Query psy8476
Match_columns 421
No_of_seqs 161 out of 2245
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 19:49:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK15429 formate hydrogenlyase 99.9 6.9E-26 1.5E-30 244.5 27.1 294 38-390 7-357 (686)
2 KOG3689|consensus 99.8 1.3E-21 2.8E-26 203.6 6.8 303 52-408 3-364 (707)
3 TIGR01817 nifA Nif-specific re 99.7 3.7E-16 8E-21 164.5 22.4 61 324-385 107-167 (534)
4 PRK15429 formate hydrogenlyase 99.7 5.4E-16 1.2E-20 167.8 20.4 176 2-230 140-322 (686)
5 PRK11061 fused phosphoenolpyru 99.7 5.7E-16 1.2E-20 167.5 18.6 60 324-385 106-165 (748)
6 PRK05022 anaerobic nitric oxid 99.4 1.4E-11 3E-16 129.0 22.7 121 289-412 73-202 (509)
7 PF01590 GAF: GAF domain; Int 99.4 1.3E-12 2.8E-17 113.5 8.4 131 243-374 7-154 (154)
8 PF13492 GAF_3: GAF domain; PD 99.3 2.1E-11 4.5E-16 102.6 11.5 118 245-376 9-129 (129)
9 smart00065 GAF Domain present 99.3 1E-10 2.2E-15 98.0 13.8 137 242-383 6-148 (149)
10 COG3605 PtsP Signal transducti 99.3 8.5E-12 1.8E-16 126.1 7.6 137 240-381 20-161 (756)
11 PF13185 GAF_2: GAF domain; PD 99.2 2.4E-10 5.2E-15 98.4 11.0 127 241-375 3-148 (148)
12 COG3605 PtsP Signal transducti 99.1 2.6E-10 5.7E-15 115.5 8.9 133 40-230 3-135 (756)
13 KOG3689|consensus 99.0 1.9E-10 4.1E-15 120.8 5.3 181 2-229 129-309 (707)
14 COG1956 GAF domain-containing 99.0 6.2E-09 1.3E-13 89.8 11.4 110 255-374 51-160 (163)
15 PF01590 GAF: GAF domain; Int 98.9 4.5E-09 9.7E-14 91.1 8.6 122 55-230 1-135 (154)
16 PF13492 GAF_3: GAF domain; PD 98.7 1.3E-07 2.9E-12 79.2 10.8 108 55-230 1-108 (129)
17 COG3604 FhlA Transcriptional r 98.7 1.5E-06 3.2E-11 88.0 18.4 63 324-388 140-202 (550)
18 COG2203 FhlA FOG: GAF domain [ 98.7 8.8E-08 1.9E-12 82.9 8.7 95 288-385 79-173 (175)
19 COG1956 GAF domain-containing 98.6 7.3E-07 1.6E-11 77.1 12.9 63 161-231 80-142 (163)
20 TIGR02916 PEP_his_kin putative 98.6 1E-05 2.3E-10 88.0 23.3 62 325-387 409-470 (679)
21 PF13185 GAF_2: GAF domain; PD 98.6 5.1E-07 1.1E-11 77.5 10.4 125 55-230 3-128 (148)
22 smart00065 GAF Domain present 98.4 5.9E-06 1.3E-10 68.7 13.1 117 55-230 1-120 (149)
23 PRK13558 bacterio-opsin activa 98.3 4.2E-05 9.1E-10 83.0 18.3 170 200-380 236-441 (665)
24 PRK10490 sensor protein KdpD; 98.0 0.00068 1.5E-08 76.1 22.4 59 326-385 595-653 (895)
25 COG2205 KdpD Osmosensitive K+ 97.8 0.0022 4.7E-08 69.0 19.5 75 326-402 592-669 (890)
26 COG2203 FhlA FOG: GAF domain [ 97.3 0.001 2.2E-08 57.1 8.0 137 39-229 3-141 (175)
27 PRK13558 bacterio-opsin activa 97.1 0.015 3.2E-07 63.1 16.0 126 41-230 289-416 (665)
28 PRK13837 two-component VirA-li 96.9 0.18 3.9E-06 56.3 23.0 67 324-391 376-442 (828)
29 TIGR02851 spore_V_T stage V sp 96.8 0.03 6.6E-07 50.5 12.7 107 259-373 72-178 (180)
30 PRK05022 anaerobic nitric oxid 96.8 0.0033 7.1E-08 66.2 7.4 133 39-230 3-137 (509)
31 PF11849 DUF3369: Domain of un 96.3 0.78 1.7E-05 41.1 18.7 58 22-80 4-61 (174)
32 PRK10600 nitrate/nitrite senso 96.0 1.3 2.9E-05 47.1 21.9 54 32-86 212-265 (569)
33 PRK11061 fused phosphoenolpyru 96.0 0.009 1.9E-07 65.6 5.3 77 236-312 12-97 (748)
34 PRK04158 transcriptional repre 95.0 0.35 7.5E-06 45.7 11.6 60 322-384 106-165 (256)
35 PRK11388 DNA-binding transcrip 94.8 0.4 8.7E-06 52.0 13.0 115 258-385 73-200 (638)
36 TIGR01817 nifA Nif-specific re 94.1 0.076 1.7E-06 56.3 5.5 77 235-311 13-97 (534)
37 PF04340 DUF484: Protein of un 93.6 0.4 8.6E-06 44.9 8.8 46 40-86 78-123 (225)
38 COG3604 FhlA Transcriptional r 93.4 0.18 3.9E-06 51.9 6.4 135 39-230 33-169 (550)
39 PF06018 CodY: CodY GAF-like d 92.2 1.4 3.1E-05 39.5 9.8 55 323-380 105-159 (177)
40 COG3850 NarQ Signal transducti 91.8 10 0.00022 39.8 16.4 55 31-86 237-291 (574)
41 COG3284 AcoR Transcriptional a 91.2 0.58 1.3E-05 49.5 7.1 88 286-386 129-216 (606)
42 COG3275 LytS Putative regulato 90.1 3.4 7.5E-05 42.5 11.1 88 283-380 266-353 (557)
43 TIGR02787 codY_Gpos GTP-sensin 89.1 3.3 7.1E-05 38.9 9.5 56 322-380 103-158 (251)
44 TIGR02851 spore_V_T stage V sp 88.5 7.9 0.00017 34.9 11.4 57 163-225 98-154 (180)
45 PF14215 bHLH-MYC_N: bHLH-MYC 87.6 0.54 1.2E-05 41.7 3.3 60 160-226 88-147 (163)
46 PF11152 DUF2930: Protein of u 87.4 2.6 5.6E-05 38.5 7.5 73 287-369 121-193 (195)
47 PRK11388 DNA-binding transcrip 86.8 2.6 5.7E-05 45.7 8.7 55 161-226 113-167 (638)
48 COG4465 CodY Pleiotropic trans 84.8 5.2 0.00011 36.8 8.0 50 328-380 115-164 (261)
49 PF05651 Diacid_rec: Putative 84.6 11 0.00023 32.4 9.6 87 289-394 45-131 (135)
50 PF04340 DUF484: Protein of un 84.1 2.7 5.9E-05 39.2 6.3 51 324-376 172-222 (225)
51 PF02743 Cache_1: Cache domain 81.1 4.8 0.0001 30.7 5.7 55 199-269 11-65 (81)
52 PF03472 Autoind_bind: Autoind 79.7 10 0.00022 32.0 7.9 127 241-370 4-145 (149)
53 PF14215 bHLH-MYC_N: bHLH-MYC 79.6 2 4.3E-05 38.1 3.4 59 286-351 90-148 (163)
54 COG4251 Bacteriophytochrome (l 79.3 98 0.0021 33.5 17.5 38 48-86 141-178 (750)
55 PRK11477 carbohydrate diacid t 78.6 24 0.00052 35.6 11.4 127 244-397 13-140 (385)
56 PF09884 DUF2111: Uncharacteri 77.0 9.4 0.0002 29.6 5.8 47 165-225 36-82 (84)
57 PF01614 IclR: Bacterial trans 73.2 13 0.00029 30.8 6.7 35 326-362 79-113 (129)
58 COG3284 AcoR Transcriptional a 72.7 22 0.00048 38.0 9.4 56 161-227 128-183 (606)
59 PRK10963 hypothetical protein; 72.0 74 0.0016 29.6 12.0 41 42-84 77-117 (223)
60 TIGR02916 PEP_his_kin putative 68.8 23 0.0005 38.6 9.1 46 3-49 437-482 (679)
61 PRK10163 DNA-binding transcrip 66.5 22 0.00047 34.1 7.4 33 326-360 215-247 (271)
62 COG1414 IclR Transcriptional r 66.1 25 0.00055 33.2 7.6 43 41-85 63-105 (246)
63 PRK10963 hypothetical protein; 64.5 15 0.00033 34.2 5.7 51 324-376 168-218 (223)
64 PRK15090 DNA-binding transcrip 64.3 27 0.00059 33.1 7.5 33 326-360 203-235 (257)
65 PF07614 DUF1577: Protein of u 64.2 21 0.00046 33.9 6.5 71 292-365 162-255 (256)
66 TIGR02431 pcaR_pcaU beta-ketoa 59.6 26 0.00056 33.0 6.4 32 326-359 197-228 (248)
67 PRK11569 transcriptional repre 59.1 39 0.00086 32.4 7.7 34 326-361 220-253 (274)
68 COG1414 IclR Transcriptional r 58.9 88 0.0019 29.6 9.9 25 201-225 193-217 (246)
69 PRK09834 DNA-binding transcrip 58.6 29 0.00063 33.0 6.6 46 326-374 205-255 (263)
70 COG2205 KdpD Osmosensitive K+ 58.5 33 0.00071 38.0 7.4 31 4-34 619-649 (890)
71 PF11031 Phage_holin_T: Bacter 51.7 52 0.0011 30.0 6.5 121 246-377 84-215 (216)
72 PF10114 PocR: Sensory domain 51.6 1.2E+02 0.0026 26.5 9.0 46 327-375 85-130 (173)
73 PF02743 Cache_1: Cache domain 50.9 23 0.0005 26.8 3.7 22 326-347 14-35 (81)
74 PF09884 DUF2111: Uncharacteri 49.9 31 0.00068 26.8 4.1 46 289-348 36-81 (84)
75 COG4702 Uncharacterized conser 47.6 27 0.00058 30.5 3.8 43 330-376 121-163 (168)
76 COG3290 CitA Signal transducti 44.5 4.2E+02 0.009 28.2 19.1 32 55-88 70-101 (537)
77 PF14827 Cache_3: Sensory doma 40.9 31 0.00067 28.3 3.3 32 55-88 21-52 (116)
78 COG4048 Uncharacterized protei 40.3 37 0.00081 27.7 3.4 51 165-230 54-104 (123)
79 PF00571 CBS: CBS domain CBS d 37.9 39 0.00085 23.2 3.0 21 326-346 28-48 (57)
80 PF14827 Cache_3: Sensory doma 37.9 42 0.00092 27.5 3.6 23 327-349 90-112 (116)
81 PF12282 H_kinase_N: Signal tr 35.9 1.4E+02 0.003 25.8 6.6 47 287-347 78-124 (145)
82 PRK12705 hypothetical protein; 35.1 1.8 4E-05 45.3 -6.1 95 288-387 220-315 (508)
83 PRK11359 cyclic-di-GMP phospho 34.7 1.8E+02 0.0039 32.0 9.1 59 325-384 315-373 (799)
84 COG4048 Uncharacterized protei 34.1 71 0.0015 26.2 4.1 49 289-352 54-102 (123)
85 PF07614 DUF1577: Protein of u 33.9 77 0.0017 30.2 5.0 59 168-227 162-243 (256)
86 PF01614 IclR: Bacterial trans 33.1 65 0.0014 26.5 4.1 24 202-225 79-102 (129)
87 PF12631 GTPase_Cys_C: Catalyt 31.1 2.3E+02 0.0049 21.2 6.6 64 354-417 9-72 (73)
88 COG3159 Uncharacterized protei 31.1 1.1E+02 0.0024 28.3 5.3 52 323-376 164-215 (218)
89 PF08448 PAS_4: PAS fold; Int 29.4 1.4E+02 0.0031 22.7 5.4 52 163-225 53-104 (110)
90 PRK11477 carbohydrate diacid t 29.3 1.3E+02 0.0029 30.2 6.3 47 165-224 50-96 (385)
91 COG3275 LytS Putative regulato 28.4 7.2E+02 0.016 26.2 11.7 61 161-230 268-328 (557)
92 PRK15090 DNA-binding transcrip 26.9 74 0.0016 30.1 3.7 42 41-84 72-113 (257)
93 PRK10163 DNA-binding transcrip 25.6 79 0.0017 30.2 3.7 43 41-85 84-126 (271)
94 TIGR02431 pcaR_pcaU beta-ketoa 24.5 86 0.0019 29.4 3.7 42 41-84 66-107 (248)
95 PRK10935 nitrate/nitrite senso 24.0 4.4E+02 0.0095 27.5 9.4 54 326-385 304-357 (565)
96 PF12282 H_kinase_N: Signal tr 23.7 1.3E+02 0.0028 25.9 4.4 49 162-224 77-125 (145)
97 COG3835 CdaR Sugar diacid util 23.2 4.7E+02 0.01 26.3 8.4 76 293-387 51-126 (376)
98 PRK11569 transcriptional repre 21.2 1.1E+02 0.0024 29.3 3.7 42 41-84 87-128 (274)
99 TIGR03020 EpsA transcriptional 20.1 1.8E+02 0.004 27.5 4.9 85 289-377 85-170 (247)
No 1
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=99.95 E-value=6.9e-26 Score=244.52 Aligned_cols=294 Identities=12% Similarity=0.067 Sum_probs=210.7
Q ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcc
Q psy8476 38 RNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVD 117 (421)
Q Consensus 38 ~~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 117 (421)
..++|++|++.+ .+..|+++++..+...+.+++.||+++|.|+|+.++.+.+ |.|
T Consensus 7 ~~~~l~~is~~~-~~~~~~~~l~~~l~~~~~~~~~ad~~~i~l~d~~~~~~~~------------------------~~~ 61 (686)
T PRK15429 7 GQQGLFDITRTL-LQQPDLASLCEALSQLVKRSALADNAAIVLWQAQTQRASY------------------------YAS 61 (686)
T ss_pred HHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHhhcccceEEEEEEcCCCCeeee------------------------eec
Confidence 357899999988 7788999999999999999999999999999998876521 111
Q ss_pred hhhhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCC
Q psy8476 118 IEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEES 197 (421)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~ 197 (421)
-.+. +++ -..| ....++|++|||+++++|+.+++..-...+ +.-.+...
T Consensus 62 ~~~~--~~~---------------------~~~~------~~~~~~g~~g~vl~~~~~l~~~~~~~~~~~--~~l~~~~~ 110 (686)
T PRK15429 62 REKG--TPV---------------------KYED------ETVLAHGPVRRILSRPDTLHCSYEEFCETW--PQLAAGGL 110 (686)
T ss_pred cccc--cch---------------------hccc------hhhhccCcceEEeecCceEEEchHHhhhcc--HHHhhccc
Confidence 1110 000 0011 112579999999999999998885432221 11111112
Q ss_pred CceeeeeEEeeeEeCCCcEEEEEEeeecccCCcch-------------------hh------------------------
Q psy8476 198 DFTTRCILCMPIFNGQKTVIGVAQLINKISERKPL-------------------CR------------------------ 234 (421)
Q Consensus 198 ~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~~~-------------------~~------------------------ 234 (421)
....++|++|||+.. |+|+|++++.++.++.|+- .+
T Consensus 111 ~~~~~~~lgvPl~~~-~~v~G~l~l~~~~~~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~e 189 (686)
T PRK15429 111 YPKFGHYCLMPLAAE-GHIFGGCEFIRYDDRPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVA 189 (686)
T ss_pred ccCccceEEeceeeC-CeeEEEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 244678999999996 5999999999998766620 00
Q ss_pred ---hccccccHHHHHh----cCCCCCCcceeEEEEEcCCCCeeeeecCCC---Cc----ccccCCCchHHHHHHHhCCEE
Q psy8476 235 ---RESNNVDIEDILA----HTPEDPSIAFSTVFELGGPGGEALVKSPGN---TV----CNTHSRLATIAKYVASTGQIL 300 (421)
Q Consensus 235 ---~~~~~~dl~~IL~----~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~---~~----~~~~~~~~gi~g~v~~tg~~v 300 (421)
...+..++++++. .+.+.++++.++|+++|.++..+.+....+ .. ....+...|++|+|+++|+|+
T Consensus 190 Is~~l~s~~dl~ell~~I~~~i~~~~~a~~~~I~L~d~~~~~L~~~aa~g~~~~~~~~~~~~~~~~~~l~g~V~~~~~p~ 269 (686)
T PRK15429 190 ITNAVLSRLDMDELVSEVAKEIHYYFDIDAISIVLRSHRKNKLNIYSTHYLDKQHPAHEQSEVDEAGTLTERVFKSKEML 269 (686)
T ss_pred HHHHHccCCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCcEEEEEecccChhhcccccccCCcccchHHHHHhcCceE
Confidence 0124566666554 456788999999999999988765533221 11 112344569999999999999
Q ss_pred EEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 301 NIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 301 ~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~ 380 (421)
.++|...++...+........+...+|+++|||.. .|+++|||.+.++.. ..|+++|+++|+.||+|+|+||+|+++|
T Consensus 270 lv~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPL~~-~~~v~GvL~l~~~~~-~~F~~~dl~lL~~iA~~~A~Aie~a~~~ 347 (686)
T PRK15429 270 LINLHERDDLAPYERMLFDTWGNQIQTLCLLPLMS-GDTMLGVLKLAQCEE-KVFTTTNLKLLRQIAERVAIAVDNALAY 347 (686)
T ss_pred EEECccCcccchhhhhhhhcccccceEEEEEeEEE-CCEEEEEEEEeeCCC-CcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99887765432221111112223468999999999 469999999998765 6899999999999999999999999999
Q ss_pred HHHHHHHHHH
Q psy8476 381 ENACKLMAKQ 390 (421)
Q Consensus 381 ~e~~~~~~~~ 390 (421)
+++++..++.
