Query psy17885
Match_columns 95
No_of_seqs 146 out of 1017
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 16:38:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17885.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17885hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0501|consensus 99.1 2E-11 4.4E-16 101.8 3.2 77 7-90 2-78 (971)
2 PF00989 PAS: PAS fold; Inter 98.9 2.3E-09 5.1E-14 66.9 4.0 44 27-73 1-44 (113)
3 PF13426 PAS_9: PAS domain; PD 98.7 2E-08 4.3E-13 61.6 4.1 41 37-84 1-41 (104)
4 PRK13557 histidine kinase; Pro 98.5 1.7E-07 3.6E-12 73.0 5.5 56 25-84 28-83 (540)
5 PF13188 PAS_8: PAS domain; PD 98.4 7.4E-07 1.6E-11 52.4 5.8 39 28-73 2-40 (64)
6 TIGR02040 PpsR-CrtJ transcript 98.4 6.2E-07 1.3E-11 70.1 5.4 43 28-73 253-296 (442)
7 PRK13559 hypothetical protein; 98.3 1.1E-06 2.4E-11 66.2 5.2 53 28-84 44-96 (361)
8 PRK13560 hypothetical protein; 98.2 4.5E-06 9.7E-11 68.0 6.7 62 9-73 181-247 (807)
9 TIGR02966 phoR_proteo phosphat 98.1 5.2E-06 1.1E-10 60.2 5.1 47 24-73 3-49 (333)
10 PRK10060 RNase II stability mo 98.0 8.6E-06 1.9E-10 67.6 5.0 45 26-73 110-154 (663)
11 PRK09776 putative diguanylate 98.0 1.3E-05 2.8E-10 68.1 6.1 69 3-74 507-580 (1092)
12 PF08448 PAS_4: PAS fold; Int 97.9 6.2E-06 1.3E-10 51.0 1.9 38 33-73 1-38 (110)
13 TIGR00229 sensory_box PAS doma 97.9 3.5E-05 7.6E-10 44.1 4.7 43 28-73 4-46 (124)
14 TIGR02040 PpsR-CrtJ transcript 97.9 2E-05 4.4E-10 61.6 4.5 44 28-73 134-177 (442)
15 PRK11073 glnL nitrogen regulat 97.8 1.4E-05 3E-10 59.7 3.3 45 26-73 6-50 (348)
16 PRK11006 phoR phosphate regulo 97.8 2.9E-05 6.4E-10 60.3 4.0 44 27-73 98-141 (430)
17 PRK11091 aerobic respiration c 97.7 5.4E-05 1.2E-09 63.0 4.5 43 28-73 156-198 (779)
18 PRK11359 cyclic-di-GMP phospho 97.7 9.1E-05 2E-09 61.0 5.7 58 13-73 122-179 (799)
19 TIGR02938 nifL_nitrog nitrogen 97.6 5.4E-05 1.2E-09 57.8 3.7 44 27-73 4-47 (494)
20 PRK13558 bacterio-opsin activa 97.6 0.00011 2.4E-09 60.1 5.2 53 28-84 149-201 (665)
21 PRK13560 hypothetical protein; 97.5 0.00021 4.5E-09 58.3 6.0 69 3-74 303-377 (807)
22 TIGR02938 nifL_nitrog nitrogen 97.5 0.00022 4.7E-09 54.4 5.0 68 3-73 101-173 (494)
23 PRK09776 putative diguanylate 97.4 0.00016 3.4E-09 61.6 4.3 44 27-73 283-326 (1092)
24 PRK11359 cyclic-di-GMP phospho 97.4 0.00016 3.4E-09 59.6 3.7 43 28-73 13-55 (799)
25 cd00130 PAS PAS domain; PAS mo 97.4 0.00033 7.1E-09 37.8 3.6 34 37-73 2-35 (103)
26 PRK10820 DNA-binding transcrip 97.1 0.00043 9.3E-09 56.6 3.4 49 22-73 75-123 (520)
27 smart00091 PAS PAS domain. PAS 97.1 0.0013 2.8E-08 33.2 4.1 42 29-73 3-44 (67)
28 PF12860 PAS_7: PAS fold 97.0 0.00086 1.9E-08 43.2 3.2 38 33-73 1-39 (115)
29 PRK11360 sensory histidine kin 97.0 0.0013 2.8E-08 51.3 4.7 43 28-73 263-305 (607)
30 KOG1229|consensus 97.0 0.00025 5.5E-09 58.7 0.8 42 30-74 160-201 (775)
31 COG3829 RocR Transcriptional r 96.9 0.0015 3.2E-08 54.5 4.7 70 1-73 85-160 (560)
32 COG2202 AtoS FOG: PAS/PAC doma 96.6 0.0074 1.6E-07 37.2 5.3 42 29-73 114-155 (232)
33 PRK11388 DNA-binding transcrip 96.4 0.0036 7.9E-08 51.9 4.0 41 30-73 206-246 (638)
