeeccccccccCCChhhhccCccc
Q psy8265 245 QNRKLEEPPLALFAICTPFGPPSLLEIP------------HKEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGY 312 (630)
Q Consensus 245 ~~rkse~p~lcLVAIarPL~~ps~~Ei~------------l~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~y 312 (630)
.....+.....++++++.|......|.. ......+...+.||+++++|+++..++||.++|++|+++.
T Consensus 171 ~~~~~~~g~~~~~g~~~DIT~rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~~g~~~~ 250 (807)
T PRK13560 171 RFERHAHADDQVDGFAEDITERKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRREEIIGMSIH 250 (807)
T ss_pred eeeecCCCceEEEEEEEccchHHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHHcCCcch
Confidence 2222223345678888888765432211 1223445567899999999999999999999999999999
Q ss_pred ceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEE--Ee-CCCceEEEEEEEecCchh-hHHHHhhh
Q psy8265 313 DLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLV--YK-NSKPDFVISTHRPLMEEE-GRDLLGKR 388 (630)
Q Consensus 313 dlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li--~~-nGkpe~IVgt~rdISErE-~~E~L~~r 388 (630)
++.++++...........+..+.....++++++++|.++|++.....+ .+ +|...+++++.+|||+++ .++.|++.
T Consensus 251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~s 330 (807)
T PRK13560 251 DFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEK 330 (807)
T ss_pred hcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHH
Confidence 998877666665555555656666678899999999999887766543 23 677889999999999976 45567766
Q ss_pred cccccccc
Q psy8265 389 TMDFKVSY 396 (630)
Q Consensus 389 ~~elk~sf 396 (630)
++.|+..+
T Consensus 331 e~~l~~l~ 338 (807)
T PRK13560 331 EDMLRAII 338 (807)
T ss_pred HHHHHHHH
Confidence 66665444
No 15
>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=99.09 E-value=2.9e-10 Score=123.60 Aligned_cols=206 Identities=9% Similarity=-0.032 Sum_probs=130.2
Q ss_pred CCCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC---ccc-cCCCCCCe---EEeee-e
Q psy8265 166 RSPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS---YYQ-SYNENGPS---ERLDI-R 236 (630)
Q Consensus 166 ~~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~---~~c-~ld~rSfF---~RMk~-r 236 (630)
..+|. .+++.+|+|++|+++...++||+.+| |+|+.+.+++||...++. +.. ..+....+ ++... .
T Consensus 4 ~~~d~~~~~d~~g~i~~~n~~~~~~~g~~~~e-----l~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 78 (442)
T TIGR02040 4 TAADVTLLLDAEGVVREVAANPHHPSFEQLSE-----WEGRRWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPS 78 (442)
T ss_pred ccCcEEEEECCCCcEEEEEECCCccccccccc-----CCCCcHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCC
Confidence 34444 46799999999999999999999999 599999999999753320 000 00011111 11111 1
Q ss_pred eeEEEeecccccCCCCCeEEEEEEeeCCCCC-----------Ccc----------cc-----ccceeeEEeecc-Cceee
Q psy8265 237 GRIKILHGQNRKLEEPPLALFAICTPFGPPS-----------LLE----------IP-----HKEVMFKSKHKL-DLSLV 289 (630)
Q Consensus 237 GRlKvLhg~~rkse~p~lcLVAIarPL~~ps-----------~~E----------i~-----l~s~~FiTRhsl-DGkft 289 (630)
|.+..+..+...... ...++++++++.... ..| .. ......+...+. +|+++
T Consensus 79 g~~~~~~~~~~~~~~-~~~~~~i~rDi~~~~~~~~~l~~~~~~~e~~~~~l~~~e~r~~~l~e~~~~~i~~~d~~~g~i~ 157 (442)
T TIGR02040 79 SFELPMRFILVRLGA-DRGVLALGRDLRAVAELQQQLVAAQQAMERDYWTLREMETRYRVVLEVSSDAVLLVDMSTGRIV 157 (442)
T ss_pred CCccCeEEEEEEeCC-CCeEEEEecccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCceEEEEECCCCEEE
Confidence 222211111100011 125677888774210 000 00 012334455666 79999
Q ss_pred eeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEeCCCceEE
Q psy8265 290 SMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYKNSKPDFV 369 (630)
Q Consensus 290 yVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~nGkpe~I 369 (630)
++|+++..++||.++|++|+++.+++||+|...+...+......|... .+++..++|++.|. ..+.++..++.+ .+
T Consensus 158 ~~N~a~~~l~G~~~~el~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~~--~~~~~~~~~~~~~~-~~~~~~~~~~~~-~~ 233 (442)
T TIGR02040 158 EANSAAAALLGGVGQSLVGRAFPQEFEGRRREELMLTLRNVRATGSAA--PVRILLRRSQKRLL-VVVSVFRQDGES-LF 233 (442)
T ss_pred EEcHHHHHHhCcCHHHHcCCCHHHhCCHHHHHHHHHHHHHHHhcCCCc--ceEEEEcCCCeEEE-EEEEEEEeCCce-EE
Confidence 999999999999999999999999999999999999888887777643 34555666666663 344444444544 45
Q ss_pred EEEEEecCchhh
Q psy8265 370 ISTHRPLMEEEG 381 (630)
Q Consensus 370 Vgt~rdISErE~ 381 (630)
++..+||++++.
T Consensus 234 l~~~~dit~~~~ 245 (442)
T TIGR02040 234 LCQLSPAGATQP 245 (442)
T ss_pred EEEEcccchhhh
Confidence 667788888653
No 16
>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=99.01 E-value=2.6e-09 Score=91.18 Aligned_cols=101 Identities=21% Similarity=0.230 Sum_probs=89.6
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~ 358 (630)
+...+.||+++++|+++..++|+.+++++|+++.+++++++.+.+...++++++++........+.. +|+..|++....
T Consensus 8 i~v~D~~~~i~~~N~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 86 (110)
T PF08448_consen 8 IFVIDPDGRIVYANQAAAELFGVSPEELIGRSLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DGEERWFEVSIS 86 (110)
T ss_dssp EEEEETTSBEEEE-HHHHHHHTSTHHHHTTSBHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TSCEEEEEEEEE
T ss_pred eEEECCCCEEEEEHHHHHHHhCCCHHHHhhccchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cCCcEEEEEEEE
Confidence 4455899999999999999999999999999999999999999999999999988877666665555 999999999999
Q ss_pred EEEe-CCCceEEEEEEEecCchh
Q psy8265 359 LVYK-NSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 359 li~~-nGkpe~IVgt~rdISErE 380 (630)
++.+ +|++.+++++.+|||+++
T Consensus 87 Pi~~~~g~~~g~~~~~~DiT~~r 109 (110)
T PF08448_consen 87 PIFDEDGEVVGVLVIIRDITERR 109 (110)
T ss_dssp EEECTTTCEEEEEEEEEEECCHH
T ss_pred EeEcCCCCEEEEEEEEEECchhh
Confidence 9986 899999999999999975
No 17
>PRK13560 hypothetical protein; Provisional
Probab=98.97 E-value=2e-09 Score=123.03 Aligned_cols=219 Identities=11% Similarity=-0.025 Sum_probs=139.0
Q ss_pred CCCCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCCC----ccccCCCCCCeE--E-eeee
Q psy8265 165 SRSPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPKS----YYQSYNENGPSE--R-LDIR 236 (630)
Q Consensus 165 ~~~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k~----~~c~ld~rSfF~--R-Mk~r 236 (630)
...++. .+++.+|+|+|+|+...+++||+.+|+ +|.++.++.++...... ........+... + ....
T Consensus 211 e~~~~~i~~~d~~g~i~~~N~~~~~~~G~~~~e~-----~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~d 285 (807)
T PRK13560 211 DNIADPAFWKDEDAKVFGCNDAACLACGFRREEI-----IGMSIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKD 285 (807)
T ss_pred hhCCCeEEEEcCCCCEEEEhHHHHHHhCCCHHHH-----cCCcchhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCC
Confidence 344444 467999999999999999999999994 89999998766422110 000111111111 1 2234
Q ss_pred eeEEEeeccc-----ccCCCCCeEEEEEEeeCCCCCCcccc------------ccceeeEEeeccCceeeee-ccccccc
Q psy8265 237 GRIKILHGQN-----RKLEEPPLALFAICTPFGPPSLLEIP------------HKEVMFKSKHKLDLSLVSM-DQRGKML 298 (630)
Q Consensus 237 GRlKvLhg~~-----rkse~p~lcLVAIarPL~~ps~~Ei~------------l~s~~FiTRhslDGkftyV-Dprv~~L 298 (630)
|+..++.... ........+++++++.+......|.. ......+...+.+|.++++ ++.+..+
T Consensus 286 G~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~~i~~~d~~g~i~~~nn~~~~~~ 365 (807)
T PRK13560 286 GRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAERM 365 (807)
T ss_pred CCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcccEEEEcCCCCEEEecCHHHHHH
Confidence 5544221110 01112234688899998764332211 1223445667889999998 4667779
Q ss_pred cCCChhhhccCcccceecc---------------ccHHHHHHH--HHHHHhcCCc-eeeEEEEEecCCcEEEEEEEEEEE
Q psy8265 299 LGYSDTELANMGGYDLVHY---------------DDLAYVASA--HQELLKTGAS-GMIAYRFQTNDGGWQWLQTSSRLV 360 (630)
Q Consensus 299 LGYspEELlG~S~ydlIHP---------------DDl~~V~ea--h~~lLkkGqs-~s~eYRfrtKdGswVWVeTsa~li 360 (630)
+||.++|++|+++..+.+. ++....... ....+..|.. ...++++..++|.++|+...+.++
T Consensus 366 ~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~p~ 445 (807)
T PRK13560 366 LGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEPL 445 (807)
T ss_pred hCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCceEEEEcCCCCeEEEEEEEeee
Confidence 9999999999987665322 221111111 1223455554 346889999999999999999988
Q ss_pred Ee-CCCceEEEEEEEecCchh-hHHHHhhh
Q psy8265 361 YK-NSKPDFVISTHRPLMEEE-GRDLLGKR 388 (630)
Q Consensus 361 ~~-nGkpe~IVgt~rdISErE-~~E~L~~r 388 (630)
.+ +|++.+++++.+|||+++ .++.|++.
T Consensus 446 ~d~~g~~~~~~~~~~DITerk~~E~~L~~~ 475 (807)
T PRK13560 446 HDADGNIIGAIALLVDITERKQVEEQLLLA 475 (807)
T ss_pred ECCCCCEEEEEEEeehhhhHHHHHHHHHHH
Confidence 76 789999999999999976 44455543
No 18
>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=98.80 E-value=7.9e-08 Score=72.39 Aligned_cols=99 Identities=22% Similarity=0.282 Sum_probs=83.1
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa 357 (630)
.+...+.+|.++++|+++..++|+..++++|..+.+++++++...+.+.+...+..+......+++..++|.++|+....