T Consensus 348 ~~~~~~~~~L 357 (686)
T PRK15429 348 QEIHRLKERL 357 (686)
T ss_pred HHHHHHhhhh
Confidence 9987755543
No 2
>KOG3689|consensus
Probab=99.84 E-value=1.3e-21 Score=203.64 Aligned_cols=303 Identities=32% Similarity=0.437 Sum_probs=223.2
Q ss_pred ccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCc
Q psy8476 52 EQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSI 131 (421)
Q Consensus 52 ~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~ 131 (421)
+.+++..+..+++..++-+++|++|+.|++-.. ..+.+. .+...++ .|
T Consensus 3 ~~l~~~~~~~~~l~~~~~l~~a~r~~~f~~~~g-~~~~~~-~~~~~~~--------~~---------------------- 50 (707)
T KOG3689|consen 3 SSLDTEALCHKILQRVAGLLQADRCSLFLVRNG-AELASR-LISVLPD--------VC---------------------- 50 (707)
T ss_pred cccccccccchhhhhccccCCCCCcCeeeeccC-cccccc-ccccCcc--------cc----------------------
Confidence 345778888999999999999999999999333 332110 0000000 00
Q ss_pred cceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEe
Q psy8476 132 AFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFN 211 (421)
Q Consensus 132 ~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~ 211 (421)
.+++..+...+. +.+.|++|||+.+|++++++|++.++++ ..+.|..++|++.+.+|.|+.+
T Consensus 51 -------~~~~~~~~~~~~---------~~~~~~~g~~a~~~~~~~~~~~~~~~~f--~~~~d~~t~~~~~~~l~~pi~~ 112 (707)
T KOG3689|consen 51 -------EESTLEEPDNRF---------PWGKGIVGHVAETGETLNIPDAYEDSRF--NSETDKLTGYKTKSILCMPIVN 112 (707)
T ss_pred -------cccccccccccc---------cccceeeeeecccccccCcccccccccc--ccccccccCCCccceeeccccc
Confidence 011100000122 3789999999999999999999998875 5678999999999999999999
Q ss_pred CCCcEEEEEEeeecccCCcc-------------h-------hhh----------ccccccHHHH---------------H
Q psy8476 212 GQKTVIGVAQLINKISERKP-------------L-------CRR----------ESNNVDIEDI---------------L 246 (421)
Q Consensus 212 ~~~~vIGVl~l~~~~~~~~~-------------~-------~~~----------~~~~~dl~~I---------------L 246 (421)
.. +++|+...+|+..+... + .|. ...-+++.+. +
T Consensus 113 ~~-~~~~~~~~~~k~~~~~~~~~~~~~~~~~l~~~~i~~~~~ql~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 191 (707)
T KOG3689|consen 113 SR-EVVGVAQAINKSNGPTFTERDESVFSAYLGFCSIVLKNAQLLASSRIERKRNQVLLDLADLMFEEQTDRESIFPKIL 191 (707)
T ss_pred hh-HHHHHHHhhccccccccccccHHHHHhhcCCceeeccHHHHHHHhhhHHHHHHHHhhhhhHHHHHhcchhcccchhh
Confidence 88 99999999999665430 1 110 0011111111 1
Q ss_pred hcCCCCCCcceeEEEEEcCCCCeeee--ec--------CCCC----cccccCCCchHHHHHHHhCCEEEEcCCCCccccc
Q psy8476 247 AHTPEDPSIAFSTVFELGGPGGEALV--KS--------PGNT----VCNTHSRLATIAKYVASTGQILNIGDVPSWMREE 312 (421)
Q Consensus 247 ~~~~~~l~a~~~~i~l~d~~~~~~~~--~~--------~~~~----~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~ 312 (421)
..+.....+..|++.+++..+...+. ++ +... .......+.++.|+|+.+|++++|.|++.++.
T Consensus 192 ~~~~~~~~~~~~si~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~l~g~va~t~~~~ni~~~~~~~~-- 269 (707)
T KOG3689|consen 192 YTARSLLQCTRCSIQLLDMSTLEEFSWVLDVLETEQTKPSTSDMAEIEFKKLLDYGLRGYVASTGEGLNISNAIADPR-- 269 (707)
T ss_pred hhhhhhhhhcccceeeeccccchhhhhhhHHHhhhhcCCCCchhhhHHHHhhhhhhhhheeecccCcCCCCCcccccc--
Confidence 11223455778888888888776321 11 0000 11223567899999999999999999999865
Q ss_pred cCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 313 VCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMAKQKV 392 (421)
Q Consensus 313 f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~~~~~~ 392 (421)
|....|. .+.+.+.++|+|++++++++|||.+++|+.++.+|+..|..+++.++..+|+++.|+++|..+.++..|..+
T Consensus 270 f~~q~d~-~~~~~~~il~~pi~~~~~~~igv~~~~nk~~g~~f~~~de~~~~~~~~~~gl~i~~~~~y~~~~~s~~r~~v 348 (707)
T KOG3689|consen 270 FDKQVDE-DGTGIRPILCIPIKNKKGEVIGVQQLVNKEDGNPFSRNDEDLFEAFTIFCGLSIHNTHMYSKINKSEPRQGV 348 (707)
T ss_pred ccccccc-cccccceeEEEecccccCceecceeeeccccCCccccchHHHHHHHHHHHhhhhhhhhhHHHHhhhccccch
Confidence 4455565 555667799999999889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcccchhHH
Q psy8476 393 FQRYLTFCGIGIQNAQ 408 (421)
Q Consensus 393 ~~e~~~~~~~~~~~~~ 408 (421)
..|++.||+++.+.|-
T Consensus 349 ~~e~l~~h~~~~~~e~ 364 (707)
T KOG3689|consen 349 ALEFLSYHAKALEEEV 364 (707)
T ss_pred hHHHHHHHHhhhHHhh
Confidence 9999999999877653
No 3
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=99.73 E-value=3.7e-16 Score=164.55 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=54.3
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACK 385 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~ 385 (421)
.++|+|||||.. +|+++|||++.++.+...|+++|+++|+.+|.++|+||++++++.+.++
T Consensus 107 ~~~S~l~VPL~~-~g~viGvL~v~s~~~~~~ft~~d~~lL~~lA~~ia~aI~~~~~~~~~~~ 167 (534)
T TIGR01817 107 GPVPFIGVPIKA-DSETIGVLAADRDFRSRERLEEEVRFLEMVANLIGQTVRLHRLVAQRRE 167 (534)
T ss_pred CcceEEEEEEcC-CCEEEEEEEEEeccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999997 6899999999999776679999999999999999999999999885443
No 4
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=99.70 E-value=5.4e-16 Score=167.80 Aligned_cols=176 Identities=12% Similarity=0.130 Sum_probs=135.7
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHH-------HHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCC
Q psy8476 2 SILEFERNQVFQRYLTFCGIGIQNAQLFEMSILEFERN-------QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCE 74 (421)
Q Consensus 2 ~~~~~~d~~~~~~~a~~~~ial~na~l~~~~~~~~~~~-------~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~ 74 (421)
..|++.|+++++.+|.++|+|++|++++++.+++.+.+ ++|.+|++.+ .+..|++++++.|++.+.++++++
T Consensus 140 ~~Ft~~d~~ll~~la~~a~~aie~~~~~e~~~~~~~~L~~~r~~~~~L~eIs~~l-~s~~dl~ell~~I~~~i~~~~~a~ 218 (686)
T PRK15429 140 RPWSEKEFNRLQTFTQIVSVVTEQIQSRVVNNVDYELLCRERDNFRILVAITNAV-LSRLDMDELVSEVAKEIHYYFDID 218 (686)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH-ccCCCHHHHHHHHHHHHHHHhCCC
Confidence 47999999999999999999999999999988877777 9999999999 667799999999999999999999
Q ss_pred eEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccceeeeecCCCCCCccccCCCCc
Q psy8476 75 RCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNT 154 (421)
Q Consensus 75 ~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~ 154 (421)
.|+|+|+|++++.|.+.. .. ++|-+. +. .+ ....|
T Consensus 219 ~~~I~L~d~~~~~L~~~a--a~------------------g~~~~~-----~~-----------~~------~~~~~--- 253 (686)
T PRK15429 219 AISIVLRSHRKNKLNIYS--TH------------------YLDKQH-----PA-----------HE------QSEVD--- 253 (686)
T ss_pred EEEEEEEECCCCcEEEEE--ec------------------ccChhh-----cc-----------cc------cccCC---
Confidence 999999999988763210 00 000000 00 00 01122
Q ss_pred ccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 155 VCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 155 ~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
.+.|++|+|+++|+|+.++|...|+.....+.........++|+++|||+.+ |+++|||.+.++....|
T Consensus 254 ------~~~~l~g~V~~~~~p~lv~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPL~~~-~~v~GvL~l~~~~~~~F 322 (686)
T PRK15429 254 ------EAGTLTERVFKSKEMLLINLHERDDLAPYERMLFDTWGNQIQTLCLLPLMSG-DTMLGVLKLAQCEEKVF 322 (686)
T ss_pred ------cccchHHHHHhcCceEEEECccCcccchhhhhhhhcccccceEEEEEeEEEC-CEEEEEEEEeeCCCCcC
Confidence 4569999999999999999988876543222122222356899999999986 59999999998876666
No 5
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=99.69 E-value=5.7e-16 Score=167.55 Aligned_cols=60 Identities=17% Similarity=0.267 Sum_probs=54.7
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACK 385 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~ 385 (421)
.++|+|||||.. +|+++|||+++++.+ +.|+++|+++|..+|+|+|+||+|+++.+.+..
T Consensus 106 ~~~S~L~VPL~~-~geVIGVL~v~~~~~-~~Fs~~d~~lL~~LA~~aAiAL~na~l~~~~~~ 165 (748)
T PRK11061 106 RFRAFLGVPIIY-RRQLLGVLVVQQREL-RQFDESEESFLVTLATQLAAILSQSQLTALFGQ 165 (748)
T ss_pred cceEEEEEEEee-CCEEEEEEEEeeCCC-CCCCHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 468999999998 579999999999988 589999999999999999999999999877743
No 6
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=99.44 E-value=1.4e-11 Score=129.05 Aligned_cols=121 Identities=12% Similarity=0.098 Sum_probs=90.6
Q ss_pred HHHHHHHhCCEEEEcCCCCccccccCCcccc-cCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHH
Q psy8476 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDE-ESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFA 367 (421)
Q Consensus 289 i~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~-~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA 367 (421)
..+.+..+|+++.+++...+|++ +...... ......+|+|||||.. +|+++|||.+++...+ .|+++|+++|+.+|
T Consensus 73 ~l~av~~~g~~v~v~~~~~~p~~-~~~~~~~~~~~~gi~S~l~vPL~~-~~~~~GvL~l~~~~~~-~f~~~~~~~l~~~a 149 (509)
T PRK05022 73 RLEAILRAGDPVRFPADSELPDP-YDGLIPGVQESLPVHDCMGLPLFV-DGRLIGALTLDALDPG-QFDAFSDEELRALA 149 (509)
T ss_pred HHHHHHhcCCeEEEecCCCCCcc-cccccccccccCCcceEEEEEEEE-CCEEEEEEEEeeCCCC-cCCHHHHHHHHHHH
Confidence 66778878999999887766653 2111111 1223468999999999 5799999999998775 89999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------hhhcccchhHHHHHH
Q psy8476 368 IFCGLGIHNTQMYENACKLMAKQKVFQRYL--------TFCGIGIQNAQLFEM 412 (421)
Q Consensus 368 ~q~aiAlena~L~~e~~~~~~~~~~~~e~~--------~~~~~~~~~~~~~~~ 412 (421)
.++|.|+.|++++++.++..++++...+.+ ..++.+..+.++++.
T Consensus 150 ~~~a~Al~~a~~~~~l~~~~~~~~~~~~~~~~~~~~~~~iig~s~~~~~~~~~ 202 (509)
T PRK05022 150 ALAAATLRNALLIEQLESQAELPQDVAEFLRQEALKEGEMIGQSPAMQQLKKE 202 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCceeecCHHHHHHHHH
Confidence 999999999999999988777666555433 234555556555544
No 7
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=99.38 E-value=1.3e-12 Score=113.52 Aligned_cols=131 Identities=23% Similarity=0.279 Sum_probs=98.4
Q ss_pred HHHHhcCCCCCCcceeEEEEEcCCCCeeeeecCCCC--c---ccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcc
Q psy8476 243 EDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNT--V---CNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDE 317 (421)
Q Consensus 243 ~~IL~~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~~--~---~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~ 317 (421)
++++..+.+.++++++.++++|.++.........+. . ....+...++.+.++.+++++.+.|+..++++......
T Consensus 7 ~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~ 86 (154)
T PF01590_consen 7 QRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPPGGRRLSMDESICGQVLQSREPIVISDVAADPRFAPQIAA 86 (154)
T ss_dssp HHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEHHHEEEETTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHH
T ss_pred HHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeecccccccccccccccccHHHHHHhCCCeEeeccccccccccccccc
Confidence 334555667889999999999999998754433221 1 12234557889999999999999999988764321111
Q ss_pred cccC------------CCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy8476 318 DEES------------DFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGI 374 (421)
Q Consensus 318 d~~~------------~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAl 374 (421)
.... .+..+|++++||.. +|+++|+|.+.+..+.+.|+++|+.+++.+|.++|+||
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~-~g~~~G~l~l~~~~~~~~~~~~d~~ll~~~a~~~a~ai 154 (154)
T PF01590_consen 87 QSALRALSSAERPFLAEYGVRSYLCVPIIS-GGRLIGVLSLYRTRPGRPFTEEDLALLESFAQQLAIAI 154 (154)
T ss_dssp HHTTBTTTHHHHHHHHTTTESEEEEEEEEE-TTEEEEEEEEEEESSSSS--HHHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccCceeeEeeeec-ccCcEEEEEEEECCCCCCcCHHHHHHHHHHHHHHHhhC
Confidence 1111 45679999999998 57999999999999877999999999999999999987
No 8
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=99.31 E-value=2.1e-11 Score=102.58 Aligned_cols=118 Identities=20% Similarity=0.256 Sum_probs=90.2
Q ss_pred HHhcCCCCCCcceeEEEEEcCCCCeeeeecCCCC---cccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccC
Q psy8476 245 ILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNT---VCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEES 321 (421)
Q Consensus 245 IL~~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~~---~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~ 321 (421)
++..+.+.++++.+.||++|+++..+....+.+. .....+...++.++++++++++.+++....+.
T Consensus 9 i~~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~----------- 77 (129)
T PF13492_consen 9 ILELLRELLGADRAALFLLDEDGNRLRVVAGWGGDPRLSESLPEDDPLIGRALETGEPVSVPDIDERDF----------- 77 (129)
T ss_dssp HHHHHHHHST-SEEEEEEEETTCECEEEEEEESS-GCGHHCEETTSHHHHHHHHHTS-EEESTCCC-TT-----------
T ss_pred HHHHHHHHhCCCEEEEEEEECCCCEEEEEEEeCCCccccccCCCCccHHHHHHhhCCeEEecccccccC-----------
Confidence 4455667789999999999999887665544322 12244677999999999999998888655311
Q ss_pred CCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy8476 322 DFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376 (421)
Q Consensus 322 ~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlen 376 (421)
...+|++++||..++ +++|+|.+....+ ..|+++|+++|+.+|+++|+||+|
T Consensus 78 -~~~~s~~~vPl~~~~-~~~Gvl~~~~~~~-~~~~~~d~~~l~~~a~~~a~alen 129 (129)
T PF13492_consen 78 -LGIRSLLVVPLRSRD-RVIGVLCLDSREP-EEFSDEDLQLLESLANQLAIALEN 129 (129)
T ss_dssp -TTTCEEEEEEEEETT-EEEEEEEEEECTT-CG-SHHHHHHHHHHHHHHHHHHH-
T ss_pred -CCCCEEEEEEEeECC-EEEEEEEEEECCC-CCCCHHHHHHHHHHHHHHHHHhCC
Confidence 245899999999965 9999999977766 589999999999999999999997
No 9
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=99.27 E-value=1e-10 Score=98.01 Aligned_cols=137 Identities=24% Similarity=0.295 Sum_probs=101.3
Q ss_pred HHHHHhcCCCCCCcceeEEEEEcCC-CCeeeeec--CCCC--cccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCc
Q psy8476 242 IEDILAHTPEDPSIAFSTVFELGGP-GGEALVKS--PGNT--VCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCND 316 (421)
Q Consensus 242 l~~IL~~~~~~l~a~~~~i~l~d~~-~~~~~~~~--~~~~--~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~ 316 (421)
++.++..+.+.++.+++.+++++.+ +....... +... .....+...+..++++++++++.+.|...++. ....
T Consensus 6 ~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~ 83 (149)
T smart00065 6 LQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPLLGLRYPLGEGLAGRVAETGRPLNIPDVEADPV--FALD 83 (149)
T ss_pred HHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCcccceEEecCCCChHHHHHHcCCeEEeechhhCCc--cccc
Confidence 3445666677889999999999984 44433322 2111 11234555689999999999999998876541 1111
Q ss_pred ccccCCCc-cceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 317 EDEESDFT-TRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENA 383 (421)
Q Consensus 317 ~d~~~~~~-~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~ 383 (421)
....+. .+|++++||.. +|+++|++.+.++...+.|+.+|+.+|+.++.+++.+++|.++++++
T Consensus 84 --~~~~~~~~~s~~~~Pl~~-~~~~~G~l~~~~~~~~~~~~~~~~~~l~~~~~~i~~~l~~~~~~~~~ 148 (149)
T smart00065 84 --LLGRYQGVRSFLAVPLVA-DGELVGVLALHNKDSPRPFTEEDEELLQALANQLAIALANAQLYEEL 148 (149)
T ss_pred --cccceeceeeEEEeeeee-cCEEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 112223 69999999999 57999999999984446899999999999999999999999998764
No 10
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=99.26 E-value=8.5e-12 Score=126.14 Aligned_cols=137 Identities=12% Similarity=0.135 Sum_probs=114.1
Q ss_pred ccHHHHHhcCCCCCCcceeEEEEEcCCCCeeeeecCCCCcc-----cccCCCchHHHHHHHhCCEEEEcCCCCccccccC
Q psy8476 240 VDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVC-----NTHSRLATIAKYVASTGQILNIGDVPSWMREEVC 314 (421)
Q Consensus 240 ~dl~~IL~~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~~~~-----~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~ 314 (421)
..|+.|+..+...+.++.|++|+.+.++..+..+...+... ....+++|++|.+.+..+|+|..|++++|.|.+.
T Consensus 20 e~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~ATeGLnk~av~~~~l~~~eGLVG~v~~~aePlNLsdAqsHPsF~Y~ 99 (756)
T COG3605 20 EALDIIVRDIALAMVTEVCSVYLLRADRRVLELMATEGLNKPAVHLVQLAFGEGLVGLVGRSAEPLNLADAQSHPSFKYL 99 (756)
T ss_pred HHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEEeccccCccccceEEecCCCchhhhhhhccCCCChhhhhhCCccccc
Confidence 34666777888888999999999999998776665444321 2346789999999999999999999999998876
Q ss_pred CcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 315 NDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYE 381 (421)
Q Consensus 315 ~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~ 381 (421)
++... ..| +|+|+|||+.+ |+++||+.|+||.. +.|++++++.|+++|-|+|.-+..+++-.
