Query 037089
Match_columns 211
No_of_seqs 189 out of 1031
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:33:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037089.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037089hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00989 PAS: PAS fold; Inter 98.6 5.4E-08 1.2E-12 69.5 4.7 45 163-210 1-45 (113)
2 PF13426 PAS_9: PAS domain; PD 98.3 6.2E-07 1.3E-11 62.9 3.2 36 173-211 1-36 (104)
3 PRK13557 histidine kinase; Pro 98.1 6.6E-06 1.4E-10 74.2 5.8 52 160-211 27-78 (540)
4 PF13188 PAS_8: PAS domain; PD 98.0 9.7E-06 2.1E-10 55.2 4.2 36 163-202 1-36 (64)
5 PRK13559 hypothetical protein; 97.8 2.9E-05 6.4E-10 67.9 5.6 50 162-211 42-91 (361)
6 PF08448 PAS_4: PAS fold; Int 97.8 2.2E-05 4.7E-10 55.7 3.5 40 169-211 1-40 (110)
7 TIGR02040 PpsR-CrtJ transcript 97.8 2.8E-05 6.1E-10 70.9 5.1 45 163-210 252-297 (442)
8 TIGR00229 sensory_box PAS doma 97.7 7.8E-05 1.7E-09 48.2 5.2 45 163-210 3-47 (124)
9 PRK10060 RNase II stability mo 97.6 0.00011 2.3E-09 71.8 5.4 49 159-210 107-155 (663)
10 PRK13560 hypothetical protein; 97.5 0.00015 3.3E-09 68.8 5.8 50 158-210 199-248 (807)
11 PRK11006 phoR phosphate regulo 97.4 0.00017 3.7E-09 65.3 4.6 50 158-210 93-142 (430)
12 TIGR02040 PpsR-CrtJ transcript 97.4 0.0003 6.5E-09 64.2 5.5 51 158-210 128-178 (442)
13 PRK11091 aerobic respiration c 97.3 0.00035 7.7E-09 68.1 5.6 50 158-210 150-199 (779)
14 cd00130 PAS PAS domain; PAS mo 97.1 0.00082 1.8E-08 40.9 3.8 35 173-210 2-36 (103)
15 PRK10820 DNA-binding transcrip 96.9 0.001 2.2E-08 64.0 4.1 53 156-211 73-125 (520)
16 PRK09776 putative diguanylate 96.8 0.0017 3.8E-08 64.8 5.1 50 158-210 278-327 (1092)
17 PRK13558 bacterio-opsin activa 96.7 0.0024 5.3E-08 61.2 5.6 49 163-211 148-196 (665)
18 PRK09776 putative diguanylate 96.7 0.0019 4.1E-08 64.5 4.8 50 158-210 531-580 (1092)
19 smart00091 PAS PAS domain. PAS 96.7 0.0052 1.1E-07 35.0 4.7 42 165-209 3-44 (67)
20 COG2202 AtoS FOG: PAS/PAC doma 96.5 0.0087 1.9E-07 41.9 5.8 45 163-210 112-156 (232)
21 PRK11360 sensory histidine kin 96.5 0.0045 9.8E-08 56.0 5.4 48 160-210 259-306 (607)
22 KOG1229 3'5'-cyclic nucleotide 96.5 0.00098 2.1E-08 65.1 1.0 45 163-210 157-201 (775)
23 KOG0501 K+-channel KCNQ [Inorg 96.4 0.002 4.3E-08 64.7 2.9 54 158-211 9-65 (971)
24 PF12860 PAS_7: PAS fold 96.3 0.0036 7.7E-08 46.9 3.1 39 169-210 1-40 (115)
25 PRK11359 cyclic-di-GMP phospho 96.2 0.0071 1.5E-07 58.3 5.3 50 158-210 131-180 (799)
26 PRK13560 hypothetical protein; 95.9 0.013 2.9E-07 55.7 5.3 50 158-210 327-377 (807)
27 PRK11388 DNA-binding transcrip 95.6 0.014 3.1E-07 56.8 4.5 45 163-210 203-247 (638)
28 PRK11086 sensory histidine kin 95.5 0.025 5.4E-07 51.7 5.5 50 158-210 216-268 (542)
29 COG3829 RocR Transcriptional r 95.5 0.022 4.7E-07 56.4 5.1 51 158-211 112-162 (560)
30 PRK15053 dpiB sensor histidine 95.4 0.027 5.8E-07 52.3 5.4 50 158-210 217-268 (545)
31 TIGR02938 nifL_nitrog nitrogen 94.9 0.037 8.1E-07 49.0 4.4 48 158-208 125-172 (494)
32 PF13596 PAS_10: PAS domain; P 91.2 0.21 4.5E-06 36.9 2.9 42 165-210 1-42 (106)
33 PRK09959 hybrid sensory histid 88.7 0.84 1.8E-05 47.0 5.8 39 162-203 575-613 (1197)
34 TIGR02373 photo_yellow photoac 85.9 0.8 1.7E-05 37.6 3.1 43 165-210 18-60 (124)
35 COG3283 TyrR Transcriptional r 85.1 1.6 3.5E-05 42.5 5.2 50 158-210 75-124 (511)
36 COG5002 VicK Signal transducti 83.0 2 4.3E-05 41.6 4.8 50 158-210 106-155 (459)
37 PF14598 PAS_11: PAS domain; P 78.4 1.1 2.5E-05 34.5 1.3 26 185-210 11-37 (111)
38 COG3290 CitA Signal transducti 75.6 4.9 0.00011 40.1 5.1 50 158-210 210-261 (537)
39 KOG3561 Aryl-hydrocarbon recep 74.3 3.6 7.9E-05 42.8 3.9 40 168-210 100-139 (803)
40 PF08670 MEKHLA: MEKHLA domain 72.3 7.2 0.00016 32.6 4.6 46 164-210 32-77 (148)
41 COG5000 NtrY Signal transducti 64.8 9.2 0.0002 39.2 4.4 52 156-210 363-414 (712)
42 KOG3558 Hypoxia-inducible fact 62.2 5.8 0.00013 40.9 2.5 35 176-211 275-309 (768)
43 PF08446 PAS_2: PAS fold; Int 61.1 9.6 0.00021 29.4 3.1 35 174-210 16-53 (110)
44 PRK10618 phosphotransfer inter 58.8 17 0.00037 37.9 5.2 43 158-202 338-380 (894)
45 PRK14538 putative bifunctional 51.1 29 0.00062 36.4 5.4 47 159-210 98-144 (838)
46 PRK13719 conjugal transfer tra 30.7 85 0.0018 28.0 4.4 36 162-200 18-53 (217)
47 PRK10841 hybrid sensory kinase 28.4 1.1E+02 0.0024 31.9 5.5 44 158-203 329-372 (924)