T Consensus 4 ~i~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (103)
T cd00130 4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSL 83 (103)
T ss_pred eEEEECCCCcEEEECHHHHHHhCCCHHHHcCccHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEEEEEEE
Confidence 34556789999999999999999999999999999999999988888877777765556678889999999999999988
Q ss_pred EEEEe-CCCceEEEEEEEec
Q psy8265 358 RLVYK-NSKPDFVISTHRPL 376 (630)
Q Consensus 358 ~li~~-nGkpe~IVgt~rdI 376 (630)
..+.+ +++...++++.+||
T Consensus 84 ~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 84 TPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEEecCCCCEEEEEEEEecC
Confidence 87665 56777788877765
No 19
>PRK13559 hypothetical protein; Provisional
Probab=98.63 E-value=1.2e-07 Score=99.47 Aligned_cols=102 Identities=15% Similarity=0.109 Sum_probs=86.0
Q ss_pred cCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe-
Q psy8265 284 LDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK- 362 (630)
Q Consensus 284 lDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~- 362 (630)
.+|.++++|+++..++||..+|++|+.+..++++++.......+...+..+.....+++.+.++|..+|++....++++
T Consensus 64 ~~g~i~~~N~a~~~l~G~~~~e~iG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~ 143 (361)
T PRK13559 64 PDLPIVLANQAFLDLTGYAAEEVVGRNCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGE 143 (361)
T ss_pred CCCcEEEEchHHHHHhCCCHHHHcCCChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcC
Confidence 3678999999999999999999999999888887776666666677777777777788889999999999999988875
Q ss_pred CCCceEEEEEEEecCchhhHHHH
Q psy8265 363 NSKPDFVISTHRPLMEEEGRDLL 385 (630)
Q Consensus 363 nGkpe~IVgt~rdISErE~~E~L 385 (630)
+|+..+++++.+|||+++..+.+
T Consensus 144 ~G~~~~~v~~~~DITerk~~e~~ 166 (361)
T PRK13559 144 DGRLLYFFGSQWDVTDIRAVRAL 166 (361)
T ss_pred CCCEEEeeeeeeehhcchhhHHH
Confidence 67888899999999998754433
No 20
>PRK09776 putative diguanylate cyclase; Provisional
Probab=98.60 E-value=5.7e-08 Score=115.97 Aligned_cols=116 Identities=18% Similarity=0.185 Sum_probs=97.1
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCC-ceeeEEEEEecCCcEEEEEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGA-SGMIAYRFQTNDGGWQWLQTS 356 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGq-s~s~eYRfrtKdGswVWVeTs 356 (630)
-+...+.||+++++|+++.+++||.++|++|+++.+++||+|.+...+.+.+.+..+. ....++|++++||+.+|+...
T Consensus 295 ~i~~~d~dG~i~~~N~~~~~l~G~~~~el~g~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~ 374 (1092)
T PRK09776 295 GMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYYRRDGEVVWALLA 374 (1092)
T ss_pred eEEEEcCCCcEEehhHHHHHHhCCCHHHHccCCceeccCcchhHhHHHHHHHHHcCCccceeeeeEEEcCCCCEEEEEEE
Confidence 3456789999999999999999999999999999999999999988887777665432 367899999999999999999
Q ss_pred EEEEEe-CCCceEEEEEEEecCchhh-HHHHhhhccccc
Q psy8265 357 SRLVYK-NSKPDFVISTHRPLMEEEG-RDLLGKRTMDFK 393 (630)
Q Consensus 357 a~li~~-nGkpe~IVgt~rdISErE~-~E~L~~r~~elk 393 (630)
..++.+ +|++.+++++.+|||+++. ++.+++..+++.
T Consensus 375 ~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~ 413 (1092)
T PRK09776 375 VSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERIT 413 (1092)
T ss_pred EEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHH
Confidence 998875 7888999999999999764 445555544444
No 21
>PRK13557 histidine kinase; Provisional
Probab=98.59 E-value=1.6e-07 Score=102.33 Aligned_cols=98 Identities=11% Similarity=0.062 Sum_probs=86.5
Q ss_pred cCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe-
Q psy8265 284 LDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK- 362 (630)
Q Consensus 284 lDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~- 362 (630)
.||+|+|+|+++..++||+.+|++|+++..++||++.......+...+..+.....+++..+++|+.+|+...+.++.+
T Consensus 51 ~~g~i~~~N~a~~~~~G~~~~e~~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~ 130 (540)
T PRK13557 51 PDNPIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYND 130 (540)
T ss_pred CCCCEEEEcHHHHHHhCCCHHHhcCCChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECC
Confidence 5899999999999999999999999999999999887777777777777777667788888999999999999998876
Q ss_pred CCCceEEEEEEEecCchhh
Q psy8265 363 NSKPDFVISTHRPLMEEEG 381 (630)
Q Consensus 363 nGkpe~IVgt~rdISErE~ 381 (630)
+|+..+++++.+|||+++.
T Consensus 131 ~g~~~~~~~~~~dit~~~~ 149 (540)
T PRK13557 131 AGDLVYFFGSQLDVSRRRD 149 (540)
T ss_pred CCCEEEEEEEecChHHHHH
Confidence 6888899999999999764
No 22
>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=98.58 E-value=5e-07 Score=71.71 Aligned_cols=102 Identities=20% Similarity=0.225 Sum_probs=83.8
Q ss_pred EeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCC-ceeeEEEEEecCCcEEEEEEEEE
Q psy8265 280 SKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGA-SGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 280 TRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGq-s~s~eYRfrtKdGswVWVeTsa~ 358 (630)
...+.+|+++++|+++..++|+..++++|+.+.+++++++...+...+...+..+. .....+++..++|..+|+.....
T Consensus 17 ~~~d~~~~i~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 (124)
T TIGR00229 17 IVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERLLEGEREPVSEERRVRRKDGSEIWVEVSVS 96 (124)
T ss_pred EEEcCCCcEEEEchHHHHHhCCChHHhcCcchhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeEcCCCCEEEEEEEEe
Confidence 34577899999999999999999999999999999999888877777777665332 34567777889999999998887
Q ss_pred EEEeCCCceEEEEEEEecCchhh
Q psy8265 359 LVYKNSKPDFVISTHRPLMEEEG 381 (630)
Q Consensus 359 li~~nGkpe~IVgt~rdISErE~ 381 (630)
.+..+|...+++++..||++++.
T Consensus 97 ~~~~~~~~~~~~~~~~dit~~~~ 119 (124)
T TIGR00229 97 PIRTNGGELGVVGIVRDITERKQ 119 (124)
T ss_pred ehhhCCCeeEEEEEeeehhHHHH
Confidence 76546777889999999998764
No 23
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.51 E-value=4.2e-07 Score=103.87 Aligned_cols=105 Identities=15% Similarity=0.131 Sum_probs=89.2
Q ss_pred ccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe
Q psy8265 283 KLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK 362 (630)
Q Consensus 283 slDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~ 362 (630)
..+|.++++|+++..++||.++|++|+.+..++|+++.......+...+..+.....++|+++++|.++|+...+.++.+
T Consensus 168 ~~dg~i~~~N~~~~~l~G~~~eel~g~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~d 247 (665)
T PRK13558 168 LPDEPLIYINDAFERITGYSPDEVLGRNCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD 247 (665)
T ss_pred CCCCcEEEEcHHHHHHhCcCHHHHcCCCHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEECCCCCEEEEEEEEEEEEC
Confidence 35799999999999999999999999999999988877666666666677777778899999999999999999998875
Q ss_pred -CCCceEEEEEEEecCchhhH-HHHhh
Q psy8265 363 -NSKPDFVISTHRPLMEEEGR-DLLGK 387 (630)
Q Consensus 363 -nGkpe~IVgt~rdISErE~~-E~L~~ 387 (630)
+|++.+++++.+|||+++.. +.|+.
T Consensus 248 ~~G~~~~~vgi~~DITerk~~E~~L~~ 274 (665)
T PRK13558 248 EDGTVTHYVGFQTDVTERKEAELALQR 274 (665)
T ss_pred CCCCEEEEEEEEEeCcHHHHHHHHHHH
Confidence 78889999999999998643 33443
No 24
>PRK10060 RNase II stability modulator; Provisional
Probab=98.44 E-value=7.6e-07 Score=102.77 Aligned_cols=130 Identities=13% Similarity=0.123 Sum_probs=98.4
Q ss_pred eeEEeeccCceeeeeccccccccCCChhhhccCccccee-ccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEE
Q psy8265 277 MFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLV-HYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQT 355 (630)
Q Consensus 277 ~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlI-HPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeT 355 (630)
.-+...+.||+|+++|++++.++||..+|++|+++.+++ ++++.......+..+++.|.....++++++++|..+|+..
T Consensus 122 ~gI~i~D~~g~I~~~N~a~~~l~Gy~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~ 201 (663)
T PRK10060 122 SVIVILDSRGNIQRFNRLCEEYTGLKEHDVIGQSVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFR 201 (663)
T ss_pred ceEEEEeCCCCEEEEcHHHHHHHCcCHHHHcCCCHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEe
Confidence 334556889999999999999999999999999988766 5666677777777778778777889999999999999876
Q ss_pred EEEEEEeCCC-ceEEEEEEEecCchhh-HHHHhhhccccccccccc--CcccccccCCCCC
Q psy8265 356 SSRLVYKNSK-PDFVISTHRPLMEEEG-RDLLGKRTMDFKVSYLDA--GLNNSYFSDSDQL 412 (630)
Q Consensus 356 sa~li~~nGk-pe~IVgt~rdISErE~-~E~L~~r~~elk~sf~d~--gl~~~~~~~s~~~ 412 (630)
...+...+|+ ..++|++.+|||+++. ++.|++ ..+.|. ||.|+..+.....
T Consensus 202 ~~~~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~------~a~~D~LTGL~NR~~f~~~l~ 256 (663)
T PRK10060 202 NKFVHSGSGKNEIFLICSGTDITEERRAQERLRI------LANTDSITGLPNRNAIQELID 256 (663)
T ss_pred eeEEEcCCCCceEEEEEEEEechHHHHHHHHHHH------HhhcCccCCCcCHHHHHHHHH
Confidence 5544333444 3568899999999764 333443 233443 9999987775544
No 25
>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=98.44 E-value=3.6e-07 Score=97.75 Aligned_cols=116 Identities=13% Similarity=0.094 Sum_probs=91.4
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa 357 (630)
-+..++.+|+++++|+++..++||.++|++|++...+.++.+...+.+.+.+.+..+.....+++.++++|+++|+....
T Consensus 16 ~i~~~d~~g~~~~~N~~~~~~~G~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~ 95 (494)
T TIGR02938 16 AISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRRKDGELYLAELTV 95 (494)
T ss_pred eEEEECCCCcEEEEchhheeecCCCHHHHhCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceeeccCCCccchhhheee
Confidence 45567889999999999999999999999999988888776555555555555556666667788889999999999988
Q ss_pred EEEEe-CCCceEEEEEEEecCchhh-HHHHhhhccccc
Q psy8265 358 RLVYK-NSKPDFVISTHRPLMEEEG-RDLLGKRTMDFK 393 (630)
Q Consensus 358 ~li~~-nGkpe~IVgt~rdISErE~-~E~L~~r~~elk 393 (630)
.++.+ +|+..+++++.+|||+++. ++.|+.....+.
T Consensus 96 ~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~ 133 (494)
T TIGR02938 96 APVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIE 133 (494)
T ss_pred EEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHH
Confidence 88775 7888999999999999763 445555444443
No 26
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.43 E-value=7.1e-07 Score=103.89 Aligned_cols=109 Identities=15% Similarity=0.156 Sum_probs=95.2
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa 357 (630)
.+...+.+|+++++|+++..++||..+|++|+++.+++++++...+......+++.+.....+.++..++|..+|++.+.
