Query psy8547
Match_columns 115
No_of_seqs 159 out of 620
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 21:39:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8547hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13560 hypothetical protein; 99.5 1.5E-13 3.3E-18 115.5 10.1 98 8-105 428-600 (807)
2 PRK09776 putative diguanylate 99.5 5.3E-13 1.1E-17 116.6 11.6 108 7-115 487-673 (1092)
3 PRK09776 putative diguanylate 99.3 1.1E-11 2.5E-16 108.3 8.1 94 11-105 365-533 (1092)
4 PRK13560 hypothetical protein; 99.2 1.9E-10 4E-15 96.9 10.9 95 11-105 285-474 (807)
5 TIGR02938 nifL_nitrog nitrogen 99.0 2.9E-10 6.4E-15 90.0 2.5 98 9-106 82-261 (494)
6 PRK11359 cyclic-di-GMP phospho 98.9 1.9E-08 4E-13 85.6 10.2 95 7-103 92-258 (799)
7 PF13426 PAS_9: PAS domain; PD 98.6 1.3E-07 2.8E-12 60.0 4.9 39 5-43 65-104 (104)
8 PF13426 PAS_9: PAS domain; PD 98.4 4.1E-07 9E-12 57.6 5.0 73 23-95 5-104 (104)
9 PF08448 PAS_4: PAS fold; Int 98.3 1.7E-06 3.7E-11 55.4 5.9 36 11-46 75-110 (110)
10 PF08448 PAS_4: PAS fold; Int 98.2 4.8E-06 1E-10 53.2 5.7 38 61-98 73-110 (110)
11 PRK11359 cyclic-di-GMP phospho 98.2 1.2E-05 2.6E-10 68.5 9.0 104 8-115 214-384 (799)
12 TIGR02040 PpsR-CrtJ transcript 98.1 2.9E-05 6.3E-10 62.7 10.2 40 60-101 330-369 (442)
13 PRK13559 hypothetical protein; 98.0 8.6E-06 1.9E-10 63.5 5.1 46 58-103 122-167 (361)
14 PRK13558 bacterio-opsin activa 98.0 1E-05 2.2E-10 68.4 5.9 49 57-105 226-274 (665)
15 PRK10060 RNase II stability mo 98.0 1.3E-05 2.9E-10 68.5 6.6 56 59-115 189-245 (663)
16 PRK13559 hypothetical protein; 98.0 1.6E-05 3.4E-10 62.0 5.6 44 6-49 121-165 (361)
17 KOG0501|consensus 97.9 1.1E-05 2.3E-10 69.3 4.0 45 57-101 97-141 (971)
18 smart00086 PAC Motif C-termina 97.9 0.0001 2.3E-09 35.8 5.9 34 11-44 10-43 (43)
19 PRK13557 histidine kinase; Pro 97.8 1.8E-05 3.8E-10 64.0 3.9 49 58-106 109-157 (540)
20 KOG0501|consensus 97.8 2E-05 4.3E-10 67.7 4.1 46 4-49 95-141 (971)
21 PRK13558 bacterio-opsin activa 97.8 6.3E-05 1.4E-09 63.7 6.3 43 7-49 227-270 (665)
22 smart00086 PAC Motif C-termina 97.8 0.00022 4.8E-09 34.6 6.1 39 58-96 5-43 (43)
23 TIGR02938 nifL_nitrog nitrogen 97.7 2.5E-05 5.4E-10 61.9 2.7 48 58-105 80-127 (494)
24 PRK13557 histidine kinase; Pro 97.6 0.00014 2.9E-09 58.8 5.5 44 6-49 108-152 (540)
25 PRK11091 aerobic respiration c 97.5 0.00012 2.7E-09 62.9 5.1 47 59-105 232-278 (779)
26 TIGR00229 sensory_box PAS doma 97.5 0.00019 4.2E-09 42.7 4.3 43 60-103 82-124 (124)
27 PF00989 PAS: PAS fold; Inter 97.4 0.00037 8.1E-09 44.5 4.5 32 10-41 82-113 (113)
28 PRK11091 aerobic respiration c 97.4 0.0004 8.6E-09 59.9 5.8 39 11-49 236-274 (779)
29 TIGR00229 sensory_box PAS doma 97.3 0.00054 1.2E-08 40.7 4.3 38 11-49 85-122 (124)
30 PF08447 PAS_3: PAS fold; Int 97.2 0.0013 2.8E-08 41.2 5.6 35 56-90 57-91 (91)
31 PF00989 PAS: PAS fold; Inter 97.1 0.00096 2.1E-08 42.5 4.6 70 24-93 16-113 (113)
32 PRK11360 sensory histidine kin 97.0 0.00063 1.4E-08 55.1 2.9 48 59-107 338-385 (607)
33 TIGR02040 PpsR-CrtJ transcript 96.9 0.0017 3.7E-08 52.5 4.8 37 11-49 333-369 (442)
34 PF08447 PAS_3: PAS fold; Int 96.7 0.0058 1.2E-07 38.1 5.2 27 11-37 64-90 (91)
35 PF13596 PAS_10: PAS domain; P 96.5 0.0062 1.3E-07 39.8 5.0 30 13-42 77-106 (106)
36 PRK11360 sensory histidine kin 96.0 0.018 3.9E-07 46.6 5.7 38 11-49 342-379 (607)
37 cd00130 PAS PAS domain; PAS mo 95.7 0.059 1.3E-06 29.8 5.7 31 11-41 73-103 (103)
38 PF13596 PAS_10: PAS domain; P 95.5 0.041 8.8E-07 35.8 5.0 29 66-94 78-106 (106)
39 cd00130 PAS PAS domain; PAS mo 94.9 0.15 3.3E-06 28.0 5.8 35 59-93 69-103 (103)
40 PF12860 PAS_7: PAS fold 94.4 0.058 1.3E-06 35.5 3.6 31 14-49 85-115 (115)
41 PF08348 PAS_6: YheO-like PAS 94.3 0.13 2.8E-06 35.5 5.2 84 17-105 20-118 (118)
42 PRK10060 RNase II stability mo 92.8 0.26 5.6E-06 42.5 5.7 41 8-49 189-231 (663)
43 PF12860 PAS_7: PAS fold 92.6 0.18 4E-06 33.1 3.5 34 61-101 82-115 (115)
44 PRK11073 glnL nitrogen regulat 92.5 0.055 1.2E-06 41.7 1.0 41 59-104 82-122 (348)
45 TIGR02966 phoR_proteo phosphat 90.4 0.37 8E-06 36.0 3.6 40 59-103 75-114 (333)
46 PRK11073 glnL nitrogen regulat 89.3 0.55 1.2E-05 36.1 3.9 37 7-48 81-118 (348)
47 TIGR02966 phoR_proteo phosphat 88.3 0.74 1.6E-05 34.4 3.9 34 11-49 79-112 (333)
48 PF02743 Cache_1: Cache domain 87.8 2.7 5.9E-05 25.9 5.8 35 9-43 5-40 (81)
49 COG5002 VicK Signal transducti 87.6 1.2 2.7E-05 36.9 5.0 44 6-49 179-223 (459)
50 PRK11086 sensory histidine kin 87.0 1.2 2.6E-05 36.1 4.7 36 11-49 296-331 (542)
51 PF08348 PAS_6: YheO-like PAS 86.7 2.4 5.2E-05 29.1 5.4 37 11-49 78-114 (118)
52 COG5002 VicK Signal transducti 86.5 1.1 2.5E-05 37.1 4.2 44 61-104 183-226 (459)
53 PRK11086 sensory histidine kin 86.1 1.2 2.6E-05 36.2 4.2 36 68-104 299-334 (542)
54 PF14827 Cache_3: Sensory doma 85.6 2.1 4.5E-05 28.6 4.6 30 11-40 83-112 (116)
55 COG2202 AtoS FOG: PAS/PAC doma 83.7 3.7 8.1E-05 25.9 5.0 41 59-100 191-232 (232)
56 COG2202 AtoS FOG: PAS/PAC doma 83.3 4.1 8.8E-05 25.7 5.1 40 7-47 190-231 (232)
57 PF09884 DUF2111: Uncharacteri 77.4 5 0.00011 26.3 3.9 23 16-38 58-80 (84)
58 PF08275 Toprim_N: DNA primase 76.7 2.9 6.3E-05 28.9 2.9 21 19-39 78-98 (128)
59 PF07411 DUF1508: Domain of un 75.2 2.9 6.2E-05 24.4 2.1 46 62-113 2-47 (49)
60 PF09884 DUF2111: Uncharacteri 70.8 8.6 0.00019 25.2 3.7 32 62-94 52-83 (84)
61 PF14598 PAS_11: PAS domain; P 63.4 34 0.00074 22.7 5.8 39 57-95 69-108 (111)
62 COG2461 Uncharacterized conser 62.6 7.4 0.00016 32.3 2.8 32 17-48 371-402 (409)
63 PF14827 Cache_3: Sensory doma 60.4 20 0.00044 23.7 4.2 30 64-93 84-113 (116)
64 PF00571 CBS: CBS domain CBS d 59.3 13 0.00029 20.8 2.8 18 19-36 30-47 (57)
65 PF12282 H_kinase_N: Signal tr 56.8 19 0.00041 25.4 3.7 33 16-49 103-135 (145)
66 PF14598 PAS_11: PAS domain; P 56.7 53 0.0012 21.7 5.8 33 11-43 75-108 (111)
67 PF08275 Toprim_N: DNA primase 56.2 13 0.00029 25.5 2.8 22 70-91 77-98 (128)
68 PRK10820 DNA-binding transcrip 54.7 16 0.00035 30.9 3.6 33 11-45 153-189 (520)
69 PRK13662 hypothetical protein; 53.7 19 0.00042 26.6 3.4 87 4-93 10-108 (177)
70 PF09151 DUF1936: Domain of un 52.2 19 0.00042 19.4 2.4 15 21-35 12-26 (36)
71 PRK10820 DNA-binding transcrip 48.7 31 0.00067 29.2 4.3 37 60-98 150-190 (520)
72 PRK08624 hypothetical protein; 48.0 17 0.00038 29.9 2.6 26 14-40 179-204 (373)
73 TIGR00646 MG010 DNA primase-re 45.1 22 0.00047 27.2 2.6 21 19-39 59-79 (218)
74 COG3284 AcoR Transcriptional a 44.8 19 0.00041 31.6 2.5 32 6-38 148-179 (606)
75 PF10829 DUF2554: Protein of u 42.9 7.6 0.00017 24.8 -0.1 17 97-113 33-49 (76)
76 COG2461 Uncharacterized conser 42.7 19 0.0004 30.1 2.0 34 69-102 371-404 (409)
77 KOG1229|consensus 41.8 19 0.00041 31.0 2.0 31 59-89 235-265 (775)
78 PRK11388 DNA-binding transcrip 39.5 47 0.001 28.6 4.1 35 62-98 277-311 (638)
79 PRK15053 dpiB sensor histidine 36.4 77 0.0017 26.0 4.8 37 68-105 298-334 (545)
80 PRK14591 rimM 16S rRNA-process 34.0 83 0.0018 22.6 4.2 30 11-43 97-126 (169)
81 PF12282 H_kinase_N: Signal tr 33.4 71 0.0015 22.4 3.6 31 68-99 103-133 (145)
82 PHA02540 61 DNA primase; Provi 33.2 40 0.00086 27.4 2.6 21 19-39 173-193 (337)
83 COG3290 CitA Signal transducti 31.8 52 0.0011 28.5 3.1 37 68-105 293-329 (537)
84 TIGR02273 16S_RimM 16S rRNA pr 31.6 48 0.001 23.6 2.6 29 11-39 92-120 (165)
85 COG3290 CitA Signal transducti 31.5 64 0.0014 27.9 3.6 33 16-49 293-325 (537)
86 COG2964 Uncharacterized protei 31.2 91 0.002 24.0 4.1 78 17-99 29-122 (220)
87 COG3829 RocR Transcriptional r 30.4 92 0.002 27.2 4.4 32 70-102 197-228 (560)
88 PF00949 Peptidase_S7: Peptida 29.8 57 0.0012 23.0 2.6 20 20-39 99-118 (132)
89 TIGR01391 dnaG DNA primase, ca 29.3 57 0.0012 26.8 2.9 21 20-40 203-223 (415)
90 COG0806 RimM RimM protein, req 28.6 1.2E+02 0.0025 22.3 4.1 30 10-39 97-126 (174)
91 PRK15053 dpiB sensor histidine 27.4 76 0.0016 26.0 3.4 32 11-42 139-170 (545)
92 PF07370 DUF1489: Protein of u 26.4 1.1E+02 0.0024 21.8 3.6 23 11-33 47-79 (137)
93 PRK11006 phoR phosphate regulo 26.1 77 0.0017 25.3 3.1 32 68-104 174-205 (430)
94 PRK13828 rimM 16S rRNA-process 25.3 73 0.0016 22.7 2.6 30 11-43 77-106 (161)
95 smart00116 CBS Domain in cysta 24.4 84 0.0018 15.5 2.2 17 20-36 24-40 (49)
96 PRK05667 dnaG DNA primase; Val 24.1 77 0.0017 27.5 2.9 21 20-40 199-219 (580)
97 PRK00122 rimM 16S rRNA-process 23.8 62 0.0013 23.2 1.9 28 11-38 97-124 (172)
98 PRK14590 rimM 16S rRNA-process 23.3 81 0.0018 22.8 2.5 30 11-42 94-123 (171)
99 cd04620 CBS_pair_7 The CBS dom 23.0 92 0.002 19.3 2.5 19 18-36 90-108 (115)
100 COG0093 RplN Ribosomal protein 22.6 86 0.0019 21.9 2.4 27 59-85 69-95 (122)
101 COG4048 Uncharacterized protei 22.4 1.4E+02 0.003 20.7 3.3 26 17-44 77-102 (123)
102 COG3284 AcoR Transcriptional a 22.0 87 0.0019 27.6 2.8 21 70-90 159-179 (606)
103 PF07310 PAS_5: PAS domain; I 21.8 1.3E+02 0.0027 20.6 3.1 28 11-38 109-136 (137)
104 PF12101 DUF3577: Protein of u 21.5 1.2E+02 0.0026 21.6 3.0 22 61-83 28-49 (137)
105 cd04627 CBS_pair_14 The CBS do 21.2 1E+02 0.0022 19.6 2.5 19 18-36 98-116 (123)
106 PF11736 DUF3299: Protein of u 20.8 2.2E+02 0.0047 20.3 4.3 27 11-37 54-80 (146)
107 PRK15215 fimbriae biosynthesis 20.4 5.4 0.00012 27.0 -3.9 18 11-28 32-49 (100)
108 cd04610 CBS_pair_ParBc_assoc T 20.2 98 0.0021 18.8 2.2 17 20-36 84-100 (107)
109 cd04590 CBS_pair_CorC_HlyC_ass 20.1 1.1E+02 0.0024 18.7 2.4 18 19-36 87-104 (111)
No 1
>PRK13560 hypothetical protein; Provisional
Probab=99.49 E-value=1.5e-13 Score=115.49 Aligned_cols=98 Identities=16% Similarity=0.211 Sum_probs=84.7
Q ss_pred ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------------------C--------------
Q psy8547 8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------------------N-------------- 52 (115)
Q Consensus 8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------~-------------- 52 (115)
..+ ||+.+|+.+...|++|++|++++++++..|||++|++|+++ .