48 PF06785 UPF0242: Uncharacteri 27.2 30 0.00064 33.3 1.0 41 165-207 285-329 (401)
49 PF02387 IncFII_repA: IncFII R 20.1 2.1E+02 0.0046 26.3 5.1 47 158-206 118-170 (281)
No 1
>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=98.62 E-value=5.4e-08 Score=69.49 Aligned_cols=45 Identities=31% Similarity=0.508 Sum_probs=40.9
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+.++.++++++++|++.|. ++.|+|+|++|++|+||+.++++|++
T Consensus 1 e~~~~i~~~~~~~i~~~d~---~g~I~~~N~a~~~l~g~~~~~~~g~~ 45 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDE---DGRILYVNQAAEELLGYSREELIGKS 45 (113)
T ss_dssp HHHHHHHHCSSSEEEEEET---TSBEEEECHHHHHHHSS-HHHHTTSB
T ss_pred CHHHHHHhcCCceEEEEeC---cCeEEEECHHHHHHHccCHHHHcCCc
Confidence 3578999999999999998 77899999999999999999999986
No 2
>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=98.28 E-value=6.2e-07 Score=62.88 Aligned_cols=36 Identities=31% Similarity=0.592 Sum_probs=30.6
Q ss_pred CCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 173 QQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 173 ~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
+++|+|+|. ++.|+|||++|++|+||+.+|++|+++
T Consensus 1 p~~i~i~d~---~g~i~~~N~~~~~~~g~~~~~~~g~~~ 36 (104)
T PF13426_consen 1 PDGIFILDP---DGRILYVNPAFERLFGYSREELIGKSI 36 (104)
T ss_dssp -SEEEEEET---TSBEEEE-HHHHHHHTS-HHHHTTSBG
T ss_pred CEEEEEECC---cCcEEehhHHHHHHHCcCHHHHcCCCc
Confidence 578999999 688999999999999999999999863
No 3
>PRK13557 histidine kinase; Provisional
Probab=98.06 E-value=6.6e-06 Score=74.24 Aligned_cols=52 Identities=38% Similarity=0.712 Sum_probs=46.5
Q ss_pred hhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 160 RVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 160 rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
.....+..+++.++.+|+|.|....+++|+|+|++|++|+||+.+|++|++|
T Consensus 27 ~~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~~~ 78 (540)
T PRK13557 27 HRSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGNNC 78 (540)
T ss_pred hhhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCCCh
Confidence 4467789999999999999998666789999999999999999999999874
No 4
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.98 E-value=9.7e-06 Score=55.18 Aligned_cols=36 Identities=22% Similarity=0.444 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYS 202 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS 202 (211)
+++..++++++.+|+|.| . ..|+++|++|++|+||+
T Consensus 1 e~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 1 ERYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS 36 (64)
T ss_dssp HHHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS-
T ss_pred CHHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC
Confidence 357899999999999999 3 27999999999999998
No 5
>PRK13559 hypothetical protein; Provisional
Probab=97.83 E-value=2.9e-05 Score=67.87 Aligned_cols=50 Identities=32% Similarity=0.688 Sum_probs=44.1
Q ss_pred HHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 162 SEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 162 srlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
.+.+..+++..+++|+++|....++.|+|+|++|++|+||+.+|++|+++
T Consensus 42 ~~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~~~ 91 (361)
T PRK13559 42 GRLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGRNC 91 (361)
T ss_pred hhHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCCCh
Confidence 35577789999999999998665778999999999999999999999863
No 6
>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=97.80 E-value=2.2e-05 Score=55.71 Aligned_cols=40 Identities=33% Similarity=0.468 Sum_probs=36.1
Q ss_pred HHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 169 LATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 169 Ldss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
|++++++|++.|. ++.|+|+|+++.+++|+..++++|+++
T Consensus 1 l~~~p~~i~v~D~---~~~i~~~N~~~~~~~~~~~~~~~G~~~ 40 (110)
T PF08448_consen 1 LDSSPDGIFVIDP---DGRIVYANQAAAELFGVSPEELIGRSL 40 (110)
T ss_dssp HHHCSSEEEEEET---TSBEEEE-HHHHHHHTSTHHHHTTSBH
T ss_pred CCCCCceeEEECC---CCEEEEEHHHHHHHhCCCHHHHhhccc
Confidence 6789999999999 788999999999999999999999863
No 7