T Consensus 167 ~i~~~D~~g~i~~~N~a~~~l~G~~~~eliG~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~ 246 (779)
T PRK11091 167 LVYYRNEDGEFSGCNRAMELLTGKSEKQLIGLTPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRK 246 (779)
T ss_pred eEEEECCCCcEEeEcHHHHHHhCcCHHHHcCCChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEe
Confidence 34556889999999999999999999999999999999999888888888888888877788899999999999999999
Q ss_pred EEEEe-CCCceEEEEEEEecCchhh-HHHHh
Q psy8265 358 RLVYK-NSKPDFVISTHRPLMEEEG-RDLLG 386 (630)
Q Consensus 358 ~li~~-nGkpe~IVgt~rdISErE~-~E~L~ 386 (630)
.++.+ +|+..+++++.+|||+++. ++.++
T Consensus 247 ~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~ 277 (779)
T PRK11091 247 VPFYDRVGKRHGLMGFGRDITERKRYQDALE 277 (779)
T ss_pred eeEEcCCCCEEEEEEEEeehhHHHHHHHHHH
Confidence 98875 7888899999999999764 33344
No 27
>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=98.10 E-value=1.2e-06 Score=93.81 Aligned_cols=202 Identities=12% Similarity=0.049 Sum_probs=121.4
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCC---Cc-cccCCCCC--C-eEEeeeeeeEEEee
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPK---SY-YQSYNENG--P-SERLDIRGRIKILH 243 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k---~~-~c~ld~rS--f-F~RMk~rGRlKvLh 243 (630)
.+++.+|+++|+|+...+++|++.+|+ +|.+.+.+.++..... .+ .+...... + +......|+..++.
T Consensus 18 ~~~d~~g~~~~~N~~~~~~~G~~~~~~-----~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 92 (494)
T TIGR02938 18 SITDLKANILYANDAFTRITGYTKEEI-----IGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRRKDGELYLAE 92 (494)
T ss_pred EEECCCCcEEEEchhheeecCCCHHHH-----hCCCchhhcCCCCCHHHHHHHHHHHHhCCcccceeeccCCCccchhhh
Confidence 467999999999999999999999884 7988777665532221 00 01111111 1 11122344433221
Q ss_pred ccc---ccCCCCCeEEEEEEeeCCCCCCcccc------------ccceeeEEeeccCceeeeeccccccccCCChhhhcc
Q psy8265 244 GQN---RKLEEPPLALFAICTPFGPPSLLEIP------------HKEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELAN 308 (630)
Q Consensus 244 g~~---rkse~p~lcLVAIarPL~~ps~~Ei~------------l~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG 308 (630)
... ........+++++++.+......+.. -....-+...+.+|+++++|+++..++|+...+..+
T Consensus 93 ~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~~~~~~~~ 172 (494)
T TIGR02938 93 LTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKKLATDLRVKEPA 172 (494)
T ss_pred eeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHHhhchhhhhHHH
Confidence 110 11112234677888877653211110 012223445678999999999999999999998888
Q ss_pred CcccceeccccHHHHHHHHHHHHhcCCc-eeeEEEEEecCCc-EEEEEEEEEEEEe-CC---------CceEEEEEEEec
Q psy8265 309 MGGYDLVHYDDLAYVASAHQELLKTGAS-GMIAYRFQTNDGG-WQWLQTSSRLVYK-NS---------KPDFVISTHRPL 376 (630)
Q Consensus 309 ~S~ydlIHPDDl~~V~eah~~lLkkGqs-~s~eYRfrtKdGs-wVWVeTsa~li~~-nG---------kpe~IVgt~rdI 376 (630)
..+.+++|+++...+...+ ..+.. .....++..++|. ++|+...+..+.. .+ ...+++++.+||
T Consensus 173 ~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 248 (494)
T TIGR02938 173 HTVLDLLREAWREALAENW----PQQLAFSNREARFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYLLLTIADI 248 (494)
T ss_pred HHHHHHhhHHhhhhhhhcc----hhhhccccceeeeccCCCceeeEEEecCceEEeecchhhheeccCCCchheehHHHH
Confidence 8888888877655443321 11211 2245666666665 8999888776643 22 234567788999
Q ss_pred Cchhh
Q psy8265 377 MEEEG 381 (630)
Q Consensus 377 SErE~ 381 (630)
|+++.
T Consensus 249 Te~k~ 253 (494)
T TIGR02938 249 SNLRE 253 (494)
T ss_pred HHHHH
Confidence 99764
No 28
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.00 E-value=1.6e-05 Score=92.14 Aligned_cols=99 Identities=14% Similarity=0.100 Sum_probs=78.6
Q ss_pred eeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCc----eeeEEEEEecCCcEEEEEEE
Q psy8265 281 KHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGAS----GMIAYRFQTNDGGWQWLQTS 356 (630)
Q Consensus 281 RhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs----~s~eYRfrtKdGswVWVeTs 356 (630)
..+.+|+++++|+++..++||+++|++|+++.+++|+++..............+.. ...++|++++||+++|+...
T Consensus 27 ~~d~~g~i~~~N~~~~~l~G~s~eeliG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~~ 106 (799)
T PRK11359 27 LINENDEVLFFNPAAEKLWGYKREEVIGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFA 106 (799)
T ss_pred EEcCCCeEEEEcHHHHHHhCCCHHHHcCCCHHHhcCccccccchHHHhhhhccCCccccccceeeEEecCCcCEEEEEEE
Confidence 35788999999999999999999999999999999998776555555555544432 34589999999999999988
Q ss_pred EEEEEeCCCceEEEEEEEecCchh
Q psy8265 357 SRLVYKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 357 a~li~~nGkpe~IVgt~rdISErE 380 (630)
...+..+|.. .++++.+|||+++
T Consensus 107 ~~~~~~~g~~-~~~~~~~DiT~~~ 129 (799)
T PRK11359 107 LSKVSAEGKV-YYLALVRDASVEM 129 (799)
T ss_pred eeeeccCCce-EEEEEEeeccchh
Confidence 8765435554 5678889999864
No 29
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=97.39 E-value=0.00019 Score=65.15 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=35.6
Q ss_pred ccCCCCcEEecccc-chhhcCCChhhhhhhccccCccccCCCCCCCC
Q psy8265 172 PILPNGHINYPSQE-IKKYNGDPLKSLAEMNTIGENKWKESPPVVSP 217 (630)
Q Consensus 172 Vls~dGkIlYVSEn-Vs~~LGysqeEL~q~~liGqSi~D~vHP~ls~ 217 (630)
-.+.||+|+||.++ |+.+|||.++|| +|+|+|+|+||.+-.
T Consensus 7 rhs~dgki~~~d~~~v~~~lgy~~~eL-----vG~s~y~~~H~~D~~ 48 (111)
T PF14598_consen 7 RHSLDGKITYVDSRAVSSLLGYLPEEL-----VGRSIYDFVHPDDLQ 48 (111)
T ss_dssp EEETTSBEEEEETTHHHHHHSS-HHHH-----TTSBGGGGBSCCTHH
T ss_pred EECCCcEEEEEcCccChhhcCCCcHHH-----cCCchHHhCCHhhhh
Confidence 45789999999999 899999999995 899999999998543
No 30
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=97.33 E-value=0.00046 Score=69.98 Aligned_cols=93 Identities=9% Similarity=-0.027 Sum_probs=68.3
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~ 358 (630)
+...+.+|+++++|+++..++||.++|++|+.+.+++++++...+ +..+.. ....+++.++|...|+.....
T Consensus 19 i~~~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~-------l~~~~~-~~~~~~~~~~~~~~~~~~~~~ 90 (333)
T TIGR02966 19 VVVLDEEGQIEWCNPAAERLLGLRWPDDLGQRITNLIRHPEFVEY-------LAAGRF-SEPLELPSPINSERVLEIRIA 90 (333)
T ss_pred EEEECCCCcEEEEcHHHHHHhCCChHHHcCCcHHHHccCHHHHHH-------HHhccc-CCCeEeecCCCCceEEEEEEE
Confidence 455688999999999999999999999999999999988654332 222222 223555667888888888877
Q ss_pred EEEeCCCceEEEEEEEecCchhhHH
Q psy8265 359 LVYKNSKPDFVISTHRPLMEEEGRD 383 (630)
Q Consensus 359 li~~nGkpe~IVgt~rdISErE~~E 383 (630)
++.+ +. ++++.+||++.+..+
T Consensus 91 p~~~-~~---~~~~~~dit~~~~~~ 111 (333)
T TIGR02966 91 PYGE-EQ---KLLVARDVTRLRRLE 111 (333)
T ss_pred EcCC-Cc---eEEEEeCchHHHHHH
Confidence 6533 22 778889999876433
No 31
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=97.31 E-value=0.0011 Score=72.82 Aligned_cols=100 Identities=16% Similarity=0.143 Sum_probs=77.8
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCc-eeeEEEEEecCCcEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGAS-GMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs-~s~eYRfrtKdGswVWVeTsa 357 (630)
+...+.+|+++++|+++..++||.+++++|+.+.++++++.. ......+.+..+.. ....+++..++|... +..+.
T Consensus 275 i~~~d~~g~i~~~N~~~~~l~g~~~~~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 351 (607)
T PRK11360 275 VIAIDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTP--FASPLLDTLEHGTEHVDLEISFPGRDRTIE-LSVST 351 (607)
T ss_pred EEEEcCCCCEEEECHHHHHHhCCChHHhcCCcHHHHcCCchh--HHHHHHHHHhcCCCccceEEEEEcCCCcEE-EEEEE
Confidence 344678999999999999999999999999999888775432 22333444555543 456788999998876 77777
Q ss_pred EEEEe-CCCceEEEEEEEecCchhh
Q psy8265 358 RLVYK-NSKPDFVISTHRPLMEEEG 381 (630)
Q Consensus 358 ~li~~-nGkpe~IVgt~rdISErE~ 381 (630)
.++.+ +|+..+++++.+|||+++.
T Consensus 352 ~~i~~~~g~~~~~i~~~~Dite~~~ 376 (607)
T PRK11360 352 SLLHNTHGEMIGALVIFSDLTERKR 376 (607)
T ss_pred eeEEcCCCCEEEEEEEEeechHHHH
Confidence 77775 7888999999999999653
No 32
>KOG3558|consensus
Probab=97.26 E-value=0.00018 Score=82.15 Aligned_cols=59 Identities=25% Similarity=0.391 Sum_probs=54.6
Q ss_pred ccCcccccccccccCCCCCeEEEeeeecccCCCCccCCCCCCccchhhhhhhccccCHHHHHHhhhccCC
Q psy8265 534 VSNGFSLPTYEVNKSNDCDKLYCHQTLTADQNSKGYSSPFESDIVHQSVYELVHSEDREELQRQLMWNSF 603 (630)
Q Consensus 534 ~~nGF~l~~~~~~~~~~~~~~y~~~~~~~~~~~~~ylg~hqsdv~hqsv~elih~edr~~f~~qlhw~~~ 603 (630)
++.||++++ .+||+.+|.+ ++|-.|||-.|-|+.=-|||++||--|-+||+.||---..