34 PRK15053 dpiB sensor histidine 95.9 0.015 3.2E-07 46.2 5.0 43 28-73 223-267 (545)
35 PRK11086 sensory histidine kin 95.8 0.018 3.9E-07 45.2 4.9 44 27-73 221-267 (542)
36 PF08447 PAS_3: PAS fold; Int 95.4 0.0076 1.6E-07 36.5 1.1 21 52-73 1-21 (91)
37 PF14598 PAS_11: PAS domain; P 93.9 0.038 8.1E-07 36.5 1.8 38 48-88 10-48 (111)
38 PRK09959 hybrid sensory histid 92.6 0.24 5.1E-06 43.4 5.2 41 28-71 577-617 (1197)
39 KOG3561|consensus 90.7 0.17 3.6E-06 44.2 2.1 57 28-89 95-151 (803)
40 COG3852 NtrB Signal transducti 90.6 0.21 4.7E-06 39.8 2.5 41 30-73 10-50 (363)
41 PF13596 PAS_10: PAS domain; P 89.9 0.23 5E-06 31.3 1.9 41 29-73 1-41 (106)
42 COG3283 TyrR Transcriptional r 89.6 0.6 1.3E-05 38.3 4.3 46 25-73 78-123 (511)
43 COG3290 CitA Signal transducti 88.7 0.83 1.8E-05 38.4 4.7 43 28-73 216-260 (537)
44 TIGR02373 photo_yellow photoac 87.3 0.64 1.4E-05 32.1 2.8 40 31-73 20-59 (124)
45 PF08446 PAS_2: PAS fold; Int 86.1 0.79 1.7E-05 30.1 2.6 42 37-84 15-59 (110)
46 KOG3558|consensus 80.7 0.89 1.9E-05 39.4 1.4 37 45-84 279-315 (768)
47 COG5002 VicK Signal transducti 79.2 2.3 5.1E-05 34.7 3.3 52 28-85 112-163 (459)
48 PF06785 UPF0242: Uncharacteri 77.5 0.89 1.9E-05 36.5 0.5 50 22-73 278-331 (401)
49 PF08670 MEKHLA: MEKHLA domain 75.0 5.7 0.00012 28.0 4.0 44 29-74 34-77 (148)
50 PRK10618 phosphotransfer inter 74.0 6.9 0.00015 34.5 5.0 37 28-66 344-380 (894)
51 PRK14538 putative bifunctional 64.9 16 0.00034 32.4 5.3 41 28-73 103-143 (838)
52 COG5000 NtrY Signal transducti 56.2 15 0.00032 31.9 3.5 40 31-73 374-413 (712)
53 COG4224 Uncharacterized protei 44.8 29 0.00063 22.1 2.7 32 18-49 29-60 (77)
54 PRK13719 conjugal transfer tra 43.7 30 0.00065 26.0 3.1 36 28-66 20-55 (217)
55 KOG3558|consensus 38.8 38 0.00082 29.8 3.3 48 35-87 126-173 (768)
56 COG4170 SapD ABC-type antimicr 37.4 19 0.00041 28.0 1.2 62 2-80 31-92 (330)
57 PRK10841 hybrid sensory kinase 36.9 77 0.0017 28.0 5.0 40 28-69 335-374 (924)
58 COG4863 Uncharacterized protei 36.3 29 0.00063 28.6 2.2 43 38-84 257-299 (439)
59 PRK01631 hypothetical protein; 30.6 51 0.0011 20.9 2.2 31 18-48 28-58 (76)
60 PRK01546 hypothetical protein; 26.9 67 0.0015 20.5 2.3 31 18-48 30-60 (79)
61 KOG3560|consensus 24.8 61 0.0013 28.0 2.3 47 33-85 117-163 (712)
62 PF13992 YecR: YecR-like lipop 23.6 66 0.0014 20.1 1.8 29 58-87 35-63 (74)
63 PF14877 mIF3: Mitochondrial t 23.2 1.1E+02 0.0025 22.3 3.2 60 7-66 31-94 (181)
64 PRK02539 hypothetical protein; 23.1 88 0.0019 20.3 2.3 30 18-47 29-58 (85)
65 PF05979 DUF896: Bacterial pro 22.3 26 0.00056 21.6 -0.2 31 18-48 27-57 (65)
No 1
>KOG0501|consensus
Probab=99.15 E-value=2e-11 Score=101.81 Aligned_cols=77 Identities=44% Similarity=0.739 Sum_probs=69.0
Q ss_pred cccceeecccchhhhhhhhHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccCCC
Q psy17885 7 KRGWRKNTAPEVELVRRTYMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSY 86 (95)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g~~ 86 (95)
+-|+||.+||+++ +++-+-+.-+.....+++.+++..|.||+|||+.||+++||+|.|++.+| |+|.|++|..