>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=97.80 E-value=2.8e-05 Score=70.91 Aligned_cols=45 Identities=33% Similarity=0.381 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCC-cccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYS-SKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS-~eELIGRN 210 (211)
..+..+++.++++|+|+|. ++.|+++|++|++|+||+ .++++|++
T Consensus 252 ~~~~~l~e~~~d~I~v~D~---~G~I~~~N~a~~~l~G~~~~~~l~G~~ 297 (442)
T TIGR02040 252 ENLARLYHEAPDAIVFSDA---DGTIRGANEAFLELTDSSSLEAVRGRT 297 (442)
T ss_pred HHHHHHHHhCCceEEEEcC---CCcEEehhHHHHHHhCCCChHHHcCCC
Confidence 3688899999999999999 678999999999999997 57899986
No 8
>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=97.74 E-value=7.8e-05 Score=48.23 Aligned_cols=45 Identities=33% Similarity=0.619 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+.+..+++..+.++++.|. ++.|+++|++|++++||...+++|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~d~---~~~i~~~n~~~~~~~g~~~~~~~~~~ 47 (124)
T TIGR00229 3 ERYRAIFESSPDAIIVIDL---EGNILYVNPAFEEIFGYSAEELIGRN 47 (124)
T ss_pred hHHHHHHhhCCceEEEEcC---CCcEEEEchHHHHHhCCChHHhcCcc
Confidence 3567889999999999998 66799999999999999999988864
No 9
>PRK10060 RNase II stability modulator; Provisional
Probab=97.55 E-value=0.00011 Score=71.77 Aligned_cols=49 Identities=16% Similarity=0.151 Sum_probs=43.3
Q ss_pred hhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 159 PRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 159 ~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
......+..+++.+.++|+|+|. ++.|+|+|++|++|+||+.+|++|++
T Consensus 107 ~~~~~~~~~v~~~~~~gI~i~D~---~g~I~~~N~a~~~l~Gy~~~eliG~~ 155 (663)
T PRK10060 107 SHGLSFAEQVVSEANSVIVILDS---RGNIQRFNRLCEEYTGLKEHDVIGQS 155 (663)
T ss_pred HHHHHHHHHHHhhCCceEEEEeC---CCCEEEEcHHHHHHHCcCHHHHcCCC
Confidence 34445677789999999999999 67899999999999999999999986
No 10
>PRK13560 hypothetical protein; Provisional
Probab=97.52 E-value=0.00015 Score=68.84 Aligned_cols=50 Identities=16% Similarity=0.251 Sum_probs=45.7
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+....+.+..++++++++|++.|. ++.|+|+|++|++|+||+.+|++|++
T Consensus 199 l~~~~~~l~~l~e~~~~~i~~~d~---~g~i~~~N~~~~~~~G~~~~e~~g~~ 248 (807)
T PRK13560 199 IDEALHFLQQLLDNIADPAFWKDE---DAKVFGCNDAACLACGFRREEIIGMS 248 (807)
T ss_pred HHHHHHHHHHHHhhCCCeEEEEcC---CCCEEEEhHHHHHHhCCCHHHHcCCc
Confidence 566677889999999999999998 67899999999999999999999985
No 11
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.42 E-value=0.00017 Score=65.32 Aligned_cols=50 Identities=14% Similarity=0.282 Sum_probs=45.5
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+....+.+..++++.+++|++.|. ++.|+|+|++|++|+||..+|++|++
T Consensus 93 l~~~~~~~~~~~~~~~~~i~~~d~---~g~i~~~N~~a~~l~g~~~~~~~g~~ 142 (430)
T PRK11006 93 LGNLIKRFRSGAESLPDAVVLTTE---EGNIFWCNGLAQQLLGFRWPEDNGQN 142 (430)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEcC---CCceeHHHHHHHHHhCCCChHhCCCc
Confidence 666677889999999999999998 67899999999999999999999975
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=97.36 E-value=0.0003 Score=64.24 Aligned_cols=51 Identities=16% Similarity=0.275 Sum_probs=43.7
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+....+.+..+++.++++|++.|.. ++.|+|+|++|++|+||+.+|++|++
T Consensus 128 l~~~e~r~~~l~e~~~~~i~~~d~~--~g~i~~~N~a~~~l~G~~~~el~g~~ 178 (442)
T TIGR02040 128 LREMETRYRVVLEVSSDAVLLVDMS--TGRIVEANSAAAALLGGVGQSLVGRA 178 (442)
T ss_pred HHHHHHHHHHHHhhCCceEEEEECC--CCEEEEEcHHHHHHhCcCHHHHcCCC
Confidence 3344567889999999999999973 46799999999999999999999985
No 13
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.30 E-value=0.00035 Score=68.12 Aligned_cols=50 Identities=20% Similarity=0.209 Sum_probs=45.0
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+.+..+.+..+++.++++|++.|. ++.|+++|++|++|+||+.++++|++
T Consensus 150 l~~~~~~l~~il~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~eliG~~ 199 (779)
T PRK11091 150 LEQQSSLLRSFLDASPDLVYYRNE---DGEFSGCNRAMELLTGKSEKQLIGLT 199 (779)
T ss_pred HHHHHHHHHHHHhcCcceEEEECC---CCcEEeEcHHHHHHhCcCHHHHcCCC
Confidence 455567788999999999999999 67899999999999999999999985
No 14
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=97.10 E-value=0.00082 Score=40.93 Aligned_cols=35 Identities=34% Similarity=0.586 Sum_probs=30.8
Q ss_pred CCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 173 QQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 173 ~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+.++++.|. ++.++++|++|++++||...+++|+.