T Consensus 127 sLDGFVm~l-----~~dG~~lYiS------EtVS~yLGLSQvELTG~SvFDfiHP~DheE~~eqL~l~~~ 185 (768)
T KOG3558|consen 127 SLDGFVMAL-----TQDGDFLYIS------ETVSIYLGLSQVELTGSSVFDFIHPCDHEEIAEQLGLRLT 185 (768)
T ss_pred hccceEEEE-----ccCCCEEEEe------chhHhhhCccceeeecchhhhccCccCHHHHHHHhccccC
Confidence 999999997 6899999998 6689999999999999999999999999999999976643
No 33
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.22 E-value=0.0043 Score=54.53 Aligned_cols=93 Identities=11% Similarity=0.090 Sum_probs=63.0
Q ss_pred EeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEE
Q psy8265 280 SKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRL 359 (630)
Q Consensus 280 TRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~l 359 (630)
.-.+.|+++.+.++++.++++..+. .+|+++.++..+.+.+.+.+.++.+. .|+....++.+ .++|. |+..+..+
T Consensus 13 ~~vD~~~~I~~~n~~a~~~f~~~~~-~iGr~l~~~~~~~~~~~l~~~i~~~~-~~~~~~~~~~~-~~~~~--~~~~~~~P 87 (106)
T PF13596_consen 13 IFVDRNLRIRYFNPAAARLFNLSPS-DIGRPLFDIHPPLSYPNLKKIIEQVR-SGKEEEFEIVI-PNGGR--WYLVRYRP 87 (106)
T ss_dssp EEEETTSBEEEE-SCGC-SS---GG-GTTSBCCCSS-HHHHHHHHHHHHHHH-TTSBSEEEEEE-EETTE--EEEEEEEE
T ss_pred EEEcCCCeEEEeChhHhhhcCCChH-HCCCCHHHcCCccchHHHHHHHHHHH-cCCCceEEEEe-cCCCE--EEEEEEEE
Confidence 4458899999999999999998754 47999999988878888888887766 45433333333 35665 55556677
Q ss_pred EEe-CCCceEEEEEEEecC
Q psy8265 360 VYK-NSKPDFVISTHRPLM 377 (630)
Q Consensus 360 i~~-nGkpe~IVgt~rdIS 377 (630)
+++ +|+..+++.+..|||
T Consensus 88 ~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 88 YRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp EE-TTS-EEEEEEEEEE-G
T ss_pred EECCCCCEEEEEEEEEecC
Confidence 775 799999999999986
No 34
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=96.92 E-value=0.003 Score=65.85 Aligned_cols=96 Identities=17% Similarity=0.114 Sum_probs=68.4
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~ 358 (630)
+...+.||+|+++|+++..++||..++++|+.+.++++..+.. .....+.+..++..........++|...|+.....
T Consensus 20 i~~~d~~~~i~~~N~a~~~~~g~~~~~~~g~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 97 (348)
T PRK11073 20 ILLLDDDLAIHYANPAAQQLLAQSSRKLFGTPLPELLSYFSLN--IELMRESLQAGQGFTDNEVTLVIDGRSHILSLTAQ 97 (348)
T ss_pred EEEECCCCeEeeEcHHHHHHhCCCHHHHcCCCHHHHcCcchhh--HHHHHHHHHcCCcccccceEEEECCceEEEEEEEE
Confidence 4456789999999999999999999999999999888754322 12233445555543322223346899999988887
Q ss_pred EEEeCCCceEEEEEEEecCchh
Q psy8265 359 LVYKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 359 li~~nGkpe~IVgt~rdISErE 380 (630)
++. ...++...+|+++++
T Consensus 98 ~~~----~~~~~~~~~dit~~~ 115 (348)
T PRK11073 98 RLP----EGMILLEMAPMDNQR 115 (348)
T ss_pred Ecc----CceeEEEEechhHHH
Confidence 764 245677788998864
No 35
>KOG3561|consensus
Probab=96.78 E-value=0.00024 Score=83.43 Aligned_cols=105 Identities=25% Similarity=0.347 Sum_probs=91.2
Q ss_pred cceeeEEeeccCceeeeeccccccccCCChhhhccCcc-cceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEE
Q psy8265 274 KEVMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGG-YDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQW 352 (630)
Q Consensus 274 ~s~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~-ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVW 352 (630)
+..+|. |++..++|.+++.|+..+.||.+.++.|++- +++.|-+|.+..+..|..++.++....+.||+++|+-.|+|
T Consensus 240 ~~~~~a-Rrsfe~r~r~~~~r~~p~~gy~~~~~~g~~~~~~~~~~~~~~~y~~~h~~g~~~s~~~~c~~~~~t~~~q~~~ 318 (803)
T KOG3561|consen 240 RLCEGA-RRSFECRMRFCDHRAPPIIGYEPFEVLGTSRNYDYYHKDDLPNYRVIHCTGYIKSAGPSCKYRFLTKGQQWIW 318 (803)
T ss_pred cccccc-ccchhhhhhhccccCCccccccceeeccccccccccccCcccceEEEeeeeeEeccCCcceeccccccccccc
Confidence 456676 9999999999999999999999999999885 99999999998888888888778777889999999999999
Q ss_pred EEEEEEEEE--eCCCceEEEEEEEecCch
Q psy8265 353 LQTSSRLVY--KNSKPDFVISTHRPLMEE 379 (630)
Q Consensus 353 VeTsa~li~--~nGkpe~IVgt~rdISEr 379 (630)
++....+-+ .++++.+|+|.+.+++-.
T Consensus 319 ~~~d~~i~~~~~~s~p~~v~~~~~~vs~~ 347 (803)
T KOG3561|consen 319 LPQDDYISYHQWNSKPCLVAIGRLVVSYA 347 (803)
T ss_pred cCccccccccccCCCcceeEecccccchh
Confidence 998876433 278899999999888643
No 36
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.37 E-value=0.024 Score=48.84 Aligned_cols=104 Identities=23% Similarity=0.260 Sum_probs=73.6
Q ss_pred eEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHH-HHHHHHHHHh-cCCceeeEEEEEecCCcE-EEEE
Q psy8265 278 FKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAY-VASAHQELLK-TGASGMIAYRFQTNDGGW-QWLQ 354 (630)
Q Consensus 278 FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~-V~eah~~lLk-kGqs~s~eYRfrtKdGsw-VWVe 354 (630)
.+...+.+|++.++|+++..++|+...+..+.....+.+...... .......... .+......+++..++|.. .|+.
T Consensus 124 ~~~~~d~~~~~~~~n~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 203 (232)
T COG2202 124 GIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYRVRRKDGERVRWIL 203 (232)
T ss_pred eEEEEeCCCCEEEeCHHHHHHhCCChHHhcCCChhheEecCCCchhhHHHHHHhhccCCCCcceEEEEEecCCCEEEEEE
Confidence 344556689999999999999999988888887777766432221 1122222222 223467899999999995 8888
Q ss_pred EEEEEEEeCCCceEEEEEEEecCchhh
Q psy8265 355 TSSRLVYKNSKPDFVISTHRPLMEEEG 381 (630)
Q Consensus 355 Tsa~li~~nGkpe~IVgt~rdISErE~ 381 (630)
.........|....+++...|+++++.
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~d~~~~~~ 230 (232)
T COG2202 204 SRISPVRDDGEIVGVVGIARDITERKQ 230 (232)
T ss_pred eeeeEecCCCceEEEEEEEechHHHhh
Confidence 887765446788888888888887653
No 37
>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=95.94 E-value=0.0027 Score=54.13 Aligned_cols=40 Identities=23% Similarity=0.230 Sum_probs=35.7
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV 215 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l 215 (630)
.+++.+|+|+|+|++..++||++.+| ++|+++++++|+..
T Consensus 15 ~~~d~~g~I~~~N~a~~~l~g~~~~~-----~~g~~~~~~~~~~~ 54 (113)
T PF00989_consen 15 FVIDEDGRILYVNQAAEELLGYSREE-----LIGKSLFDLIHPED 54 (113)
T ss_dssp EEEETTSBEEEECHHHHHHHSS-HHH-----HTTSBGGGGCSGGG
T ss_pred EEEeCcCeEEEECHHHHHHHccCHHH-----HcCCcHHHhcCchh
Confidence 47789999999999999999999999 59999999999874
No 38
>PF12860 PAS_7: PAS fold
Probab=95.93 E-value=0.035 Score=49.36 Aligned_cols=95 Identities=20% Similarity=0.229 Sum_probs=62.6
Q ss_pred EEeeccCceeeeeccccccccCCChhhh-ccCcccceec---------cccH-HHHHHHHHHHHhcCCceeeEEEEEecC
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTEL-ANMGGYDLVH---------YDDL-AYVASAHQELLKTGASGMIAYRFQTND 347 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEEL-lG~S~ydlIH---------PDDl-~~V~eah~~lLkkGqs~s~eYRfrtKd 347 (630)
+...+.|++++++|+++..++|+.++.+ .|.++.+++. +++. ..+.+.+.. +..+ ....+.+...|
T Consensus 8 v~v~D~~~rl~~~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~d 84 (115)
T PF12860_consen 8 VAVFDSDGRLVFWNQRFRELFGLPPEMLRPGASFRDLLRRLAERGEFPPGDPEAWVRQRLAR-LRRR--QPRSFELRLPD 84 (115)
T ss_pred EEEEcCCCeEEeEcHHHHHHhCCCHHHhcCCCCHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HhcC--CCceeEEECCC
Confidence 4556889999999999999999999998 7888666552 2332 233333322 2222 23455667788
Q ss_pred CcEEEEEEEEEEEEeCCCceEEEEEEEecCchhhH
Q psy8265 348 GGWQWLQTSSRLVYKNSKPDFVISTHRPLMEEEGR 382 (630)
Q Consensus 348 GswVWVeTsa~li~~nGkpe~IVgt~rdISErE~~ 382 (630)
|.|+ +....... + .++|.+..|||+++..
T Consensus 85 gr~l--~~~~~~~~-~---Gg~v~~~~DVT~~~~~ 113 (115)
T PF12860_consen 85 GRWL--EVRAQPLP-D---GGFVLTFTDVTERRRA 113 (115)
T ss_pred CEEE--EEEeEECC-C---CCEEEEEEeCCHHHHh
Confidence 8754 55444431 2 3678999999997653
No 39
>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=95.58 E-value=0.086 Score=33.20 Aligned_cols=40 Identities=20% Similarity=0.536 Sum_probs=33.2
Q ss_pred eEEEEEecCCcEEEEEEEEEEEEe-CCCceEEEEEEEecCc
Q psy8265 339 IAYRFQTNDGGWQWLQTSSRLVYK-NSKPDFVISTHRPLME 378 (630)
Q Consensus 339 ~eYRfrtKdGswVWVeTsa~li~~-nGkpe~IVgt~rdISE 378 (630)
..+++..++|.++|+......+.+ ++....++++..||++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~ 42 (43)
T smart00086 2 VEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITE 42 (43)
T ss_pred eEEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccC
Confidence 357788999999999998887765 5777889999999886
No 40
>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=94.48 E-value=0.052 Score=37.46 Aligned_cols=51 Identities=31% Similarity=0.348 Sum_probs=42.9
Q ss_pred EeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHH
Q psy8265 280 SKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQEL 330 (630)
Q Consensus 280 TRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~l 330 (630)
...+.++++.++|+.+..++|+...++.+..+.+++++++...+...+...
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
T smart00091 15 FVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDREEVQEALQRL 65 (67)
T ss_pred EEEcCCCeEEEECHHHHHHhCCCHHHHcCCcHHHhcCcccHHHHHHHHHHH
Confidence 345678899999999999999999999999999999999987776665443
No 41
>KOG3559|consensus
Probab=93.96 E-value=0.036 Score=60.63 Aligned_cols=51 Identities=20% Similarity=0.216 Sum_probs=45.0
Q ss_pred eeeEEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHH
Q psy8265 276 VMFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASA 326 (630)
Q Consensus 276 ~~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~ea 326 (630)
.-|+...+.||+|.|++..+.-.||.+.-||-|.++++||||.|...+..+
T Consensus 89 DGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~ 139 (598)
T KOG3559|consen 89 DGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAV 139 (598)
T ss_pred cceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHH
Confidence 346667899999999999999999999999999999999999998765544
No 42
>KOG0501|consensus
Probab=93.85 E-value=0.17 Score=57.84 Aligned_cols=92 Identities=13% Similarity=0.161 Sum_probs=71.2
Q ss_pred cCceeeeeccccccccCCChhhhccCc-ccceeccc--c---HHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEE
Q psy8265 284 LDLSLVSMDQRGKMLLGYSDTELANMG-GYDLVHYD--D---LAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 284 lDGkftyVDprv~~LLGYspEELlG~S-~ydlIHPD--D---l~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa 357 (630)
.|+-|+|+|..++.+.||...|++.++ .-.|+|.| | ++.+++.++ .-+....+.-+-.|+-..+|+-.+.