T Consensus 100 petgE-E~Y--~sFLGvPIi~~-~r~lGVLVVQqk~~-R~y~E~Eve~L~T~A~~lA~iva~~el~~ 161 (756)
T COG3605 100 PETGE-ERY--HSFLGVPIIRR-GRLLGVLVVQQREL-RQYDEDEVEFLVTLAMQLAEIVAQSQLTG 161 (756)
T ss_pred cccch-HHH--HHhhccceeec-CceeEEEEEecccc-cccchHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 65433 224 89999999994 79999999999987 69999999999999999999999988763
No 11
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=99.16 E-value=2.4e-10 Score=98.44 Aligned_cols=127 Identities=24% Similarity=0.298 Sum_probs=81.0
Q ss_pred cHHHHHh----cCCCCCCcceeEEEEEcCCCCeeeee-cCCCC--cccc--cCCC---------chHHHHHHHhCCEEEE
Q psy8476 241 DIEDILA----HTPEDPSIAFSTVFELGGPGGEALVK-SPGNT--VCNT--HSRL---------ATIAKYVASTGQILNI 302 (421)
Q Consensus 241 dl~~IL~----~~~~~l~a~~~~i~l~d~~~~~~~~~-~~~~~--~~~~--~~~~---------~gi~g~v~~tg~~v~i 302 (421)
+++++++ .+.+..+++.+.|+++|+++...... .+... .... .+.. .++.+.++++|+|+++
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDPSEFLKEEIPLPPPPDEPPAYAAVGLWEGVLRTGEPIII 82 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSSCTSTCCECCCCCCCESCHHHCCEETTSHHHHHTS-EEE
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCchhhhhhhcccCcccccccchhhhhHHHHHHhcCceEEE
Confidence 4555544 44566789999999999988443322 22111 1111 1111 2333345999999999
Q ss_pred c-CCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy8476 303 G-DVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIH 375 (421)
Q Consensus 303 ~-D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAle 375 (421)
+ +.+... . .........+|++|+||..+ |+++|||.+.++.. ..|+++|+++|+.+|+|+|+|||
T Consensus 83 ~~~~~~~~---~---~~~~~~~~~~s~l~vPl~~~-~~~~Gvl~l~~~~~-~~f~~~~~~~l~~la~~~a~aie 148 (148)
T PF13185_consen 83 NDDDSSFP---P---WELARHPGIRSILCVPLRSG-GEVIGVLSLYSKEP-NAFSEEDLELLEALADQIAIAIE 148 (148)
T ss_dssp SCCCGGGS---T---THHHCCTT-SEEEEEEEEET-TEEEEEEEEEESST-T---HHHHHHHHHHHHHHHHHHH
T ss_pred eCcccccc---c---hhhhccccCCEEEEEEEeEC-CEEEEEEEEeeCCC-CCcCHHHHHHHHHHHHHHHHHhC
Confidence 9 222211 1 12234456799999999994 69999999999877 59999999999999999999996
No 12
>COG3605 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]
Probab=99.09 E-value=2.6e-10 Score=115.52 Aligned_cols=133 Identities=17% Similarity=0.233 Sum_probs=104.5
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchh
Q psy8476 40 QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIE 119 (421)
Q Consensus 40 ~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~ 119 (421)
..|-+|...+ ++..++.+-|+.|++.++..|.++.|+|||.+.+...|+.+ ..-|-- +|
T Consensus 3 ~~Lr~i~E~v-a~~~~~qe~Ld~iVr~i~~aM~tEVCSvYl~~~d~~~leL~----ATeGLn----k~------------ 61 (756)
T COG3605 3 TRLRRIVEKV-ASALELQEALDIIVRDIALAMVTEVCSVYLLRADRRVLELM----ATEGLN----KP------------ 61 (756)
T ss_pred hHHHHHHHHH-hcccCHHHHHHHHHHHHHHHhhhhheeEEEEcCCCcEEEEE----eccccC----cc------------
Confidence 3477888887 77889999999999999999999999999999998665422 111100 00
Q ss_pred hhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCc
Q psy8476 120 DILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDF 199 (421)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~ 199 (421)
-+ ..+.+ +.++|++|-|.+..+|+|+.|+..+|.|.+.|.+. ..
T Consensus 62 -------------------av-----~~~~l---------~~~eGLVG~v~~~aePlNLsdAqsHPsF~Y~petg---EE 105 (756)
T COG3605 62 -------------------AV-----HLVQL---------AFGEGLVGLVGRSAEPLNLADAQSHPSFKYLPETG---EE 105 (756)
T ss_pred -------------------cc-----ceEEe---------cCCCchhhhhhhccCCCChhhhhhCCccccccccc---hH
Confidence 00 01122 37899999999999999999999999998766542 35
Q ss_pred eeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 200 TTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 200 ~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
..+|+|+|||+.. |+++||++++|+....+
T Consensus 106 ~Y~sFLGvPIi~~-~r~lGVLVVQqk~~R~y 135 (756)
T COG3605 106 RYHSFLGVPIIRR-GRLLGVLVVQQRELRQY 135 (756)
T ss_pred HHHHhhccceeec-CceeEEEEEeccccccc
Confidence 6789999999986 69999999999998765
No 13
>KOG3689|consensus
Probab=99.03 E-value=1.9e-10 Score=120.85 Aligned_cols=181 Identities=37% Similarity=0.481 Sum_probs=144.9
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEE
Q psy8476 2 SILEFERNQVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLL 81 (421)
Q Consensus 2 ~~~~~~d~~~~~~~a~~~~ial~na~l~~~~~~~~~~~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~ 81 (421)
..|+..|+..++.+..++++.+.++++.+..+.+.++.+.|++++..++....+++..+.+++..+..+..+.+|++.++
T Consensus 129 ~~~~~~~~~~~~~~l~~~~i~~~~~ql~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~si~~~ 208 (707)
T KOG3689|consen 129 PTFTERDESVFSAYLGFCSIVLKNAQLLASSRIERKRNQVLLDLADLMFEEQTDRESIFPKILYTARSLLQCTRCSIQLL 208 (707)
T ss_pred cccccccHHHHHhhcCCceeeccHHHHHHHhhhHHHHHHHHhhhhhHHHHHhcchhcccchhhhhhhhhhhhcccceeee
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCC
Q psy8476 82 KSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSR 161 (421)
Q Consensus 82 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~ 161 (421)
+..+..+..+- +....+.... .-+++..++. . ....
T Consensus 209 ~~~~~~~~~~~-~~~~~~~~~~-------------------~~~~~~~~~~---------------~---------~~~l 244 (707)
T KOG3689|consen 209 DMSTLEEFSWV-LDVLETEQTK-------------------PSTSDMAEIE---------------F---------KKLL 244 (707)
T ss_pred ccccchhhhhh-hHHHhhhhcC-------------------CCCchhhhHH---------------H---------Hhhh
Confidence 99887652211 1110000000 0000111111 1 1126
Q ss_pred CCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecccCC
Q psy8476 162 LATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISER 229 (421)
Q Consensus 162 ~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~ 229 (421)
+.++.|+|+.+|+.++|.|++.+|.|... .|. .+.+++.++|+|+.+..+++|||.+++|+.++.
T Consensus 245 d~~l~g~va~t~~~~ni~~~~~~~~f~~q--~d~-~~~~~~~il~~pi~~~~~~~igv~~~~nk~~g~ 309 (707)
T KOG3689|consen 245 DYGLRGYVASTGEGLNISNAIADPRFDKQ--VDE-DGTGIRPILCIPIKNKKGEVIGVQQLVNKEDGN 309 (707)
T ss_pred hhhhhheeecccCcCCCCCcccccccccc--ccc-cccccceeEEEecccccCceecceeeeccccCC
Confidence 78999999999999999999999987543 454 677788899999999989999999999999985
No 14
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=98.97 E-value=6.2e-09 Score=89.83 Aligned_cols=110 Identities=17% Similarity=0.246 Sum_probs=89.2
Q ss_pred cceeEEEEEcCCCCeeeeecCCCCcccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEee
Q psy8476 255 IAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIF 334 (421)
Q Consensus 255 a~~~~i~l~d~~~~~~~~~~~~~~~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~ 334 (421)
..+..+|+++.+...+=.|.|. ..+...+.++|+-|.++++++.+++.|+...|.+ .. ....++|.++|||+
T Consensus 51 ~nW~GFYl~~~~~LvLgPFqG~-~acv~I~~GkGVCg~A~~~~~t~~V~DV~~~~gh-ia------CD~as~SEIVvPi~ 122 (163)
T COG1956 51 VNWVGFYLLEGDELVLGPFQGK-VACVRIPFGKGVCGTAAATGETVRVDDVHAFPGH-IA------CDAASNSEIVVPIF 122 (163)
T ss_pred CceEEEEEecCCeEEEecccCC-cceEEeccCcchhHHHHhcCCeEEecccccCCCc-cc------cccccCceEEEEEE
Confidence 6889999999555444445554 2245678899999999999999999999887652 22 22357999999999
Q ss_pred eCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy8476 335 NGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGI 374 (421)
Q Consensus 335 ~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAl 374 (421)
. +|++||||-+.+...+ .|+++|+..|+.+|..++..+
T Consensus 123 ~-~g~~iGvlDiDS~~~~-~Fd~~D~~~Le~~~~~l~~~~ 160 (163)
T COG1956 123 K-DGKLIGVLDIDSPTPG-RFDEEDEAGLEKLAALLEKSL 160 (163)
T ss_pred E-CCEEEEEEecCCCCcc-cCCHHHHHHHHHHHHHHHHHh
Confidence 9 7899999999999886 899999999999998877654
No 15
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=98.91 E-value=4.5e-09 Score=91.10 Aligned_cols=122 Identities=24% Similarity=0.356 Sum_probs=87.5
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccce
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFS 134 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 134 (421)
|++++++.+++.+.+++++++|+++++|++.+.+... .. .+
T Consensus 1 Dl~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~---~~-~~----------------------------------- 41 (154)
T PF01590_consen 1 DLDELLQRILRELAELLGADRASIFLLDPDGNRLYSV---AG-VG----------------------------------- 41 (154)
T ss_dssp SHHHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEE---EE-EE-----------------------------------
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEE---Ee-ec-----------------------------------
Confidence 7899999999999999999999999999988765210 00 00
Q ss_pred eeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccC------------CCceee
Q psy8476 135 TVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEE------------SDFTTR 202 (421)
Q Consensus 135 ~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~------------~~~~~~ 202 (421)
...+. ......+ ...++.++++++++++.+.|+..+|++......... ..+.++
T Consensus 42 ----~~~~~-~~~~~~~---------~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 (154)
T PF01590_consen 42 ----LPDPP-PGGRRLS---------MDESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVR 107 (154)
T ss_dssp ----GGGSE-HHHEEEE---------TTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTES
T ss_pred ----ccccc-ccccccc---------ccccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccccccCc
Confidence 00000 0001111 357889999999999999999999986432211111 157899
Q ss_pred eeEEeeeEeCCCcEEEEEEeeeccc-CCc
Q psy8476 203 CILCMPIFNGQKTVIGVAQLINKIS-ERK 230 (421)
Q Consensus 203 s~l~vPl~~~~~~vIGVl~l~~~~~-~~~ 230 (421)
|++++||..+ |+++|+|.+.+..+ ..|
T Consensus 108 s~l~vPi~~~-g~~~G~l~l~~~~~~~~~ 135 (154)
T PF01590_consen 108 SYLCVPIISG-GRLIGVLSLYRTRPGRPF 135 (154)
T ss_dssp EEEEEEEEET-TEEEEEEEEEEESSSSS-
T ss_pred eeeEeeeecc-cCcEEEEEEEECCCCCCc
Confidence 9999998875 79999999999988 444
No 16
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=98.71 E-value=1.3e-07 Score=79.21 Aligned_cols=108 Identities=24% Similarity=0.344 Sum_probs=76.7
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccce
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFS 134 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 134 (421)
|++++++.+++.+.+.+++++++|+++|++.+.+...
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~~~~~~------------------------------------------- 37 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDEDGNRLRVV------------------------------------------- 37 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEETTCECEEEE-------------------------------------------
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEE-------------------------------------------
Confidence 7899999999999999999999999999987765311
Q ss_pred eeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCC
Q psy8476 135 TVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQK 214 (421)
Q Consensus 135 ~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~ 214 (421)
...++... ..-.+| .+.++++++.++++++.+++....+. ...++++++||..++
T Consensus 38 --~~~~~~~~-~~~~l~---------~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~s~~~vPl~~~~- 92 (129)
T PF13492_consen 38 --AGWGGDPR-LSESLP---------EDDPLIGRALETGEPVSVPDIDERDF------------LGIRSLLVVPLRSRD- 92 (129)
T ss_dssp --EEESS-GC-GHHCEE---------TTSHHHHHHHHHTS-EEESTCCC-TT------------TTTCEEEEEEEEETT-
T ss_pred --EEeCCCcc-ccccCC---------CCccHHHHHHhhCCeEEecccccccC------------CCCCEEEEEEEeECC-
Confidence 00000000 000122 57899999999999999988665332 345899999999986
Q ss_pred cEEEEEEeeecccCCc
Q psy8476 215 TVIGVAQLINKISERK 230 (421)
Q Consensus 215 ~vIGVl~l~~~~~~~~ 230 (421)
+++|++.+.......+
T Consensus 93 ~~~Gvl~~~~~~~~~~ 108 (129)
T PF13492_consen 93 RVIGVLCLDSREPEEF 108 (129)
T ss_dssp EEEEEEEEEECTTCG-
T ss_pred EEEEEEEEEECCCCCC
Confidence 9999999977665544
No 17
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=98.67 E-value=1.5e-06 Score=87.98 Aligned_cols=63 Identities=16% Similarity=0.241 Sum_probs=56.1
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMA 388 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~~ 388 (421)
...|+|++||+++ ++++|++++.....+ .|+.+-.+.++.+|..++.|..|+++++++.+..+
T Consensus 140 ~~~a~i~~PL~~~-~~~~G~Ltld~~~~~-~f~~~~~~~lr~La~~a~la~~~~~l~~~l~~~~~ 202 (550)
T COG3604 140 KKHACIGVPLKSG-DKLIGALTLDHTEPD-QFDEDLDEELRFLAALAALAVANALLHRELSSLKE 202 (550)
T ss_pred cceeEEeeeeeeC-CeeeeeEEeeeeccc-ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999995 699999999988874 79999999999999999999999999999977653
No 18
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=98.67 E-value=8.8e-08 Score=82.93 Aligned_cols=95 Identities=15% Similarity=0.231 Sum_probs=76.0
Q ss_pred hHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHH
Q psy8476 288 TIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFA 367 (421)
Q Consensus 288 gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA 367 (421)
+..+++.+.++++.++|...+++..- ..... .....++.+++||..+ ++++|++.+.+....+.|+++++.+++.+|
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~i~~~l~vPl~~~-~~~~G~l~~~~~~~~~~~~~~e~~ll~~la 155 (175)
T COG2203 79 CLIGIALREGRPVVVEDILQDPRFRD-NPLVL-LEPPIRSYLGVPLIAQ-GELLGLLCVHDSEPRRQWSEEELELLEELA 155 (175)
T ss_pred hhhhhhhcCCceEEeeccccCccccc-CHHHH-HHHHHHHheeeeeeEC-CEeeEEeeeeccCCCCCCCHHHHHHHHHHH
Confidence 36778899999999999998765321 11111 1111589999999994 699999999999876579999999999999
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy8476 368 IFCGLGIHNTQMYENACK 385 (421)
Q Consensus 368 ~q~aiAlena~L~~e~~~ 385 (421)
.++|+|+++++++++.+.
T Consensus 156 ~~~a~ai~~~~~~~~~~~ 173 (175)
T COG2203 156 EQVAIAIERARLYEELQE 173 (175)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999988543
No 19
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=98.63 E-value=7.3e-07 Score=77.14 Aligned_cols=63 Identities=21% Similarity=0.304 Sum_probs=56.2
Q ss_pred CCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecccCCcc
Q psy8476 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISERKP 231 (421)
Q Consensus 161 ~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~~ 231 (421)
.|+|++|.++++|+.+++.|++..|.+. .....++|.++||++. +|++||||-+.+...++|+
T Consensus 80 ~GkGVCg~A~~~~~t~~V~DV~~~~ghi-------aCD~as~SEIVvPi~~-~g~~iGvlDiDS~~~~~Fd 142 (163)
T COG1956 80 FGKGVCGTAAATGETVRVDDVHAFPGHI-------ACDAASNSEIVVPIFK-DGKLIGVLDIDSPTPGRFD 142 (163)
T ss_pred cCcchhHHHHhcCCeEEecccccCCCcc-------ccccccCceEEEEEEE-CCEEEEEEecCCCCcccCC
Confidence 8999999999999999999999988753 3446789999999998 5799999999999998884
No 20
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=98.57 E-value=1e-05 Score=87.98 Aligned_cols=62 Identities=11% Similarity=0.105 Sum_probs=55.4
Q ss_pred cceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 325 TRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLM 387 (421)
Q Consensus 325 ~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~ 387 (421)
.++++|+||.. +|+++|++.+.++.....|+.+|.++|+.++.|++.+++|.++.++.++..