T Consensus 2 ~~~i~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~ 36 (103)
T cd00130 2 PDGVIVLDL---DGRILYANPAAEQLLGYSPEELIGKS 36 (103)
T ss_pred CceEEEECC---CCcEEEECHHHHHHhCCCHHHHcCcc
Confidence 467889998 66799999999999999999998864
No 15
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=96.87 E-value=0.001 Score=63.97 Aligned_cols=53 Identities=17% Similarity=0.144 Sum_probs=47.6
Q ss_pred CCchhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 156 GAFPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 156 ~al~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
.-+++..+.+..+|++++++|++.|. ++.|+++|+++++|+|++.++++|+++
T Consensus 73 ~~~e~e~~~L~aIL~sm~eGVi~vD~---~G~I~~iN~aA~~Llg~~~eel~Gk~i 125 (520)
T PRK10820 73 MPSEREHRALSALLEALPEPVLSIDM---KGKVELANPASCQLFGQSEEKLRNHTA 125 (520)
T ss_pred ChHHHHHHHHHHHHHhCCCcEEEECC---CCeeeHhHHHHHHHHCcCHHHHCCCcH
Confidence 44667788899999999999999999 667999999999999999999999863
No 16
>PRK09776 putative diguanylate cyclase; Provisional
Probab=96.78 E-value=0.0017 Score=64.78 Aligned_cols=50 Identities=12% Similarity=0.241 Sum_probs=44.3
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+....+.+..+++..+.+|++.|. ++.|+|+|++|++|+||+.+|++|++
T Consensus 278 l~~~e~r~~~l~e~~~~~i~~~d~---dG~i~~~N~~~~~l~G~~~~el~g~~ 327 (1092)
T PRK09776 278 ISESETRFRNAMEYSAIGMALVGT---EGQWLQVNKALCQFLGYSQEELRGLT 327 (1092)
T ss_pred HHHHHHHHHHHHHhCCceEEEEcC---CCcEEehhHHHHHHhCCCHHHHccCC
Confidence 444556788999999999999999 67899999999999999999999975
No 17
>PRK13558 bacterio-opsin activator; Provisional
Probab=96.74 E-value=0.0024 Score=61.20 Aligned_cols=49 Identities=39% Similarity=0.621 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
+.+..+++..+.+|++.|....++.|+|+|++|++|+||+.++++|+++
T Consensus 148 r~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~~~ 196 (665)
T PRK13558 148 RLKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGRNC 196 (665)
T ss_pred HHHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCCCH
Confidence 3456789999999999987555788999999999999999999999863
No 18
>PRK09776 putative diguanylate cyclase; Provisional
Probab=96.71 E-value=0.0019 Score=64.50 Aligned_cols=50 Identities=20% Similarity=0.349 Sum_probs=44.4
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+.+..+.+..+++..+++|++.|. ++.|+|+|++|++|+||+.+|++|++
T Consensus 531 L~~~~~~l~~~l~~~~~~i~~~D~---~g~i~~~N~a~~~l~G~~~~e~iG~~ 580 (1092)
T PRK09776 531 LFQEKERLHITLDSIGEAVVCTDM---AMKVTFMNPVAEKMTGWTQEEALGVP 580 (1092)
T ss_pred HHHHHHHHHHHHhccccEEEEECC---CCeEEEEcHHHHHHhCCCHHHHcCCC
Confidence 445566788899999999999999 66799999999999999999999985
No 19
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=96.69 E-value=0.0052 Score=35.03 Aligned_cols=42 Identities=38% Similarity=0.606 Sum_probs=36.0
Q ss_pred HHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCC
Q 037089 165 LKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGR 209 (211)
Q Consensus 165 L~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGR 209 (211)
+..+++....++++.|. ...++++|+.+..++|+...+++|+
T Consensus 3 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (67)
T smart00091 3 LRAILESLPDGIFVLDL---DGRILYANPAAEELLGYSPEELIGK 44 (67)
T ss_pred HHHHHhhCCceEEEEcC---CCeEEEECHHHHHHhCCCHHHHcCC
Confidence 45677888899999997 5669999999999999998888775
No 20
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.52 E-value=0.0087 Score=41.87 Aligned_cols=45 Identities=36% Similarity=0.511 Sum_probs=38.9
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
..+..+++..+.++++.|. ++.|+++|++|++++||...+.+++.
T Consensus 112 ~~~~~~~~~~~~~~~~~d~---~~~~~~~n~~~~~~~g~~~~~~~~~~ 156 (232)
T COG2202 112 ERLRALLEASPDGIWVLDE---DGRILYANPAAEELLGYSPEEELGRG 156 (232)
T ss_pred HHHHHHHhhCCceEEEEeC---CCCEEEeCHHHHHHhCCChHHhcCCC
Confidence 3477899999999999998 67899999999999999988777654
No 21
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.52 E-value=0.0045 Score=55.96 Aligned_cols=48 Identities=15% Similarity=0.211 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 160 RVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 160 rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.....+..+++..++++++.|. ++.|+++|++|++|+||..++++|++
T Consensus 259 ~~~~~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~l~g~~~~~~~g~~ 306 (607)
T PRK11360 259 ETRSLNELILESIADGVIAIDR---QGKITTMNPAAEVITGLQRHELVGKP 306 (607)
T ss_pred HHHHHHHHHHHhccCeEEEEcC---CCCEEEECHHHHHHhCCChHHhcCCc
Confidence 3334567788999999999998 66799999999999999999999875
No 22
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.47 E-value=0.00098 Score=65.13 Aligned_cols=45 Identities=31% Similarity=0.482 Sum_probs=40.0
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
..+-.+|+...++|-|+|. +.-|.|||+||++|+||.+.|+||+.