T Consensus 38 VD~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~e----N~~~~qfEillyKKN~TPvW~~vqi 113 (971)
T KOG0501|consen 38 VDWPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLE----NYETNQFEILLYKKNRTPVWLLVQI 113 (971)
T ss_pred eccceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHH----hhhhcceeeEeeecCCCceEEEEEe
Confidence 478899999999999999999999887 55777765 3 444444443 3334456667778999999999999
Q ss_pred EEEEe-CCCceEEEEEEEecCch
Q psy8265 358 RLVYK-NSKPDFVISTHRPLMEE 379 (630)
Q Consensus 358 ~li~~-nGkpe~IVgt~rdISEr 379 (630)
.++++ ..++..++|+.+|||--
T Consensus 114 APIrNe~d~VVLfLctFkDIT~~ 136 (971)
T KOG0501|consen 114 APIRNEKDKVVLFLCTFKDITAL 136 (971)
T ss_pred ecccCCCceEEEEEeecccchhh
Confidence 99875 45677889999999953
No 43
>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=93.74 E-value=0.028 Score=46.98 Aligned_cols=41 Identities=22% Similarity=0.250 Sum_probs=34.2
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVS 216 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls 216 (630)
.+++.+|+|+|+|+...+++|++.+|+ +|+++.++.++...
T Consensus 5 ~i~d~~g~i~~~N~~~~~~~g~~~~~~-----~g~~~~~~~~~~~~ 45 (104)
T PF13426_consen 5 FILDPDGRILYVNPAFERLFGYSREEL-----IGKSISDFFPEEDR 45 (104)
T ss_dssp EEEETTSBEEEE-HHHHHHHTS-HHHH-----TTSBGGGGCSTTSC
T ss_pred EEECCcCcEEehhHHHHHHHCcCHHHH-----cCCCcccccCcccc
Confidence 367889999999999999999999984 89999999987643
No 44
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=92.85 E-value=0.3 Score=53.32 Aligned_cols=107 Identities=10% Similarity=0.149 Sum_probs=78.7
Q ss_pred ccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe
Q psy8265 283 KLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK 362 (630)
Q Consensus 283 slDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~ 362 (630)
+.-|+++-+|..+..+||...|+++|+++.+++--+|--. +++++.+..+..... .+ +++.+-++.++.++.+
T Consensus 128 dRrG~iI~iN~~A~k~L~~~~E~~~~~~i~elL~i~d~y~----~~dL~e~~~s~lld~--~~-~~E~~~lrv~Fs~i~r 200 (459)
T COG5002 128 DRRGKIILINKPALKMLGVSKEDALGRSILELLKIEDTYT----FEDLVEKNDSLLLDS--SD-EEEGYVLRVNFSVIQR 200 (459)
T ss_pred cCCCcEEEeccHHHHHhCcCHHHHhcccHHHHhCCcccee----HHHHHhcCCcEEEee--cC-CCccEEEEEEEEEEee
Confidence 4569999999999999999999999999998887665332 345554433333332 23 7888999999998876
Q ss_pred -CCCceEEEEEEEecCchhhHHH-----Hhhhcccccccc
Q psy8265 363 -NSKPDFVISTHRPLMEEEGRDL-----LGKRTMDFKVSY 396 (630)
Q Consensus 363 -nGkpe~IVgt~rdISErE~~E~-----L~~r~~elk~sf 396 (630)
.|-..++|++..|+||++..|. ..+-+.+|+++.
T Consensus 201 EsGfisGlIaVlhDvTEqek~e~ErRefvanvSHElRTPl 240 (459)
T COG5002 201 ESGFISGLIAVLHDVTEQEKVERERREFVANVSHELRTPL 240 (459)
T ss_pred cccccceeEEEEecccHHHHHHHHHHHHHHhcchhhcCch
Confidence 7889999999999999764433 333445665554
No 45
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=92.19 E-value=0.25 Score=53.79 Aligned_cols=91 Identities=13% Similarity=0.098 Sum_probs=59.3
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~ 358 (630)
+...+.+|+|+++|+++..++||..+|++|+++.+++.++|.... +.... .....++..++|.++.+.. .
T Consensus 111 i~~~d~~g~i~~~N~~a~~l~g~~~~~~~g~~~~~~~~~~~~~~~-------~~~~~-~~~~~~~~~~~~~~~~~~~--~ 180 (430)
T PRK11006 111 VVLTTEEGNIFWCNGLAQQLLGFRWPEDNGQNILNLLRYPEFTQY-------LKTRD-FSRPLTLVLNNGRHLEIRV--M 180 (430)
T ss_pred EEEEcCCCceeHHHHHHHHHhCCCChHhCCCcHHHHhcCHHHHHH-------HHhcc-cCCCeEEEcCCCCEEEEEE--E
Confidence 445678999999999999999999999999998888765554321 21111 1223344566777554432 2
Q ss_pred EEEeCCCceEEEEEEEecCchhhHH
Q psy8265 359 LVYKNSKPDFVISTHRPLMEEEGRD 383 (630)
Q Consensus 359 li~~nGkpe~IVgt~rdISErE~~E 383 (630)
.. .++ .++.+.+|||+++..+
T Consensus 181 ~~-~~~---~~~~~~~dit~~~~~e 201 (430)
T PRK11006 181 PY-TEG---QLLMVARDVTQMHQLE 201 (430)
T ss_pred Ec-CCC---cEEEEEehhhHHHHHH
Confidence 22 122 3567789999876433
No 46
>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=91.73 E-value=0.029 Score=46.91 Aligned_cols=38 Identities=16% Similarity=0.040 Sum_probs=24.6
Q ss_pred EEeccccchhhcCCChhhhhhhccccCccccCCCCCCCCC
Q psy8265 179 INYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSPK 218 (630)
Q Consensus 179 IlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~k 218 (630)
|+|+|+++.+++||+++|+ . ..-...+.+++||.+..+
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~-~~~~~~~~~~ihpdD~~~ 38 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-G-KPDFEEWLERIHPDDRER 38 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-T-CBEHHHHHHHB-TTTHHH
T ss_pred CEEEeHHHHHHhCCCHHHh-c-cCCHHHHHhhcCHHHHHH
Confidence 7999999999999999884 0 011223788999986543
No 47
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=91.42 E-value=0.35 Score=55.17 Aligned_cols=91 Identities=13% Similarity=0.079 Sum_probs=61.6
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSR 358 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~ 358 (630)
+.-.+.+|+|+++|+++..++|+..++++|+++.++++..++. +.+.++...... .-...+|..+++.. .
T Consensus 93 Vi~vD~~G~I~~iN~aA~~Llg~~~eel~Gk~i~eli~~~~l~-------~~le~~~~~~~~-~~v~~~g~~~~v~~--~ 162 (520)
T PRK10820 93 VLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFNFL-------RWLESEPQDSHN-EHVVINGQDFLMEI--T 162 (520)
T ss_pred EEEECCCCeeeHhHHHHHHHHCcCHHHHCCCcHHHHcCcchHH-------HHHHcCCCccce-EEEEECCEEEEEEE--E
Confidence 4456889999999999999999999999999999999876543 234444431111 22344677666554 4
Q ss_pred EEE--e-CCCc--eEEEEEEEecCch
Q psy8265 359 LVY--K-NSKP--DFVISTHRPLMEE 379 (630)
Q Consensus 359 li~--~-nGkp--e~IVgt~rdISEr 379 (630)
++. + +|+. .++|.+.+++++.
T Consensus 163 PI~~~d~~g~~~~~GaVivlrd~~~l 188 (520)
T PRK10820 163 PVYLQDENDQHVLVGAVVMLRSTARM 188 (520)
T ss_pred eeeecCCCCceeEEEEEEEeccHHHH
Confidence 444 3 3443 5677777777763
No 48
>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=90.31 E-value=0.94 Score=42.70 Aligned_cols=59 Identities=8% Similarity=0.012 Sum_probs=50.9
Q ss_pred eeEEeeccCceeeeeccccccccCCChhhhccCcccceeccc-cHHHHHHHHHHHHhcCC
Q psy8265 277 MFKSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYD-DLAYVASAHQELLKTGA 335 (630)
Q Consensus 277 ~FiTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPD-Dl~~V~eah~~lLkkGq 335 (630)
.=+.+.+.+|+++.-|..-..+.|+.++.++|++++.=|-|. +...+...+.+..+.|.
T Consensus 27 FGvI~lD~~G~V~~YN~aE~~~sg~~p~~vlGr~FF~eVAPC~~~~~f~gRF~~g~~~g~ 86 (124)
T TIGR02373 27 FGAIQLDGSGVILRYNAAEGRITGRDPERVIGRNFFKEVAPCTDIPEFSGRFMEGVASGT 86 (124)
T ss_pred cceEEECCCCEEEEEecchhhhcCCChhhhhchhhhhhcccccCCHHHHHHHHhhhhcCC
Confidence 336788999999999999999999999999999999888886 56678888888777775
No 49
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=89.38 E-value=1.2 Score=41.72 Aligned_cols=84 Identities=15% Similarity=0.088 Sum_probs=69.9
Q ss_pred ceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEEEEEEe-CC
Q psy8265 286 LSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSSRLVYK-NS 364 (630)
Q Consensus 286 GkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa~li~~-nG 364 (630)
.++..+-.++..++|+ |+.|+.+.+++.+++...+...++.++..+.+.....++...+|.++.++.-.-++.+ +|
T Consensus 51 ~r~RLaGt~i~~~~G~---d~tG~~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~~~~ 127 (137)
T PF07310_consen 51 FRYRLAGTRIVELFGR---DLTGRRLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRSDGG 127 (137)
T ss_pred eEEEEecHHHHHHhCC---CCCCCCHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCCCCC
Confidence 4455677888888888 6779999999999999999999999998888888888999999999888876666655 56
Q ss_pred CceEEEEE
Q psy8265 365 KPDFVIST 372 (630)
Q Consensus 365 kpe~IVgt 372 (630)
.++.|+|.
T Consensus 128 ~v~rilG~ 135 (137)
T PF07310_consen 128 TVDRILGA 135 (137)
T ss_pred CccEEEEe
Confidence 78888885
No 50
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=89.22 E-value=1.4 Score=48.64 Aligned_cols=90 Identities=17% Similarity=0.103 Sum_probs=61.5
Q ss_pred EEeeccCceeeeeccccccccCCC---hhhhccCcccceeccccHHHHHHHHHHHHhcCCce-eeEEEEEecCCcEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYS---DTELANMGGYDLVHYDDLAYVASAHQELLKTGASG-MIAYRFQTNDGGWQWLQ 354 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYs---pEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~-s~eYRfrtKdGswVWVe 354 (630)
+...+.+|+++++|+++..++|+. +++++|..+.++...+.+ .++++.+... ..+.+ .+|.++++.