T Consensus 409 ~~~~l~vPL~~-~~~~~G~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~l~~~~~~~~l~~~~ 470 (679)
T TIGR02916 409 PNAWLIVPLIS-GEELVGFVVLARPRTAGEFNWEVRDLLKTAGRQAASYLAQMEASEALAEAR 470 (679)
T ss_pred CCceEEEEecc-CCEEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46799999999 469999999998877678999999999999999999999999998876543
No 21
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=98.56 E-value=5.1e-07 Score=77.50 Aligned_cols=125 Identities=21% Similarity=0.215 Sum_probs=72.6
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccce
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAFS 134 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~ 134 (421)
|++++++.+++.+.++++++.++|+++|++++.+.. ... +.. +.. +
T Consensus 3 ~~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~----~~~-~~~------------------------~~~----~- 48 (148)
T PF13185_consen 3 DLEELLQQILDALLELTGADAGAIYLYDPDGQLLPV----AAS-GDP------------------------SEF----L- 48 (148)
T ss_dssp HHHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEE----EEE-SSS------------------------CTS----T-
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEE----EEe-CCc------------------------hhh----h-
Confidence 789999999999999999999999999998742210 000 000 000 0
Q ss_pred eeeecCCCCCCccccCCCCcccC-CCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCC
Q psy8476 135 TVFELGGPGGEALVKSPGNTVCN-THSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQ 213 (421)
Q Consensus 135 ~~~~~g~~~~~~~~~~p~~~~~~-~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~ 213 (421)
......+...... .... .++.+.++++|+|+.++ ..++.+.. ........++|++|+||+.++
T Consensus 49 ----------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~---~~~~~~~~~~s~l~vPl~~~~ 112 (148)
T PF13185_consen 49 ----------KEEIPLPPPPDEPPAYAA-VGLWEGVLRTGEPIIIN--DDDSSFPP---WELARHPGIRSILCVPLRSGG 112 (148)
T ss_dssp ----------CCECCCCCCCESCHHHCC-EETTSHHHHHTS-EEES--CCCGGGST---THHHCCTT-SEEEEEEEEETT
T ss_pred ----------hhhcccCcccccccchhh-hhHHHHHHhcCceEEEe--Cccccccc---hhhhccccCCEEEEEEEeECC
Confidence 0000111000000 0000 34445559999999999 22212111 123356789999999999875
Q ss_pred CcEEEEEEeeecccCCc
Q psy8476 214 KTVIGVAQLINKISERK 230 (421)
Q Consensus 214 ~~vIGVl~l~~~~~~~~ 230 (421)
+++|||.+.++....|
T Consensus 113 -~~~Gvl~l~~~~~~~f 128 (148)
T PF13185_consen 113 -EVIGVLSLYSKEPNAF 128 (148)
T ss_dssp -EEEEEEEEEESSTT--
T ss_pred -EEEEEEEEeeCCCCCc
Confidence 9999999999877655
No 22
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=98.42 E-value=5.9e-06 Score=68.73 Aligned_cols=117 Identities=27% Similarity=0.321 Sum_probs=79.8
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCC-CchhhhHHHHHhCCCcccccCCcccccCCCCcchhhhccCCCCCCCccc
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSE-TSEASHLERILERPGRVISERKPLCRRESNNVDIEDILAHTPEDPSIAF 133 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~ 133 (421)
|++++++.++..+.+.+++++|+|++++++ +..+... ... +
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~--~~~--~---------------------------------- 42 (149)
T smart00065 1 DLEELLQTILEELRQLLGADRVLIYLVDEDDRGELVLV--AAD--G---------------------------------- 42 (149)
T ss_pred CHHHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEE--Eec--C----------------------------------
Confidence 578999999999999999999999999994 3322100 000 0
Q ss_pred eeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCce-eeeeEEeeeEeC
Q psy8476 134 STVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFT-TRCILCMPIFNG 212 (421)
Q Consensus 134 ~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~-~~s~l~vPl~~~ 212 (421)
.........+| ...+..++++++++++.+.|+..++... ......+. .++++++||..+
T Consensus 43 -------~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~s~~~~Pl~~~ 102 (149)
T smart00065 43 -------LTLPLLGLRYP---------LGEGLAGRVAETGRPLNIPDVEADPVFA----LDLLGRYQGVRSFLAVPLVAD 102 (149)
T ss_pred -------CCcccceEEec---------CCCChHHHHHHcCCeEEeechhhCCccc----cccccceeceeeEEEeeeeec
Confidence 00000011122 4568999999999999999988765221 11222334 899999999995
Q ss_pred CCcEEEEEEeeec-ccCCc
Q psy8476 213 QKTVIGVAQLINK-ISERK 230 (421)
Q Consensus 213 ~~~vIGVl~l~~~-~~~~~ 230 (421)
|+++|++.+.+. ....+
T Consensus 103 -~~~~G~l~~~~~~~~~~~ 120 (149)
T smart00065 103 -GELVGVLALHNKDSPRPF 120 (149)
T ss_pred -CEEEEEEEEEecCCCCCC
Confidence 699999999987 44444
No 23
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.26 E-value=4.2e-05 Score=82.95 Aligned_cols=170 Identities=15% Similarity=0.088 Sum_probs=107.1
Q ss_pred eeeeeEEeeeEeCCCcEEEEEEeeecccCCcchhh-------------------------hccccccHHHHHh----cCC
Q psy8476 200 TTRCILCMPIFNGQKTVIGVAQLINKISERKPLCR-------------------------RESNNVDIEDILA----HTP 250 (421)
Q Consensus 200 ~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~~~~~-------------------------~~~~~~dl~~IL~----~~~ 250 (421)
.+..+.+.|+.+.+|++.|++.+......+..... ......+.++++. .+.
T Consensus 236 ~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~~~~~L~~l~~~~~~ll~~v~~~l~~~~~~~~l~~~v~~~l~ 315 (665)
T PRK13558 236 FWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQRERRKLQRLLERVEGLVNDVTSALVRATDREEIEAAVCDRVG 315 (665)
T ss_pred EEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 34566678999888999998887654443321100 0011222233332 233
Q ss_pred CCCCcceeEEEEEcCCCCeeeee--cCCCCc--cc-ccCCCchHHHHHHHh--CCEEEEcCCCCccccccCCcccccCCC
Q psy8476 251 EDPSIAFSTVFELGGPGGEALVK--SPGNTV--CN-THSRLATIAKYVAST--GQILNIGDVPSWMREEVCNDEDEESDF 323 (421)
Q Consensus 251 ~~l~a~~~~i~l~d~~~~~~~~~--~~~~~~--~~-~~~~~~gi~g~v~~t--g~~v~i~D~~~~~~~~f~~~~d~~~~~ 323 (421)
+..+..+..+.++|++.+.+... .+.... .. ......+..+.++++ |++..+.+...++. . . ...+
T Consensus 316 ~~~~~~~awi~~~d~~~~~l~~~~~~g~~~~~~~~~~~~~~~~p~~~a~~~~~~~~~~~~~~~~~~~--~-~---~~~~- 388 (665)
T PRK13558 316 AGGEYDGAWIGEYDPTSGTITVAEAAGGCDGADGDVLDLAAAGPAAAALQSVVAETEAVESTDVDGV--S-G---TVDG- 388 (665)
T ss_pred hccCcceEEEeeecCCCCeEeeeecccCCcccccccccccccCchHHHHHhccCceEEecCCCcccc--c-c---ccCC-
Confidence 44556677788888887765322 221111 11 112245667788888 88877765432211 0 0 0112
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~ 380 (421)
.|++|+||.. +|+++|||.++...+ ..|+++++.+|+.+|.++|.||++.+.-
T Consensus 389 --~s~~~vPL~~-~g~~~GvL~v~~~~~-~~f~~~e~~ll~~la~~ia~aI~~~~~~ 441 (665)
T PRK13558 389 --SAVAAVPLVY-RETTYGVLVVYTAEP-DEIDDRERVVLEALGRAVGAAINALESR 441 (665)
T ss_pred --ceEEEEeEEE-CCEEEEEEEEeeCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2999999998 579999999999876 5899999999999999999999875543
No 24
>PRK10490 sensor protein KdpD; Provisional
Probab=98.03 E-value=0.00068 Score=76.07 Aligned_cols=59 Identities=10% Similarity=0.149 Sum_probs=51.2
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACK 385 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~ 385 (421)
.+++++||.. .++++||+.+.++.....|+.++.++++.++.|++.++++..+.++.++
T Consensus 595 ~~~~~lPl~~-~~~~~Gvl~l~~~~~~~~~~~~~~~ll~~la~~~a~aler~~l~~~~~~ 653 (895)
T PRK10490 595 VPYQILPLKS-AQKTYGLLAVEPGNLRQLMIPEQQRLLETFTLLIANALERLTLTASEEQ 653 (895)
T ss_pred CceEEEEEEE-CCEEEEEEEEecCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999 4699999999877655689999999999999999999999988766543
No 25
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=97.78 E-value=0.0022 Score=68.96 Aligned_cols=75 Identities=15% Similarity=0.188 Sum_probs=59.5
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhhhcc
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKL---MAKQKVFQRYLTFCGI 402 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~---~~~~~~~~e~~~~~~~ 402 (421)
-.+++.||.+. +.++||+.+... .....+.++.++|.++++|+|+|+++.+|.++.++. .++.++--.+++.++.
T Consensus 592 ~~~~~lPl~~~-~~~~gvlgv~~~-~~~ll~p~~~rlL~a~~~q~AlAler~~L~~~~~~a~l~~e~E~lRsaLL~sISH 669 (890)
T COG2205 592 AKYLYLPLKSG-GKVLGVLGVEPG-LSPLLAPEQRRLLDAVLTQIALALERVTLAEEAEQARLAAERERLRSALLASISH 669 (890)
T ss_pred CceeEeecccC-CceEEEEEecCC-CCccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45899999984 699999999877 445799999999999999999999999999998773 3344444444554444
No 26
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=97.30 E-value=0.001 Score=57.10 Aligned_cols=137 Identities=17% Similarity=0.182 Sum_probs=92.8
Q ss_pred HHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCc-hhhhHHHHHhCCCcccccCCcccccCCCCcc
Q psy8476 39 NQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETS-EASHLERILERPGRVISERKPLCRRESNNVD 117 (421)
Q Consensus 39 ~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~-~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 117 (421)
...+.++++.+ ....++++++..+++.+.+.+++++|.++.++++.. ....+....... ... .
T Consensus 3 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~--~~~-------------~ 66 (175)
T COG2203 3 EALLNELAAKI-AQDLDLEEILQAALELLAELLGADRGLIYLLDEDGLLDGALVAEAAEAG--LEQ-------------L 66 (175)
T ss_pred HHHHHHHHHHH-HHHCCHHHHHHHHHHHHHHHhhccHHhhheeccccccchHHHHHHhcch--hhh-------------h
Confidence 45677888887 556699999999999999999999999999999863 111111111100 000 0
Q ss_pred hhhhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccCcccccCC
Q psy8476 118 IEDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEES 197 (421)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~ 197 (421)
+.+ ....+ +...+..+++...++++.++|+..+|.+...+ ...
T Consensus 67 ~~~--------------------------~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~ 109 (175)
T COG2203 67 IDE--------------------------LFGLV--------ILPACLIGIALREGRPVVVEDILQDPRFRDNP---LVL 109 (175)
T ss_pred HHH--------------------------Hhccc--------CcchhhhhhhhcCCceEEeeccccCcccccCH---HHH
Confidence 000 00000 12334788999999999999999998764211 111
Q ss_pred Cce-eeeeEEeeeEeCCCcEEEEEEeeecccCC
Q psy8476 198 DFT-TRCILCMPIFNGQKTVIGVAQLINKISER 229 (421)
Q Consensus 198 ~~~-~~s~l~vPl~~~~~~vIGVl~l~~~~~~~ 229 (421)
... +++.+++||+.++ +++|++.+.+....+
T Consensus 110 ~~~~i~~~l~vPl~~~~-~~~G~l~~~~~~~~~ 141 (175)
T COG2203 110 LEPPIRSYLGVPLIAQG-ELLGLLCVHDSEPRR 141 (175)
T ss_pred HHHHHHHheeeeeeECC-EeeEEeeeeccCCCC
Confidence 122 7999999999975 999999999887774
No 27
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.07 E-value=0.015 Score=63.14 Aligned_cols=126 Identities=8% Similarity=0.036 Sum_probs=83.3
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcchhh
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDIED 120 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~ 120 (421)
.+.++...+ ....+.+++++.+++.+....+.+.++|+++|++.+.+... ... |.
T Consensus 289 ll~~v~~~l-~~~~~~~~l~~~v~~~l~~~~~~~~awi~~~d~~~~~l~~~---~~~-g~-------------------- 343 (665)
T PRK13558 289 LVNDVTSAL-VRATDREEIEAAVCDRVGAGGEYDGAWIGEYDPTSGTITVA---EAA-GG-------------------- 343 (665)
T ss_pred hHHHHHHHH-HhcCCHHHHHHHHHHHHHhccCcceEEEeeecCCCCeEeee---ecc-cC--------------------
Confidence 344566666 45569999999999999999999999999999988765210 000 00
Q ss_pred hccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhc--CCEEeecCCCCccccccCcccccCCC
Q psy8476 121 ILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVAST--GQILNIGDVPSWMREEVCNDEDEESD 198 (421)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~--g~~~~i~d~~~~p~~~~~~~~d~~~~ 198 (421)
.+. . .+. .+. ....|..+.++++ |++..+.+...++... ...+
T Consensus 344 -----~~~---~------~~~-----~~~----------~~~~~p~~~a~~~~~~~~~~~~~~~~~~~~~------~~~~ 388 (665)
T PRK13558 344 -----CDG---A------DGD-----VLD----------LAAAGPAAAALQSVVAETEAVESTDVDGVSG------TVDG 388 (665)
T ss_pred -----Ccc---c------ccc-----ccc----------ccccCchHHHHHhccCceEEecCCCcccccc------ccCC
Confidence 000 0 000 000 1235667788888 8888887765432211 0111
Q ss_pred ceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 199 FTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 199 ~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
.|++++||..+ |+++|||.+++..++.|
T Consensus 389 ---~s~~~vPL~~~-g~~~GvL~v~~~~~~~f 416 (665)
T PRK13558 389 ---SAVAAVPLVYR-ETTYGVLVVYTAEPDEI 416 (665)
T ss_pred ---ceEEEEeEEEC-CEEEEEEEEeeCCCCCC
Confidence 29999999986 69999999999888777
No 28
>PRK13837 two-component VirA-like sensor kinase; Provisional
Probab=96.91 E-value=0.18 Score=56.35 Aligned_cols=67 Identities=9% Similarity=0.082 Sum_probs=57.4
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMAKQK 391 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~~~~~ 391 (421)
...+++|+|+..+ ++++|++.+........+..+++.+++.++.+++.++++.++.++.++..++..
T Consensus 376 ~~~~~~~~~~~~~-~~~~g~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~e~~~l~~~l~ 442 (828)
T PRK13837 376 GPALWACLAFKSG-DRIVALLGLGRQRYGLRPPAGELQLLELALDCLAHAIERRRLETERDALERRLE 442 (828)
T ss_pred CcceEEEEEeccC-CceEEEEEecccccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3478999999984 699999999887766678899999999999999999999999988877655443
No 29
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=96.78 E-value=0.03 Score=50.52 Aligned_cols=107 Identities=14% Similarity=0.148 Sum_probs=71.6
Q ss_pred EEEEEcCCCCeeeeecCCCCcccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCC
Q psy8476 259 TVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQK 338 (421)
Q Consensus 259 ~i~l~d~~~~~~~~~~~~~~~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g 338 (421)
.+.+-|.++-..++-.+....... + .......++.+|+.....+... +...... .......|.+++||+. +|
T Consensus 72 aVaITDr~~ILA~~G~g~d~~~~~-~-is~~t~~~i~~gk~~~~~~~~~-~~i~c~~----~~~~~l~s~ii~Pl~~-~g 143 (180)
T TIGR02851 72 IVLITDRDTVIAVAGVSKKEYLNK-P-ISDELEDTMEERKTVILSDTKD-GPIEIID----GQEFEYTSQVIAPIIA-EG 143 (180)
T ss_pred EEEEECCCcEEEEECCChhhcCCC-c-cCHHHHHHHHcCCEEEecCCcc-ceecccc----CCCCCcceEEEEEEEE-CC
Confidence 677788877666654443332222 3 4556677999999988776321 1011110 0111247999999998 57
Q ss_pred cEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHH
Q psy8476 339 TVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLG 373 (421)
Q Consensus 339 ~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiA 373 (421)
+++|+|.++.+..+..|++-+..|.+.+|+.++.=
T Consensus 144 ~viGtLkly~k~~~~~~~~~e~~la~glA~lLS~Q 178 (180)
T TIGR02851 144 DPIGAVIIFSKEPGEKLGEVEQKAAETAAAFLGKQ 178 (180)
T ss_pred eEEEEEEEEECCccCCCCHHHHHHHHHHHHHHHHh
Confidence 99999999944434489999999999999887753
No 30
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=96.77 E-value=0.0033 Score=66.22 Aligned_cols=133 Identities=13% Similarity=0.100 Sum_probs=95.8
Q ss_pred HHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcch
Q psy8476 39 NQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDI 118 (421)
Q Consensus 39 ~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 118 (421)
+..|+++++.| ++.+|++++|+.+++.+.+.++++.|+|++++++ .+.. ....|.+.
T Consensus 3 ~~~l~eis~~L-~~s~d~~e~L~~vl~~l~~~l~~~~~~l~l~~~~--~l~~----~as~gl~~---------------- 59 (509)
T PRK05022 3 LDALLPIALDL-SRGLPHQDRFQRLLTTLRQVLPCDASALLRLDGD--QLVP----LAIDGLSP---------------- 59 (509)
T ss_pred HHHHHHHHHHH-hcCCCHHHHHHHHHHHHHHHcCCCEEEEEecCCC--cEEE----EEEcCCCh----------------
Confidence 46799999999 6777999999999999999999999999999864 3311 01000000
Q ss_pred hhhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCc-chhhhhhcCCEEeecCCCCccccccCcccc-cC
Q psy8476 119 EDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLAT-IAKYVASTGQILNIGDVPSWMREEVCNDED-EE 196 (421)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~g-i~g~v~~~g~~~~i~d~~~~p~~~~~~~~d-~~ 196 (421)
+ .. .. ..+.+.| .++.++++|+|+.++|...||.+. ++... ..
T Consensus 60 ~------~~-------------------~~---------~~~~geGP~l~av~~~g~~v~v~~~~~~p~~~-~~~~~~~~ 104 (509)
T PRK05022 60 D------VL-------------------GR---------RFALEEHPRLEAILRAGDPVRFPADSELPDPY-DGLIPGVQ 104 (509)
T ss_pred H------hh-------------------CC---------ccCCCcchHHHHHHhcCCeEEEecCCCCCccc-cccccccc
Confidence 0 00 00 1125677 789999889999999988888741 11111 12
Q ss_pred CCceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 197 SDFTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 197 ~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
...+++|+|||||..+ |+++|||.+++..++.|
T Consensus 105 ~~~gi~S~l~vPL~~~-~~~~GvL~l~~~~~~~f 137 (509)
T PRK05022 105 ESLPVHDCMGLPLFVD-GRLIGALTLDALDPGQF 137 (509)
T ss_pred ccCCcceEEEEEEEEC-CEEEEEEEEeeCCCCcC
Confidence 3457889999999996 59999999999887766
No 31
>PF11849 DUF3369: Domain of unknown function (DUF3369); InterPro: IPR021800 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 170 amino acids in length.
Probab=96.29 E-value=0.78 Score=41.08 Aligned_cols=58 Identities=12% Similarity=0.191 Sum_probs=46.3
Q ss_pred HHHhhHhHHHHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEE
Q psy8476 22 GIQNAQLFEMSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFL 80 (421)
Q Consensus 22 al~na~l~~~~~~~~~~~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L 80 (421)
||...+-........+-++.+++.+..|+.. .+++++...++.++..+++.+...++.
T Consensus 4 aLRsYrdi~~Ie~~R~GLe~Ii~as~~L~~~-~sl~~fa~gvL~Ql~~Ll~~~~~~l~~ 61 (174)
T PF11849_consen 4 ALRSYRDIRTIERNRQGLEKIIEASASLFQI-RSLQEFASGVLTQLSALLGLEDDGLYC 61 (174)
T ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHHHHHcc-CCHHHHHHHHHHHHHHHhCCCCCeEEE
Confidence 4455555555666677788999999999654 599999999999999999988777766
No 32
>PRK10600 nitrate/nitrite sensor protein NarX; Provisional
Probab=96.00 E-value=1.3 Score=47.14 Aligned_cols=54 Identities=7% Similarity=0.081 Sum_probs=46.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCc
Q psy8476 32 SILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETS 86 (421)
Q Consensus 32 ~~~~~~~~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~ 86 (421)
.++..+.++.|++.++.+ ....++.+.++.++..+..+++++.+.+.+++++.+
T Consensus 212 l~~~~~~l~~ly~~~~~l-~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~ 265 (569)
T PRK10600 212 LEQKNQILSFLWQANRRL-HSRAPLCERLSPVLNGLQNLTLLRDIELRVYETDDE 265 (569)
T ss_pred HHHHHHHHHHHHHHHHHH-hcCcchHHHHHHHHHHHHHhcCCCceEEEEeccccc
Confidence 444556778999999998 566689999999999999999999999999997654
No 33
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=95.97 E-value=0.009 Score=65.62 Aligned_cols=77 Identities=10% Similarity=0.003 Sum_probs=58.1
Q ss_pred ccccccHHHHHh----cCCCCCCcceeEEEEEcCCCCeeeeecCCCC---c--ccccCCCchHHHHHHHhCCEEEEcCCC
Q psy8476 236 ESNNVDIEDILA----HTPEDPSIAFSTVFELGGPGGEALVKSPGNT---V--CNTHSRLATIAKYVASTGQILNIGDVP 306 (421)
Q Consensus 236 ~~~~~dl~~IL~----~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~~---~--~~~~~~~~gi~g~v~~tg~~v~i~D~~ 306 (421)
.....+++++|. .+.+.++++.|+||++|+++..++.....+. . ....+.++|++|+|+++|+|++++|++
T Consensus 12 L~s~~dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~geGi~G~Va~tg~pV~V~Dv~ 91 (748)
T PRK11061 12 VASAPRLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDEGIVGLVGRLAEPINLADAQ 91 (748)
T ss_pred HhccCCHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCcchHHHHhccCceEEECCcc
Confidence 345566666554 4567789999999999999987655443332 1 124577899999999999999999999
Q ss_pred Cccccc
Q psy8476 307 SWMREE 312 (421)
Q Consensus 307 ~~~~~~ 312 (421)
.||++.