T Consensus 428 ~~~~~g~~~~~~~~~~p~~d~~g~~~~~~~~~~DITerk~~E~~L~~~~~~~e~~~~~i~~~~~~~~~~~~~~~~~~~~~ 507 (807)
T PRK13560 428 IEREDDGPADCSAYAEPLHDADGNIIGAIALLVDITERKQVEEQLLLANLIVENSPLVLFRWKAEEGWPVELVSKNITQF 507 (807)
T ss_pred EEcCCCCeEEEEEEEeeeECCCCCEEEEEEEeehhhhHHHHHHHHHHHHHHHhcCCceEEEEecCCCceEEEecchhhhc
Confidence 335 99999999999999999999999999999999999988732 0
Q ss_pred ---------CC-------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeee
Q psy8547 53 ---------GE-------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKD 92 (115)
Q Consensus 53 ---------~~-------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~D 92 (115)
+. ..++..+|||+.+|......|++|++|++.+++++..|
T Consensus 508 G~~~~e~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~~~D 587 (807)
T PRK13560 508 GYEPDEFISGKRMFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGIVID 587 (807)
T ss_pred CCCHHHhhcccchHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEEEec
Confidence 00 01123579999999999999999999999999999999
Q ss_pred cccchhhchhhcc
Q psy8547 93 VTNTKMAQMADNG 105 (115)
Q Consensus 93 IT~~k~~E~~~~~ 105 (115)
||++|++|++++.
T Consensus 588 ITerK~aE~~L~~ 600 (807)
T PRK13560 588 ISERKHAEEKIKA 600 (807)
T ss_pred hHHHHHHHHHHHH
Confidence 9999999998764
No 2
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.46 E-value=5.3e-13 Score=116.64 Aligned_cols=108 Identities=16% Similarity=0.047 Sum_probs=92.7
Q ss_pred eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------C----------
Q psy8547 7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------N---------- 52 (115)
Q Consensus 7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~---------- 52 (115)
..++ || ..|+.....|++|++|++.+++++.+|||++|++++++ +
T Consensus 487 r~~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~g~i~~~N~a~ 565 (1092)
T PRK09776 487 RIVVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDMAMKVTFMNPVA 565 (1092)
T ss_pred EEEcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECCCCeEEEEcHHH
Confidence 3445 99 99999999999999999999999999999999877631 0
Q ss_pred ------------CC---------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEE
Q psy8547 53 ------------GE---------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYL 87 (115)
Q Consensus 53 ------------~~---------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i 87 (115)
|. ......+|||..+|...+++|+++++|++.+++
T Consensus 566 ~~l~G~~~~e~iG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v 645 (1092)
T PRK09776 566 EKMTGWTQEEALGVPLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLSTLDGENIGSV 645 (1092)
T ss_pred HHHhCCCHHHHcCCCHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEEEEeeeeecCCCCEEEEE
Confidence 00 011235799999999999999999999999999
Q ss_pred EEeeecccchhhchhhccCCCccccccC
Q psy8547 88 ASHKDVTNTKMAQMADNGEGDYEDMQEL 115 (115)
Q Consensus 88 ~~~~DIT~~k~~E~~~~~~~~~~~~~~~ 115 (115)
++++|||++|+.|+++++.+.+|.|-.|
T Consensus 646 ~~~~DITe~k~~e~~L~~~a~~D~lTgl 673 (1092)
T PRK09776 646 LVIQDVTESRKMLRQLSYSASHDALTHL 673 (1092)
T ss_pred EEEEecchHHHHHHHHHhhcCCCcccCC
Confidence 9999999999999999999999987543
No 3
>PRK09776 putative diguanylate cyclase; Provisional
Probab=99.27 E-value=1.1e-11 Score=108.30 Aligned_cols=94 Identities=15% Similarity=0.180 Sum_probs=82.2
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------C--------------C
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------N--------------G 53 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~--------------~ 53 (115)
||+.+|+.++++|+++++|.+.+++++.+|||++|++|+.+ . |
T Consensus 365 dG~~~~~~~~~~~~~~~~g~~~~~i~~~~DITerk~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~~~~~n~~~~~l~G 444 (1092)
T PRK09776 365 DGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLMERITLANEAGGIGIWEWDLKPNIISWDKRMFELYE 444 (1092)
T ss_pred CCCEEEEEEEEEEEECCCCCEeeehhhHHhhHHHHHHHHHHHHHHHHHHHHHHhcCceEEEEecCCCeEeeCHHHHHHhC
Confidence 99999999999999999999999999999999999988631 0 0
Q ss_pred ---C-----------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeeccc
Q psy8547 54 ---E-----------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 95 (115)
Q Consensus 54 ---~-----------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~ 95 (115)
+ ..++.++||| .+|......|++|++|++..++++..|||+
T Consensus 445 ~~~~~~~~~~~~~~~~~p~d~~~~~~~~~~~~~~~~~~~~e~r~~~~dG-~~w~~~~~~~~~d~~G~~~~~ig~~~DITe 523 (1092)
T PRK09776 445 IPPHIKPTWQVWYACLHPEDRQRVEKEIRDALQGRSPFKLEFRIVVKDG-VRHIRALANRVLNKDGEVERLLGINMDMTE 523 (1092)
T ss_pred CCcccCCCHHHHHHhcCHhHHHHHHHHHHHHHhcCCCeeEEEEEEcCCc-eEEEEEeeEEEECCCCCEEEEEeeeeehhH
Confidence 0 0123468999 999999999999999999999999999999
Q ss_pred chhhchhhcc
Q psy8547 96 TKMAQMADNG 105 (115)
Q Consensus 96 ~k~~E~~~~~ 105 (115)
+|++|+++++
T Consensus 524 rk~~e~~L~~ 533 (1092)
T PRK09776 524 VRQLNEALFQ 533 (1092)
T ss_pred HHHHHHHHHH
Confidence 9999988764
No 4
>PRK13560 hypothetical protein; Provisional
Probab=99.19 E-value=1.9e-10 Score=96.92 Aligned_cols=95 Identities=12% Similarity=0.041 Sum_probs=79.3
Q ss_pred CCCceeEEEE--EEEeeCCCCCEEEEEEEEEeccchhhhhhhc------------------------------CCC--C-
Q psy8547 11 QRTPFWCLLD--IVPIKNEKREVVLYLASHKDVTNTKMAQMAD------------------------------NGE--G- 55 (115)
Q Consensus 11 dG~~fw~~~~--i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------------~~~--e- 55 (115)
||+.+|+.+. ..|+.|++|.+.+++++.+|||++|.+++++ ++. +
T Consensus 285 dG~~~~~~~~~~~~~~~~~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~~i~~~d~~g~i~~~nn~~~~~ 364 (807)
T PRK13560 285 DGRTRPVDVIFNHAEFDDKENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPIAAIGLDADGNICFVNNNAAER 364 (807)
T ss_pred CCCEEEEEEEecceEEEcCCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcccEEEEcCCCCEEEecCHHHHH
Confidence 9999976555 4667899999999999999999999988732 000 0
Q ss_pred ------------------------------------------------------------ceeceecCCceeEEEEEeEE
Q psy8547 56 ------------------------------------------------------------DYEDMQELGTPFWCLLDIVP 75 (115)
Q Consensus 56 ------------------------------------------------------------~~~~yrKdGs~f~~~~~i~p 75 (115)
.....+++|+.+|+.....|
T Consensus 365 ~~G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~p 444 (807)
T PRK13560 365 MLGWSAAEVMGKPLPGMDPELNEEFWCGDFQEWYPDGRPMAFDACPMAKTIKGGKIFDGQEVLIEREDDGPADCSAYAEP 444 (807)
T ss_pred HhCCCHHHHcCCCccccChhhhhhhhhchhhhcCCcCCcchhhhhhHHHHHhcCCcccCceEEEEcCCCCeEEEEEEEee
Confidence 01124689999999999999
Q ss_pred eeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 76 IKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 76 irde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
++|++|++..+++++.|||++|++|+++++
T Consensus 445 ~~d~~g~~~~~~~~~~DITerk~~E~~L~~ 474 (807)
T PRK13560 445 LHDADGNIIGAIALLVDITERKQVEEQLLL 474 (807)
T ss_pred eECCCCCEEEEEEEeehhhhHHHHHHHHHH
Confidence 999999999999999999999999998875
No 5
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=98.96 E-value=2.9e-10 Score=90.00 Aligned_cols=98 Identities=19% Similarity=0.220 Sum_probs=74.6
Q ss_pred cc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc-----------------------CC-----------
Q psy8547 9 YR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD-----------------------NG----------- 53 (115)
Q Consensus 9 Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~-----------------------~~----------- 53 (115)
.+ +|+.+|..+.++|+++++|.+.+++++++|||++|++++.+ .+
T Consensus 82 ~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~~~i~~~N~~~~~ 161 (494)
T TIGR02938 82 RRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKK 161 (494)
T ss_pred cCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccceEEEEcCCCCEEEechhHHH
Confidence 45 99999999999999999999999999999999999877621 00
Q ss_pred -------C-----------C------------------ceece-ecCCc-eeEEEEEeEEeeCCCCCEE---------EE
Q psy8547 54 -------E-----------G------------------DYEDM-QELGT-PFWCLLDIVPIKNEKREVV---------LY 86 (115)
Q Consensus 54 -------~-----------e------------------~~~~y-rKdGs-~f~~~~~i~pirde~G~v~---------~~ 86 (115)
+ + ....+ +++|. .+|......|+.+..|.+. ++
T Consensus 162 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (494)
T TIGR02938 162 LATDLRVKEPAHTVLDLLREAWREALAENWPQQLAFSNREARFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYL 241 (494)
T ss_pred hhchhhhhHHHHHHHHHhhHHhhhhhhhcchhhhccccceeeeccCCCceeeEEEecCceEEeecchhhheeccCCCchh
Confidence 0 0 00012 33444 7999999999988877653 45
Q ss_pred EEEeeecccchhhchhhccC
Q psy8547 87 LASHKDVTNTKMAQMADNGE 106 (115)
Q Consensus 87 i~~~~DIT~~k~~E~~~~~~ 106 (115)
++++.|||++|++|++++..
T Consensus 242 ~~~~~DITe~k~~ee~l~~~ 261 (494)
T TIGR02938 242 LLTIADISNLREEQERARLS 261 (494)
T ss_pred eehHHHHHHHHHHHHHHHHH
Confidence 66899999999999877643
No 6
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.86 E-value=1.9e-08 Score=85.62 Aligned_cols=95 Identities=15% Similarity=0.307 Sum_probs=74.6
Q ss_pred eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------------------------C-------
Q psy8547 7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------------------------N------- 52 (115)
Q Consensus 7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------------------------~------- 52 (115)
..++ ||+.+|+.+.+.|+. ..|.. +++++.+|||++++.++.. +
T Consensus 92 ~~~~~dG~~~~v~~~~~~~~-~~g~~-~~~~~~~DiT~~~~~~~~~~~~~~~~~~~~~~i~~~d~~g~i~~~N~~~~~l~ 169 (799)
T PRK11359 92 QLEKKDGSKIWTRFALSKVS-AEGKV-YYLALVRDASVEMAQKEQTRQLIIAVDHLDRPVIVLDPERRIVQCNRAFTEMF 169 (799)
T ss_pred EEecCCcCEEEEEEEeeeec-cCCce-EEEEEEeeccchhhhHHHHHHHHHHHhcCCCcEEEEcCCCcEEEEChhhHhhh
Confidence 3445 999999999999984 45654 6789999999987765521 0
Q ss_pred --------CC------------------------------CceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547 53 --------GE------------------------------GDYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94 (115)
Q Consensus 53 --------~~------------------------------e~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT 94 (115)
|. ..+...+++|..+|+..+..|+.+++|.+.+++++..|||
T Consensus 170 G~~~~e~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DIT 249 (799)
T PRK11359 170 GYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDIT 249 (799)
T ss_pred CCCHHHHCCCChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhh
Confidence 00 0012357899999999999999999999999999999999
Q ss_pred cchhhchhh
Q psy8547 95 NTKMAQMAD 103 (115)
Q Consensus 95 ~~k~~E~~~ 103 (115)
++|++++..