T Consensus 234 Ii~~D~~g~I~~~N~~a~~llg~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~---~~g~~~~~~ 303 (542)
T PRK11086 234 VIAVDDRGEVTLINDEAKRLFNYKKGLEDDPLGTDVESWMPVSRL-------KEVLRTGTPRRDEEIN---INGRLLLTN 303 (542)
T ss_pred EEEECCCCeEEEEhHHHHHHhCCCcCCcccccCCcHHHhCCchhH-------HHHHhcCCCccceEEE---ECCEEEEEE
Confidence 445688999999999999999765 457778777776654432 3345555542 22232 356555443
Q ss_pred EEEEEEEeCCCceEEEEEEEecCchh
Q psy8265 355 TSSRLVYKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 355 Tsa~li~~nGkpe~IVgt~rdISErE 380 (630)
..++.++|+..++|++.+|+++.+
T Consensus 304 --~~pi~~~g~~~g~v~~~rDite~~ 327 (542)
T PRK11086 304 --TVPVRVNGEIIGAIATFRDKTEVR 327 (542)
T ss_pred --EEEEeECCEEEEEEEEEEEchHHH
Confidence 456666888889999999999864
No 51
>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=87.25 E-value=0.19 Score=45.76 Aligned_cols=47 Identities=15% Similarity=0.091 Sum_probs=36.3
Q ss_pred eeeeccCCCCCCCCCCcc-CCCCcEEeccccchhhcCCC---hhhhhhhccccCccccCCCCC
Q psy8265 156 TVLMWGSNPSRSPPASPI-LPNGHINYPSQEIKKYNGDP---LKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 156 ~~L~~gfll~~~~~~~Vl-s~dGkIlYVSEnVs~~LGys---qeEL~q~~liGqSi~D~vHP~ 214 (630)
.+.-.|+|+ |+ ..+++|+++|+|+..+||.+ .++ ++|+++-++..+.
T Consensus 11 ~IQphG~LL-------a~d~~~~~I~~~S~N~~~~lg~~~~~~~~-----llG~~l~~ll~~~ 61 (110)
T PF08446_consen 11 SIQPHGALL-------ALDPDDLRIVQASENIAELLGIPPELPEE-----LLGRPLSELLGAE 61 (110)
T ss_dssp EE-TTSEEE-------EEETTTTBEEEEETTHHHHHSS----HHH-----HTTCBHHHHSCCC
T ss_pred ccCCCEEEE-------EEECCCCEEEEEcCCHHHHhCCccccchh-----hcccCHHHHhCHH
Confidence 344468888 77 46799999999999999999 777 4899988877543
No 52
>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=87.16 E-value=0.19 Score=42.53 Aligned_cols=39 Identities=28% Similarity=0.403 Sum_probs=34.7
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
.|++.+|+|+|++....+++|++.++ ++|+++.++.++.
T Consensus 9 ~v~D~~~~i~~~N~~~~~~~~~~~~~-----~~G~~~~~~~~~~ 47 (110)
T PF08448_consen 9 FVIDPDGRIVYANQAAAELFGVSPEE-----LIGRSLFDLLPPE 47 (110)
T ss_dssp EEEETTSBEEEE-HHHHHHHTSTHHH-----HTTSBHHHHSCCG
T ss_pred EEECCCCEEEEEHHHHHHHhCCCHHH-----Hhhccchhccccc
Confidence 47799999999999999999999888 5999999988875
No 53
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=84.97 E-value=0.48 Score=34.86 Aligned_cols=41 Identities=17% Similarity=0.167 Sum_probs=35.4
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVS 216 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls 216 (630)
.+++.+|+++++++...+++|++..+ ++|..+++++|+...
T Consensus 6 ~~~d~~~~~~~~n~~~~~~~g~~~~~-----~~~~~~~~~~~~~~~ 46 (103)
T cd00130 6 IVLDLDGRILYANPAAEQLLGYSPEE-----LIGKSLLDLIHPEDR 46 (103)
T ss_pred EEECCCCcEEEECHHHHHHhCCCHHH-----HcCccHHHhcCCccc
Confidence 36689999999999999999999888 479999999888644
No 54
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=82.81 E-value=2.9 Score=48.65 Aligned_cols=92 Identities=12% Similarity=0.084 Sum_probs=59.2
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCcee-eEEEEEecCCcEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGASGM-IAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s-~eYRfrtKdGswVWVeTsa 357 (630)
+.-.+.||+|+++|+++..++|+..++++|+.+.++++... .+.+++.++.... .+..+ ..+|..+|+....
T Consensus 216 Vl~vD~~G~I~~~N~aa~~llg~s~~~l~G~~i~~l~~~~~------~l~~vl~~~~~~~~~~~~l-~~~g~~~~~~v~~ 288 (638)
T PRK11388 216 VIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELLTLPA------VLQQAIKQAHPLKHVEVTF-ESQGQFIDAVITL 288 (638)
T ss_pred EEEECCCCeEehhhHHHHHHhCcCHHHHCCCcHHHHhccch------HHHHHHhcCCceeeEEEEE-ecCCceEEEEEEE
Confidence 34567889999999999999999999999999888774221 1234555665432 22222 3457777888777
Q ss_pred EEEEeCCCceEEEEEEEecCc
Q psy8265 358 RLVYKNSKPDFVISTHRPLME 378 (630)
Q Consensus 358 ~li~~nGkpe~IVgt~rdISE 378 (630)
.++.+ +....++.+.++++.
T Consensus 289 ~Pi~~-~~g~~~v~~l~~~~~ 308 (638)
T PRK11388 289 KPIIE-GQGTSFILLLHPVEQ 308 (638)
T ss_pred Eeecc-cCceEEEEEehhhHH
Confidence 77643 222224444445443
No 55
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=82.78 E-value=1.7 Score=50.06 Aligned_cols=93 Identities=24% Similarity=0.172 Sum_probs=65.0
Q ss_pred EEeeccCceeeeeccccccccCCChhhhccCccccee-ccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLV-HYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTSS 357 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYspEELlG~S~ydlI-HPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTsa 357 (630)
+...|.+|+++++|.+...++|..+++++|+++.+++ -.+| ..+.+++.+|+... -..++..|... +. +.
T Consensus 130 l~vvD~~G~~i~~N~~~~~~~gl~~e~~~gk~~~~v~~~~~~-----s~~l~vl~~~kp~~--~~~~~~~~~~~-i~-~~ 200 (560)
T COG3829 130 LLVVDEDGIIIYYNKAYAKLLGLSPEEVLGKHLLDVVSAGED-----STLLEVLRTGKPIR--DVVQTYNGNKI-IV-NV 200 (560)
T ss_pred eEEEcCCCcEEEEcHHHHHHhCCCHHHHcCCcHHHHHhccCC-----ceehhhhhcCCcce--eeeeeecCCce-eE-ee
Confidence 5567889999999999999999999999999877765 1111 22345566666532 33444555444 33 33
Q ss_pred EEEEeCCCceEEEEEEEecCchh
Q psy8265 358 RLVYKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 358 ~li~~nGkpe~IVgt~rdISErE 380 (630)
.+++.+|...+.|.+.+++++.+
T Consensus 201 ~pv~~~g~l~G~v~~~~~~~~l~ 223 (560)
T COG3829 201 APVYADGQLIGVVGISKDVSELE 223 (560)
T ss_pred ccEecCCcEEEEEEeecchHHHH
Confidence 34556888899999999999854
No 56
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=82.02 E-value=8.2 Score=37.51 Aligned_cols=87 Identities=13% Similarity=0.038 Sum_probs=63.4
Q ss_pred ccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCc-eeeEEEEEecCCcEEEEEE--EEEE
Q psy8265 283 KLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGAS-GMIAYRFQTNDGGWQWLQT--SSRL 359 (630)
Q Consensus 283 slDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs-~s~eYRfrtKdGswVWVeT--sa~l 359 (630)
..|=.|+|.|.++..+++++-+||++.+..--.-+.++....+.+.++.+.|-. ...-.|+ .+.|+-+|++- .|++
T Consensus 50 ~~dP~f~yaN~aaL~l~e~~w~el~~lPsr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRi-ss~Grrf~ie~a~vW~l 128 (148)
T PF08670_consen 50 KADPIFIYANQAALDLFETTWDELVGLPSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRI-SSTGRRFRIERATVWNL 128 (148)
T ss_pred CCCCEEEehhHHHHHHhcCCHHHHhcCcHhhccChhhHHHHHHHHHHHHHhCCccCCCeEEE-cCCCCeEEEeceEEEEE
Confidence 356679999999999999999999999877666677777777888888888864 2344565 67788888763 3444
Q ss_pred EEeCCCceEEE
Q psy8265 360 VYKNSKPDFVI 370 (630)
Q Consensus 360 i~~nGkpe~IV 370 (630)
+-.+|...+.-
T Consensus 129 ~D~~g~~~GqA 139 (148)
T PF08670_consen 129 IDEDGNYCGQA 139 (148)
T ss_pred EcCCCCEEEEE
Confidence 42356654443
No 57
>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=75.82 E-value=1.6 Score=34.00 Aligned_cols=40 Identities=23% Similarity=0.206 Sum_probs=34.0
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV 215 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l 215 (630)
.+++.+|+|+|+++...+++|++..+ ++|.++.++.++..
T Consensus 17 ~~~d~~~~i~~~n~~~~~~~g~~~~~-----~~~~~~~~~~~~~~ 56 (124)
T TIGR00229 17 IVIDLEGNILYVNPAFEEIFGYSAEE-----LIGRNVLELIPEED 56 (124)
T ss_pred EEEcCCCcEEEEchHHHHHhCCChHH-----hcCcchhhhcChhh
Confidence 46789999999999999999998877 47988888777653
No 58
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=73.92 E-value=9.5 Score=44.72 Aligned_cols=92 Identities=8% Similarity=0.055 Sum_probs=59.1
Q ss_pred eccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHHHHHHHhcCCc-eeeEEEEEecCCcEEEEEEEEEEE
Q psy8265 282 HKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASAHQELLKTGAS-GMIAYRFQTNDGGWQWLQTSSRLV 360 (630)
Q Consensus 282 hslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs-~s~eYRfrtKdGswVWVeTsa~li 360 (630)
.+-+|++.-+|+++..+||....+++|+++..+ .+.+.+.+.+.-..+.. ...+..+ .+.|+..-+..+++..
T Consensus 386 ~d~~g~i~t~N~~ae~~l~~~~~~~~G~~lsa~-----ap~~~~vf~~~~a~~~~~~~~ev~~-~r~g~~rtl~Vq~t~~ 459 (712)
T COG5000 386 FDNRGCITTVNPSAEQILGKPFDQLLGQSLSAI-----APELEEVFAEAGAAARTDKRVEVKL-AREGEERTLNVQATRE 459 (712)
T ss_pred EcCCCeeEeecchHHHHhcCChhHhhcchhhhh-----hhHHHHHHHHhhhhcCCCccceeec-ccCCCceeeeeeeeec
Confidence 466899999999999999999999999985543 23344444433222222 2223333 4456666677766654
Q ss_pred EeCCCceEEEEEEEecCchh
Q psy8265 361 YKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 361 ~~nGkpe~IVgt~rdISErE 380 (630)
..+ ...+.|.+..|||+.-
T Consensus 460 ~~d-~~~gyVvt~DDITdLV 478 (712)
T COG5000 460 PED-NGNGYVVTFDDITDLV 478 (712)
T ss_pred ccc-cCCceEEEecchHHHH
Confidence 322 3446788899999854
No 59
>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=70.91 E-value=14 Score=34.44 Aligned_cols=48 Identities=23% Similarity=0.302 Sum_probs=36.2
Q ss_pred eeeEEEEEecCCcEEEEEEEEEEEEe-CCCceEEEEEEEecCchh-hHHHHh
Q psy8265 337 GMIAYRFQTNDGGWQWLQTSSRLVYK-NSKPDFVISTHRPLMEEE-GRDLLG 386 (630)
Q Consensus 337 ~s~eYRfrtKdGswVWVeTsa~li~~-nGkpe~IVgt~rdISErE-~~E~L~ 386 (630)
....|+-++++|+ -+.++...+++ +|++.+++|+|.|+|..+ ..+.|.