T Consensus 157 nalFaaLD~c~eAiEI~~d---dhViQYVNpAfE~mmG~hkgEliGke 201 (775)
T KOG1229|consen 157 NALFAALDECDEAIEICDD---DHVIQYVNPAFENMMGCHKGELIGKE 201 (775)
T ss_pred HHHHHHHhhhhhhheeccc---hhHHHHhcHHHHhhhcchhhhhcCCc
Confidence 4456678889999999998 77899999999999999999999974
No 23
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=96.44 E-value=0.002 Score=64.70 Aligned_cols=54 Identities=24% Similarity=0.507 Sum_probs=42.4
Q ss_pred chhhHHHHHHHHHhcC---CeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 158 FPRVSEELKAALATLQ---QTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 158 l~rlsrlL~~aLdss~---dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
+.-....|..++.... -.+++.++..-|+||+|+|++||++.||.+.|++.+.|
T Consensus 9 VAPQNTFLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs~ 65 (971)
T KOG0501|consen 9 VAPQNTFLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKSC 65 (971)
T ss_pred cccchhHHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhcccc
Confidence 3334445555555444 46888888888999999999999999999999998876
No 24
>PF12860 PAS_7: PAS fold
Probab=96.33 E-value=0.0036 Score=46.88 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=34.0
Q ss_pred HHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccc-cCCC
Q 037089 169 LATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEV-IGRN 210 (211)
Q Consensus 169 Ldss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eEL-IGRN 210 (211)
|+++++||+|.|. ++.++++|++|.+|+|+..+.+ .|..
T Consensus 1 Ld~l~~Gv~v~D~---~~rl~~~N~~~~~l~~~~~~~~~~G~~ 40 (115)
T PF12860_consen 1 LDSLPQGVAVFDS---DGRLVFWNQRFRELFGLPPEMLRPGAS 40 (115)
T ss_pred CCCcCceEEEEcC---CCeEEeEcHHHHHHhCCCHHHhcCCCC
Confidence 4678899999999 7789999999999999999887 5643
No 25
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=96.22 E-value=0.0071 Score=58.35 Aligned_cols=50 Identities=24% Similarity=0.352 Sum_probs=43.0
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.....+.+..+++..+.+|++.|. ++.|+++|++|++|+||+.++++|+.
T Consensus 131 ~~~~~~~~~~~~~~~~~~i~~~d~---~g~i~~~N~~~~~l~G~~~~e~~g~~ 180 (799)
T PRK11359 131 QKEQTRQLIIAVDHLDRPVIVLDP---ERRIVQCNRAFTEMFGYCISEASGMQ 180 (799)
T ss_pred hHHHHHHHHHHHhcCCCcEEEEcC---CCcEEEEChhhHhhhCCCHHHHCCCC
Confidence 344455667789999999999998 67899999999999999999999975
No 26
>PRK13560 hypothetical protein; Provisional
Probab=95.87 E-value=0.013 Score=55.74 Aligned_cols=50 Identities=24% Similarity=0.343 Sum_probs=42.7
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEE-cHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYA-SSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYV-N~AFerMTGYS~eELIGRN 210 (211)
+....+.+..+++.++.+|++.|. ++.|+++ |+++++|+||+.+|++|++
T Consensus 327 L~~se~~l~~l~~~~~~~i~~~d~---~g~i~~~nn~~~~~~~G~~~~e~~g~~ 377 (807)
T PRK13560 327 LLEKEDMLRAIIEAAPIAAIGLDA---DGNICFVNNNAAERMLGWSAAEVMGKP 377 (807)
T ss_pred HHHHHHHHHHHHHhCcccEEEEcC---CCCEEEecCHHHHHHhCCCHHHHcCCC
Confidence 445567788999999999999999 5679987 6788889999999999975
No 27
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=95.61 E-value=0.014 Score=56.81 Aligned_cols=45 Identities=13% Similarity=0.242 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 163 EELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 163 rlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
..+..+++...++|++.|. ++.|+++|+++++|+|++.++++|++
T Consensus 203 ~~~~~il~~~~~gVl~vD~---~G~I~~~N~aa~~llg~s~~~l~G~~ 247 (638)
T PRK11388 203 NQLNALLESMDDGVIAWDE---QGNLQFLNAQAARLLRLDATASQGRA 247 (638)
T ss_pred HHHHHHHhccCCcEEEECC---CCeEehhhHHHHHHhCcCHHHHCCCc
Confidence 3445588889999999999 67899999999999999999999985
No 28
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=95.51 E-value=0.025 Score=51.67 Aligned_cols=50 Identities=12% Similarity=0.261 Sum_probs=40.7
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCc---ccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSS---KEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~---eELIGRN 210 (211)
+.++.+.+..+++.+.++|++.|. ++.|+|+|+++++|+||.. .+.+|+.