T Consensus 250 erk~~e~~~ 258 (799)
T PRK11359 250 EERQIRQLE 258 (799)
T ss_pred hHHHHHHHH
Confidence 999887643
No 7
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=98.56 E-value=1.3e-07 Score=59.96 Aligned_cols=39 Identities=23% Similarity=0.442 Sum_probs=35.3
Q ss_pred ceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547 5 PDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 43 (115)
Q Consensus 5 ~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~ 43 (115)
....++ ||+.+|+.++++|+++++|++.+++++++|||+
T Consensus 65 e~~~~~~~g~~~~~~~~~~~i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 65 EVRLRRKDGETFWVEVSASPIRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEEEEETTSEEEEEEEEEEEEEETTSSEEEEEEEEEEEHH
T ss_pred EEEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEEEECCC
Confidence 344556 999999999999999999999999999999995
No 8
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=98.45 E-value=4.1e-07 Score=57.57 Aligned_cols=73 Identities=16% Similarity=0.336 Sum_probs=52.4
Q ss_pred EeeCCCCCEEEEEEEEEeccchhhhhhhc------------------------CCC---CceeceecCCceeEEEEEeEE
Q psy8547 23 PIKNEKREVVLYLASHKDVTNTKMAQMAD------------------------NGE---GDYEDMQELGTPFWCLLDIVP 75 (115)
Q Consensus 23 Pi~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~---e~~~~yrKdGs~f~~~~~i~p 75 (115)
-+.|.+|.++.+=..+..++.....+-.. ++. .....++++|+.+|+.++++|
T Consensus 5 ~i~d~~g~i~~~N~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~ 84 (104)
T PF13426_consen 5 FILDPDGRILYVNPAFERLFGYSREELIGKSISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFWVEVSASP 84 (104)
T ss_dssp EEEETTSBEEEE-HHHHHHHTS-HHHHTTSBGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEEEEEEEEE
T ss_pred EEECCcCcEEehhHHHHHHHCcCHHHHcCCCcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEEEEEEEEE
Confidence 35677888877666666666544322210 011 122347899999999999999
Q ss_pred eeCCCCCEEEEEEEeeeccc
Q psy8547 76 IKNEKREVVLYLASHKDVTN 95 (115)
Q Consensus 76 irde~G~v~~~i~~~~DIT~ 95 (115)
+++++|++.++++++.|||+
T Consensus 85 i~~~~g~~~~~i~~~~DiTe 104 (104)
T PF13426_consen 85 IRDEDGEITGIIGIFRDITE 104 (104)
T ss_dssp EEETTSSEEEEEEEEEEEHH
T ss_pred EECCCCCEEEEEEEEEECCC
Confidence 99999999999999999996
No 9
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=98.34 E-value=1.7e-06 Score=55.37 Aligned_cols=36 Identities=31% Similarity=0.421 Sum_probs=34.8
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 46 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~ 46 (115)
+|...|..++++|++|++|++.+++.+.+|||++|+
T Consensus 75 ~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 75 DGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp TSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred cCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 899999999999999999999999999999999985
No 10
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=98.19 E-value=4.8e-06 Score=53.21 Aligned_cols=38 Identities=32% Similarity=0.412 Sum_probs=35.8
Q ss_pred ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchh
Q psy8547 61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 98 (115)
Q Consensus 61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~ 98 (115)
..+|...|..++++|++|++|++.+++.+..|||++|+
T Consensus 73 ~~~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~DiT~~rr 110 (110)
T PF08448_consen 73 LRDGEERWFEVSISPIFDEDGEVVGVLVIIRDITERRR 110 (110)
T ss_dssp CTTSCEEEEEEEEEEEECTTTCEEEEEEEEEEECCHHH
T ss_pred eecCCcEEEEEEEEEeEcCCCCEEEEEEEEEECchhhC
Confidence 34899999999999999999999999999999999985
No 11
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.16 E-value=1.2e-05 Score=68.55 Aligned_cols=104 Identities=10% Similarity=0.175 Sum_probs=74.2
Q ss_pred ecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc--------CC-------------------CCc---
Q psy8547 8 NYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD--------NG-------------------EGD--- 56 (115)
Q Consensus 8 ~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~--------~~-------------------~e~--- 56 (115)
..+ ||..+|+.+...|+.+++|.+.+++++.+|||++++++++. .+ ...
T Consensus 214 ~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~~~DITerk~~e~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 (799)
T PRK11359 214 LLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEERQIRQLEGNILAAMCSSPPFHEMGEIICRNIESVLNESHVSL 293 (799)
T ss_pred EeCCCCCEEEEEeeeeeeecCCCceeEEEEEeehhhhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCceeeE
Confidence 334 99999999999999999999999999999999999876521 00 000
Q ss_pred ----------e----eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc----------------------cchhhc
Q psy8547 57 ----------Y----EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT----------------------NTKMAQ 100 (115)
Q Consensus 57 ----------~----~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT----------------------~~k~~E 100 (115)
+ ......|...|. .|+++.+|.+.+++.+..+.. ++++.+
T Consensus 294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~i~~~dG~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 369 (799)
T PRK11359 294 FALRNGMPIHWASSSHGAEYQNAQSWS----ATIRQRDGAPAGTLQIKTSSGAETSAFIERVADISQHLAALALEQEKSR 369 (799)
T ss_pred EEecCCceeeccCCCCCHHHhhcccee----eeeecCCCcEEEEEEEEECCCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 001223334443 688889999988888876532 455566
Q ss_pred hhhccCCCccccccC
Q psy8547 101 MADNGEGDYEDMQEL 115 (115)
Q Consensus 101 ~~~~~~~~~~~~~~~ 115 (115)
.++++.+.+|.|..|
T Consensus 370 ~~l~~~~~~D~lTgl 384 (799)
T PRK11359 370 QHIEQLIQFDPLTGL 384 (799)
T ss_pred HHHHHHhCcCCCCCC
Confidence 778888888887543
No 12
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=98.13 E-value=2.9e-05 Score=62.74 Aligned_cols=40 Identities=13% Similarity=0.126 Sum_probs=35.2
Q ss_pred eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547 60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 101 (115)
Q Consensus 60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~ 101 (115)
.+|||+.+|+.++++|+++..+ ..++++++|||++|+.+.
T Consensus 330 ~~~~G~~~~ve~s~~~i~~~~~--~~~~~v~rDITeR~~~~~ 369 (442)
T TIGR02040 330 TGEFGAQTEVEISAAWVDQGER--PLIVLVIRDISRRLTMRD 369 (442)
T ss_pred EcCCCCEEEEEEEEEEeccCCc--eEEEEEEecchhhccCCC
Confidence 5899999999999999987665 468899999999999865
No 13
>PRK13559 hypothetical protein; Provisional
Probab=98.03 E-value=8.6e-06 Score=63.47 Aligned_cols=46 Identities=24% Similarity=0.539 Sum_probs=41.7
Q ss_pred eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547 58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD 103 (115)
Q Consensus 58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~ 103 (115)
..+++||+.||+.++++|++++.|.+..+++++.|||++|++|+..
T Consensus 122 ~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~~~ 167 (361)
T PRK13559 122 LNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRALE 167 (361)
T ss_pred EEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHHHH
Confidence 3478999999999999999999999999999999999999876643
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.02 E-value=1e-05 Score=68.44 Aligned_cols=49 Identities=33% Similarity=0.578 Sum_probs=45.3
Q ss_pred eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
++.++|||+.+|+.+++.|++++.|.+..++++..|||++|++|+++++
T Consensus 226 ~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~~L~~ 274 (665)
T PRK13558 226 LRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAELALQR 274 (665)
T ss_pred EEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHHHHHH
Confidence 3457899999999999999999999999999999999999999998774
No 15
>PRK10060 RNase II stability modulator; Provisional
Probab=98.02 E-value=1.3e-05 Score=68.50 Aligned_cols=56 Identities=13% Similarity=0.167 Sum_probs=45.2
Q ss_pred ceecCCceeEEEEEeEEeeCCCCC-EEEEEEEeeecccchhhchhhccCCCccccccC
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKRE-VVLYLASHKDVTNTKMAQMADNGEGDYEDMQEL 115 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~-v~~~i~~~~DIT~~k~~E~~~~~~~~~~~~~~~ 115 (115)
..+|+|+.+|...... +.+..|. ..+++++..|||++|.+|+++++++.+|.|-.|
T Consensus 189 ~~~~~G~~~~~~~~~~-~~~~~g~~~~~~i~~~~DITe~k~~e~~l~~~a~~D~LTGL 245 (663)
T PRK10060 189 IKTRKGQRLFLFRNKF-VHSGSGKNEIFLICSGTDITEERRAQERLRILANTDSITGL 245 (663)
T ss_pred EEeCCCCEEEEEeeeE-EEcCCCCceEEEEEEEEechHHHHHHHHHHHHhhcCccCCC
Confidence 3689999999876644 4544554 567889999999999999999999999998654
No 16
>PRK13559 hypothetical protein; Provisional
Probab=97.97 E-value=1.6e-05 Score=62.00 Aligned_cols=44 Identities=30% Similarity=0.601 Sum_probs=39.6
Q ss_pred eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
..+++ ||+.+|+.++++|+++++|.+.+++++.+|||++|++++
T Consensus 121 ~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~~DITerk~~e~ 165 (361)
T PRK13559 121 LLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIRAVRA 165 (361)
T ss_pred EEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeeeeehhcchhhHH
Confidence 34556 999999999999999999999999999999999997654
No 17
>KOG0501|consensus
Probab=97.91 E-value=1.1e-05 Score=69.27 Aligned_cols=45 Identities=40% Similarity=0.606 Sum_probs=41.5
Q ss_pred eeceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547 57 YEDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 101 (115)
Q Consensus 57 ~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~ 101 (115)
...|+|+.+|.|..+.|+||||+...|+.|+..|+|||..||.-+
T Consensus 97 illyKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQPid 141 (971)
T KOG0501|consen 97 ILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQPID 141 (971)
T ss_pred eEeeecCCCceEEEEEeecccCCCceEEEEEeecccchhhcCCCc
Confidence 346999999999999999999999999999999999999988654
No 18
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=97.87 E-value=0.0001 Score=35.81 Aligned_cols=34 Identities=29% Similarity=0.518 Sum_probs=31.8
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT 44 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~ 44 (115)
+|..+|+.....|+.+.+|.+.+++++..|||++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 10 DGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 (43)
T ss_pred CCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence 9999999999999999999999999999999863
No 19
>PRK13557 histidine kinase; Provisional
Probab=97.83 E-value=1.8e-05 Score=63.96 Aligned_cols=49 Identities=24% Similarity=0.443 Sum_probs=44.4
Q ss_pred eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccC
Q psy8547 58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGE 106 (115)
Q Consensus 58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~ 106 (115)
..++|+|+.+|..++++|+++.+|.+++++++..|||+++++|++++..
T Consensus 109 ~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~~l~~~ 157 (540)
T PRK13557 109 LNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAEDALRQA 157 (540)
T ss_pred EEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHHHHHHH
Confidence 3478999999999999999999999999999999999999998876543
No 20
>KOG0501|consensus
Probab=97.81 E-value=2e-05 Score=67.67 Aligned_cols=46 Identities=43% Similarity=0.710 Sum_probs=42.8
Q ss_pred cceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 4 HPDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 4 ~~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
-+.+.|| +-+|.|..+.|.||+|+...++.|+..|+|||..|++-.