T Consensus 92 ~dprf~ 97 (748)
T PRK11061 92 KHPSFK 97 (748)
T ss_pred cCcccc
Confidence 988764
No 34
>PRK04158 transcriptional repressor CodY; Validated
Probab=95.05 E-value=0.35 Score=45.73 Aligned_cols=60 Identities=25% Similarity=0.268 Sum_probs=49.9
Q ss_pred CCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 322 DFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENAC 384 (421)
Q Consensus 322 ~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~ 384 (421)
.+..+-+..+||..+ |+-+|.|.+.... .+|+++|+-+++.-|.-+|+.+.+.+.-+..+
T Consensus 106 ~~~~~~~tIvPI~gg-GeRLGTLvl~r~~--~~f~~dDliL~EyaATVVgLEIlR~~a~e~eE 165 (256)
T PRK04158 106 LFPDKLTTIVPIIGG-GERLGTLILARFD--KEFTDDDLILAEYAATVVGMEILREKAEEIEE 165 (256)
T ss_pred cccCceEEEEEEecC-CeEEEEEEEEecC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567999999995 7999999998665 48999999999999999999999877655444
No 35
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=94.75 E-value=0.4 Score=51.97 Aligned_cols=115 Identities=12% Similarity=0.121 Sum_probs=72.5
Q ss_pred eEEEEEcCCCCeeeeecCCC---------C----cccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCc
Q psy8476 258 STVFELGGPGGEALVKSPGN---------T----VCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFT 324 (421)
Q Consensus 258 ~~i~l~d~~~~~~~~~~~~~---------~----~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~ 324 (421)
+.+.+.|.++..+....... . ...+...+..-.|.+..+++|+.+....+ |.. .++
T Consensus 73 ~~~~l~D~~G~vL~~~g~~~~~~~~~~~~~~~G~~w~E~~~GTnaig~al~~~~pv~v~g~EH-----~~~------~~~ 141 (638)
T PRK11388 73 CALLILDETGCILSRNGDPQTLQQLSALGFNDGTYCAEGIIGTNALSLAAISGQPVKTMGDQH-----FKQ------ALH 141 (638)
T ss_pred cEEEEEcCCceEEEEeCCHHHHHHHHHcCCccCCccchhccCcCHHHHHHhcCCceEEecHHH-----HHH------hcc
Confidence 67788888777655332110 0 00112244568888999999999875432 321 123
Q ss_pred cceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 325 TRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACK 385 (421)
Q Consensus 325 ~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~ 385 (421)
.-++.++||+..+|+++|||.+..... .++...+.++..+|.++...+......++.+.
T Consensus 142 ~~~c~aaPI~d~~G~liGvl~l~~~~~--~~~~~~l~lv~~~a~~Ie~~l~~~~~~~~~~~ 200 (638)
T PRK11388 142 NWAFCATPVFDSKGRLTGTIALACPVE--QTSAADLPLTLSIAREVGNLLLTDSLLAESNR 200 (638)
T ss_pred CceEEeeEEEcCCCCEEEEEEEEeccc--ccChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357999999998899999999987653 46666777666666666665544333333333
No 36
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=94.10 E-value=0.076 Score=56.28 Aligned_cols=77 Identities=17% Similarity=0.027 Sum_probs=55.4
Q ss_pred hccccccHHHHHhc----CCCCCCcceeEEEEEcCCCCeeeee-cCCCC---cccccCCCchHHHHHHHhCCEEEEcCCC
Q psy8476 235 RESNNVDIEDILAH----TPEDPSIAFSTVFELGGPGGEALVK-SPGNT---VCNTHSRLATIAKYVASTGQILNIGDVP 306 (421)
Q Consensus 235 ~~~~~~dl~~IL~~----~~~~l~a~~~~i~l~d~~~~~~~~~-~~~~~---~~~~~~~~~gi~g~v~~tg~~v~i~D~~ 306 (421)
......++++++.. +.+.+++++|+|+++|.++...... .+... .....+.++|++|+|+++|+|++++|+.
T Consensus 13 ~l~~~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~aa~g~~~~~~~~~~~~~~~gi~g~v~~~~~pvii~Dv~ 92 (534)
T TIGR01817 13 ILSAPTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLVAAIGWSEEGFAPIRYRVGEGAIGQIVATGNSLVVPDVA 92 (534)
T ss_pred HHhccCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEEEEeCCChhhcccccccCCccHHHHHHhcCCeEEecccc
Confidence 34556777776554 5567899999999999987764332 22211 1124567799999999999999999999
Q ss_pred Ccccc
Q psy8476 307 SWMRE 311 (421)
Q Consensus 307 ~~~~~ 311 (421)
.|+++
T Consensus 93 ~d~~~ 97 (534)
T TIGR01817 93 AEPLF 97 (534)
T ss_pred cCchh
Confidence 87654
No 37
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=93.58 E-value=0.4 Score=44.86 Aligned_cols=46 Identities=15% Similarity=0.269 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCc
Q psy8476 40 QILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETS 86 (421)
Q Consensus 40 ~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~ 86 (421)
+.+.++...+.+. .+++++++.+...+++.++.+.+++.|+++...
T Consensus 78 ~~~~~l~l~LL~a-~sl~~l~~~L~~~l~~~f~~~~v~L~L~~~~~~ 123 (225)
T PF04340_consen 78 QRLHRLVLALLAA-RSLQELLQALDDGLREDFDVDAVRLRLFDDDAA 123 (225)
T ss_dssp HHHHHHHHHHHC---SHHHHHHHHHHHHHHTS--SEEEEEEE-SS--
T ss_pred HHHHHHHHHHhcC-CCHHHHHHHHHHHHHHhcCCCeEEEEeeccccc
Confidence 4556666677555 499999999999999999999999999998654
No 38
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=93.37 E-value=0.18 Score=51.91 Aligned_cols=135 Identities=16% Similarity=0.151 Sum_probs=93.0
Q ss_pred HHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchhhhHHHHHhCCCcccccCCcccccCCCCcch
Q psy8476 39 NQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETSEASHLERILERPGRVISERKPLCRRESNNVDI 118 (421)
Q Consensus 39 ~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~ 118 (421)
.+.+.+++..+ .+..++++++..+.+.+..+++|+++.|.++|.++-..+ ...+.+ ..
T Consensus 33 ~~~l~el~~~l-~~~~~~e~ll~~v~~~l~~~~~~~~~~ll~~d~~~l~~~----~~~gl~--~~--------------- 90 (550)
T COG3604 33 IRILVELTNAL-LSPLRLERLLAEVAKELHSLFGCDASALLRLDSKNLIPL----ATDGLS--KD--------------- 90 (550)
T ss_pred hHHHHHhhhhh-cCchhHHHHHHHHHHHHHHHhcCCeeEEEEecccccchh----hhhccc--cc---------------
Confidence 56899999998 666799999999999999999999999999999871111 111111 00
Q ss_pred hhhccCCCCCCCccceeeeecCCCCCCccccCCCCcccCCCCCCCcchhhhhhcCCEEeecCCCCccccccC--cccccC
Q psy8476 119 EDILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVC--NDEDEE 196 (421)
Q Consensus 119 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~p~~~~~~~~~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~--~~~d~~ 196 (421)
.+|.. .... ..++++++.|+++|.|+.+ +..|+.+... .-....
T Consensus 91 --------------------~~~~~---~~~~---------~~~~~~l~~i~~~~~p~~~--~~~d~~~~~~~~~l~~~~ 136 (550)
T COG3604 91 --------------------HLGRE---QRFV---------VEGHPLLEQILKAGRPLVF--HPADSLFPDPYDGLLPDT 136 (550)
T ss_pred --------------------ccccc---cccc---------cCcchHHHHHHhCCCcEEE--ecCCcccCCcccccccCc
Confidence 00000 0001 2468899999999999999 3333332111 111112
Q ss_pred CCceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 197 SDFTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 197 ~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
.+...++++++||+.++ +++|++.+....++.|
T Consensus 137 ~~~~~~a~i~~PL~~~~-~~~G~Ltld~~~~~~f 169 (550)
T COG3604 137 EGNKKHACIGVPLKSGD-KLIGALTLDHTEPDQF 169 (550)
T ss_pred cCCcceeEEeeeeeeCC-eeeeeEEeeeeccccc
Confidence 23357999999999975 9999999999888766
No 39
>PF06018 CodY: CodY GAF-like domain; InterPro: IPR010312 This family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; GO: 0003677 DNA binding, 0005525 GTP binding; PDB: 2HGV_A 2GX5_D 2B0L_C 2B18_A.
Probab=92.24 E-value=1.4 Score=39.50 Aligned_cols=55 Identities=25% Similarity=0.353 Sum_probs=42.0
Q ss_pred CccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 323 FTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 323 ~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~ 380 (421)
+..+-...|||..+ |+-+|.|.+.... .+|+++|+-|.+.-|--+|+-+-+++.=
T Consensus 105 ~~~k~~tivPI~g~-GeRLGTLvl~r~~--~~F~ddDLILaEY~ATVVGmEiLr~~~e 159 (177)
T PF06018_consen 105 FPNKYTTIVPIYGG-GERLGTLVLARFD--KEFTDDDLILAEYGATVVGMEILRSKSE 159 (177)
T ss_dssp GSSSEEEEEEEEET-TEEEEEEEEEESS------HHHHHHHHHHHHHHHHHHHHHHT-
T ss_pred ccCCcEEEEEEeeC-CeEEEEEEEEEcC--CCCChhhhHHHHHHHHHHHHHHHHHHHH
Confidence 44456789999994 8999999998764 4899999999999999999888876543
No 40
>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]
Probab=91.78 E-value=10 Score=39.77 Aligned_cols=55 Identities=9% Similarity=0.069 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCc
Q psy8476 31 MSILEFERNQILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETS 86 (421)
Q Consensus 31 ~~~~~~~~~~~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~ 86 (421)
..++...++..|++.++.+ ++....++.+.-+++.+..+.++....+.+++++..
T Consensus 237 ~L~~~Nq~Ls~LYqssr~L-~ts~~~~~~l~~vLn~l~~~~~~~~~~l~l~~~~~e 291 (574)
T COG3850 237 DLEQKNQRLSFLYQSSRRL-HTSQIDDERLRHVLNRLQNLTGLAAVRLELYGGDDE 291 (574)
T ss_pred HHHHhhhHHHHHHHHHHHh-ccCCChHHHHHHHHHHHHHhhcccceEEEEecCcch
Confidence 3445567889999999999 666799999999999999999999999999998653
No 41
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=91.15 E-value=0.58 Score=49.52 Aligned_cols=88 Identities=11% Similarity=0.068 Sum_probs=69.5
Q ss_pred CchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHH
Q psy8476 286 LATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEA 365 (421)
Q Consensus 286 ~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~ 365 (421)
+..-+|.++.++++|.|---+ +|. ..+..=||-++||+..+|++.|||.+...+. +-++....++..
T Consensus 129 GTNgIGTcLve~~aVtI~~~q-----HF~------~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~--~~~~~s~~~~~~ 195 (606)
T COG3284 129 GTNGIGTCLVEGEAVTIHGDQ-----HFI------QAHHGLSCSAAPIFDEQGELVGVLDISSCRS--DLSEASQPLTLA 195 (606)
T ss_pred cccchhhhhccCcceEEehhh-----hHh------hcccCceeeeeccccCCCcEEEEEEeccCCc--chhhhhhHHHHH
Confidence 344567889999999875422 232 2234468999999999999999999987764 578899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy8476 366 FAIFCGLGIHNTQMYENACKL 386 (421)
Q Consensus 366 lA~q~aiAlena~L~~e~~~~ 386 (421)
+...+|..+|+..+.+..+..
T Consensus 196 iV~~~ar~IE~~~~~~~~~~~ 216 (606)
T COG3284 196 IVTDAARRIEAELFLAAFEGH 216 (606)
T ss_pred HHHHHHHHHHHHHHHHhcCcc
Confidence 999999999998888776663
No 42
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=90.07 E-value=3.4 Score=42.50 Aligned_cols=88 Identities=14% Similarity=0.203 Sum_probs=65.3
Q ss_pred cCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHH
Q psy8476 283 HSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSI 362 (421)
Q Consensus 283 ~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~l 362 (421)
.+...+.+..++.+|+.+....-.. +..+. ..-+.+|.+..|+..+ |+|+|.|-++-++. +.|+.-...+
T Consensus 266 ~~i~s~~t~~ai~~g~vv~~~~~e~---~~csh-----~~c~l~s~lViPL~~~-g~ViGTiK~y~~~~-~lis~~~r~l 335 (557)
T COG3275 266 KPIISSLTRKAIKTGEVVYADGNEV---YECSH-----PTCKLGSALVIPLRGK-GRVIGTIKLYEAKA-RLISSINREL 335 (557)
T ss_pred CeeccHHHHHHHhhCCEEEEccchh---hccCC-----CCCCcCCceEeecccC-CceeeeEEEEeccH-hHhhHHHHHH
Confidence 3455778888999999876543222 11110 1124689999999995 89999999998887 5899999999
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy8476 363 FEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 363 L~~lA~q~aiAlena~L~ 380 (421)
.+.+|+.++-=++-.+.-
T Consensus 336 a~Gia~l~SaQie~ge~e 353 (557)
T COG3275 336 AEGIAQLLSAQIEAGEAE 353 (557)
T ss_pred HHHHHHHHHHHHHHhHHH
Confidence 999998888777755543
No 43
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=89.13 E-value=3.3 Score=38.94 Aligned_cols=56 Identities=21% Similarity=0.275 Sum_probs=46.3
Q ss_pred CCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 322 DFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 322 ~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~ 380 (421)
.|..+-...|||.. .|+=+|.+.+.... .+|+++|+-|.+.-|--+|+-+-+.+.-
T Consensus 103 ~~~~~~~tivPI~g-~g~RLGTl~l~r~~--~~F~~dDliLaEy~aTVVG~Eilr~~~~ 158 (251)
T TIGR02787 103 LFPKGLTTIVPIYG-GGERLGTLILARSD--KEFNDDDLVLAEYAATVVGMELLRAQAE 158 (251)
T ss_pred hccCCcEEEEeeec-CCceeEEEEEEEcC--CCCCcccchhhhhHhHHHHHHHHHHHHH
Confidence 34456688999998 47899999997664 4899999999999999999988876643
No 44
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=88.48 E-value=7.9 Score=34.94 Aligned_cols=57 Identities=14% Similarity=0.197 Sum_probs=38.3
Q ss_pred CcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeec
Q psy8476 163 ATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINK 225 (421)
Q Consensus 163 ~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~ 225 (421)
.-.+-.++.+|+.....+... +.+... ........+.+++||+.+ |+++|+|.++.+
T Consensus 98 s~~t~~~i~~gk~~~~~~~~~-~~i~c~----~~~~~~l~s~ii~Pl~~~-g~viGtLkly~k 154 (180)
T TIGR02851 98 SDELEDTMEERKTVILSDTKD-GPIEII----DGQEFEYTSQVIAPIIAE-GDPIGAVIIFSK 154 (180)
T ss_pred CHHHHHHHHcCCEEEecCCcc-ceeccc----cCCCCCcceEEEEEEEEC-CeEEEEEEEEEC
Confidence 345678999999998886321 111111 011234689999999976 599999999933
No 45
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=87.61 E-value=0.54 Score=41.73 Aligned_cols=60 Identities=22% Similarity=0.149 Sum_probs=42.9
Q ss_pred CCCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecc
Q psy8476 160 SRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKI 226 (421)
Q Consensus 160 ~~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~ 226 (421)
+.|.|+.|+++.+|+++.|.+....+...+.+.. .......+.++|+|+.+ ||+++.+..
T Consensus 88 sfg~G~~G~a~~sg~~~Wi~~~~~~~~~~~~r~~-~aq~~~~~Tiv~IPv~~------GVvELGSt~ 147 (163)
T PF14215_consen 88 SFGEGIPGRAAASGQHIWISGANELDSSYCERAW-LAQFAGIQTIVCIPVPN------GVVELGSTE 147 (163)
T ss_pred EecCCccEEEeecCccEEEeCCCccccccchhhh-hhcccccceEEEEEecC------CEEEeeeee
Confidence 3589999999999999999998765443333221 11234566999999943 688887654
No 46
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=87.38 E-value=2.6 Score=38.46 Aligned_cols=73 Identities=18% Similarity=0.225 Sum_probs=53.7
Q ss_pred chHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHH
Q psy8476 287 ATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAF 366 (421)
Q Consensus 287 ~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~l 366 (421)
..+...++++++++-..|..--|... ++|. ....+.|++|.|+-. + |++.+..... +.||+.|...++.+
T Consensus 121 g~i~~~~~~~~~~~yL~nl~lyPGr~---Ef~~-lP~ntq~VlvqP~g~-~----G~lvlgs~~~-R~ft~~D~~Wi~~i 190 (195)
T PF11152_consen 121 GPICQRAMESGKLIYLVNLKLYPGRV---EFDY-LPENTQSVLVQPLGQ-N----GVLVLGSNSP-RAFTKSDEAWIAGI 190 (195)
T ss_pred HHHHHHHHhcCCceeccccccCCCch---hhhh-cCCCCcEEEEEEcCC-C----eEEEEeeCCc-cccCHHHHHHHHHH
Confidence 35677789999998877764333221 2221 223579999999987 3 8999988877 69999999999999
Q ss_pred HHH
Q psy8476 367 AIF 369 (421)
Q Consensus 367 A~q 369 (421)
|+.
T Consensus 191 A~K 193 (195)
T PF11152_consen 191 ADK 193 (195)
T ss_pred HHh
Confidence 974
No 47
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=86.82 E-value=2.6 Score=45.68 Aligned_cols=55 Identities=13% Similarity=0.157 Sum_probs=42.4
Q ss_pred CCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecc
Q psy8476 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKI 226 (421)
Q Consensus 161 ~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~ 226 (421)
.|..-+|-+..+++|+.|....+ |. ..+..-++.++||++.+|+++|||.+....