T Consensus 216 i~~l~~~~~~il~~~~~gIi~~D~---~g~I~~~N~~a~~llg~~~~~~~~~~~~~ 268 (542)
T PRK11086 216 ISTLFEQRQAMLQSIKEGVIAVDD---RGEVTLINDEAKRLFNYKKGLEDDPLGTD 268 (542)
T ss_pred HHHHHHHHHHHHHHhcCcEEEECC---CCeEEEEhHHHHHHhCCCcCCcccccCCc
Confidence 455566778899999999999999 7789999999999998763 4556543
No 29
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=95.45 E-value=0.022 Score=56.40 Aligned_cols=51 Identities=25% Similarity=0.529 Sum_probs=45.9
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
+.+..+.+..+++.+.+++++.|. ++.|+++|.+...++|++.++++|+++
T Consensus 112 l~~~~~~l~~il~~~~~~l~vvD~---~G~~i~~N~~~~~~~gl~~e~~~gk~~ 162 (560)
T COG3829 112 LRQLRQRLEAILDSIDDGLLVVDE---DGIIIYYNKAYAKLLGLSPEEVLGKHL 162 (560)
T ss_pred HHHHHHHHHHHHhhccCceEEEcC---CCcEEEEcHHHHHHhCCCHHHHcCCcH
Confidence 455668899999999999999999 667999999999999999999999863
No 30
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=95.43 E-value=0.027 Score=52.27 Aligned_cols=50 Identities=20% Similarity=0.296 Sum_probs=41.6
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCc--ccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSS--KEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~--eELIGRN 210 (211)
+....+.+..+++...++|++.|. ++.|+++|+++++|+|+.. ++++|++
T Consensus 217 ~~~~~~~~~~il~~~~egii~~D~---~g~I~~~N~~a~~ll~~~~~~~~~~g~~ 268 (545)
T PRK15053 217 IARVVRQQEALFSSVYEGLIAVDP---HGYITAINRNARKMLGLSSPGRQWLGKP 268 (545)
T ss_pred HHHHHHHHHHHHHHhCceEEEECC---CCeEEeecHHHHHHhCCCCcchhhcCCc
Confidence 344456677799999999999999 6789999999999999975 4688875
No 31
>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=94.86 E-value=0.037 Score=48.98 Aligned_cols=48 Identities=6% Similarity=0.079 Sum_probs=40.2
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIG 208 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIG 208 (211)
+......+..+++..+.+|++.|. ++.|+|+|++|++++||...+..+
T Consensus 125 l~~~~~~~~~~~~~~~~~i~~~d~---~~~i~~~N~~~~~~~g~~~~~~~~ 172 (494)
T TIGR02938 125 VANQKLLIESVVDAAPVAFVLLDP---TGRVILDNQEYKKLATDLRVKEPA 172 (494)
T ss_pred HHHHHHHHHHHHhcccceEEEEcC---CCCEEEechhHHHhhchhhhhHHH
Confidence 445556788899999999999998 678999999999999998776544
No 32
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=91.24 E-value=0.21 Score=36.86 Aligned_cols=42 Identities=21% Similarity=0.285 Sum_probs=31.6
Q ss_pred HHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 165 LKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 165 L~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
|..+|++++.++++.|. +..|.|.|++..++++... ..+|++
T Consensus 1 L~~il~s~~~~i~~vD~---~~~I~~~n~~a~~~f~~~~-~~iGr~ 42 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDR---NLRIRYFNPAAARLFNLSP-SDIGRP 42 (106)
T ss_dssp HHHHHHHSSSEEEEEET---TSBEEEE-SCGC-SS---G-GGTTSB
T ss_pred ChHHHhcCCCCEEEEcC---CCeEEEeChhHhhhcCCCh-HHCCCC
Confidence 46789999999999999 7789999999999998764 557875
No 33
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=88.74 E-value=0.84 Score=47.03 Aligned_cols=39 Identities=15% Similarity=-0.011 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCc
Q 037089 162 SEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSS 203 (211)
Q Consensus 162 srlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~ 203 (211)
.+.+..+++.++.+|++.|. ++.|+++|++|++++|+..
T Consensus 575 ~~~~~~i~~~~~~~i~~~d~---~g~i~~~N~~~~~~~g~~~ 613 (1197)
T PRK09959 575 ISFRKALSDSLPNPTYVVNW---QGNVISHNSAFEHYFTADY 613 (1197)
T ss_pred HHHHHHHHhhCCCcEEEEcC---CCcEEEehHHHHHHhCccc
Confidence 34567788999999999998 6789999999999999874
No 34
>TIGR02373 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc.
Probab=85.92 E-value=0.8 Score=37.55 Aligned_cols=43 Identities=26% Similarity=0.239 Sum_probs=39.1
Q ss_pred HHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 165 LKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 165 L~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
-.+-++.++-||+-.|. ++.|+..|.+=.+++|++++.+||++
T Consensus 18 s~eelD~lpFGvI~lD~---~G~V~~YN~aE~~~sg~~p~~vlGr~ 60 (124)
T TIGR02373 18 GDAQFDALPFGAIQLDG---SGVILRYNAAEGRITGRDPERVIGRN 60 (124)
T ss_pred CHhHhhcCCcceEEECC---CCEEEEEecchhhhcCCChhhhhchh
Confidence 34678999999999999 67799999999999999999999986
No 35
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=85.15 E-value=1.6 Score=42.52 Aligned_cols=50 Identities=18% Similarity=0.193 Sum_probs=44.4
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.+|-...|..++++.++.|+-.|- .+.|..+|+|++.++|.+.+++.|+.
T Consensus 75 seR~hl~L~aLL~al~~pVlsvd~---kg~v~~aNpAa~~l~~~~~~~~~g~~ 124 (511)
T COG3283 75 SEREHLALSALLEALPEPVLSVDM---KGKVDMANPAACQLFGRKEDRLRGHT 124 (511)
T ss_pred chhHhHHHHHHHHhCCCceEEecc---cCceeecCHHHHHHhCCChhhhcCcc
Confidence 556677789999999999999999 55699999999999999999999874
No 36
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=82.96 E-value=2 Score=41.57 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=44.6
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
++...+.|..+|....+||+.+|.. +.|+.+|....+|+|.+.++++|++
T Consensus 106 ~e~Er~kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~ 155 (459)
T COG5002 106 TEQERRKLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRS 155 (459)
T ss_pred HHHHHHHHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhccc
Confidence 5566678888999999999999994 5699999999999999999999986
No 37
>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=78.43 E-value=1.1 Score=34.53 Aligned_cols=26 Identities=38% Similarity=0.650 Sum_probs=23.1
Q ss_pred CCCEEEEcHH-HHHhhCCCcccccCCC
Q 037089 185 DCPIMYASSG-FFSMTGYSSKEVIGRN 210 (211)
Q Consensus 185 D~pIVYVN~A-FerMTGYS~eELIGRN 210 (211)
++.|+||.+. ...++||.++|++|+.