T Consensus 95 fEillyKKN~TPvW~~vqiAPIrNe~d~VVLfLctFkDIT~~KQPid 141 (971)
T KOG0501|consen 95 FEILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTFKDITALKQPID 141 (971)
T ss_pred eeeEeeecCCCceEEEEEeecccCCCceEEEEEeecccchhhcCCCc
Confidence 3578899 999999999999999999999999999999999999755
No 21
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.76 E-value=6.3e-05 Score=63.66 Aligned_cols=43 Identities=40% Similarity=0.737 Sum_probs=40.0
Q ss_pred eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
..++ ||+.+|+.+.+.|+++++|.+.+++++.+|||++|++++
T Consensus 227 ~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~~DITerk~~E~ 270 (665)
T PRK13558 227 RNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTERKEAEL 270 (665)
T ss_pred EEECCCCCEEEEEEEEEEEECCCCCEEEEEEEEEeCcHHHHHHH
Confidence 4456 999999999999999999999999999999999999877
No 22
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=97.76 E-value=0.00022 Score=34.56 Aligned_cols=39 Identities=28% Similarity=0.453 Sum_probs=34.6
Q ss_pred eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccc
Q psy8547 58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNT 96 (115)
Q Consensus 58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~ 96 (115)
...+++|..+|+.....++.+..|.+..++++..|||++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 5 RLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence 346788999999999999999999999999999999863
No 23
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=97.69 E-value=2.5e-05 Score=61.89 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=43.8
Q ss_pred eceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 58 EDMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 58 ~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
..++|+|..+|..+.++|+++++|.+..+++++.|||++|++|+++++
T Consensus 80 ~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~DIt~~k~~e~~l~~ 127 (494)
T TIGR02938 80 LNRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELHRLEQVVAN 127 (494)
T ss_pred eccCCCccchhhheeeEEEECCCCCEEEEEEehhhhhHHHHHHHHHHH
Confidence 347899999999999999999999999999999999999999987654
No 24
>PRK13557 histidine kinase; Provisional
Probab=97.58 E-value=0.00014 Score=58.80 Aligned_cols=44 Identities=30% Similarity=0.560 Sum_probs=40.1
Q ss_pred eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
..+++ ||+.+|..++++|+++++|.+++++++..|||+++.+++
T Consensus 108 ~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~~dit~~~~~e~ 152 (540)
T PRK13557 108 ILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVSRRRDAED 152 (540)
T ss_pred EEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEecChHHHHHHHH
Confidence 34567 999999999999999999999999999999999988765
No 25
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.55 E-value=0.00012 Score=62.93 Aligned_cols=47 Identities=19% Similarity=0.002 Sum_probs=43.1
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
..++||+.+|..++.+|+++++|.+.++++++.|||++|++|++++.
T Consensus 232 ~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~~l~~ 278 (779)
T PRK11091 232 LDYPDGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQDALEK 278 (779)
T ss_pred EEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHHHHHH
Confidence 36789999999999999999999999999999999999999987653
No 26
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=97.51 E-value=0.00019 Score=42.69 Aligned_cols=43 Identities=21% Similarity=0.342 Sum_probs=38.7
Q ss_pred eecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547 60 MQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD 103 (115)
Q Consensus 60 yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~ 103 (115)
..++|..+|+.+...|+. +.|.+..+++++.|||++++++.++
T Consensus 82 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~~l 124 (124)
T TIGR00229 82 RRKDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEEAL 124 (124)
T ss_pred EcCCCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHhcC
Confidence 478999999999999999 8899999999999999999988653
No 27
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=97.36 E-value=0.00037 Score=44.47 Aligned_cols=32 Identities=22% Similarity=0.564 Sum_probs=30.0
Q ss_pred cCCCceeEEEEEEEeeCCCCCEEEEEEEEEec
Q psy8547 10 RQRTPFWCLLDIVPIKNEKREVVLYLASHKDV 41 (115)
Q Consensus 10 rdG~~fw~~~~i~Pi~de~G~~~~fi~~~~DI 41 (115)
++|+.+|+.+..+|+++.+|++.+++++.+||
T Consensus 82 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 82 RDGRPRWVEVRASPVRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp TTSCEEEEEEEEEEEEETTEEEEEEEEEEEE-
T ss_pred cCCcEEEEEEEEEEEEeCCCCEEEEEEEEEeC
Confidence 49999999999999999999999999999997
No 28
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.35 E-value=0.0004 Score=59.86 Aligned_cols=39 Identities=18% Similarity=0.072 Sum_probs=37.7
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
||+.+|+.++.+|+++++|.+.+++++.+|||++|++++
T Consensus 236 ~G~~~~~~~~~~pi~~~~g~~~g~v~~~~DITe~k~~e~ 274 (779)
T PRK11091 236 DGRKACFELRKVPFYDRVGKRHGLMGFGRDITERKRYQD 274 (779)
T ss_pred CCCEEEEEEEeeeEEcCCCCEEEEEEEEeehhHHHHHHH
Confidence 999999999999999999999999999999999999875
No 29
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=97.28 E-value=0.00054 Score=40.68 Aligned_cols=38 Identities=18% Similarity=0.368 Sum_probs=35.5
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
+|..+|+.+...|+. ++|...+++++..|||+++.+++
T Consensus 85 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~dit~~~~~~~ 122 (124)
T TIGR00229 85 DGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERKQAEE 122 (124)
T ss_pred CCCEEEEEEEEeehh-hCCCeeEEEEEeeehhHHHHHHh
Confidence 999999999999999 88999999999999999998764
No 30
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=97.20 E-value=0.0013 Score=41.18 Aligned_cols=35 Identities=17% Similarity=0.223 Sum_probs=30.9
Q ss_pred ceeceecCCceeEEEEEeEEeeCCCCCEEEEEEEe
Q psy8547 56 DYEDMQELGTPFWCLLDIVPIKNEKREVVLYLASH 90 (115)
Q Consensus 56 ~~~~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~ 90 (115)
.++.++|||+..|+.....|++|++|+++.++|+.
T Consensus 57 e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 57 EYRIRRKDGEYRWIEVRGRPIFDENGKPIRIIGVI 91 (91)
T ss_dssp EEEEEGTTSTEEEEEEEEEEEETTTS-EEEEEEEE
T ss_pred EEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEC
Confidence 45678899999999999999999999999999874
No 31
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=97.13 E-value=0.00096 Score=42.52 Aligned_cols=70 Identities=14% Similarity=0.332 Sum_probs=48.0
Q ss_pred eeCCCCCEEEEEEEEEeccchhhhhhhc------------------------CCC--C--ceeceecCCceeEEEEEeEE
Q psy8547 24 IKNEKREVVLYLASHKDVTNTKMAQMAD------------------------NGE--G--DYEDMQELGTPFWCLLDIVP 75 (115)
Q Consensus 24 i~de~G~~~~fi~~~~DIT~~k~~e~~~------------------------~~~--e--~~~~yrKdGs~f~~~~~i~p 75 (115)
+.|.+|+++++-..+.+++.....+..- .+. . ......++|+.+|+.++.+|
T Consensus 16 ~~d~~g~I~~~N~a~~~l~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~ 95 (113)
T PF00989_consen 16 VIDEDGRILYVNQAAEELLGYSREELIGKSLFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRDGRPRWVEVRASP 95 (113)
T ss_dssp EEETTSBEEEECHHHHHHHSS-HHHHTTSBGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETTSCEEEEEEEEEE
T ss_pred EEeCcCeEEEECHHHHHHHccCHHHHcCCcHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecCCcEEEEEEEEEE
Confidence 4678888887666666666554433210 000 0 01112359999999999999
Q ss_pred eeCCCCCEEEEEEEeeec
Q psy8547 76 IKNEKREVVLYLASHKDV 93 (115)
Q Consensus 76 irde~G~v~~~i~~~~DI 93 (115)
+++.+|++.++++++.||
T Consensus 96 ~~~~~~~~~~~~~~~~DI 113 (113)
T PF00989_consen 96 VRDEDGQIIGILVIFRDI 113 (113)
T ss_dssp EEETTEEEEEEEEEEEE-
T ss_pred EEeCCCCEEEEEEEEEeC
Confidence 999999999999999997
No 32
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.95 E-value=0.00063 Score=55.05 Aligned_cols=48 Identities=17% Similarity=-0.024 Sum_probs=42.3
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCC
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEG 107 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~ 107 (115)
..+++|..+ +.++.+|+.+++|++..+++++.|||++|++|+++++..
T Consensus 338 ~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~~l~~~~ 385 (607)
T PRK11360 338 FPGRDRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQRRVARQE 385 (607)
T ss_pred EEcCCCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHHHHHHHH
Confidence 356778777 899999999999999999999999999999999887643
No 33
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=96.87 E-value=0.0017 Score=52.48 Aligned_cols=37 Identities=8% Similarity=0.008 Sum_probs=32.6
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
||+.+|+.++++|+.+..+ ..++++.+|||++++++.
T Consensus 333 ~G~~~~ve~s~~~i~~~~~--~~~~~v~rDITeR~~~~~ 369 (442)
T TIGR02040 333 FGAQTEVEISAAWVDQGER--PLIVLVIRDISRRLTMRD 369 (442)
T ss_pred CCCEEEEEEEEEEeccCCc--eEEEEEEecchhhccCCC
Confidence 9999999999999998666 457889999999999853
No 34
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=96.67 E-value=0.0058 Score=38.15 Aligned_cols=27 Identities=15% Similarity=0.182 Sum_probs=25.3
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEE
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLAS 37 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~ 37 (115)
||+..|+.....|++|++|+++.++++
T Consensus 64 ~G~~~wi~~~~~~~~d~~g~~~~~~Gv 90 (91)
T PF08447_consen 64 DGEYRWIEVRGRPIFDENGKPIRIIGV 90 (91)
T ss_dssp TSTEEEEEEEEEEEETTTS-EEEEEEE
T ss_pred CCCEEEEEEEEEEEECCCCCEEEEEEE
Confidence 999999999999999999999999987
No 35
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=96.55 E-value=0.0062 Score=39.79 Aligned_cols=30 Identities=23% Similarity=0.398 Sum_probs=24.2
Q ss_pred CceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547 13 TPFWCLLDIVPIKNEKREVVLYLASHKDVT 42 (115)
Q Consensus 13 ~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT 42 (115)
...|..+.+.|+++++|+..|.+.++.|||
T Consensus 77 ~~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 77 GGRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp TTEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred CCEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 355668899999999999999999999998
No 36
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=95.96 E-value=0.018 Score=46.60 Aligned_cols=38 Identities=24% Similarity=0.161 Sum_probs=34.8
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
+|..+ +.++.+|++|++|++.+++++++|||+++++++
T Consensus 342 ~~~~~-~~~~~~~i~~~~g~~~~~i~~~~Dite~~~~e~ 379 (607)
T PRK11360 342 DRTIE-LSVSTSLLHNTHGEMIGALVIFSDLTERKRLQR 379 (607)
T ss_pred CCcEE-EEEEEeeEEcCCCCEEEEEEEEeechHHHHHHH
Confidence 77766 899999999999999999999999999988775
No 37
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=95.70 E-value=0.059 Score=29.78 Aligned_cols=31 Identities=29% Similarity=0.641 Sum_probs=29.1
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEec
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDV 41 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DI 41 (115)
+|...|+.+...|+.+..|...+++++..||
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 73 DGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred CCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 7999999999999999999999999998886
No 38
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=95.47 E-value=0.041 Score=35.85 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=22.9
Q ss_pred eeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547 66 PFWCLLDIVPIKNEKREVVLYLASHKDVT 94 (115)
Q Consensus 66 ~f~~~~~i~pirde~G~v~~~i~~~~DIT 94 (115)
-.|..+.+.|+++++|++.+.+.++.|||
T Consensus 78 ~~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 78 GRWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp TEEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred CEEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 34556799999999999999999999998
No 39
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=94.92 E-value=0.15 Score=27.98 Aligned_cols=35 Identities=29% Similarity=0.565 Sum_probs=31.0
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeec
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDV 93 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DI 93 (115)
...++|...|+.+...|+.+..|....++++..||
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di 103 (103)
T cd00130 69 LRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVVRDI 103 (103)
T ss_pred EEccCCCEEEEEEEEEEEecCCCCEEEEEEEEecC
Confidence 35677999999999999999999999999998886
No 40
>PF12860 PAS_7: PAS fold
Probab=94.43 E-value=0.058 Score=35.53 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=24.8
Q ss_pred ceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 14 PFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 14 ~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
--|..+...|.-+ | +++.++.|||+++++|+
T Consensus 85 gr~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 85 GRWLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred CEEEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 3467788888854 5 67899999999999874
No 41
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=94.30 E-value=0.13 Score=35.47 Aligned_cols=84 Identities=15% Similarity=0.206 Sum_probs=58.5
Q ss_pred EEEEEEEeeCCCCCEEEEEEEEEe-ccchhhhhhh-------c-CC--C-C---ceeceecCCceeEEEEEeEEeeCCCC
Q psy8547 17 CLLDIVPIKNEKREVVLYLASHKD-VTNTKMAQMA-------D-NG--E-G---DYEDMQELGTPFWCLLDIVPIKNEKR 81 (115)
Q Consensus 17 ~~~~i~Pi~de~G~~~~fi~~~~D-IT~~k~~e~~-------~-~~--~-e---~~~~yrKdGs~f~~~~~i~pirde~G 81 (115)
|++.+-=+.+.+..++. +..- ||.|+.=... + +. + . .|...-|||..+.+ +-..|||++|
T Consensus 20 ~EVVLHDl~~~~~sIv~---I~Ng~vsgR~vGdp~t~~~l~~l~~~~~~~~~~~nY~~~~~~Gk~lrS--sT~~Ird~~g 94 (118)
T PF08348_consen 20 CEVVLHDLSDPEHSIVA---IANGHVSGRKVGDPITDLALELLKEKQYEEDYIINYKTKTKDGKILRS--STFFIRDENG 94 (118)
T ss_pred eEEEEEECCCCCCEEEE---EECCCccCCccCCchhHHHHHHHhccccCCCccccccccCCCCCEEEE--EEEEEECCCC
Confidence 67777777777776653 4444 7777653221 1 11 1 1 23345689988876 5678999999
Q ss_pred CEEEEEEEeeecccchhhchhhcc
Q psy8547 82 EVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 82 ~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
++++.+++-.|+|...++..-|+|
T Consensus 95 ~~iG~LCIN~D~s~~~~~~~~L~q 118 (118)
T PF08348_consen 95 KLIGALCINFDISALEQAQNFLDQ 118 (118)
T ss_pred CEEEEEEEEeccHHHHHHHHHHcC
Confidence 999999999999999988776654
No 42
>PRK10060 RNase II stability modulator; Provisional
Probab=92.85 E-value=0.26 Score=42.46 Aligned_cols=41 Identities=12% Similarity=0.176 Sum_probs=30.6
Q ss_pred ecc-CCCceeEEEEEEEeeCCCCC-EEEEEEEEEeccchhhhhh
Q psy8547 8 NYR-QRTPFWCLLDIVPIKNEKRE-VVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 8 ~Yr-dG~~fw~~~~i~Pi~de~G~-~~~fi~~~~DIT~~k~~e~ 49 (115)
+.+ +|+.+|+.... |+.+.+|. ..+++++.+|||+++.+++
T Consensus 189 ~~~~~G~~~~~~~~~-~~~~~~g~~~~~~i~~~~DITe~k~~e~ 231 (663)
T PRK10060 189 IKTRKGQRLFLFRNK-FVHSGSGKNEIFLICSGTDITEERRAQE 231 (663)
T ss_pred EEeCCCCEEEEEeee-EEEcCCCCceEEEEEEEEechHHHHHHH
Confidence 334 99999987664 45555554 4678899999999998776
No 43
>PF12860 PAS_7: PAS fold
Probab=92.57 E-value=0.18 Score=33.11 Aligned_cols=34 Identities=21% Similarity=0.370 Sum_probs=25.2
Q ss_pred ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhch
Q psy8547 61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 101 (115)
Q Consensus 61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~ 101 (115)
..||. |..++.+|.-+ | .++.++.|||+.+++|+
T Consensus 82 ~~dgr--~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E~ 115 (115)
T PF12860_consen 82 LPDGR--WLEVRAQPLPD--G---GFVLTFTDVTERRRAEE 115 (115)
T ss_pred CCCCE--EEEEEeEECCC--C---CEEEEEEeCCHHHHhcC
Confidence 34554 55667778743 4 48899999999999985
No 44
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=92.48 E-value=0.055 Score=41.69 Aligned_cols=41 Identities=10% Similarity=0.017 Sum_probs=32.9
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~ 104 (115)
.+.+||..+|+.++.+|+. . ..++..+.|+|++++.+.++.