T Consensus 113 ~GTnaig~al~~~~pv~v~g~EH-----~~------~~~~~~~c~aaPI~d~~G~liGvl~l~~~~ 167 (638)
T PRK11388 113 IGTNALSLAAISGQPVKTMGDQH-----FK------QALHNWAFCATPVFDSKGRLTGTIALACPV 167 (638)
T ss_pred cCcCHHHHHHhcCCceEEecHHH-----HH------HhccCceEEeeEEEcCCCCEEEEEEEEecc
Confidence 56778999999999998875332 11 124456888999999999999999987643
No 48
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=84.83 E-value=5.2 Score=36.78 Aligned_cols=50 Identities=24% Similarity=0.312 Sum_probs=41.6
Q ss_pred EEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 328 ILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMY 380 (421)
Q Consensus 328 ~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~ 380 (421)
--.+||.. .|+-+|.+.+....+ .|+++|+-|.+.-|-.+|+-+-|.++-
T Consensus 115 tTi~PI~G-~g~RLGTLil~R~d~--~F~ddDLiL~E~~aTvvG~qil~~k~e 164 (261)
T COG4465 115 TTIVPIYG-GGERLGTLILWRLDD--KFTDDDLILVEYAATVVGMQILREKLE 164 (261)
T ss_pred eEEEEEec-CCeeeeeEEEEecCC--CCCccceehhhhhhHHHHHHHHHHHHH
Confidence 34689998 589999999876543 799999999999999999988876654
No 49
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=84.64 E-value=11 Score=32.42 Aligned_cols=87 Identities=16% Similarity=0.104 Sum_probs=56.4
Q ss_pred HHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHH
Q psy8476 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAI 368 (421)
Q Consensus 289 i~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~ 368 (421)
-+-.++++++++.+..-... .+ . ..+.=+.+||.. +|+++||+-+.-. .++-..+...+..
T Consensus 45 gA~~~i~~~~~~~i~~~~~~---~~-------~--g~k~GinlPI~~-~g~~iGviGItG~------p~eV~~~~~lvk~ 105 (135)
T PF05651_consen 45 GAKEVIRTNKEIEITEEDAE---QY-------P--GVKPGINLPIIF-NGEVIGVIGITGE------PEEVRPYAQLVKK 105 (135)
T ss_pred HHHHHHHcCCcccccHhHHh---hc-------c--CCCcceeeeEEE-CCEEEEEEEEecC------HHHHHHHHHHHHH
Confidence 45567888888776542210 11 1 246678899999 6899999999633 2355566666677
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 369 FCGLGIHNTQMYENACKLMAKQKVFQ 394 (421)
Q Consensus 369 q~aiAlena~L~~e~~~~~~~~~~~~ 394 (421)
++-+-|+...+.++.+.....++.++
T Consensus 106 ~~Elll~e~~~~~~~~~~~~~~~~~l 131 (135)
T PF05651_consen 106 MAELLLEEEYLKEQLQWRERARESFL 131 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777887777766666555444443
No 50
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=84.12 E-value=2.7 Score=39.21 Aligned_cols=51 Identities=14% Similarity=0.174 Sum_probs=42.2
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlen 376 (421)
..+|+..+||. +++.+|+|.+.++.+.+--.+-+-.+|+.+|..++.+|+.
T Consensus 172 ~v~S~AlipL~--~~~~~G~LalGS~D~~rF~p~mgT~fL~~La~vv~~~L~r 222 (225)
T PF04340_consen 172 QVGSVALIPLG--SGRPIGLLALGSRDPDRFQPDMGTDFLEQLAEVVSAALER 222 (225)
T ss_dssp C-SEEEEEEEE--SSSEEEEEEEEESSTTCCCSTTTTHHHHHHHHHHHHHGGG
T ss_pred cccchheeecc--CCCceEEEEecCCChhhCCCCccHHHHHHHHHHHHHHHhc
Confidence 56999999999 4689999999999987444455788999999999998864
No 51
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=81.12 E-value=4.8 Score=30.66 Aligned_cols=55 Identities=13% Similarity=0.145 Sum_probs=36.6
Q ss_pred ceeeeeEEeeeEeCCCcEEEEEEeeecccCCcchhhhccccccHHHHHhcCCCCCCcceeEEEEEcCCCCe
Q psy8476 199 FTTRCILCMPIFNGQKTVIGVAQLINKISERKPLCRRESNNVDIEDILAHTPEDPSIAFSTVFELGGPGGE 269 (421)
Q Consensus 199 ~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~~~~~~~~~~~dl~~IL~~~~~~l~a~~~~i~l~d~~~~~ 269 (421)
...--.+++|+.+.+|+++||+.+.- +++.+...+.+.---.-+.+|++|.++..
T Consensus 11 ~~~vi~~s~pi~~~~g~~~Gvv~~di----------------~l~~l~~~i~~~~~~~~g~~~ivd~~G~i 65 (81)
T PF02743_consen 11 GQPVITISVPIYDDDGKIIGVVGIDI----------------SLDQLSEIISNIKFGNNGYAFIVDKNGTI 65 (81)
T ss_dssp TEEEEEEEEEEEETTTEEEEEEEEEE----------------EHHHHHHHHTTSBBTTTBEEEEEETTSBB
T ss_pred CcEEEEEEEEEECCCCCEEEEEEEEe----------------ccceeeeEEEeeEECCCEEEEEEECCCCE
Confidence 34556789999998899999999853 34444433333322345678888887654
No 52
>PF03472 Autoind_bind: Autoinducer binding domain; InterPro: IPR005143 This domain binds N-acyl homoserine lactones (AHLs), which are also known as autoinducers. These are small, diffusible molecules used as communication signals in a large variety of proteobacteria. It is almost always found in association with the DNA-binding LuxR domain (IPR000792 from INTERPRO). The autoinducer binding domain forms the N-terminal region of the protein, while the DNA-binding domain forms the C-terminal region. In most cases, binding of AHL by this N-terminal domain leads to unmasking of the DNA-binding domain, allowing it to bind DNA and activate transcription []. In rare cases, some LuxR proteins such as EsaR, act as repressors []. In these proteins binding of AHL to this domain leads to inactivation of the protein as a transcriptional regulator. A large number of processes have been shown to be regulated by LuxR proteins, including bioluminescence, production of virulence factors in plant and animal pathogens, antibiotic production and plasmid transfer. Structural studies of TraR from Agrobacterium tumefaciens [, ] show that the functional protein is a homodimer. Binding of the cognate AHL is required for protein folding, resistance to proteases and dimerisation. The autoinducer binding domain binds its cognate AHL in an alpha/beta/alpha sandwich and provides an extensive dimerisation surface, though residues from the C-terminal region also make some contribution to dimerisation. The autoinducer binding domain is also required for interaction with RpoA, allowing transcription to occur []. There are some proteins which consist solely of the autoinducer binding domain. The function of these is not known, but TrlR from Agrobacterium has been shown to inhibit the activity of TraR by the formation of inactive heterodimers [].; PDB: 3SZT_A 1H0M_A 1L3L_B 2Q0O_B 2UV0_F 3IX8_A 3IX4_C 3IX3_A 3JPU_D 3QP8_A ....
Probab=79.72 E-value=10 Score=31.96 Aligned_cols=127 Identities=12% Similarity=0.019 Sum_probs=72.1
Q ss_pred cHHHHHhcCCCCCCcceeEEEEEcCCCCe---eeeecCCCC-cc-----cccCCCchHHHHHHHhCCEEEEcCCCCccc-
Q psy8476 241 DIEDILAHTPEDPSIAFSTVFELGGPGGE---ALVKSPGNT-VC-----NTHSRLATIAKYVASTGQILNIGDVPSWMR- 310 (421)
Q Consensus 241 dl~~IL~~~~~~l~a~~~~i~l~d~~~~~---~~~~~~~~~-~~-----~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~- 310 (421)
++.+++..+...++.+...+......... ..++...+. +. .......-+..++..+..|+...+......
T Consensus 4 ~l~~~l~~~~~~~Gf~~~~~~~~~~~~~~~~~~~~~~~~p~~w~~~Y~~~~~~~~DPv~~~~~~~~~p~~W~~~~~~~~~ 83 (149)
T PF03472_consen 4 ELWDLLERLAARLGFDRFAYGAPSPDPRGDSDFLLISNYPDEWLEHYEERGYFRIDPVVRHARRSSGPFFWSDLFERDAL 83 (149)
T ss_dssp HHHHHHHHHHHCTTTSEEEEEEEETTSCECEEEEEEESS-HHHHHHHHHTTGGGT-HHHHHHCHTSSEEEEECHCTSSSS
T ss_pred HHHHHHHHHHHHcCCCEEEEEeccCCCCCCccEEEEecCCHHHHHHHHHcCCcCCCHHHHHHHhCCCCEEEccchhhhhh
Confidence 45556666667777776666643443333 333333332 21 122344667777788888998877654311
Q ss_pred -cccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHH----HHHHHHHHHHHH
Q psy8476 311 -EEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDC----DVSIFEAFAIFC 370 (421)
Q Consensus 311 -~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~----d~~lL~~lA~q~ 370 (421)
+....-.+....+..++-+++|+...+|.. |++.+...... .... +...|+.+|..+
T Consensus 84 ~~~~~~~~~~a~~~Gl~~G~~~p~~~~~g~~-~~~s~~~~~~~--~~~~~~~~~~~~l~~la~~~ 145 (149)
T PF03472_consen 84 SPEQRRFFDEARDFGLRSGVSVPLHGPDGRF-GALSFAGDERD--PDAEELLWHRADLRLLAHYF 145 (149)
T ss_dssp SHHHHHHHHHHHHTTTSEEEEEEEEECCGCE-EEEEEEESSSS--CCHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHcCCCceEEEEeEcCCCCE-EEEEEECCCCC--CChHHHHHHHHHHHHHHHHH
Confidence 000011122234566999999999976555 99999777653 3444 555666666543
No 53
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=79.62 E-value=2 Score=38.14 Aligned_cols=59 Identities=19% Similarity=0.138 Sum_probs=39.3
Q ss_pred CchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCC
Q psy8476 286 LATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVT 351 (421)
Q Consensus 286 ~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~ 351 (421)
+.|+.|+++.+|+++.+.+....+...+...... .-.....++|+|+. + |||.+.+...
T Consensus 90 g~G~~G~a~~sg~~~Wi~~~~~~~~~~~~r~~~a-q~~~~~Tiv~IPv~--~----GVvELGSt~~ 148 (163)
T PF14215_consen 90 GEGIPGRAAASGQHIWISGANELDSSYCERAWLA-QFAGIQTIVCIPVP--N----GVVELGSTEK 148 (163)
T ss_pred cCCccEEEeecCccEEEeCCCccccccchhhhhh-cccccceEEEEEec--C----CEEEeeeeee
Confidence 6899999999999999987755322222211111 11223589999994 3 6999987765
No 54
>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]
Probab=79.31 E-value=98 Score=33.45 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=34.0
Q ss_pred HHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCc
Q psy8476 48 SIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSETS 86 (421)
Q Consensus 48 ~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~ 86 (421)
.+ .++-++.+++..+.+.+++..|.|+..+|-+|++..
T Consensus 141 ~l-q~a~~l~~l~~~~tqeVr~~tGfDRVMlYrF~~d~~ 178 (750)
T COG4251 141 RL-QSAANLRDLLSRTTQEVRRMTGFDRVMLYRFDEDGS 178 (750)
T ss_pred HH-hcCccHHHHHHHHHHHHHHhcCCceEEEEeecCCCC
Confidence 45 566799999999999999999999999999999764
No 55
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=78.58 E-value=24 Score=35.60 Aligned_cols=127 Identities=13% Similarity=0.139 Sum_probs=65.1
Q ss_pred HHHhcCCCCCCcceeEEEEEcCCCCeeeeecCCCCcccccCCCchHHHHHHHhCCEEEEcCCCCccccccCCcccccCCC
Q psy8476 244 DILAHTPEDPSIAFSTVFELGGPGGEALVKSPGNTVCNTHSRLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDF 323 (421)
Q Consensus 244 ~IL~~~~~~l~a~~~~i~l~d~~~~~~~~~~~~~~~~~~~~~~~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~ 323 (421)
+|+.++++.++. .|-++|.++.....-++. ..-..++| +-.++++++++.|...... .+ .
T Consensus 13 ~IV~~~~~ii~~---ninimd~~G~IIaS~d~~----Rig~~Heg-A~~~~~~~~~~~i~~~~~~---~~-------~-- 72 (385)
T PRK11477 13 DIVARTMRIIDT---NINVMDARGRIIGSGDRE----RIGELHEG-ALLVLSQGRVVDIDDAVAR---HL-------H-- 72 (385)
T ss_pred HHHHHHHHHcCC---CeEEECCCCEEEecCChH----HcccccHH-HHHHHhcCCeeeecHHHHh---hc-------C--
Confidence 455555555543 355566655432211110 01112223 3346888999887542110 11 1
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMA-KQKVFQRYL 397 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~~-~~~~~~e~~ 397 (421)
..+.=+.+||.. +|+++|||-+... .++=..+.+.+...+-+.++.+.+.++.+.... +...+.+.+
T Consensus 73 g~k~GiN~Pi~~-~~~viGvIgItG~------p~ev~~~~~lv~~~aEllleq~~~~~~~~~~~~~~~~fl~~LL 140 (385)
T PRK11477 73 GVRQGINLPLRL-EGEIVGVIGLTGE------PENLRKYGELVCMTAEMMLEQSRLMHLLAQDSRLREELVMNLI 140 (385)
T ss_pred CCCcCceeeEEE-CCEEEEEEecCCC------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 236678999999 6899999987521 223333444444455566666666654444333 333444443
No 56
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=76.95 E-value=9.4 Score=29.58 Aligned_cols=47 Identities=15% Similarity=0.342 Sum_probs=34.0
Q ss_pred chhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeec
Q psy8476 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINK 225 (421)
Q Consensus 165 i~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~ 225 (421)
+.-.|+++|+.+...-.. -.|.-..++.+||.+++|++||++-+++-
T Consensus 36 VLe~vl~~g~v~r~~P~~--------------G~Y~G~PViV~PI~~~~g~viaAiGvVD~ 82 (84)
T PF09884_consen 36 VLEEVLETGKVIRVTPIE--------------GPYKGVPVIVAPIKDEDGEVIAAIGVVDL 82 (84)
T ss_pred HHHHHHHcCCEEEeccCC--------------cccCCeeEEEEEEEcCCCCEEEEEEEEEc
Confidence 445667777777633221 23667789999999998999999988753
No 57
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=73.22 E-value=13 Score=30.83 Aligned_cols=35 Identities=14% Similarity=0.297 Sum_probs=28.4
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSI 362 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~l 362 (421)
-+.+++||...+|+++|+|.+..... .|+++....
T Consensus 79 v~~iA~Pi~~~~g~~~~alsv~~~~~--~~~~~~~~~ 113 (129)
T PF01614_consen 79 VAAIAVPIFDPNGQVVAALSVSGPSE--RFDEERLEE 113 (129)
T ss_dssp EEEEEEEEEETTSCEEEEEEEEEEGG--GSHHHHHHH
T ss_pred cceEEEEEECCCCCEEEEEEEeeEhH--hCCHHHHHH
Confidence 46899999998899999999988764 577766554
No 58
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=72.73 E-value=22 Score=37.97 Aligned_cols=56 Identities=16% Similarity=0.113 Sum_probs=43.5
Q ss_pred CCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeeccc
Q psy8476 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKIS 227 (421)
Q Consensus 161 ~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~ 227 (421)
.|..-+|-++..++|+.|.--.. | . ..+..-|+.++||++.+|+++|||.+.+...
T Consensus 128 ~GTNgIGTcLve~~aVtI~~~qH---F--~------~~~~~lsCsAaPI~D~qG~L~gVLDISs~r~ 183 (606)
T COG3284 128 EGTNGIGTCLVEGEAVTIHGDQH---F--I------QAHHGLSCSAAPIFDEQGELVGVLDISSCRS 183 (606)
T ss_pred ccccchhhhhccCcceEEehhhh---H--h------hcccCceeeeeccccCCCcEEEEEEeccCCc
Confidence 46777899999999998765221 2 1 2455679999999999999999999986553
No 59
>PRK10963 hypothetical protein; Provisional
Probab=72.00 E-value=74 Score=29.61 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=31.4
Q ss_pred HHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCC
Q psy8476 42 LLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSE 84 (421)
Q Consensus 42 L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~ 84 (421)
+..+...+... .+++++++.+. ..++-++.+.+++.|+++.
T Consensus 77 ~~~l~l~Ll~a-~~~~~l~~~L~-~~~~~f~~~~v~l~L~~~~ 117 (223)
T PRK10963 77 LLPLQSRLAAA-DSLQDMLMRLH-RWARDLGLAGAKIRLFPDR 117 (223)
T ss_pred HHHHHHHHhcC-CCHHHHHHHHH-HHHHHcCCCceEEEEeccc
Confidence 34444555344 49999999996 5799999999999998873
No 60
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=68.84 E-value=23 Score=38.63 Aligned_cols=46 Identities=4% Similarity=0.003 Sum_probs=35.1
Q ss_pred CCchhhHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHH
Q psy8476 3 ILEFERNQVFQRYLTFCGIGIQNAQLFEMSILEFERNQILLKLARSI 49 (421)
Q Consensus 3 ~~~~~d~~~~~~~a~~~~ial~na~l~~~~~~~~~~~~~L~~i~~~l 49 (421)
.|+.+|.++++.+++|++.+++|.++.++..+. ++++.+.+++..+
T Consensus 437 ~~~~e~~~lL~~l~~q~a~~l~~~~~~~~l~~~-~~~~~~~~~~a~i 482 (679)
T TIGR02916 437 EFNWEVRDLLKTAGRQAASYLAQMEASEALAEA-RQFEAFNRMSAFV 482 (679)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 588999999999999999999999988776543 3344555554444
No 61
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=66.54 E-value=22 Score=34.13 Aligned_cols=33 Identities=9% Similarity=0.185 Sum_probs=26.7
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDV 360 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~ 360 (421)
-+++++||+..+|+++|.|.+.-... .|+++..
T Consensus 215 v~~vAvPI~~~~g~~~aalsvs~p~~--r~~~~~~ 247 (271)
T PRK10163 215 LNCIASAIYDDVGSVVAAISISGPSS--RLTEDRF 247 (271)
T ss_pred CeEEEEEEECCCCCEEEEEEEEEecc--cCCHHHH
Confidence 47999999998899999999987754 4666543
No 62
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=66.11 E-value=25 Score=33.21 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCC
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSET 85 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~ 85 (421)
.+++++... .+..|+-++..-+++.+++..+ +.|.+.++|.+.
T Consensus 63 ~~~~lg~~~-l~~~~l~~~a~p~l~~L~~~tg-etv~L~v~dg~~ 105 (246)
T COG1414 63 RLLELGAAA-LSSLDLVSLARPLLEELAEETG-ETVHLSVLDGDE 105 (246)
T ss_pred HHHHHHHHH-HhcCCHHHHhHHHHHHHHHHhC-CcEEEEEEeCCE
Confidence 678888876 5566999999999999999999 889999999654
No 63
>PRK10963 hypothetical protein; Provisional
Probab=64.47 E-value=15 Score=34.21 Aligned_cols=51 Identities=6% Similarity=0.043 Sum_probs=41.8
Q ss_pred ccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy8476 324 TTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376 (421)
Q Consensus 324 ~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlen 376 (421)
..+|+-++|+.. +..+|+|.+.+..+.+--+.-+-.+|+.+|..++..|..