T Consensus 11 dgki~~~d~~~v~~~lgy~~~eLvG~s 37 (111)
T PF14598_consen 11 DGKITYVDSRAVSSLLGYLPEELVGRS 37 (111)
T ss_dssp TSBEEEEETTHHHHHHSS-HHHHTTSB
T ss_pred CcEEEEEcCccChhhcCCCcHHHcCCc
Confidence 7889999999 7999999999999985
No 38
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=75.61 E-value=4.9 Score=40.09 Aligned_cols=50 Identities=20% Similarity=0.311 Sum_probs=43.0
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcc--cccCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSK--EVIGRN 210 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~e--ELIGRN 210 (211)
+.++.+.....|++..+||+..|. .+.|..+|.+.++|.|+... +++|++
T Consensus 210 Ia~l~~er~A~l~si~EGviAvd~---~G~It~~N~~A~~ll~~~~~~~~~ig~~ 261 (537)
T COG3290 210 IATLLEERQAMLQSIKEGVIAVDK---KGVITLINQAAQKLLGLRQPSGDPIGRS 261 (537)
T ss_pred HHHHHHHHHHHHHHhhceEEEECC---CCeEeehhHHHHHHhcccCcCccccccc
Confidence 667777888899999999999999 56799999999999999886 577764
No 39
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=74.31 E-value=3.6 Score=42.77 Aligned_cols=40 Identities=28% Similarity=0.499 Sum_probs=32.1
Q ss_pred HHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 168 ALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 168 aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
+|+++..-++|... ++.||||.+.-..++||.-+|++|++
T Consensus 100 mLeAlDGF~fvV~c---dG~IvyVSeSVT~~L~y~QsDL~~qS 139 (803)
T KOG3561|consen 100 ILEALDGFLFVVNC---DGRIVYVSESVTSVLGYLQSDLMGQS 139 (803)
T ss_pred HHHHhcCeEEEEec---CceEEEEecchHHhhCcCHHHHhcch
Confidence 34444455667776 57899999999999999999999985
No 40
>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Probab=72.28 E-value=7.2 Score=32.64 Aligned_cols=46 Identities=20% Similarity=0.231 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 164 ELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 164 lL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.+.+.|-+.+.+|+-.+.. +|-.++|+|.+...|++|+-+|+++.+
T Consensus 32 ~~~~~L~~ap~ailsh~~~-~dP~f~yaN~aaL~l~e~~w~el~~lP 77 (148)
T PF08670_consen 32 ELAKALWHAPFAILSHGTK-ADPIFIYANQAALDLFETTWDELVGLP 77 (148)
T ss_pred HHHHHHHcCCCEEEEcCCC-CCCEEEehhHHHHHHhcCCHHHHhcCc
Confidence 3555666688888877775 356678999999999999999998864
No 41
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=64.83 E-value=9.2 Score=39.22 Aligned_cols=52 Identities=17% Similarity=0.173 Sum_probs=43.9
Q ss_pred CCchhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 156 GAFPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 156 ~al~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.++++..+.+..+|+....||+..|. ++.|.-+|++-++|+|.+.++++|++
T Consensus 363 ~~~e~rr~f~E~VLsgvtaGVi~~d~---~g~i~t~N~~ae~~l~~~~~~~~G~~ 414 (712)
T COG5000 363 DALEQRRRFLEAVLSGLTAGVIGFDN---RGCITTVNPSAEQILGKPFDQLLGQS 414 (712)
T ss_pred HHHHHHHHHHHHHHhcCceeEEEEcC---CCeeEeecchHHHHhcCChhHhhcch
Confidence 33556667777899999999999999 56688889999999999999999964
No 42
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=62.18 E-value=5.8 Score=40.92 Aligned_cols=35 Identities=23% Similarity=0.475 Sum_probs=29.2
Q ss_pred EEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCCC
Q 037089 176 FVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRNW 211 (211)
Q Consensus 176 IvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRNc 211 (211)
++++-... |.+|+||.+.|..+.||..+||||+.|
T Consensus 275 ~FvtRhs~-DmkityCedRisdlm~y~PeeLvGrS~ 309 (768)
T KOG3558|consen 275 MFVTRHSL-DMKITYCEDRISDLMDYEPEELVGRSC 309 (768)
T ss_pred eeEEeeec-ceeEEEEchhHHHHhcCCHHHhhchhH
Confidence 45555443 678999999999999999999999975
No 43
>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3S7O_A 2O9B_A 3S7P_A 1ZTU_A 3S7N_A 3S7Q_A 2O9C_A 2OOL_A 3C2W_G 3NHQ_B ....
Probab=61.14 E-value=9.6 Score=29.43 Aligned_cols=35 Identities=26% Similarity=0.427 Sum_probs=28.9
Q ss_pred CeEEEEcCCCCCCCEEEEcHHHHHhhCCC---cccccCCC
Q 037089 174 QTFVVSDATKPDCPIMYASSGFFSMTGYS---SKEVIGRN 210 (211)
Q Consensus 174 dgIvItDa~~~D~pIVYVN~AFerMTGYS---~eELIGRN 210 (211)
..+++.|.. +..|++|+.....++|.. .++++|++
T Consensus 16 G~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~~ 53 (110)
T PF08446_consen 16 GALLALDPD--DLRIVQASENIAELLGIPPELPEELLGRP 53 (110)
T ss_dssp SEEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTCB
T ss_pred EEEEEEECC--CCEEEEEcCCHHHHhCCccccchhhcccC
Confidence 456677764 688999999999999999 99999985
No 44
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=58.81 E-value=17 Score=37.91 Aligned_cols=43 Identities=7% Similarity=-0.065 Sum_probs=36.3
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCC
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYS 202 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS 202 (211)
+.........+++.++.||++.|.. ++.|+++|+++++++|+.