T Consensus 68 ~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~~~~L~ 117 (118)
T PF08348_consen 68 YIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQAQNFLD 117 (118)
T ss_pred ccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHHHHHHc
Confidence 5678999999996 45666666665 688999999999999865 344443
No 60
>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=70.76 E-value=1.9 Score=43.71 Aligned_cols=39 Identities=10% Similarity=0.088 Sum_probs=34.7
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
.+++.+|+|+|+++.+.+++|++.+| ++|+.+.+++++.
T Consensus 20 ~~~d~~g~i~~~N~~~~~~~g~~~~~-----~~g~~~~~~~~~~ 58 (333)
T TIGR02966 20 VVLDEEGQIEWCNPAAERLLGLRWPD-----DLGQRITNLIRHP 58 (333)
T ss_pred EEECCCCcEEEEcHHHHHHhCCChHH-----HcCCcHHHHccCH
Confidence 57799999999999999999999888 5899998888764
No 61
>KOG1229|consensus
Probab=65.56 E-value=2.4 Score=47.49 Aligned_cols=68 Identities=16% Similarity=0.133 Sum_probs=53.2
Q ss_pred eccCceeeeeccccccccCCChhhhccCcccceeccc-cHHHHHHHHHHHHhcCCceeeEEEEEecCCc
Q psy8265 282 HKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYD-DLAYVASAHQELLKTGASGMIAYRFQTNDGG 349 (630)
Q Consensus 282 hslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPD-Dl~~V~eah~~lLkkGqs~s~eYRfrtKdGs 349 (630)
.+-|-.+.||||+...++||...||+|+...++--.+ .+..+...+...+++|.....++.-++|.|.
T Consensus 173 ~~ddhViQYVNpAfE~mmG~hkgEliGke~adlpkkdknradlldtintcikkgke~qG~~~aRRksgd 241 (775)
T KOG1229|consen 173 CDDDHVIQYVNPAFENMMGCHKGELIGKEEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEARRKSGD 241 (775)
T ss_pred ccchhHHHHhcHHHHhhhcchhhhhcCCchhhccccccchhhhhhhhhHhhhcCccccchHHHhhccCC
Confidence 3556778899999999999999999999888775544 4567777788888888776666666677664
No 62
>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=65.03 E-value=3.2 Score=28.12 Aligned_cols=39 Identities=21% Similarity=0.241 Sum_probs=31.9
Q ss_pred ccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC
Q psy8265 172 PILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV 215 (630)
Q Consensus 172 Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l 215 (630)
+++.+|+++++++...+++|+...++ +|.++.++.++..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~ 54 (67)
T smart00091 16 VLDLDGRILYANPAAEELLGYSPEEL-----IGKSLLELIHPED 54 (67)
T ss_pred EEcCCCeEEEECHHHHHHhCCCHHHH-----cCCcHHHhcCccc
Confidence 55789999999999999999987773 6877777777653
No 63
>PRK13557 histidine kinase; Provisional
Probab=64.40 E-value=3.4 Score=45.42 Aligned_cols=36 Identities=19% Similarity=0.297 Sum_probs=32.3
Q ss_pred CCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC
Q psy8265 175 PNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV 215 (630)
Q Consensus 175 ~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l 215 (630)
.+|.|+|+|+...+++||+.+| ++|+++.+++||..
T Consensus 51 ~~g~i~~~N~a~~~~~G~~~~e-----~~g~~~~~l~~~~~ 86 (540)
T PRK13557 51 PDNPIVFANRAFLEMTGYAAEE-----IIGNNCRFLQGPET 86 (540)
T ss_pred CCCCEEEEcHHHHHHhCCCHHH-----hcCCChHhhcCCCC
Confidence 4899999999999999999999 48999999988854
No 64
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=64.19 E-value=10 Score=43.74 Aligned_cols=87 Identities=21% Similarity=0.166 Sum_probs=63.7
Q ss_pred eeccCceeeeeccccccccCCChh--hhccCcccceeccc-cHHHHHHHHHHHHhcCCc-eeeEEEEEecCCcEEEEEEE
Q psy8265 281 KHKLDLSLVSMDQRGKMLLGYSDT--ELANMGGYDLVHYD-DLAYVASAHQELLKTGAS-GMIAYRFQTNDGGWQWLQTS 356 (630)
Q Consensus 281 RhslDGkftyVDprv~~LLGYspE--ELlG~S~ydlIHPD-Dl~~V~eah~~lLkkGqs-~s~eYRfrtKdGswVWVeTs 356 (630)
-.+..|+++.+|.+++.++|+... +++|+++.+.+-|+ |+..+ ++.|+. ..-+.|+ +|. |+-.+
T Consensus 230 Avd~~G~It~~N~~A~~ll~~~~~~~~~ig~~i~~v~~p~~~l~~v-------l~~~~~~~~~e~~~---ng~--~~i~n 297 (537)
T COG3290 230 AVDKKGVITLINQAAQKLLGLRQPSGDPIGRSIVEVLPPDSDLPEV-------LETGKPQHDEEIRI---NGR--LLVAN 297 (537)
T ss_pred EECCCCeEeehhHHHHHHhcccCcCcccccccceEeeccccCcHHH-------HhcCCcccchhhhc---CCe--EEEEE
Confidence 346779999999999999999865 79999999999873 45544 445554 2233443 454 44455
Q ss_pred EEEEEeCCCceEEEEEEEecCch
Q psy8265 357 SRLVYKNSKPDFVISTHRPLMEE 379 (630)
Q Consensus 357 a~li~~nGkpe~IVgt~rdISEr 379 (630)
-.+++.+++..+.|.+.||-+|.
T Consensus 298 r~pI~~~~~~~GaI~tFRdktei 320 (537)
T COG3290 298 RVPIRSGGQIVGAIITFRDKTEI 320 (537)
T ss_pred eccEEECCEEeEEEEEEecHHHH
Confidence 55666788999999999998885
No 65
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=64.16 E-value=4.3 Score=35.44 Aligned_cols=37 Identities=19% Similarity=0.178 Sum_probs=27.2
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPP 213 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP 213 (630)
.+++.+++|.|.|+.+.++++..+.+ +|++|.++.++
T Consensus 13 ~~vD~~~~I~~~n~~a~~~f~~~~~~------iGr~l~~~~~~ 49 (106)
T PF13596_consen 13 IFVDRNLRIRYFNPAAARLFNLSPSD------IGRPLFDIHPP 49 (106)
T ss_dssp EEEETTSBEEEE-SCGC-SS---GGG------TTSBCCCSS-H
T ss_pred EEEcCCCeEEEeChhHhhhcCCChHH------CCCCHHHcCCc
Confidence 47899999999999999999987655 79999988765
No 66
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=64.13 E-value=17 Score=40.61 Aligned_cols=90 Identities=11% Similarity=0.045 Sum_probs=57.4
Q ss_pred EEeeccCceeeeeccccccccCCCh--hhhccCcccceeccccHHHHHHHHHHHHhcCCceeeEEEEEecCCcEEEEEEE
Q psy8265 279 KSKHKLDLSLVSMDQRGKMLLGYSD--TELANMGGYDLVHYDDLAYVASAHQELLKTGASGMIAYRFQTNDGGWQWLQTS 356 (630)
Q Consensus 279 iTRhslDGkftyVDprv~~LLGYsp--EELlG~S~ydlIHPDDl~~V~eah~~lLkkGqs~s~eYRfrtKdGswVWVeTs 356 (630)
+.-.+.+|+++++|+++..++|+.. ++++|+.+.+++++.+... ...... ....... .+|. . +...
T Consensus 235 ii~~D~~g~I~~~N~~a~~ll~~~~~~~~~~g~~~~~~~~~~~~~~------~~~~~~-~~~~~~~---~~~~-~-~~~~ 302 (545)
T PRK15053 235 LIAVDPHGYITAINRNARKMLGLSSPGRQWLGKPIAEVVRPADFFT------EQIDEK-RQDVVAN---FNGL-S-VIAN 302 (545)
T ss_pred EEEECCCCeEEeecHHHHHHhCCCCcchhhcCCcHHHhCCCchhhh------hhcCCc-ccceEEE---ECCE-E-EEEE
Confidence 4456889999999999999999965 5799999888876543211 111111 1111122 2442 2 2334
Q ss_pred EEEEEeCCCceEEEEEEEecCchh
Q psy8265 357 SRLVYKNSKPDFVISTHRPLMEEE 380 (630)
Q Consensus 357 a~li~~nGkpe~IVgt~rdISErE 380 (630)
..++..+++..++|.+.+|++|..
T Consensus 303 ~~~i~~~~~~~G~v~~~~d~te~~ 326 (545)
T PRK15053 303 REAIRSGDDLLGAIISFRSKDEIS 326 (545)
T ss_pred eeeEEECCeEEEEEEEEEchHHHH
Confidence 445556677778888999999853
No 67
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=63.24 E-value=2.4 Score=44.23 Aligned_cols=39 Identities=8% Similarity=-0.012 Sum_probs=33.9
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
.|++.+|+|++++....+++|++.++ ++|..+.+..++.
T Consensus 21 ~~~d~~~~i~~~N~a~~~~~g~~~~~-----~~g~~~~~~~~~~ 59 (348)
T PRK11073 21 LLLDDDLAIHYANPAAQQLLAQSSRK-----LFGTPLPELLSYF 59 (348)
T ss_pred EEECCCCeEeeEcHHHHHHhCCCHHH-----HcCCCHHHHcCcc
Confidence 57899999999999999999999888 4799888887653
No 68
>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=63.05 E-value=4.8 Score=36.59 Aligned_cols=43 Identities=23% Similarity=0.199 Sum_probs=37.1
Q ss_pred cCceeeeeccccccccCCC---hhhhccCcccceeccccHHHHHHH
Q psy8265 284 LDLSLVSMDQRGKMLLGYS---DTELANMGGYDLVHYDDLAYVASA 326 (630)
Q Consensus 284 lDGkftyVDprv~~LLGYs---pEELlG~S~ydlIHPDDl~~V~ea 326 (630)
.|++|+.++..+..+||.. +++++|+++.+++-++....+++.
T Consensus 24 ~~~~I~~~S~N~~~~lg~~~~~~~~llG~~l~~ll~~~~~~~l~~~ 69 (110)
T PF08446_consen 24 DDLRIVQASENIAELLGIPPELPEELLGRPLSELLGAESAERLREA 69 (110)
T ss_dssp TTTBEEEEETTHHHHHSS----HHHHTTCBHHHHSCCCCHHHHHHH
T ss_pred CCCEEEEEcCCHHHHhCCccccchhhcccCHHHHhCHHHHHHHHHh
Confidence 4799999999999999999 999999999999988877766654
No 69
>PRK10060 RNase II stability modulator; Provisional
Probab=58.17 E-value=3.9 Score=47.85 Aligned_cols=43 Identities=16% Similarity=0.189 Sum_probs=35.5
Q ss_pred CCCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCC
Q psy8265 166 RSPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPP 213 (630)
Q Consensus 166 ~~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP 213 (630)
..++. .+++.+|+|+|+++...+++||+.+| ++|++++++.++
T Consensus 119 ~~~~gI~i~D~~g~I~~~N~a~~~l~Gy~~~e-----liG~~~~~l~~~ 162 (663)
T PRK10060 119 EANSVIVILDSRGNIQRFNRLCEEYTGLKEHD-----VIGQSVFKLFMS 162 (663)
T ss_pred hCCceEEEEeCCCCEEEEcHHHHHHHCcCHHH-----HcCCCHHHHhCC
Confidence 34443 46789999999999999999999999 489999887643
No 70
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=50.45 E-value=7.2 Score=30.81 Aligned_cols=28 Identities=18% Similarity=0.113 Sum_probs=20.1
Q ss_pred eeccCceeeeeccccccccCCChhhhccCccc
Q psy8265 281 KHKLDLSLVSMDQRGKMLLGYSDTELANMGGY 312 (630)
Q Consensus 281 RhslDGkftyVDprv~~LLGYspEELlG~S~y 312 (630)
..+ +++++++|+++..++||. +.|+.+.