T Consensus 168 ~v~S~AllpL~~--~~~~GlLalGS~D~~rF~~~mgT~fL~~la~vvs~~L~~ 218 (223)
T PRK10963 168 AVGSVAMSLLGS--DGDLGVLLFSSRDAQHYQQGQGTQLLQHLALMLPELLER 218 (223)
T ss_pred cCceeEEEeccC--CCceEEEEEeCCChhhcCCCccHHHHHHHHHHHHHHHHH
Confidence 458999999965 345999999999987555566888999999999988764
No 64
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=64.31 E-value=27 Score=33.05 Aligned_cols=33 Identities=15% Similarity=0.199 Sum_probs=27.2
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDV 360 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~ 360 (421)
-+++++||++.+|+++|.|.+.-... .|+++..
T Consensus 203 v~~vA~Pv~~~~g~~~aalsv~~p~~--r~~~~~~ 235 (257)
T PRK15090 203 LRCIAVPVFDRFGVVIAGLSISFPTL--RFSEERK 235 (257)
T ss_pred CEEEEEEEECCCCCEEEEEEEEeehh--hcCHHHH
Confidence 47999999998899999999987654 5776654
No 65
>PF07614 DUF1577: Protein of unknown function (DUF1577); InterPro: IPR011471 This is a family of hypothetical proteins found in Leptospira interrogans.
Probab=64.21 E-value=21 Score=33.88 Aligned_cols=71 Identities=18% Similarity=0.162 Sum_probs=47.7
Q ss_pred HHHHhCCEEEEcCCCCcccc------ccC---Ccc-c----c----cCCCccceEEEEEeeeCCCc-----EEEEEEEEe
Q psy8476 292 YVASTGQILNIGDVPSWMRE------EVC---NDE-D----E----ESDFTTRCILCMPIFNGQKT-----VIGVAQLIN 348 (421)
Q Consensus 292 ~v~~tg~~v~i~D~~~~~~~------~f~---~~~-d----~----~~~~~~~S~L~vPI~~~~g~-----vIGVl~v~~ 348 (421)
-|=+|++++.|+|+....-+ .|. .++ + . ...-.++|.|.+||+..+ . ++|.+.+++
T Consensus 162 lVKkt~K~i~I~dt~~~eSy~~~~~~~~id~~~elge~~l~~~i~~yk~~kI~SelI~PI~y~n-~~~~~ipiGYi~vqs 240 (256)
T PF07614_consen 162 LVKKTKKIIYIEDTSDPESYKNNYNEEFIDYEKELGEDDLDSFIREYKNQKIRSELIYPIIYKN-HSEESIPIGYIWVQS 240 (256)
T ss_pred HHHhhCCeEEecCCCCcccccccCccccccHHHHHHHHHHHHHHHHHhhhceeeEEEEEEEEec-CCCceeeeEEEEEec
Confidence 35788999999998742111 110 111 0 0 011247899999999954 6 999999999
Q ss_pred cCCCCCCCHHHHHHHHH
Q psy8476 349 KVTRQPFTDCDVSIFEA 365 (421)
Q Consensus 349 ~~~~~~Fs~~d~~lL~~ 365 (421)
+.. .|+..++..+..
T Consensus 241 ~~~--~i~~~~~~~~~e 255 (256)
T PF07614_consen 241 KEK--SIDQSVLMEIKE 255 (256)
T ss_pred cCc--ccCHHHHHHHhh
Confidence 865 799998876643
No 66
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=59.58 E-value=26 Score=33.01 Aligned_cols=32 Identities=16% Similarity=0.196 Sum_probs=26.0
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCD 359 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d 359 (421)
-+.+++||...+|+++|.|.+..... .|++++
T Consensus 197 ~~~vA~Pv~~~~g~~~aalsv~~p~~--r~~~~~ 228 (248)
T TIGR02431 197 LRSIAVPIRNARGQVVAALNVSTHAA--RTTPEE 228 (248)
T ss_pred CeEEEEEEECCCCCEEEEEEEeeecc--cCCHHH
Confidence 47999999988899999999986654 577654
No 67
>PRK11569 transcriptional repressor IclR; Provisional
Probab=59.09 E-value=39 Score=32.36 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=27.1
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVS 361 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~ 361 (421)
-+++++||++.+|+++|+|.+..... .|+++.+.
T Consensus 220 v~~iA~Pi~~~~g~~~aalsvs~p~~--r~~~~~~~ 253 (274)
T PRK11569 220 LRCVAACIFDEHREPFAAISISGPIS--RITDDRVT 253 (274)
T ss_pred cEEEEEEEECCCCCEEEEEEEEeehh--hCCHHHHH
Confidence 47999999998889999999986653 57766543
No 68
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=58.87 E-value=88 Score=29.55 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=21.4
Q ss_pred eeeeEEeeeEeCCCcEEEEEEeeec
Q psy8476 201 TRCILCMPIFNGQKTVIGVAQLINK 225 (421)
Q Consensus 201 ~~s~l~vPl~~~~~~vIGVl~l~~~ 225 (421)
--+.+++||++.+|+++|+|.+...
T Consensus 193 gv~~iAaPi~~~~g~v~aaisv~~p 217 (246)
T COG1414 193 GVRCIAAPIFDAGGEVVAAISVSGP 217 (246)
T ss_pred CcEEEEEEEECCCCCEEEEEEEeec
Confidence 3488999999999999999998643
No 69
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=58.63 E-value=29 Score=33.03 Aligned_cols=46 Identities=15% Similarity=0.285 Sum_probs=30.6
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHH-H----HHHHHHHHHHHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCD-V----SIFEAFAIFCGLGI 374 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d-~----~lL~~lA~q~aiAl 374 (421)
-+.+++||+.. |+++|.|.+..... .|+.++ . ..|...|.++...+
T Consensus 205 v~~iA~PV~~~-g~~vaalsv~~p~~--r~~~~~~~~~~~~~l~~aa~~is~~l 255 (263)
T PRK09834 205 IASIAVPVRSG-QRVLGCLNLVYIAS--AMSIEEAAKRYLPALQRAAKQIEAGV 255 (263)
T ss_pred ceEEEeeEecC-CceEEEEEeeehhh--cCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999986 99999999987654 466543 2 33334444444444
No 70
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=58.46 E-value=33 Score=38.00 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=28.1
Q ss_pred CchhhHHHHHHHHHHHHHHHHhhHhHHHHHH
Q psy8476 4 LEFERNQVFQRYLTFCGIGIQNAQLFEMSIL 34 (421)
Q Consensus 4 ~~~~d~~~~~~~a~~~~ial~na~l~~~~~~ 34 (421)
..+++..+|..+++|+++|++|.+|.++.++
T Consensus 619 l~p~~~rlL~a~~~q~AlAler~~L~~~~~~ 649 (890)
T COG2205 619 LAPEQRRLLDAVLTQIALALERVTLAEEAEQ 649 (890)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678899999999999999999999988765
No 71
>PF11031 Phage_holin_T: Bacteriophage T holin; InterPro: IPR020982 One mechanism by which bacteriophages effect host lysis begins with the accumulation of a holin in the host membrane and an endolysin in the host cytoplasm during late gene expression. At an allele-specific time, the holin disrupts the membrane, thus allowing the endolysin to enter the periplasm and degrade the cell wall peptidoglycan. This entry represents a specific holin, known as T, which has an unusual C-terminal periplasmic domain thought to be involved in the transduction of environmental information for the real-time control of lysis timing [].
Probab=51.68 E-value=52 Score=30.02 Aligned_cols=121 Identities=13% Similarity=0.047 Sum_probs=68.1
Q ss_pred HhcCCCCCCcceeEEEEEcCCCCeee----eecCCCC------cccccCCCchHHHH-HHHhCCEEEEcCCCCccccccC
Q psy8476 246 LAHTPEDPSIAFSTVFELGGPGGEAL----VKSPGNT------VCNTHSRLATIAKY-VASTGQILNIGDVPSWMREEVC 314 (421)
Q Consensus 246 L~~~~~~l~a~~~~i~l~d~~~~~~~----~~~~~~~------~~~~~~~~~gi~g~-v~~tg~~v~i~D~~~~~~~~f~ 314 (421)
|+.+.-..+++|+.+|-+-+.....+ ...|.-+ ..+..|.++.-..+ +-..|.- -..+..+.|.
T Consensus 84 lqIvhvss~ADfsaV~sfRPknlNyfvDivAyEGklP~~vd~knlgg~pIdKTS~eY~~Hl~G~~-----f~s~~e~~fl 158 (216)
T PF11031_consen 84 LQIVHVSSGADFSAVYSFRPKNLNYFVDIVAYEGKLPSTVDPKNLGGFPIDKTSEEYMRHLNGRY-----FSSDTEFAFL 158 (216)
T ss_pred hhheeeecCCCEEEEEEecCcchhHHHHHHhhccCCccccCHhHcCCCCCccchHHHHHhhcCcc-----cccccceeec
Confidence 33344456899999988877654411 1122111 01334444333332 2222321 1112223343
Q ss_pred CcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy8476 315 NDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNT 377 (421)
Q Consensus 315 ~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena 377 (421)
+.-+... ...-+..+|+.+-++-=-|.+.+.|.++. . -+..-|..+|+|+|.+|-.+
T Consensus 159 pt~~~~~--~~~YmySCPyFNLdNvYsGtV~m~W~~kP-~---i~~~~L~~iC~qaaR~LGR~ 215 (216)
T PF11031_consen 159 PTKDKSF--EIKYMYSCPYFNLDNVYSGTVSMYWYKKP-V---IDDERLEAICNQAARILGRA 215 (216)
T ss_pred cCCCCCc--ceeEEEeCCcccccccccceeEEEEecCC-C---ccHHHHHHHhhHHHHHhccC
Confidence 3322222 24568999999988667799999999852 2 33378999999999988654
No 72
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=51.63 E-value=1.2e+02 Score=26.47 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=29.9
Q ss_pred eEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHH
Q psy8476 327 CILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIH 375 (421)
Q Consensus 327 S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAle 375 (421)
..+++||+. +|+.+|.+....-... . .+++...+...+...++..+
T Consensus 85 ~~~~~PI~~-~g~~iG~i~~G~v~~~-~-~~~~~~~~~~~a~~~~~~~~ 130 (173)
T PF10114_consen 85 VDIAVPIIV-DGEYIGYIICGQVLLE-D-PDDESELIRELAKKYGIDPE 130 (173)
T ss_pred eeeeeeEEE-CCEEEEEEEEEEeecC-C-CchhHHHHHHHHHHcCCCHH
Confidence 589999999 6799999988766543 2 22233345556655555443
No 73
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=50.90 E-value=23 Score=26.75 Aligned_cols=22 Identities=23% Similarity=0.530 Sum_probs=18.9
Q ss_pred ceEEEEEeeeCCCcEEEEEEEE
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLI 347 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~ 347 (421)
.-.+++||+..+|+++||+.+.
T Consensus 14 vi~~s~pi~~~~g~~~Gvv~~d 35 (81)
T PF02743_consen 14 VITISVPIYDDDGKIIGVVGID 35 (81)
T ss_dssp EEEEEEEEEETTTEEEEEEEEE
T ss_pred EEEEEEEEECCCCCEEEEEEEE
Confidence 4578999999778999999874
No 74
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=49.95 E-value=31 Score=26.76 Aligned_cols=46 Identities=17% Similarity=0.394 Sum_probs=33.0
Q ss_pred HHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEe
Q psy8476 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 348 (421)
Q Consensus 289 i~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~ 348 (421)
+...++++++.+...-. ...|.-..++.+||...+|+++|.|-+.+
T Consensus 36 VLe~vl~~g~v~r~~P~--------------~G~Y~G~PViV~PI~~~~g~viaAiGvVD 81 (84)
T PF09884_consen 36 VLEEVLETGKVIRVTPI--------------EGPYKGVPVIVAPIKDEDGEVIAAIGVVD 81 (84)
T ss_pred HHHHHHHcCCEEEeccC--------------CcccCCeeEEEEEEEcCCCCEEEEEEEEE
Confidence 45567888887663221 12245578999999998799999998765
No 75
>COG4702 Uncharacterized conserved protein [Function unknown]
Probab=47.65 E-value=27 Score=30.50 Aligned_cols=43 Identities=23% Similarity=0.286 Sum_probs=33.7
Q ss_pred EEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy8476 330 CMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376 (421)
Q Consensus 330 ~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlen 376 (421)
++||.++..-+||++++. |-+=-+++--+++.+|.++++.++.
T Consensus 121 ~fpI~vk~ag~iG~v~VS----GlpqreDHnlvv~aL~~~lg~~~~~ 163 (168)
T COG4702 121 GFPIQVKGAGVIGVVTVS----GLPQREDHNLVVRALADHLGIDLES 163 (168)
T ss_pred ceeEEEeccceEEEEEec----CCCcccchhHHHHHHHHHhCCChhh
Confidence 579999777899999984 3344677888899999999876654
No 76
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=44.45 E-value=4.2e+02 Score=28.18 Aligned_cols=32 Identities=9% Similarity=0.137 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchh
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEA 88 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l 88 (421)
+.+.-+..+.+.+++..+++ +|.+.|.+.=++
T Consensus 70 ~~~~~iq~~~~~i~~~t~a~--fIVV~d~~gIR~ 101 (537)
T COG3290 70 DQEARIQAIAEAIRSITDAD--FIVVGDMKGIRL 101 (537)
T ss_pred CcchhHHHHHHHHHhhcCce--EEEEecCCccee
Confidence 55567788899999999887 788888876444
No 77
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=40.87 E-value=31 Score=28.29 Aligned_cols=32 Identities=6% Similarity=0.101 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHhhhCCCeEEEEEEeCCCchh
Q psy8476 55 NLECLVTKIMTEARDLLKCERCAVFLLKSETSEA 88 (421)
Q Consensus 55 dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~~~l 88 (421)
|..+.+..+++.+++..+++ ++++.|.+.-.+
T Consensus 21 ~~~~~lq~~~~~~~~~~~~~--~i~v~D~~g~~l 52 (116)
T PF14827_consen 21 DPEAELQALLEQLRKESDID--YIVVTDRDGIVL 52 (116)
T ss_dssp GHHSCCCCHHHHHHHHCT-S--EEEEECTTSBEC
T ss_pred CccHHHHHHHHHHHhhcCCe--EEEEEcCCCCEE
Confidence 66656788888888886666 788999977544
No 78
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.30 E-value=37 Score=27.74 Aligned_cols=51 Identities=12% Similarity=0.145 Sum_probs=34.8
Q ss_pred chhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 165 i~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
+...|+++|+.+.-. ...--|.-...+.+||+ ++|++|+++.+++-..+-|
T Consensus 54 VLeevle~gevvr~v--------------P~~GpY~G~pVVV~Pik-~~g~viaAiGiVDlt~gi~ 104 (123)
T COG4048 54 VLEEVLEKGEVVREV--------------PIIGPYRGLPVVVAPIK-DEGEVIAAIGIVDLTAGIF 104 (123)
T ss_pred HHHHHHhhCceeeeC--------------CCCCccCCceEEEEEec-cCCeEEEEEEeeehhhhhc
Confidence 445566777766411 11123667889999999 5689999999987665543
No 79
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=37.94 E-value=39 Score=23.21 Aligned_cols=21 Identities=14% Similarity=0.393 Sum_probs=17.4
Q ss_pred ceEEEEEeeeCCCcEEEEEEE
Q psy8476 326 RCILCMPIFNGQKTVIGVAQL 346 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v 346 (421)
...-++|+.+.+|+++|++..
T Consensus 28 ~~~~~~~V~d~~~~~~G~is~ 48 (57)
T PF00571_consen 28 NGISRLPVVDEDGKLVGIISR 48 (57)
T ss_dssp HTSSEEEEESTTSBEEEEEEH
T ss_pred cCCcEEEEEecCCEEEEEEEH
Confidence 446789999878999999974
No 80
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=37.89 E-value=42 Score=27.48 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=17.1
Q ss_pred eEEEEEeeeCCCcEEEEEEEEec
Q psy8476 327 CILCMPIFNGQKTVIGVAQLINK 349 (421)
Q Consensus 327 S~L~vPI~~~~g~vIGVl~v~~~ 349 (421)
-...+||++.+|++||++.+.-.
T Consensus 90 ~~~~~PV~d~~g~viG~V~VG~~ 112 (116)
T PF14827_consen 90 LRAFAPVYDSDGKVIGVVSVGVS 112 (116)
T ss_dssp EEEEEEEE-TTS-EEEEEEEEEE
T ss_pred EEEEEeeECCCCcEEEEEEEEEE
Confidence 36789999668999999998643
No 81
>PF12282 H_kinase_N: Signal transduction histidine kinase; InterPro: IPR022066 This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with PF07568 from PFAM, PF08448 from PFAM, PF02518 from PFAM. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this. ; PDB: 2YKH_B 2YKF_A.
Probab=35.90 E-value=1.4e+02 Score=25.82 Aligned_cols=47 Identities=17% Similarity=0.046 Sum_probs=24.2
Q ss_pred chHHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEE
Q psy8476 287 ATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLI 347 (421)
Q Consensus 287 ~gi~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~ 347 (421)
+..+-+++.+|+++...+...- .+ ..-..=.+||.. +|++||||...
T Consensus 78 ep~v~~a~~tg~~~~~~~~~~~------------~~-~~v~~~~~PI~~-~~~vIaVl~~~ 124 (145)
T PF12282_consen 78 EPAVDRALETGRPVRGGRAVWQ------------GG-VPVRQEVVPIRR-NGRVIAVLIRE 124 (145)
T ss_dssp SHHHHHHHH-------------------------------EEEEEEEEE-TTEEEEEEEEE
T ss_pred cHHHHHHHHhCCceecCCcccc------------CC-ceeEEEEEEEEE-CCEEEEEEEEE
Confidence 5678889999988765443210 11 134577899999 57999999954
No 82
>PRK12705 hypothetical protein; Provisional
Probab=35.07 E-value=1.8 Score=45.29 Aligned_cols=95 Identities=18% Similarity=0.061 Sum_probs=71.9
Q ss_pred hHHHHHHHhCCEEEEcCCCCcc-ccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHH
Q psy8476 288 TIAKYVASTGQILNIGDVPSWM-REEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAF 366 (421)
Q Consensus 288 gi~g~v~~tg~~v~i~D~~~~~-~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~l 366 (421)
.|-..=..||..++|+|.+..- -..|.+.-+...++.++++++.|.... +++.+++...++ .|+....+..+..
T Consensus 220 Nir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~p-~rIeevv~~~~~----~~~~~i~~~ge~a 294 (508)
T PRK12705 220 NIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIHP-ARIEEYVQKANE----EFKQKIYEIGEEV 294 (508)
T ss_pred hHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCCh-HHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 3444456679999999998750 023544444556677899999999885 688888876544 4899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy8476 367 AIFCGLGIHNTQMYENACKLM 387 (421)
Q Consensus 367 A~q~aiAlena~L~~e~~~~~ 387 (421)
+.++|+...|..++.-+-++.