T Consensus 82 ~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~~~~~ 122 (348)
T PRK11073 82 TLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLSQEQL 122 (348)
T ss_pred EEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHHHHHH
Confidence 3678999999999999998 2 246778999999888766543
No 45
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=90.39 E-value=0.37 Score=36.02 Aligned_cols=40 Identities=18% Similarity=0.140 Sum_probs=33.3
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhh
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD 103 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~ 103 (115)
...++|..+|..+.++|+.+.. +++++.|||+.++.++..
T Consensus 75 ~~~~~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~~~ 114 (333)
T TIGR02966 75 LPSPINSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQMR 114 (333)
T ss_pred eecCCCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHHHH
Confidence 3458999999999999998754 788999999998877643
No 46
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=89.31 E-value=0.55 Score=36.10 Aligned_cols=37 Identities=8% Similarity=0.021 Sum_probs=29.5
Q ss_pred eecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhh
Q psy8547 7 TNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48 (115)
Q Consensus 7 ~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e 48 (115)
..++ ||+.+|+.++.+|+. . .+++..++|+|+++..+
T Consensus 81 ~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~~dit~~~~~~ 118 (348)
T PRK11073 81 VTLVIDGRSHILSLTAQRLP--E---GMILLEMAPMDNQRRLS 118 (348)
T ss_pred eEEEECCceEEEEEEEEEcc--C---ceeEEEEechhHHHHHH
Confidence 3455 999999999999999 2 34667899999987754
No 47
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=88.34 E-value=0.74 Score=34.38 Aligned_cols=34 Identities=21% Similarity=0.192 Sum_probs=29.5
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
+|..+|+.+.++|+.+.. ++++++|||+.++.++
T Consensus 79 ~~~~~~~~~~~~p~~~~~-----~~~~~~dit~~~~~~~ 112 (333)
T TIGR02966 79 INSERVLEIRIAPYGEEQ-----KLLVARDVTRLRRLEQ 112 (333)
T ss_pred CCCceEEEEEEEEcCCCc-----eEEEEeCchHHHHHHH
Confidence 899999999999998854 7789999999887654
No 48
>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=87.84 E-value=2.7 Score=25.92 Aligned_cols=35 Identities=14% Similarity=0.147 Sum_probs=27.2
Q ss_pred cc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547 9 YR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 43 (115)
Q Consensus 9 Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~ 43 (115)
|. ..+.-|+.....||++++|+++|++++--++..
T Consensus 5 y~~~~~~~~vi~~s~pi~~~~g~~~Gvv~~di~l~~ 40 (81)
T PF02743_consen 5 YVDAATGQPVITISVPIYDDDGKIIGVVGIDISLDQ 40 (81)
T ss_dssp EEETTTTEEEEEEEEEEEETTTEEEEEEEEEEEHHH
T ss_pred EEeCCCCcEEEEEEEEEECCCCCEEEEEEEEeccce
Confidence 44 446667889999999999999999987555443
No 49
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=87.61 E-value=1.2 Score=36.85 Aligned_cols=44 Identities=14% Similarity=0.099 Sum_probs=39.4
Q ss_pred eeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 6 DTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 6 ~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
++..+ .|+.+-..+..+.++-|.|.+.|+|++..|+|++...|+
T Consensus 179 lld~~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ 223 (459)
T COG5002 179 LLDSSDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVER 223 (459)
T ss_pred EEeecCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHH
Confidence 44556 788889999999999999999999999999999988777
No 50
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=87.05 E-value=1.2 Score=36.13 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=29.1
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
+|.. +.....|+++ +|.+.+++.+++|+|+.++.++
T Consensus 296 ~g~~--~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~ 331 (542)
T PRK11086 296 NGRL--LLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQ 331 (542)
T ss_pred CCEE--EEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHH
Confidence 5544 4556789999 8999999999999999877554
No 51
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=86.74 E-value=2.4 Score=29.14 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=31.2
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
||+.+.+ +-..|+|++|+++|.+++=.|+|....+..
T Consensus 78 ~Gk~lrS--sT~~Ird~~g~~iG~LCIN~D~s~~~~~~~ 114 (118)
T PF08348_consen 78 DGKILRS--STFFIRDENGKLIGALCINFDISALEQAQN 114 (118)
T ss_pred CCCEEEE--EEEEEECCCCCEEEEEEEEeccHHHHHHHH
Confidence 8877654 456899999999999999999999887654
No 52
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=86.51 E-value=1.1 Score=37.05 Aligned_cols=44 Identities=14% Similarity=0.117 Sum_probs=39.1
Q ss_pred ecCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547 61 QELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104 (115)
Q Consensus 61 rKdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~ 104 (115)
+..|..+-..+.-+-++-+.|-+.+++++..|+|++...|++.|
T Consensus 183 ~~~~E~~~lrv~Fs~i~rEsGfisGlIaVlhDvTEqek~e~ErR 226 (459)
T COG5002 183 SDEEEGYVLRVNFSVIQRESGFISGLIAVLHDVTEQEKVERERR 226 (459)
T ss_pred cCCCccEEEEEEEEEEeecccccceeEEEEecccHHHHHHHHHH
Confidence 44788888899999999999999999999999999988887655
No 53
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=86.08 E-value=1.2 Score=36.19 Aligned_cols=36 Identities=19% Similarity=0.301 Sum_probs=30.0
Q ss_pred EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547 68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104 (115)
Q Consensus 68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~ 104 (115)
+......|+.+ +|.+..++.+++|+|+.++.++++.
T Consensus 299 ~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~l~ 334 (542)
T PRK11086 299 LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQRLD 334 (542)
T ss_pred EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHHHH
Confidence 34556789998 8999999999999999988777654
No 54
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=85.65 E-value=2.1 Score=28.64 Aligned_cols=30 Identities=17% Similarity=0.081 Sum_probs=22.9
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEe
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKD 40 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~D 40 (115)
.|+.-+..-...||+|++|+++|++.+-..
T Consensus 83 ~~~~~~~~~~~~PV~d~~g~viG~V~VG~~ 112 (116)
T PF14827_consen 83 QGTGGPSLRAFAPVYDSDGKVIGVVSVGVS 112 (116)
T ss_dssp ECTTCEEEEEEEEEE-TTS-EEEEEEEEEE
T ss_pred ecCCceEEEEEEeeECCCCcEEEEEEEEEE
Confidence 555567788999999999999999987554
No 55
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=83.74 E-value=3.7 Score=25.89 Aligned_cols=41 Identities=27% Similarity=0.437 Sum_probs=35.1
Q ss_pred ceecCCce-eEEEEEeEEeeCCCCCEEEEEEEeeecccchhhc
Q psy8547 59 DMQELGTP-FWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 100 (115)
Q Consensus 59 ~yrKdGs~-f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E 100 (115)
...++|.. +|....+.+..+ .|.+..++....|+++.++++
T Consensus 191 ~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~ 232 (232)
T COG2202 191 VRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQAE 232 (232)
T ss_pred EEecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhcC
Confidence 36799996 999999999886 788999999999999988754
No 56
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=83.31 E-value=4.1 Score=25.72 Aligned_cols=40 Identities=28% Similarity=0.431 Sum_probs=34.2
Q ss_pred eecc-CCCc-eeEEEEEEEeeCCCCCEEEEEEEEEeccchhhh
Q psy8547 7 TNYR-QRTP-FWCLLDIVPIKNEKREVVLYLASHKDVTNTKMA 47 (115)
Q Consensus 7 ~~Yr-dG~~-fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~ 47 (115)
.... +|.. .|....+.|..+ .|.+..+.....|+|+++..
T Consensus 190 ~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~ 231 (232)
T COG2202 190 RVRRKDGERVRWILSRISPVRD-DGEIVGVVGIARDITERKQA 231 (232)
T ss_pred EEEecCCCEEEEEEeeeeEecC-CCceEEEEEEEechHHHhhc
Confidence 3444 9996 999999999988 89999999999999998764
No 57
>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=77.43 E-value=5 Score=26.33 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=20.3
Q ss_pred eEEEEEEEeeCCCCCEEEEEEEE
Q psy8547 16 WCLLDIVPIKNEKREVVLYLASH 38 (115)
Q Consensus 16 w~~~~i~Pi~de~G~~~~fi~~~ 38 (115)
=.-+.++||++++|++++-+++.
T Consensus 58 G~PViV~PI~~~~g~viaAiGvV 80 (84)
T PF09884_consen 58 GVPVIVAPIKDEDGEVIAAIGVV 80 (84)
T ss_pred CeeEEEEEEEcCCCCEEEEEEEE
Confidence 35688999999999999999886
No 58
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=76.72 E-value=2.9 Score=28.87 Aligned_cols=21 Identities=29% Similarity=0.354 Sum_probs=15.7
Q ss_pred EEEEEeeCCCCCEEEEEEEEE
Q psy8547 19 LDIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 19 ~~i~Pi~de~G~~~~fi~~~~ 39 (115)
=-|-||+|+.|++++|-+-.-
T Consensus 78 RiifPI~d~~G~vvgF~gR~l 98 (128)
T PF08275_consen 78 RIIFPIRDERGRVVGFGGRRL 98 (128)
T ss_dssp EEEEEEE-TTS-EEEEEEEES
T ss_pred eEEEEEEcCCCCEEEEecccC
Confidence 457899999999999987655
No 59
>PF07411 DUF1508: Domain of unknown function (DUF1508); InterPro: IPR010879 This domain is found in a family of proteins, which have no known function. Members of this family are often found as tandem repeats and in some cases represent the whole protein.; PDB: 3BID_H 2K49_A 2K8E_A 2K7I_A.
Probab=75.23 E-value=2.9 Score=24.35 Aligned_cols=46 Identities=9% Similarity=0.019 Sum_probs=32.8
Q ss_pred cCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhccCCCccccc
Q psy8547 62 ELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNGEGDYEDMQ 113 (115)
Q Consensus 62 KdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~~~~~~~~~ 113 (115)
++|..+|. ++..+|+|+.---.+.+-.+.+..-+.++..|-.....