T Consensus 16 i~d-~~~i~~~N~~~~~l~g~~---~~~~~~~ 43 (64)
T PF13188_consen 16 IID-GGRIIYVNPAFEELFGYS---LEGEDIG 43 (64)
T ss_dssp EEE-TSBEEEE-HHHHHHHCS----HTCCCHH
T ss_pred EEE-CCChHHhhHHHHHHhCCC---CCCCCHH
Confidence 345 779999999999999998 5555444
No 71
>KOG3753|consensus
Probab=48.33 E-value=12 Score=45.28 Aligned_cols=51 Identities=18% Similarity=0.197 Sum_probs=42.6
Q ss_pred eeeEEe-eccCceeeeeccccccccCCChhhhccCcccceeccccHHHHHHH
Q psy8265 276 VMFKSK-HKLDLSLVSMDQRGKMLLGYSDTELANMGGYDLVHYDDLAYVASA 326 (630)
Q Consensus 276 ~~FiTR-hslDGkftyVDprv~~LLGYspEELlG~S~ydlIHPDDl~~V~ea 326 (630)
..|+.- -.+||+++|+.+.+..++||..+-+.+..+-||+||.|+......
T Consensus 191 DsF~~~vS~~dG~iLyis~q~a~ilg~krDv~s~a~FvdflapqD~~vF~sf 242 (1114)
T KOG3753|consen 191 DSFVVAVSFLDGRILYISEQAALILGCKRDVLSSAKFVDFLAPQDVGVFYSF 242 (1114)
T ss_pred cceEEEEeccCCcEEEeechhhhhccCchhhhccchhhhhcchhhhhhhhhc
Confidence 444433 356899999999999999999999999999999999998765543
No 72
>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=47.14 E-value=25 Score=33.32 Aligned_cols=41 Identities=22% Similarity=0.237 Sum_probs=36.8
Q ss_pred ccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCCCC
Q psy8265 172 PILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVVSP 217 (630)
Q Consensus 172 Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ls~ 217 (630)
-++.+|+|+.-+..=+.+-|++++. ++|+++|..+=||-..
T Consensus 31 ~lD~~G~V~~YN~aE~~~sg~~p~~-----vlGr~FF~eVAPC~~~ 71 (124)
T TIGR02373 31 QLDGSGVILRYNAAEGRITGRDPER-----VIGRNFFKEVAPCTDI 71 (124)
T ss_pred EECCCCEEEEEecchhhhcCCChhh-----hhchhhhhhcccccCC
Confidence 4599999999999999999999988 6999999999998543
No 73
>PRK13559 hypothetical protein; Provisional
Probab=46.24 E-value=8.3 Score=40.62 Aligned_cols=34 Identities=15% Similarity=0.091 Sum_probs=29.2
Q ss_pred CCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 176 NGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 176 dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
+|.|+|+++...+++|++.+| ++|+++.++.++.
T Consensus 65 ~g~i~~~N~a~~~l~G~~~~e-----~iG~~~~~l~~~~ 98 (361)
T PRK13559 65 DLPIVLANQAFLDLTGYAAEE-----VVGRNCRFLQGAA 98 (361)
T ss_pred CCcEEEEchHHHHHhCCCHHH-----HcCCChhhhcCCC
Confidence 678999999999999999888 4899887776654
No 74
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=45.67 E-value=7.4 Score=45.95 Aligned_cols=46 Identities=17% Similarity=0.125 Sum_probs=38.3
Q ss_pred CCCCCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 164 PSRSPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 164 l~~~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
++..++. .+++.+|+|+++++...+++|++.+| ++|+++.++.++.
T Consensus 161 l~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~~~e-----liG~~~~~l~~~~ 207 (779)
T PRK11091 161 LDASPDLVYYRNEDGEFSGCNRAMELLTGKSEKQ-----LIGLTPKDVYSPE 207 (779)
T ss_pred HhcCcceEEEECCCCcEEeEcHHHHHHhCcCHHH-----HcCCChHHhCCHH
Confidence 3344454 47799999999999999999999888 4899999998875
No 75
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=42.57 E-value=90 Score=38.93 Aligned_cols=26 Identities=4% Similarity=-0.127 Sum_probs=21.4
Q ss_pred EeeccCceeeeeccccccccCCChhh
Q psy8265 280 SKHKLDLSLVSMDQRGKMLLGYSDTE 305 (630)
Q Consensus 280 TRhslDGkftyVDprv~~LLGYspEE 305 (630)
...+.+|+++++|+++..++|+...+
T Consensus 590 ~~~d~~g~i~~~N~~~~~~~g~~~~~ 615 (1197)
T PRK09959 590 YVVNWQGNVISHNSAFEHYFTADYYK 615 (1197)
T ss_pred EEEcCCCcEEEehHHHHHHhCccccc
Confidence 34678999999999999999976433
No 76
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=40.71 E-value=8.5 Score=41.93 Aligned_cols=41 Identities=17% Similarity=0.051 Sum_probs=33.4
Q ss_pred CCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCC
Q psy8265 167 SPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESP 212 (630)
Q Consensus 167 ~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vH 212 (630)
.++. .+++.+|+|+|+++.+.+++|++.+|+ +|+++.+...
T Consensus 107 ~~~~i~~~d~~g~i~~~N~~a~~l~g~~~~~~-----~g~~~~~~~~ 148 (430)
T PRK11006 107 LPDAVVLTTEEGNIFWCNGLAQQLLGFRWPED-----NGQNILNLLR 148 (430)
T ss_pred CCCeEEEEcCCCceeHHHHHHHHHhCCCChHh-----CCCcHHHHhc
Confidence 3444 467999999999999999999998884 7988876653
No 77
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=36.72 E-value=8 Score=30.54 Aligned_cols=21 Identities=24% Similarity=0.278 Sum_probs=17.3
Q ss_pred ccCCCCcEEeccccchhhcCCC
Q psy8265 172 PILPNGHINYPSQEIKKYNGDP 193 (630)
Q Consensus 172 Vls~dGkIlYVSEnVs~~LGys 193 (630)
|++ +|+|+++++...+++||+
T Consensus 16 i~d-~~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 16 IID-GGRIIYVNPAFEELFGYS 36 (64)
T ss_dssp EEE-TSBEEEE-HHHHHHHCS-
T ss_pred EEE-CCChHHhhHHHHHHhCCC
Confidence 567 789999999999999987
No 78
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=34.15 E-value=12 Score=42.77 Aligned_cols=39 Identities=8% Similarity=-0.021 Sum_probs=34.3
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
.+++.+|+|+++++...++||++.++ ++|+++.++++..
T Consensus 94 i~vD~~G~I~~iN~aA~~Llg~~~ee-----l~Gk~i~eli~~~ 132 (520)
T PRK10820 94 LSIDMKGKVELANPASCQLFGQSEEK-----LRNHTAAQLINGF 132 (520)
T ss_pred EEECCCCeeeHhHHHHHHHHCcCHHH-----HCCCcHHHHcCcc
Confidence 46799999999999999999998877 5899999888753
No 79
>PF12860 PAS_7: PAS fold
Probab=32.35 E-value=14 Score=32.67 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=31.8
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESP 212 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vH 212 (630)
.|.+.+|+++|+++...+++|++.+.+ ..|.++-+++.
T Consensus 9 ~v~D~~~rl~~~N~~~~~l~~~~~~~~----~~G~~~~~l~~ 46 (115)
T PF12860_consen 9 AVFDSDGRLVFWNQRFRELFGLPPEML----RPGASFRDLLR 46 (115)
T ss_pred EEEcCCCeEEeEcHHHHHHhCCCHHHh----cCCCCHHHHHH
Confidence 578999999999999999999988775 37887766653
No 80
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=27.08 E-value=28 Score=38.44 Aligned_cols=44 Identities=16% Similarity=0.123 Sum_probs=35.8
Q ss_pred CCCCC-CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCC
Q psy8265 166 RSPPA-SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPV 214 (630)
Q Consensus 166 ~~~~~-~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~ 214 (630)
..+++ .+++.+|+|+++++...+++|++.++ ++|+.+.++.++.
T Consensus 270 ~~~~~i~~~d~~g~i~~~N~~~~~l~g~~~~~-----~~g~~~~~~~~~~ 314 (607)
T PRK11360 270 SIADGVIAIDRQGKITTMNPAAEVITGLQRHE-----LVGKPYSELFPPN 314 (607)
T ss_pred hccCeEEEEcCCCCEEEECHHHHHHhCCChHH-----hcCCcHHHHcCCc
Confidence 33443 46799999999999999999999877 4899888887653
No 81
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.47 E-value=39 Score=39.19 Aligned_cols=36 Identities=14% Similarity=0.208 Sum_probs=31.7
Q ss_pred CCCcEEeccccchhhcCCChhhhhhhccccCccccCCCCCC
Q psy8265 175 PNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESPPVV 215 (630)
Q Consensus 175 ~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vHP~l 215 (630)
.+|.|+|+|+...+++|++.+|+ +|+++.++.|+..
T Consensus 169 ~dg~i~~~N~~~~~l~G~~~eel-----~g~~~~~l~~~~~ 204 (665)
T PRK13558 169 PDEPLIYINDAFERITGYSPDEV-----LGRNCRFLQGEDT 204 (665)
T ss_pred CCCcEEEEcHHHHHHhCcCHHHH-----cCCCHHHhcCCCc
Confidence 58999999999999999999984 8999888887754
No 82
>PF06531 DUF1108: Protein of unknown function (DUF1108); InterPro: IPR009494 This entry is represented by Bacteriophage 92, Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.
Probab=23.69 E-value=32 Score=30.54 Aligned_cols=20 Identities=30% Similarity=0.803 Sum_probs=16.8
Q ss_pred Cccchhhhhhhcc--ccCHHHH
Q psy8265 575 SDIVHQSVYELVH--SEDREEL 594 (630)
Q Consensus 575 sdv~hqsv~elih--~edr~~f 594 (630)
.|+|+|+|||.|- |||+.-+
T Consensus 58 ~d~i~~aiyewIE~nTDE~Drl 79 (86)
T PF06531_consen 58 MDIINQAIYEWIEENTDEQDRL 79 (86)
T ss_pred HHHHHHHHHHHHHhCcchHHHH
Confidence 7999999999996 7777654
No 83
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=22.95 E-value=26 Score=40.88 Aligned_cols=37 Identities=5% Similarity=-0.004 Sum_probs=32.3
Q ss_pred CccCCCCcEEeccccchhhcCCChhhhhhhccccCccccCCC
Q psy8265 171 SPILPNGHINYPSQEIKKYNGDPLKSLAEMNTIGENKWKESP 212 (630)
Q Consensus 171 ~Vls~dGkIlYVSEnVs~~LGysqeEL~q~~liGqSi~D~vH 212 (630)
.+++.+|+|+++++...++||.+.++ ++|+.+.++.+
T Consensus 217 l~vD~~G~I~~~N~aa~~llg~s~~~-----l~G~~i~~l~~ 253 (638)
T PRK11388 217 IAWDEQGNLQFLNAQAARLLRLDATA-----SQGRAITELLT 253 (638)
T ss_pred EEECCCCeEehhhHHHHHHhCcCHHH-----HCCCcHHHHhc
Confidence 57899999999999999999998777 58998877764
Done!