T Consensus 295 ~~~lgi~~~~~~li~~Lg~L~ 315 (508)
T PRK12705 295 LEELGIFDLKPGLVRLLGRLY 315 (508)
T ss_pred HHHhccccccHHHHHHHHHHh
Confidence 999999999999988876543
No 83
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=34.74 E-value=1.8e+02 Score=31.98 Aligned_cols=59 Identities=7% Similarity=-0.012 Sum_probs=44.5
Q ss_pred cceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 325 TRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENAC 384 (421)
Q Consensus 325 ~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~ 384 (421)
.+.+.+.|+..++|.++|.+.+....++ .-.....++.....+..+++++..+..++++
T Consensus 315 ~~~~~~~~i~~~dG~~~g~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 373 (799)
T PRK11359 315 NAQSWSATIRQRDGAPAGTLQIKTSSGA-ETSAFIERVADISQHLAALALEQEKSRQHIE 373 (799)
T ss_pred hccceeeeeecCCCcEEEEEEEEECCCC-CchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667789999999999999999887654 5566667777777777888877666554443
No 84
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.05 E-value=71 Score=26.16 Aligned_cols=49 Identities=12% Similarity=0.203 Sum_probs=33.9
Q ss_pred HHHHHHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCC
Q psy8476 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTR 352 (421)
Q Consensus 289 i~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~ 352 (421)
....|+.+|+.+.--. ....|.-+.+..+||+. +|+||+.|-+.+-..+
T Consensus 54 VLeevle~gevvr~vP--------------~~GpY~G~pVVV~Pik~-~g~viaAiGiVDlt~g 102 (123)
T COG4048 54 VLEEVLEKGEVVREVP--------------IIGPYRGLPVVVAPIKD-EGEVIAAIGIVDLTAG 102 (123)
T ss_pred HHHHHHhhCceeeeCC--------------CCCccCCceEEEEEecc-CCeEEEEEEeeehhhh
Confidence 3445778887655111 11235567899999995 8999999999877654
No 85
>PF07614 DUF1577: Protein of unknown function (DUF1577); InterPro: IPR011471 This is a family of hypothetical proteins found in Leptospira interrogans.
Probab=33.85 E-value=77 Score=30.22 Aligned_cols=59 Identities=24% Similarity=0.147 Sum_probs=40.1
Q ss_pred hhhhcCCEEeecCCCCcccccc---CcccccC---------------CCceeeeeEEeeeEeCCCc-----EEEEEEeee
Q psy8476 168 YVASTGQILNIGDVPSWMREEV---CNDEDEE---------------SDFTTRCILCMPIFNGQKT-----VIGVAQLIN 224 (421)
Q Consensus 168 ~v~~~g~~~~i~d~~~~p~~~~---~~~~d~~---------------~~~~~~s~l~vPl~~~~~~-----vIGVl~l~~ 224 (421)
-|-++++++.|+|+.+...+.. ....+.. ..-.++|.+.+||+..+ . +||.+.+++
T Consensus 162 lVKkt~K~i~I~dt~~~eSy~~~~~~~~id~~~elge~~l~~~i~~yk~~kI~SelI~PI~y~n-~~~~~ipiGYi~vqs 240 (256)
T PF07614_consen 162 LVKKTKKIIYIEDTSDPESYKNNYNEEFIDYEKELGEDDLDSFIREYKNQKIRSELIYPIIYKN-HSEESIPIGYIWVQS 240 (256)
T ss_pred HHHhhCCeEEecCCCCcccccccCccccccHHHHHHHHHHHHHHHHHhhhceeeEEEEEEEEec-CCCceeeeEEEEEec
Confidence 4678999999999985433321 0111111 12357899999999754 4 999999988
Q ss_pred ccc
Q psy8476 225 KIS 227 (421)
Q Consensus 225 ~~~ 227 (421)
+..
T Consensus 241 ~~~ 243 (256)
T PF07614_consen 241 KEK 243 (256)
T ss_pred cCc
Confidence 754
No 86
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=33.06 E-value=65 Score=26.55 Aligned_cols=24 Identities=17% Similarity=0.380 Sum_probs=20.4
Q ss_pred eeeEEeeeEeCCCcEEEEEEeeec
Q psy8476 202 RCILCMPIFNGQKTVIGVAQLINK 225 (421)
Q Consensus 202 ~s~l~vPl~~~~~~vIGVl~l~~~ 225 (421)
-+.+++||++.+|+++|+|.+.-.
T Consensus 79 v~~iA~Pi~~~~g~~~~alsv~~~ 102 (129)
T PF01614_consen 79 VAAIAVPIFDPNGQVVAALSVSGP 102 (129)
T ss_dssp EEEEEEEEEETTSCEEEEEEEEEE
T ss_pred cceEEEEEECCCCCEEEEEEEeeE
Confidence 367999999988999999998643
No 87
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=31.14 E-value=2.3e+02 Score=21.20 Aligned_cols=64 Identities=5% Similarity=-0.123 Sum_probs=45.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHH
Q psy8476 354 PFTDCDVSIFEAFAIFCGLGIHNTQMYENACKLMAKQKVFQRYLTFCGIGIQNAQLFEMSILEF 417 (421)
Q Consensus 354 ~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 417 (421)
--+.++..+|+.....+..|+....-.....-.....+.+.+.+..+.-....|+++...-.+|
T Consensus 9 l~~~Rq~~~L~~a~~~l~~a~~~l~~~~~~dl~a~~L~~A~~~L~~ItG~~~~ediLd~IFs~F 72 (73)
T PF12631_consen 9 LTNARQRQLLEQALEHLEDALEALENGLPLDLVAEDLREALESLGEITGEVVTEDILDNIFSNF 72 (73)
T ss_dssp --SHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHCTSS--HHHHHHHHCTS
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHhh
Confidence 4577888999988888888887766444445566777888888888888889999998887766
No 88
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.07 E-value=1.1e+02 Score=28.34 Aligned_cols=52 Identities=10% Similarity=0.112 Sum_probs=42.1
Q ss_pred CccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy8476 323 FTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHN 376 (421)
Q Consensus 323 ~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlen 376 (421)
..+.|+-++|+-. + ...|+|.+.+..+.+..+.-+-.+|..+|..++-+++.
T Consensus 164 ~~vgSvAi~~L~~-~-~~~gllafgS~D~~hf~~gmGT~fL~~la~vl~~~L~R 215 (218)
T COG3159 164 KAVGSVAIVPLGS-Q-APLGLLAFGSRDPRHFQPGMGTLFLRHLALVLARLLER 215 (218)
T ss_pred cccceeEEEEccC-C-CCceEEEecCCCccccCCCcchHHHHHHHHHHHHHHhh
Confidence 3578999999996 4 78999999999887555566788888888888877763
No 89
>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=29.39 E-value=1.4e+02 Score=22.65 Aligned_cols=52 Identities=15% Similarity=0.221 Sum_probs=37.4
Q ss_pred CcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeec
Q psy8476 163 ATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINK 225 (421)
Q Consensus 163 ~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~ 225 (421)
......++..+++......... ..+.....+-+.|+.+.+|++.|++.+...
T Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~D 104 (110)
T PF08448_consen 53 QAALRRALAGGEPVFFEEILLR-----------DGEERWFEVSISPIFDEDGEVVGVLVIIRD 104 (110)
T ss_dssp HHHHHHHHHHTSEEEEEEEECT-----------TSCEEEEEEEEEEEECTTTCEEEEEEEEEE
T ss_pred HHHHHHhhccCceEEEEEEEee-----------cCCcEEEEEEEEEeEcCCCCEEEEEEEEEE
Confidence 5567788888888775543331 113456677789999999999999988654
No 90
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=29.34 E-value=1.3e+02 Score=30.17 Aligned_cols=47 Identities=23% Similarity=0.289 Sum_probs=32.2
Q ss_pred chhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeee
Q psy8476 165 IAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224 (421)
Q Consensus 165 i~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~ 224 (421)
-+-.|+++|+++.|..-.. ..+ .+++.-+..||..+ |+++||+.+..
T Consensus 50 gA~~~~~~~~~~~i~~~~~-~~~-----------~g~k~GiN~Pi~~~-~~viGvIgItG 96 (385)
T PRK11477 50 GALLVLSQGRVVDIDDAVA-RHL-----------HGVRQGINLPLRLE-GEIVGVIGLTG 96 (385)
T ss_pred HHHHHHhcCCeeeecHHHH-hhc-----------CCCCcCceeeEEEC-CEEEEEEecCC
Confidence 3456788999988854322 111 23466678999986 69999999753
No 91
>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]
Probab=28.41 E-value=7.2e+02 Score=26.20 Aligned_cols=61 Identities=15% Similarity=0.219 Sum_probs=44.7
Q ss_pred CCCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeeecccCCc
Q psy8476 161 RLATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKISERK 230 (421)
Q Consensus 161 ~~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~~~~~~~ 230 (421)
...+.+..++.+|+.+....-.. +..+ -...+..|.+..|+..+ |+|+|.+.++-..+..+
T Consensus 268 i~s~~t~~ai~~g~vv~~~~~e~---~~cs-----h~~c~l~s~lViPL~~~-g~ViGTiK~y~~~~~li 328 (557)
T COG3275 268 IISSLTRKAIKTGEVVYADGNEV---YECS-----HPTCKLGSALVIPLRGK-GRVIGTIKLYEAKARLI 328 (557)
T ss_pred eccHHHHHHHhhCCEEEEccchh---hccC-----CCCCCcCCceEeecccC-CceeeeEEEEeccHhHh
Confidence 55788899999999887443221 1111 12356889999999987 79999999998777655
No 92
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=26.92 E-value=74 Score=30.08 Aligned_cols=42 Identities=19% Similarity=0.099 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCC
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSE 84 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~ 84 (421)
.+++++... ....++-+....+++.+.+-++. .|.+..+|.+
T Consensus 72 ~~~~lg~~~-~~~~~l~~~a~p~l~~La~~~~e-tv~L~v~~g~ 113 (257)
T PRK15090 72 KLFELGAKA-LQNVDLIRSADIQMREISRLTKE-TIHLGALDED 113 (257)
T ss_pred HHHHHHHHH-HhhCcHHHHHHHHHHHHHHHhCC-eEEEEEEECC
Confidence 577888876 44558888888888988888864 5666677664
No 93
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=25.65 E-value=79 Score=30.24 Aligned_cols=43 Identities=9% Similarity=0.065 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCCC
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSET 85 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~~ 85 (421)
.++.++... ....++-++..-+++.+++.++ +.|.+.+++...
T Consensus 84 ~l~~Lg~~~-~~~~~l~~~a~p~l~~La~~~g-etv~l~v~~g~~ 126 (271)
T PRK10163 84 GVFNVGAAY-IHNRDVLSVAGPFMRRLMLLSG-ETVNVAIRNGNE 126 (271)
T ss_pred HHHHHHHHH-HhcCCHHHHHHHHHHHHHHHHC-CeEEEEEEECCE
Confidence 567788877 4556899988899999888886 566777777643
No 94
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=24.47 E-value=86 Score=29.42 Aligned_cols=42 Identities=14% Similarity=0.246 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCC
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSE 84 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~ 84 (421)
.+++++... ....++-++...+++.+.+.++. .|.+.+++.+
T Consensus 66 ~~~~lg~~~-~~~~~l~~~a~p~l~~L~~~~g~-tv~L~v~~g~ 107 (248)
T TIGR02431 66 RVLRLGYAY-LSSAPLPKVAQPLLERLSAQTHE-SCSVAVLDGD 107 (248)
T ss_pred HHHHHHHHH-HhcCchHHHHHHHHHHHHHHHCC-eEEEEEEeCC
Confidence 577788776 44558999999999999998875 4566666654
No 95
>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional
Probab=23.99 E-value=4.4e+02 Score=27.51 Aligned_cols=54 Identities=17% Similarity=0.156 Sum_probs=42.4
Q ss_pred ceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8476 326 RCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGLGIHNTQMYENACK 385 (421)
Q Consensus 326 ~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~aiAlena~L~~e~~~ 385 (421)
..+...|+... ++.+|.+.+.+. ....+..+++.++.+++.++...++.++.++
T Consensus 304 ~~~~~~~~~~~-~~~~g~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (565)
T PRK10935 304 LPWQILPLTME-DTVLGYLHWQAS-----LPCPDEPLMNNVAQMLGRGLYFNQAQKQQQQ 357 (565)
T ss_pred CceEEEEEeeC-CcceEEEEecCC-----CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999985 578999987543 3457889999999999999987777766544
No 96
>PF12282 H_kinase_N: Signal transduction histidine kinase; InterPro: IPR022066 This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with PF07568 from PFAM, PF08448 from PFAM, PF02518 from PFAM. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this. ; PDB: 2YKH_B 2YKF_A.
Probab=23.74 E-value=1.3e+02 Score=25.94 Aligned_cols=49 Identities=16% Similarity=0.007 Sum_probs=24.9
Q ss_pred CCcchhhhhhcCCEEeecCCCCccccccCcccccCCCceeeeeEEeeeEeCCCcEEEEEEeee
Q psy8476 162 LATIAKYVASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLIN 224 (421)
Q Consensus 162 ~~gi~g~v~~~g~~~~i~d~~~~p~~~~~~~~d~~~~~~~~s~l~vPl~~~~~~vIGVl~l~~ 224 (421)
.+..+-+++++|++....+... .+..+-..=.+||++++ ++||||....
T Consensus 77 ~ep~v~~a~~tg~~~~~~~~~~-------------~~~~~v~~~~~PI~~~~-~vIaVl~~~~ 125 (145)
T PF12282_consen 77 NEPAVDRALETGRPVRGGRAVW-------------QGGVPVRQEVVPIRRNG-RVIAVLIRET 125 (145)
T ss_dssp GSHHHHHHHH-------------------------------EEEEEEEEETT-EEEEEEEEE-
T ss_pred ccHHHHHHHHhCCceecCCccc-------------cCCceeEEEEEEEEECC-EEEEEEEEEc
Confidence 3567889999999887554322 12224456789999975 9999999653
No 97
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=23.22 E-value=4.7e+02 Score=26.25 Aligned_cols=76 Identities=13% Similarity=0.066 Sum_probs=50.5
Q ss_pred HHHhCCEEEEcCCCCccccccCCcccccCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHH
Q psy8476 293 VASTGQILNIGDVPSWMREEVCNDEDEESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFAIFCGL 372 (421)
Q Consensus 293 v~~tg~~v~i~D~~~~~~~~f~~~~d~~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA~q~ai 372 (421)
+++.++.|.|...... .. .| .+.=+-.||.. +|+|||||-+.- .+++=..+.+.+.-.+-.
T Consensus 51 al~e~R~V~Id~~~a~----~l------~g--VkpGINLPi~~-~~~vVGViGITG------eP~~Vr~y~ELVrm~AEl 111 (376)
T COG3835 51 ALKERRVVEIDQAVAR----KL------KG--VKPGINLPIRF-DGKVVGVIGITG------EPEEVRKYGELVRMTAEL 111 (376)
T ss_pred HHhcCcEEEeeHHHHH----Hh------cC--CCCCCCcceEe-cCceEEEEeccC------ChHHHHHHHHHHHHHHHH
Confidence 6778888888754221 00 11 24566789999 689999998842 244555566666666677
Q ss_pred HHHHHHHHHHHHHHH
Q psy8476 373 GIHNTQMYENACKLM 387 (421)
Q Consensus 373 Alena~L~~e~~~~~ 387 (421)
-|+-+++.++.+-..
T Consensus 112 liEQ~~~~Eq~qw~~ 126 (376)
T COG3835 112 LIEQARLLEQLQWDR 126 (376)
T ss_pred HHHHHHHHHHHHHHH
Confidence 788888887765543
No 98
>PRK11569 transcriptional repressor IclR; Provisional
Probab=21.20 E-value=1.1e+02 Score=29.29 Aligned_cols=42 Identities=17% Similarity=0.168 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhccCCHHHHHHHHHHHHHhhhCCCeEEEEEEeCC
Q psy8476 41 ILLKLARSIFEEQSNLECLVTKIMTEARDLLKCERCAVFLLKSE 84 (421)
Q Consensus 41 ~L~~i~~~l~~~~~dl~~ll~~i~~~~~~l~~a~~~~i~L~d~~ 84 (421)
.+++++... ....++-++..-+++.+.+.++ +.+.+.++|.+
T Consensus 87 ~l~~Lg~~~-~~~~~l~~~a~p~l~~La~~~g-etv~L~v~~g~ 128 (274)
T PRK11569 87 HAFIVGSSF-LQSRNLLAIVHPILRNLMEDSG-ETVNLAVLDQS 128 (274)
T ss_pred HHHHHHHHH-HhhCcHHHHHHHHHHHHHHHHC-CeEEEEEEeCC
Confidence 477787776 4455888888899999888876 45667777764
No 99
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=20.13 E-value=1.8e+02 Score=27.53 Aligned_cols=85 Identities=6% Similarity=-0.085 Sum_probs=52.2
Q ss_pred HHHHHHHhCCEEEEcCCCCccccccCCcccc-cCCCccceEEEEEeeeCCCcEEEEEEEEecCCCCCCCHHHHHHHHHHH
Q psy8476 289 IAKYVASTGQILNIGDVPSWMREEVCNDEDE-ESDFTTRCILCMPIFNGQKTVIGVAQLINKVTRQPFTDCDVSIFEAFA 367 (421)
Q Consensus 289 i~g~v~~tg~~v~i~D~~~~~~~~f~~~~d~-~~~~~~~S~L~vPI~~~~g~vIGVl~v~~~~~~~~Fs~~d~~lL~~lA 367 (421)
...|+..+++|+.+...+.+| ..+.. ++. ......+.....+|...+|...|++.+.... ..|+.++...|+.++
T Consensus 85 ~~~W~~~~~~Pv~~~~~~~~p-~~w~~-~~~~~~~~~l~~a~~hGi~~~~g~~~~~lS~~~~~--~~~~~~~~~~L~ll~ 160 (247)
T TIGR03020 85 TNAWGAGKRQPRLVCALTLDD-DGWLR-FSVNLLLLNLKNIAFHGLSDVDGRHDCLYSFSRSS--VPLDARHAYFLELLL 160 (247)
T ss_pred HHHHHhcCCCCEEeccCccCC-Ccccc-cchHHHHHHHHHHHHcCCcCCCCCeeEEEEEecCC--CCCCHHHHHHHHHHH
Confidence 344666688998872222221 11111 010 0111235556666665567888998887653 489999999999999
Q ss_pred HHHHHHHHHH
Q psy8476 368 IFCGLGIHNT 377 (421)
Q Consensus 368 ~q~aiAlena 377 (421)
..+..++.+.
T Consensus 161 ~~l~~~l~~~ 170 (247)
T TIGR03020 161 PYLDSALRRV 170 (247)
T ss_pred HHHHHHHHHH
Confidence 9887777643
Done!