T Consensus 2 ~~g~~~f~------L~a~ng~viasse~Y~sk~~a~~~I~~Vk~~a~~a~v~ 47 (49)
T PF07411_consen 2 SDGQFRFR------LKAGNGEVIASSEGYSSKADAEKGIESVKKNAPDAEVV 47 (49)
T ss_dssp TTSEEEEE------EE-TTS-EEEEBEEBSSHHHHHHHHHHHHHHTTTSCEE
T ss_pred CCCCEEEE------EEcCCCCEEEecCCcCCHHHHHHHHHHHHHhCCCCccc
Confidence 68889997 57899999997777777777777777777666554443
No 60
>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=70.77 E-value=8.6 Score=25.21 Aligned_cols=32 Identities=28% Similarity=0.270 Sum_probs=24.0
Q ss_pred cCCceeEEEEEeEEeeCCCCCEEEEEEEeeecc
Q psy8547 62 ELGTPFWCLLDIVPIKNEKREVVLYLASHKDVT 94 (115)
Q Consensus 62 KdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT 94 (115)
+.|..--.-+.++||++++|+++..+++. |+|
T Consensus 52 ~~G~Y~G~PViV~PI~~~~g~viaAiGvV-D~t 83 (84)
T PF09884_consen 52 IEGPYKGVPVIVAPIKDEDGEVIAAIGVV-DLT 83 (84)
T ss_pred CCcccCCeeEEEEEEEcCCCCEEEEEEEE-Ecc
Confidence 33444446788999999999999999875 344
No 61
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=63.44 E-value=34 Score=22.67 Aligned_cols=39 Identities=10% Similarity=0.131 Sum_probs=28.6
Q ss_pred eeceecCCceeEEEEEeEEeeCCC-CCEEEEEEEeeeccc
Q psy8547 57 YEDMQELGTPFWCLLDIVPIKNEK-REVVLYLASHKDVTN 95 (115)
Q Consensus 57 ~~~yrKdGs~f~~~~~i~pirde~-G~v~~~i~~~~DIT~ 95 (115)
++...|+|+..|+.....++.|.. +++-+++++..=|++
T Consensus 69 yR~~~k~g~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 69 YRFRTKNGGYVWVQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp EEEE-TTSSEEEEEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred EEEEecCCcEEEEEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 566779999999999999999744 456666666654444
No 62
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=62.65 E-value=7.4 Score=32.35 Aligned_cols=32 Identities=22% Similarity=0.249 Sum_probs=28.5
Q ss_pred EEEEEEEeeCCCCCEEEEEEEEEeccchhhhh
Q psy8547 17 CLLDIVPIKNEKREVVLYLASHKDVTNTKMAQ 48 (115)
Q Consensus 17 ~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e 48 (115)
+.++-.+|+|++|+..|.+-+.+|||.-+..+
T Consensus 371 i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ 402 (409)
T COG2461 371 IHIRYFAVKDEEGEYLGTLEVVQDITRIKELE 402 (409)
T ss_pred EEEEEEEEEcCCCceeeeehhhhhhHHHHhcc
Confidence 46788999999999999999999999887754
No 63
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=60.45 E-value=20 Score=23.74 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=21.8
Q ss_pred CceeEEEEEeEEeeCCCCCEEEEEEEeeec
Q psy8547 64 GTPFWCLLDIVPIKNEKREVVLYLASHKDV 93 (115)
Q Consensus 64 Gs~f~~~~~i~pirde~G~v~~~i~~~~DI 93 (115)
|+.-+..-...||+|.+|+++.++.+-..+
T Consensus 84 ~~~~~~~~~~~PV~d~~g~viG~V~VG~~~ 113 (116)
T PF14827_consen 84 GTGGPSLRAFAPVYDSDGKVIGVVSVGVSL 113 (116)
T ss_dssp CTTCEEEEEEEEEE-TTS-EEEEEEEEEEH
T ss_pred cCCceEEEEEEeeECCCCcEEEEEEEEEEc
Confidence 444566778899999999999999876543
No 64
>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=59.29 E-value=13 Score=20.76 Aligned_cols=18 Identities=17% Similarity=0.412 Sum_probs=14.8
Q ss_pred EEEEEeeCCCCCEEEEEE
Q psy8547 19 LDIVPIKNEKREVVLYLA 36 (115)
Q Consensus 19 ~~i~Pi~de~G~~~~fi~ 36 (115)
....||.|++|+++|++.
T Consensus 30 ~~~~~V~d~~~~~~G~is 47 (57)
T PF00571_consen 30 ISRLPVVDEDGKLVGIIS 47 (57)
T ss_dssp SSEEEEESTTSBEEEEEE
T ss_pred CcEEEEEecCCEEEEEEE
Confidence 456799999999998764
No 65
>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=56.85 E-value=19 Score=25.39 Aligned_cols=33 Identities=15% Similarity=0.310 Sum_probs=21.4
Q ss_pred eEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 16 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 16 w~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
.+..++.||+++. ++++++....++...+..+.
T Consensus 103 ~v~~~~~PI~~~~-~vIaVl~~~~~~~~~~~~~~ 135 (145)
T PF12282_consen 103 PVRQEVVPIRRNG-RVIAVLIRETNLSASRTPSR 135 (145)
T ss_dssp --EEEEEEEEETT-EEEEEEEEE--GGGS----H
T ss_pred eeEEEEEEEEECC-EEEEEEEEEcccccccCCCH
Confidence 4688999999975 99999998878877766543
No 66
>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A ....
Probab=56.73 E-value=53 Score=21.73 Aligned_cols=33 Identities=6% Similarity=0.083 Sum_probs=24.4
Q ss_pred CCCceeEEEEEEEeeCCCC-CEEEEEEEEEeccc
Q psy8547 11 QRTPFWCLLDIVPIKNEKR-EVVLYLASHKDVTN 43 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G-~~~~fi~~~~DIT~ 43 (115)
+|...|+.....+++|... ++-.++++..=|++
T Consensus 75 ~g~~vwvqt~~~~~~n~~~~~~~~Iv~~n~vlse 108 (111)
T PF14598_consen 75 NGGYVWVQTKATLFYNPWTSKPEFIVCTNTVLSE 108 (111)
T ss_dssp TSSEEEEEEEEEEEEETTTTCEEEEEEEEEEESC
T ss_pred CCcEEEEEEEEEEEECCCCCCccEEEEEEEEecc
Confidence 9999999999999998655 44545555554444
No 67
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=56.18 E-value=13 Score=25.52 Aligned_cols=22 Identities=27% Similarity=0.271 Sum_probs=16.4
Q ss_pred EEEeEEeeCCCCCEEEEEEEee
Q psy8547 70 LLDIVPIKNEKREVVLYLASHK 91 (115)
Q Consensus 70 ~~~i~pirde~G~v~~~i~~~~ 91 (115)
.--|-||+|+.|+|+.|-+-..
T Consensus 77 ~RiifPI~d~~G~vvgF~gR~l 98 (128)
T PF08275_consen 77 GRIIFPIRDERGRVVGFGGRRL 98 (128)
T ss_dssp TEEEEEEE-TTS-EEEEEEEES
T ss_pred CeEEEEEEcCCCCEEEEecccC
Confidence 3467899999999999988665
No 68
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=54.69 E-value=16 Score=30.86 Aligned_cols=33 Identities=15% Similarity=0.276 Sum_probs=26.0
Q ss_pred CCCceeEEEEEEEee--CCCCCE--EEEEEEEEeccchh
Q psy8547 11 QRTPFWCLLDIVPIK--NEKREV--VLYLASHKDVTNTK 45 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~--de~G~~--~~fi~~~~DIT~~k 45 (115)
+|..|+ +.+.||+ +++|+. +|.+.+++|++...
T Consensus 153 ~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~ 189 (520)
T PRK10820 153 NGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMG 189 (520)
T ss_pred CCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHH
Confidence 787776 5678887 777764 89999999999753
No 69
>PRK13662 hypothetical protein; Provisional
Probab=53.67 E-value=19 Score=26.59 Aligned_cols=87 Identities=16% Similarity=0.158 Sum_probs=50.5
Q ss_pred cceeecc-CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhhhc---------CCCCc--eeceecCCceeEEEE
Q psy8547 4 HPDTNYR-QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMAD---------NGEGD--YEDMQELGTPFWCLL 71 (115)
Q Consensus 4 ~~~~~Yr-dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~~~---------~~~e~--~~~yrKdGs~f~~~~ 71 (115)
.....|| ||+.+|.--.-.-+.+.+|.++++-. .+=+++..-....- .+.-. ....+.+|..+.|.+
T Consensus 10 v~I~~yK~dG~lHr~w~~~~v~~~~~~~~v~~~~-~t~v~e~dG~~Wv~repai~~F~~~~wfnv~~m~~~~gv~~Y~nl 88 (177)
T PRK13662 10 IQIQSYKHDGSLHRTWRDTMVLKTTENAVIGGND-HTLVTESDGRRWVTREPAICYFHKKYWFNVIAMIREDGVYYYCNL 88 (177)
T ss_pred EEEEEEEeCCeEEEEEEcCEEEEccCCeEEEECC-cEEEEeCCCceEEecCCEEEEEeCCCCEEEEEEEcCCCeEEEEEC
Confidence 4567899 99999988888888999998877654 22233322111100 00000 012466677777777
Q ss_pred EeEEeeCCCCCEEEEEEEeeec
Q psy8547 72 DIVPIKNEKREVVLYLASHKDV 93 (115)
Q Consensus 72 ~i~pirde~G~v~~~i~~~~DI 93 (115)
.--+++++.| +.++---.||
T Consensus 89 ~~p~~~~~~~--i~~iD~dLDv 108 (177)
T PRK13662 89 ASPFVLDEEA--LKYIDYDLDI 108 (177)
T ss_pred CCCcEEcCCc--eeEEeeeeEE
Confidence 7777775443 3444444444
No 70
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=52.16 E-value=19 Score=19.43 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=10.1
Q ss_pred EEEeeCCCCCEEEEE
Q psy8547 21 IVPIKNEKREVVLYL 35 (115)
Q Consensus 21 i~Pi~de~G~~~~fi 35 (115)
+.||+|+.|++--|-
T Consensus 12 l~pvy~~kgeikvfr 26 (36)
T PF09151_consen 12 LEPVYNQKGEIKVFR 26 (36)
T ss_dssp EEEEE-TTS-EEEEE
T ss_pred EEEeecCCCcEEEEE
Confidence 579999999986543
No 71
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=48.69 E-value=31 Score=29.17 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=27.9
Q ss_pred eecCCceeEEEEEeEEee--CCCCCE--EEEEEEeeecccchh
Q psy8547 60 MQELGTPFWCLLDIVPIK--NEKREV--VLYLASHKDVTNTKM 98 (115)
Q Consensus 60 yrKdGs~f~~~~~i~pir--de~G~v--~~~i~~~~DIT~~k~ 98 (115)
...+|..|+ +.++||. ++.|.. ++.+.+++|+++..+
T Consensus 150 v~~~g~~~~--v~~~PI~~~d~~g~~~~~GaVivlrd~~~l~~ 190 (520)
T PRK10820 150 VVINGQDFL--MEITPVYLQDENDQHVLVGAVVMLRSTARMGR 190 (520)
T ss_pred EEECCEEEE--EEEEeeeecCCCCceeEEEEEEEeccHHHHHH
Confidence 456677666 5678887 777764 899999999997644
No 72
>PRK08624 hypothetical protein; Provisional
Probab=47.97 E-value=17 Score=29.93 Aligned_cols=26 Identities=19% Similarity=0.124 Sum_probs=20.0
Q ss_pred ceeEEEEEEEeeCCCCCEEEEEEEEEe
Q psy8547 14 PFWCLLDIVPIKNEKREVVLYLASHKD 40 (115)
Q Consensus 14 ~fw~~~~i~Pi~de~G~~~~fi~~~~D 40 (115)
.|+..+.+ ||+|..|++++|=+-.-|
T Consensus 179 ~Fr~RImF-PI~d~~GrvIGFgGR~l~ 204 (373)
T PRK08624 179 VISQRIII-PHRDESGELIGIRGRLLD 204 (373)
T ss_pred ccCCeeEE-EEECCCCCEEEEeCeEcC
Confidence 45555554 999999999999876543
No 73
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=45.07 E-value=22 Score=27.22 Aligned_cols=21 Identities=14% Similarity=0.175 Sum_probs=17.5
Q ss_pred EEEEEeeCCCCCEEEEEEEEE
Q psy8547 19 LDIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 19 ~~i~Pi~de~G~~~~fi~~~~ 39 (115)
--+-||+|..|++++|-+-.-
T Consensus 59 RimFPI~d~~G~vvgFgGR~l 79 (218)
T TIGR00646 59 WLNLPLYNFDGNLIGFLNRKV 79 (218)
T ss_pred EEEEEEECCCCCEEEEeccCC
Confidence 457899999999999987543
No 74
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=44.75 E-value=19 Score=31.58 Aligned_cols=32 Identities=25% Similarity=0.202 Sum_probs=23.9
Q ss_pred eeeccCCCceeEEEEEEEeeCCCCCEEEEEEEE
Q psy8547 6 DTNYRQRTPFWCLLDIVPIKNEKREVVLYLASH 38 (115)
Q Consensus 6 ~~~YrdG~~fw~~~~i~Pi~de~G~~~~fi~~~ 38 (115)
...|+.....| .-+.+||+|++|++++.+-+.
T Consensus 148 ~qHF~~~~~~l-sCsAaPI~D~qG~L~gVLDIS 179 (606)
T COG3284 148 DQHFIQAHHGL-SCSAAPIFDEQGELVGVLDIS 179 (606)
T ss_pred hhhHhhcccCc-eeeeeccccCCCcEEEEEEec
Confidence 33445555666 567899999999999988655
No 75
>PF10829 DUF2554: Protein of unknown function (DUF2554); InterPro: IPR020117 This entry contains proteins with no known function.
Probab=42.95 E-value=7.6 Score=24.82 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=14.2
Q ss_pred hhhchhhccCCCccccc
Q psy8547 97 KMAQMADNGEGDYEDMQ 113 (115)
Q Consensus 97 k~~E~~~~~~~~~~~~~ 113 (115)
+.++.+|+++||+|.|.