T Consensus 338 L~~~~~l~~~Ii~~lp~Gilv~D~~--~~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 338 LRILRALNEEIVSNLPLGLLVYDFE--SNRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHHHHHHHhCCceEEEEECC--CCeEEEEhHHHHHHhCcc
Confidence 4555567788999999999999964 678999999999999874
No 45
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=51.10 E-value=29 Score=36.38 Aligned_cols=47 Identities=17% Similarity=0.048 Sum_probs=36.1
Q ss_pred hhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCcccccCCC
Q 037089 159 PRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSSKEVIGRN 210 (211)
Q Consensus 159 ~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~eELIGRN 210 (211)
.++.+....++...+.++++.|.. ++.|+++|+.|..++| .+ ++|++
T Consensus 98 ~~~~~~~~~~l~~~p~gi~~~~~~--~~~i~W~N~~~~~~~~--~~-~~g~~ 144 (838)
T PRK14538 98 FHVSQIGEEVLNELPIGIVLIDIS--SKEIQWLNPYANFILK--NP-EINTP 144 (838)
T ss_pred HHHhHHHHHHHHhCCceEEEEeCC--CCEEEEECHHHHHHhC--cc-ccCCc
Confidence 345556678899999999999932 5679999999999977 23 67764
No 46
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=30.75 E-value=85 Score=28.02 Aligned_cols=36 Identities=11% Similarity=0.142 Sum_probs=30.8
Q ss_pred HHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhC
Q 037089 162 SEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTG 200 (211)
Q Consensus 162 srlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTG 200 (211)
.+.+..+++..+..+.|=+. ++.++|+|.+|.+++.
T Consensus 18 ~~~~~~~i~~~~~P~CiR~~---~g~fi~~N~~F~~~f~ 53 (217)
T PRK13719 18 PESLTAFIDDYSYPACIRNE---SGKFIFYNTLFLKEFL 53 (217)
T ss_pred HHHHHHHHHcCCCCeEEECC---CCCeeecchHHHHHHH
Confidence 34677899999999999998 6679999999998765
No 47
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=28.42 E-value=1.1e+02 Score=31.87 Aligned_cols=44 Identities=5% Similarity=-0.007 Sum_probs=34.8
Q ss_pred chhhHHHHHHHHHhcCCeEEEEcCCCCCCCEEEEcHHHHHhhCCCc
Q 037089 158 FPRVSEELKAALATLQQTFVVSDATKPDCPIMYASSGFFSMTGYSS 203 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvItDa~~~D~pIVYVN~AFerMTGYS~ 203 (211)
+....+....+++..+.++++.+.. ++.++++|+.+..++|+..
T Consensus 329 L~e~e~~~r~iv~~~p~gi~i~~~~--~g~~~~~N~~a~~~~~l~~ 372 (924)
T PRK10841 329 LEEHEQFNRKIVASAPVGICILRTS--DGTNILSNELAHNYLNMLT 372 (924)
T ss_pred HHHHHHHHHHHHHhCCccEEEEEcC--CCcEEEehHHHHHHhccCC
Confidence 3334455677889999999999864 6789999999999998754
No 48
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=27.20 E-value=30 Score=33.32 Aligned_cols=41 Identities=24% Similarity=0.449 Sum_probs=29.2
Q ss_pred HHHHHHhcC---C-eEEEEcCCCCCCCEEEEcHHHHHhhCCCccccc
Q 037089 165 LKAALATLQ---Q-TFVVSDATKPDCPIMYASSGFFSMTGYSSKEVI 207 (211)
Q Consensus 165 L~~aLdss~---d-gIvItDa~~~D~pIVYVN~AFerMTGYS~eELI 207 (211)
..+++|.+. . +++|-.+. ..+.+|+|.-|..+|||+.++.+
T Consensus 285 cRrLfDsLreEnlgmlfVYs~k--~qRllFAN~~fk~wtGy~~edFl 329 (401)
T PF06785_consen 285 CRRLFDSLREENLGMLFVYSPK--SQRLLFANSQFKTWTGYSSEDFL 329 (401)
T ss_pred HHHHHhhhcccccceEEEecch--hhHHHHhHHHHHHHhccCHHHHH
Confidence 444455442 2 44555553 67899999999999999998765
No 49
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=20.12 E-value=2.1e+02 Score=26.34 Aligned_cols=47 Identities=19% Similarity=0.303 Sum_probs=31.2
Q ss_pred chhhHHHHHHHHHhcCCeEEE----EcCCCCC--CCEEEEcHHHHHhhCCCcccc
Q 037089 158 FPRVSEELKAALATLQQTFVV----SDATKPD--CPIMYASSGFFSMTGYSSKEV 206 (211)
Q Consensus 158 l~rlsrlL~~aLdss~dgIvI----tDa~~~D--~pIVYVN~AFerMTGYS~eEL 206 (211)
+.|.++.+.+.|+.+ |++. .|..... ..+|++.+.|..|+|++.+.+
T Consensus 118 itRasR~i~e~le~~--Gli~~~~~~D~~~~~~~Pk~I~lT~~ff~l~gi~~~kl 170 (281)
T PF02387_consen 118 ITRASRLISEFLEPL--GLITCEKEWDPYNGNYIPKHIWLTPLFFMLLGISEDKL 170 (281)
T ss_pred HHHHHHHHHHHHHhc--CCeeeeeeechhhccccCeEEEECHHHHHHhCCCHHHH
Confidence 667777777766644 3332 3332211 247899999999999998765
Done!