T Consensus 33 q~~d~qLrHeADSDELR 49 (76)
T PF10829_consen 33 QNADHQLRHEADSDELR 49 (76)
T ss_pred ccHHHHHHhhcccHHHH
Confidence 45788999999999885
No 76
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=42.71 E-value=19 Score=30.07 Aligned_cols=34 Identities=21% Similarity=0.200 Sum_probs=29.2
Q ss_pred EEEEeEEeeCCCCCEEEEEEEeeecccchhhchh
Q psy8547 69 CLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA 102 (115)
Q Consensus 69 ~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~ 102 (115)
+.++-.+|+|+.|+-.+.+-+..|||.-+.-|-.
T Consensus 371 i~i~Y~av~de~ge~~g~le~~qdi~~i~~l~ge 404 (409)
T COG2461 371 IHIRYFAVKDEEGEYLGTLEVVQDITRIKELEGE 404 (409)
T ss_pred EEEEEEEEEcCCCceeeeehhhhhhHHHHhccch
Confidence 4678899999999999999999999988876653
No 77
>KOG1229|consensus
Probab=41.77 E-value=19 Score=31.02 Aligned_cols=31 Identities=10% Similarity=0.131 Sum_probs=28.0
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEEEEEE
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVLYLAS 89 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~~i~~ 89 (115)
.+||.|...-..+.|+|+.+..|++.+|++.
T Consensus 235 aRRksgdS~dqh~~itP~~gqggkirhfvsl 265 (775)
T KOG1229|consen 235 ARRKSGDSCDQHFIITPFAGQGGKIRHFVSL 265 (775)
T ss_pred HhhccCCcccceEEEeeecCCCCceeeehhh
Confidence 3789999999999999999999999999864
No 78
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=39.47 E-value=47 Score=28.57 Aligned_cols=35 Identities=11% Similarity=0.183 Sum_probs=24.7
Q ss_pred cCCceeEEEEEeEEeeCCCCCEEEEEEEeeecccchh
Q psy8547 62 ELGTPFWCLLDIVPIKNEKREVVLYLASHKDVTNTKM 98 (115)
Q Consensus 62 KdGs~f~~~~~i~pirde~G~v~~~i~~~~DIT~~k~ 98 (115)
++|..+++.+++.|+.+..|. .++....|++..+.
T Consensus 277 ~~g~~~~~~v~~~Pi~~~~g~--~~v~~l~~~~~~~~ 311 (638)
T PRK11388 277 SQGQFIDAVITLKPIIEGQGT--SFILLLHPVEQMRQ 311 (638)
T ss_pred cCCceEEEEEEEEeecccCce--EEEEEehhhHHHHH
Confidence 347778899999999865554 25666778876543
No 79
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=36.41 E-value=77 Score=25.97 Aligned_cols=37 Identities=5% Similarity=0.020 Sum_probs=27.5
Q ss_pred EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
.......|+.. .|++...+.+++|+|+.+..+.++..
T Consensus 298 ~~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~~l~~ 334 (545)
T PRK15053 298 SVIANREAIRS-GDDLLGAIISFRSKDEISTLNAQLTQ 334 (545)
T ss_pred EEEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHHHHHH
Confidence 34467788886 56688999999999998776655443
No 80
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional
Probab=33.99 E-value=83 Score=22.58 Aligned_cols=30 Identities=13% Similarity=0.078 Sum_probs=24.1
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 43 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~ 43 (115)
+|..||..+---.|.|++|..+| ...||-+
T Consensus 97 e~E~Y~~dLiG~~V~d~~g~~lG---~V~~v~~ 126 (169)
T PRK14591 97 EDEVYFKDLIGCSVKNINNDSFG---VVVDIIE 126 (169)
T ss_pred CCCEEeeeecCcEEEeCCCCEEE---EEEEEee
Confidence 79999999999999999998765 4454433
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=33.43 E-value=71 Score=22.44 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=20.2
Q ss_pred EEEEEeEEeeCCCCCEEEEEEEeeecccchhh
Q psy8547 68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMA 99 (115)
Q Consensus 68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~ 99 (115)
.....+.||+++. +++..+....++...+..
T Consensus 103 ~v~~~~~PI~~~~-~vIaVl~~~~~~~~~~~~ 133 (145)
T PF12282_consen 103 PVRQEVVPIRRNG-RVIAVLIRETNLSASRTP 133 (145)
T ss_dssp --EEEEEEEEETT-EEEEEEEEE--GGGS---
T ss_pred eeEEEEEEEEECC-EEEEEEEEEcccccccCC
Confidence 5678999999865 899999977777755543
No 82
>PHA02540 61 DNA primase; Provisional
Probab=33.15 E-value=40 Score=27.37 Aligned_cols=21 Identities=14% Similarity=0.224 Sum_probs=17.4
Q ss_pred EEEEEeeCCCCCEEEEEEEEE
Q psy8547 19 LDIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 19 ~~i~Pi~de~G~~~~fi~~~~ 39 (115)
=-|-||+|.+|++++|=+-.-
T Consensus 173 RImFPI~d~~G~vigFgGR~l 193 (337)
T PHA02540 173 RLVIPIFNKDGKIESFQGRAL 193 (337)
T ss_pred eeEEEEECCCCCEEEEEeEEC
Confidence 357899999999999987554
No 83
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=31.83 E-value=52 Score=28.51 Aligned_cols=37 Identities=22% Similarity=0.263 Sum_probs=30.2
Q ss_pred EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhcc
Q psy8547 68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADNG 105 (115)
Q Consensus 68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~~ 105 (115)
++.+...||+ .+|++++++.+|+|-|+-+.--++|.+
T Consensus 293 ~~i~nr~pI~-~~~~~~GaI~tFRdktei~~L~eqLt~ 329 (537)
T COG3290 293 LLVANRVPIR-SGGQIVGAIITFRDKTEIKKLTEQLTG 329 (537)
T ss_pred EEEEEeccEE-ECCEEeEEEEEEecHHHHHHHHHHHHH
Confidence 5667889998 588999999999999988876655544
No 84
>TIGR02273 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide.
Probab=31.64 E-value=48 Score=23.55 Aligned_cols=29 Identities=14% Similarity=0.123 Sum_probs=23.2
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEE
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~ 39 (115)
+|+.||+.+---.|.|++|+.+|.+.-..
T Consensus 92 e~e~y~~dLiG~~V~d~~~~~lG~V~~v~ 120 (165)
T TIGR02273 92 EDEYYWTDLIGLEVVTEEGEELGKVVEIL 120 (165)
T ss_pred CCCEEhhHhCCcEEEcCCCcEEEEEEEEe
Confidence 78999999999999999997765444333
No 85
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=31.46 E-value=64 Score=27.94 Aligned_cols=33 Identities=21% Similarity=0.272 Sum_probs=28.5
Q ss_pred eEEEEEEEeeCCCCCEEEEEEEEEeccchhhhhh
Q psy8547 16 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQM 49 (115)
Q Consensus 16 w~~~~i~Pi~de~G~~~~fi~~~~DIT~~k~~e~ 49 (115)
|+..+..||+- +|+++|.+++|+|-|+-+...+
T Consensus 293 ~~i~nr~pI~~-~~~~~GaI~tFRdktei~~L~e 325 (537)
T COG3290 293 LLVANRVPIRS-GGQIVGAIITFRDKTEIKKLTE 325 (537)
T ss_pred EEEEEeccEEE-CCEEeEEEEEEecHHHHHHHHH
Confidence 67889999987 7899999999999998876544
No 86
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.20 E-value=91 Score=23.96 Aligned_cols=78 Identities=14% Similarity=0.242 Sum_probs=47.6
Q ss_pred EEEEEEEeeCCCCCEEEEEEEEEe-ccchhhhhh----h-c-----CCC--C---ceeceecCCceeEEEEEeEEeeCCC
Q psy8547 17 CLLDIVPIKNEKREVVLYLASHKD-VTNTKMAQM----A-D-----NGE--G---DYEDMQELGTPFWCLLDIVPIKNEK 80 (115)
Q Consensus 17 ~~~~i~Pi~de~G~~~~fi~~~~D-IT~~k~~e~----~-~-----~~~--e---~~~~yrKdGs~f~~~~~i~pirde~ 80 (115)
|++..--+.+.+..++. +..- +|.|.--.. + + +++ . .|..+-|||.++.. +-..|||..
T Consensus 29 ~EIVLH~l~~~~~svi~---IaN~h~SgR~vG~piT~~al~~l~~~~~~~~~~~~~Y~~~~~~g~~ikS--sS~~Irn~~ 103 (220)
T COG2964 29 CEIVLHDLEDLEHSVIA---IANGHISGRQVGSPITDLALDLLHNKEGSEKSVIGNYFTRAKDGRLIKS--SSIFIRNKE 103 (220)
T ss_pred eEEEEEEcccCCceEEE---EecCccccCccCCchhHHHHHhcccccccchhhhhhhhhcCCCCceeee--eEEEEEcCC
Confidence 66666666776665542 3333 555443211 1 1 111 1 23345677888775 345699999
Q ss_pred CCEEEEEEEeeecccchhh
Q psy8547 81 REVVLYLASHKDVTNTKMA 99 (115)
Q Consensus 81 G~v~~~i~~~~DIT~~k~~ 99 (115)
|++++.+++-.|++-.+-.
T Consensus 104 g~~iGmLCIN~d~s~l~~~ 122 (220)
T COG2964 104 GRIIGMLCINMDLSLLVPV 122 (220)
T ss_pred CCEEEEEEEecchhhhhHH
Confidence 9999999999999954433
No 87
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=30.36 E-value=92 Score=27.16 Aligned_cols=32 Identities=13% Similarity=0.298 Sum_probs=24.8
Q ss_pred EEEeEEeeCCCCCEEEEEEEeeecccchhhchh
Q psy8547 70 LLDIVPIKNEKREVVLYLASHKDVTNTKMAQMA 102 (115)
Q Consensus 70 ~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~ 102 (115)
..+..|+. .+|.+...++++.|++..+....+
T Consensus 197 i~~~~pv~-~~g~l~G~v~~~~~~~~l~~l~~~ 228 (560)
T COG3829 197 IVNVAPVY-ADGQLIGVVGISKDVSELERLTRE 228 (560)
T ss_pred eEeeccEe-cCCcEEEEEEeecchHHHHHHHHH
Confidence 45667777 466999999999999987765543
No 88
>PF00949 Peptidase_S7: Peptidase S7, Flavivirus NS3 serine protease ; InterPro: IPR001850 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature identifies serine peptidases belong to MEROPS peptidase family S7 (flavivirin family, clan PA(S)). The protein fold of the peptidase domain for members of this family resembles that of chymotrypsin, the type example for clan PA. Flaviviruses produce a polyprotein from the ssRNA genome. The N terminus of the NS3 protein (approx. 180 aa) is required for the processing of the polyprotein. NS3 also has conserved homology with NTP-binding proteins and DEAD family of RNA helicase [, , ].; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0005524 ATP binding; PDB: 2IJO_B 3E90_D 2GGV_B 2FP7_B 2WV9_A 3U1I_B 3U1J_B 2WZQ_A 2WHX_A 3L6P_A ....
Probab=29.77 E-value=57 Score=22.98 Aligned_cols=20 Identities=25% Similarity=0.212 Sum_probs=14.9
Q ss_pred EEEEeeCCCCCEEEEEEEEE
Q psy8547 20 DIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 20 ~i~Pi~de~G~~~~fi~~~~ 39 (115)
+-|||.|.+|+++++-+.--
T Consensus 99 SGSpi~n~~g~ivGlYg~g~ 118 (132)
T PF00949_consen 99 SGSPIFNQNGEIVGLYGNGV 118 (132)
T ss_dssp TT-EEEETTSCEEEEEEEEE
T ss_pred CCCceEcCCCcEEEEEccce
Confidence 35899999999998775543
No 89
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=29.26 E-value=57 Score=26.85 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=17.1
Q ss_pred EEEEeeCCCCCEEEEEEEEEe
Q psy8547 20 DIVPIKNEKREVVLYLASHKD 40 (115)
Q Consensus 20 ~i~Pi~de~G~~~~fi~~~~D 40 (115)
-+-||+|.+|++++|-+=.-+
T Consensus 203 iifPi~d~~G~vvgf~gR~~~ 223 (415)
T TIGR01391 203 IMFPIHDPKGRVVGFGGRALG 223 (415)
T ss_pred EEEEEECCCCCEEEEEeeecC
Confidence 456999999999999876554
No 90
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=28.59 E-value=1.2e+02 Score=22.35 Aligned_cols=30 Identities=10% Similarity=0.034 Sum_probs=25.3
Q ss_pred cCCCceeEEEEEEEeeCCCCCEEEEEEEEE
Q psy8547 10 RQRTPFWCLLDIVPIKNEKREVVLYLASHK 39 (115)
Q Consensus 10 rdG~~fw~~~~i~Pi~de~G~~~~fi~~~~ 39 (115)
..|+-||+.+.-..|.+++|+.+|-+.-..
T Consensus 97 ~EdEfY~~DLiG~~V~~~~g~~lG~V~~i~ 126 (174)
T COG0806 97 EEDEFYYHDLIGLEVVTEDGELLGKVTEIL 126 (174)
T ss_pred CCCcEEeEeecCcEEEcCCCcEEEEEEEEe
Confidence 479999999999999999999887664443
No 91
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=27.45 E-value=76 Score=25.99 Aligned_cols=32 Identities=13% Similarity=0.060 Sum_probs=25.3
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT 42 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT 42 (115)
.|+.=.|....+||++++|.++|++.+...+.
T Consensus 139 ~~~~g~~~~~a~PI~~~~g~~iGvi~v~~~~~ 170 (545)
T PRK15053 139 KGSMGMAMRAKTPIFDDDGKVIGVVSIGYLVS 170 (545)
T ss_pred ccccceeeEEEeeeEcCCCCEEEEEEEEEEHH
Confidence 56666677788999999999999987766443
No 92
>PF07370 DUF1489: Protein of unknown function (DUF1489); InterPro: IPR008320 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.37 E-value=1.1e+02 Score=21.80 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=16.7
Q ss_pred CCCceeE----------EEEEEEeeCCCCCEEE
Q psy8547 11 QRTPFWC----------LLDIVPIKNEKREVVL 33 (115)
Q Consensus 11 dG~~fw~----------~~~i~Pi~de~G~~~~ 33 (115)
-||.||+ .+.+.|+.+++|.-..
T Consensus 47 GGSlYWVikg~i~~RQ~Il~i~~~~~~dG~~rc 79 (137)
T PF07370_consen 47 GGSLYWVIKGQIQCRQRILDIEEVTDGDGIRRC 79 (137)
T ss_pred CCcEEEEECCEEEEeeeeeeeeEecCCCCcccE
Confidence 5899997 4667777787775443
No 93
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=26.14 E-value=77 Score=25.27 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=23.1
Q ss_pred EEEEEeEEeeCCCCCEEEEEEEeeecccchhhchhhc
Q psy8547 68 WCLLDIVPIKNEKREVVLYLASHKDVTNTKMAQMADN 104 (115)
Q Consensus 68 ~~~~~i~pirde~G~v~~~i~~~~DIT~~k~~E~~~~ 104 (115)
+..+.+.|..+ + .++.+..|||++++.|++.+
T Consensus 174 ~~~~~~~~~~~--~---~~~~~~~dit~~~~~e~~~~ 205 (430)
T PRK11006 174 HLEIRVMPYTE--G---QLLMVARDVTQMHQLEGARR 205 (430)
T ss_pred EEEEEEEEcCC--C---cEEEEEehhhHHHHHHHHHH
Confidence 45667777753 2 26678999999999887544
No 94
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional
Probab=25.26 E-value=73 Score=22.70 Aligned_cols=30 Identities=13% Similarity=0.052 Sum_probs=24.3
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEeccc
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVTN 43 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT~ 43 (115)
+|..||..+-.-.|.|++|..+ |...||-+
T Consensus 77 e~e~y~~dLiG~~V~d~~g~~l---G~V~~V~~ 106 (161)
T PRK13828 77 DDEFYHADLIGLAAVDTGGALL---GRVKAVHN 106 (161)
T ss_pred CCCEEhhhccCCEEEeCCCCEE---EEEEEEcc
Confidence 8899999999999999999765 56666643
No 95
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=24.45 E-value=84 Score=15.48 Aligned_cols=17 Identities=18% Similarity=0.335 Sum_probs=12.3
Q ss_pred EEEEeeCCCCCEEEEEE
Q psy8547 20 DIVPIKNEKREVVLYLA 36 (115)
Q Consensus 20 ~i~Pi~de~G~~~~fi~ 36 (115)
...||.+++|++.|++.
T Consensus 24 ~~~~v~~~~~~~~g~i~ 40 (49)
T smart00116 24 RRLPVVDEEGRLVGIVT 40 (49)
T ss_pred CcccEECCCCeEEEEEE
Confidence 34588888888877664
No 96
>PRK05667 dnaG DNA primase; Validated
Probab=24.11 E-value=77 Score=27.46 Aligned_cols=21 Identities=14% Similarity=0.219 Sum_probs=17.3
Q ss_pred EEEEeeCCCCCEEEEEEEEEe
Q psy8547 20 DIVPIKNEKREVVLYLASHKD 40 (115)
Q Consensus 20 ~i~Pi~de~G~~~~fi~~~~D 40 (115)
-+-||+|..|++++|-+-.-|
T Consensus 199 imfPI~d~~G~vigF~GR~l~ 219 (580)
T PRK05667 199 IMFPIRDLRGRVIGFGGRVLG 219 (580)
T ss_pred EEEEEECCCCcEEEEEeeecC
Confidence 355999999999999876554
No 97
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional
Probab=23.77 E-value=62 Score=23.20 Aligned_cols=28 Identities=14% Similarity=0.164 Sum_probs=22.6
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEE
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASH 38 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~ 38 (115)
+|+.||..+---.|.|++|..+|-|.-.
T Consensus 97 ~~e~y~~dLiG~~V~d~~g~~lG~V~~v 124 (172)
T PRK00122 97 EDEYYWHDLIGLEVVDEDGEELGKVTDI 124 (172)
T ss_pred CCCEEHHHhCCcEEEeCCCcEEEEEEEE
Confidence 7899999999999999999876544333
No 98
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional
Probab=23.26 E-value=81 Score=22.79 Aligned_cols=30 Identities=13% Similarity=-0.089 Sum_probs=23.2
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEEEecc
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASHKDVT 42 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~~DIT 42 (115)
+|+.||..+---+|+|++|..+| +...||-
T Consensus 94 e~e~y~~dLiG~~V~d~~g~~lG--G~V~~v~ 123 (171)
T PRK14590 94 KGEFYSEDLIGLQAIDETGKPLN--WKLTDVQ 123 (171)
T ss_pred CCCEEhHHccCcEEEeCCCCEee--eEEEEEe
Confidence 68999999999999999997754 1444443
No 99
>cd04620 CBS_pair_7 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=23.01 E-value=92 Score=19.34 Aligned_cols=19 Identities=5% Similarity=0.336 Sum_probs=14.8
Q ss_pred EEEEEEeeCCCCCEEEEEE
Q psy8547 18 LLDIVPIKNEKREVVLYLA 36 (115)
Q Consensus 18 ~~~i~Pi~de~G~~~~fi~ 36 (115)
.....||.|++|+++|.+.
T Consensus 90 ~~~~~pVvd~~~~~~Gvit 108 (115)
T cd04620 90 QIRHLPVLDDQGQLIGLVT 108 (115)
T ss_pred CCceEEEEcCCCCEEEEEE
Confidence 4567899999999887653
No 100
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=22.64 E-value=86 Score=21.92 Aligned_cols=27 Identities=15% Similarity=-0.171 Sum_probs=23.5
Q ss_pred ceecCCceeEEEEEeEEeeCCCCCEEE
Q psy8547 59 DMQELGTPFWCLLDIVPIKNEKREVVL 85 (115)
Q Consensus 59 ~yrKdGs~f~~~~~i~pirde~G~v~~ 85 (115)
.+|+||+.....-+..-|.|++|++..
T Consensus 69 ~rR~DGs~i~FddNA~Viin~~g~P~G 95 (122)
T COG0093 69 VRRPDGSYIKFDDNAAVIINPDGEPRG 95 (122)
T ss_pred eEcCCCCEEEeCCceEEEECCCCCccc
Confidence 478999999999999999999998755
No 101
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.37 E-value=1.4e+02 Score=20.71 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=20.2
Q ss_pred EEEEEEEeeCCCCCEEEEEEEEEeccch
Q psy8547 17 CLLDIVPIKNEKREVVLYLASHKDVTNT 44 (115)
Q Consensus 17 ~~~~i~Pi~de~G~~~~fi~~~~DIT~~ 44 (115)
..+.+.||+ ++|+++..+++.. +|.-
T Consensus 77 ~pVVV~Pik-~~g~viaAiGiVD-lt~g 102 (123)
T COG4048 77 LPVVVAPIK-DEGEVIAAIGIVD-LTAG 102 (123)
T ss_pred ceEEEEEec-cCCeEEEEEEeee-hhhh
Confidence 467889999 6899999988764 5543
No 102
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=22.01 E-value=87 Score=27.56 Aligned_cols=21 Identities=29% Similarity=0.252 Sum_probs=18.0
Q ss_pred EEEeEEeeCCCCCEEEEEEEe
Q psy8547 70 LLDIVPIKNEKREVVLYLASH 90 (115)
Q Consensus 70 ~~~i~pirde~G~v~~~i~~~ 90 (115)
.++.+||+|+.|+++..+.+.
T Consensus 159 sCsAaPI~D~qG~L~gVLDIS 179 (606)
T COG3284 159 SCSAAPIFDEQGELVGVLDIS 179 (606)
T ss_pred eeeeeccccCCCcEEEEEEec
Confidence 578999999999998877655
No 103
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=21.78 E-value=1.3e+02 Score=20.56 Aligned_cols=28 Identities=11% Similarity=0.064 Sum_probs=25.1
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEEE
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLASH 38 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~~ 38 (115)
+|.....+..+-|+.++.|.+..+++..
T Consensus 109 ~g~~~~~e~l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 109 DGRYLEYERLLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred CCCeeEEEEEEcccCCCCCCccEEEEec
Confidence 8888889999999999999999988864
No 104
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=21.49 E-value=1.2e+02 Score=21.61 Aligned_cols=22 Identities=18% Similarity=0.366 Sum_probs=16.9
Q ss_pred ecCCceeEEEEEeEEeeCCCCCE
Q psy8547 61 QELGTPFWCLLDIVPIKNEKREV 83 (115)
Q Consensus 61 rKdGs~f~~~~~i~pirde~G~v 83 (115)
.|+|.||+ .++|+++......+
T Consensus 28 ~~kg~pFl-ac~I~AL~G~~d~~ 49 (137)
T PF12101_consen 28 PRKGDPFL-ACTIAALRGPADNP 49 (137)
T ss_pred CCCCCeeE-EEEeeeeecCCCCc
Confidence 46799999 57999999855543
No 105
>cd04627 CBS_pair_14 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=21.16 E-value=1e+02 Score=19.56 Aligned_cols=19 Identities=5% Similarity=0.172 Sum_probs=15.0
Q ss_pred EEEEEEeeCCCCCEEEEEE
Q psy8547 18 LLDIVPIKNEKREVVLYLA 36 (115)
Q Consensus 18 ~~~i~Pi~de~G~~~~fi~ 36 (115)
.....||-|++|+++|.+.
T Consensus 98 ~~~~lpVvd~~~~~vGiit 116 (123)
T cd04627 98 GISSVAVVDNQGNLIGNIS 116 (123)
T ss_pred CCceEEEECCCCcEEEEEe
Confidence 3567899999999987664
No 106
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=20.84 E-value=2.2e+02 Score=20.25 Aligned_cols=27 Identities=19% Similarity=0.208 Sum_probs=25.0
Q ss_pred CCCceeEEEEEEEeeCCCCCEEEEEEE
Q psy8547 11 QRTPFWCLLDIVPIKNEKREVVLYLAS 37 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~G~~~~fi~~ 37 (115)
||...-+.=.+.|+-++++++..|+.+
T Consensus 54 ~Gk~V~i~Gf~vPle~~~~~v~eFlLv 80 (146)
T PF11736_consen 54 DGKQVRIPGFMVPLEQEEGKVTEFLLV 80 (146)
T ss_pred CCCEEEEeeEEEeeccCCCcEEEEEEe
Confidence 899999999999999989999999887
No 107
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=20.36 E-value=5.4 Score=27.01 Aligned_cols=18 Identities=39% Similarity=0.781 Sum_probs=15.4
Q ss_pred CCCceeEEEEEEEeeCCC
Q psy8547 11 QRTPFWCLLDIVPIKNEK 28 (115)
Q Consensus 11 dG~~fw~~~~i~Pi~de~ 28 (115)
+...||+.+.|+||+-+.
T Consensus 32 ~eehF~LLieIS~IrS~K 49 (100)
T PRK15215 32 NEEHFWLLIGISSIHSEK 49 (100)
T ss_pred CHHHHHHHHHHcccchHH
Confidence 778899999999998643
No 108
>cd04610 CBS_pair_ParBc_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a ParBc (ParB-like nuclease) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=20.21 E-value=98 Score=18.79 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=13.5
Q ss_pred EEEEeeCCCCCEEEEEE
Q psy8547 20 DIVPIKNEKREVVLYLA 36 (115)
Q Consensus 20 ~i~Pi~de~G~~~~fi~ 36 (115)
...||.|++|+++|++.
T Consensus 84 ~~~~Vv~~~g~~~Gvi~ 100 (107)
T cd04610 84 SKLPVVDENNNLVGIIT 100 (107)
T ss_pred CeEeEECCCCeEEEEEE
Confidence 45689999999888764
No 109
>cd04590 CBS_pair_CorC_HlyC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role,
Probab=20.11 E-value=1.1e+02 Score=18.75 Aligned_cols=18 Identities=6% Similarity=-0.003 Sum_probs=14.3
Q ss_pred EEEEEeeCCCCCEEEEEE
Q psy8547 19 LDIVPIKNEKREVVLYLA 36 (115)
Q Consensus 19 ~~i~Pi~de~G~~~~fi~ 36 (115)
....||.|++|+++|++.
T Consensus 87 ~~~~~Vv~~~~~~~Gvit 104 (111)
T cd04590 87 SHMAIVVDEYGGTAGLVT 104 (111)
T ss_pred CcEEEEEECCCCEEEEeE
Confidence 466899999999888764
Done!