T Consensus 2 pgGkRGLVAPQNT-----FLENiiRRsn~~dtsFlL~NAQiVD~PiVY~NdgFcKlsGY~RAevMQKs--~tc~FMyGEl 74 (971)
T KOG0501|consen 2 PGGKRGLVAPQNT-----FLENIIRRSNNADTSFLLANAQIVDWPIVYCNDGFCKLSGYHRAEVMQKS--CTCSFMYGEL 74 (971)
T ss_pred CCCcccccccchh-----HHHHHHhhccCCCcceeeccceeeccceEEecCcchhccCccHHHHhccc--ceeeeeeccc
Confidence 3489999999995 78877777777788999999999999999999999999999999999996 7899999998
Q ss_pred CCCC
Q psy17885 87 LQSL 90 (95)
Q Consensus 87 ~~~~ 90 (95)
++..
T Consensus 75 tdk~ 78 (971)
T KOG0501|consen 75 TDKG 78 (971)
T ss_pred cchh
Confidence 8764
No 2
>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=98.88 E-value=2.3e-09 Score=66.90 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=40.4
Q ss_pred HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 27 ~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+.+++++++++++++++|.. +.|+|+|++|++++||+++|++|+
T Consensus 1 e~~~~i~~~~~~~i~~~d~~---g~I~~~N~a~~~l~g~~~~~~~g~ 44 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDED---GRILYVNQAAEELLGYSREELIGK 44 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETT---SBEEEECHHHHHHHSS-HHHHTTS
T ss_pred CHHHHHHhcCCceEEEEeCc---CeEEEECHHHHHHHccCHHHHcCC
Confidence 35788999999999999977 899999999999999999999999
No 3
>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=98.71 E-value=2e-08 Score=61.61 Aligned_cols=41 Identities=20% Similarity=0.397 Sum_probs=34.0
Q ss_pred CCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 37 ~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
|++++++|++ +.|+|||++|++++||+++|++|+ ++..|..
T Consensus 1 p~~i~i~d~~---g~i~~~N~~~~~~~g~~~~~~~g~----~~~~~~~ 41 (104)
T PF13426_consen 1 PDGIFILDPD---GRILYVNPAFERLFGYSREELIGK----SISDFFP 41 (104)
T ss_dssp -SEEEEEETT---SBEEEE-HHHHHHHTS-HHHHTTS----BGGGGCS
T ss_pred CEEEEEECCc---CcEEehhHHHHHHHCcCHHHHcCC----CcccccC
Confidence 6899999997 899999999999999999999999 7665554
No 4
>PRK13557 histidine kinase; Provisional
Probab=98.52 E-value=1.7e-07 Score=72.95 Aligned_cols=56 Identities=20% Similarity=0.323 Sum_probs=49.3
Q ss_pred hHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 25 YMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 25 ~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
....+..+++..+.+++++|+.+.+++|+|+|++|++++||+++|++|+ ++..+..
T Consensus 28 ~~~~~~~~~~~~~~~i~v~d~~~~~g~i~~~N~a~~~~~G~~~~e~~g~----~~~~l~~ 83 (540)
T PRK13557 28 RSDIFFAAVETTRMPMIVTDPNQPDNPIVFANRAFLEMTGYAAEEIIGN----NCRFLQG 83 (540)
T ss_pred hhHHHHHHHHhCcCcEEEEcCCCCCCCEEEEcHHHHHHhCCCHHHhcCC----ChHhhcC
Confidence 3567789999999999999987777899999999999999999999999 7665554
No 5
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=98.45 E-value=7.4e-07 Score=52.44 Aligned_cols=39 Identities=21% Similarity=0.385 Sum_probs=33.1
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.++.+++.++.+++|.| . +.|+++|++|++++||+ ..|+
T Consensus 2 ~~~~l~~~~~~~i~i~d-~---~~i~~~N~~~~~l~g~~---~~~~ 40 (64)
T PF13188_consen 2 RYRSLFDNSPDGILIID-G---GRIIYVNPAFEELFGYS---LEGE 40 (64)
T ss_dssp HHHHHHCCSSSEEEEEE-T---SBEEEE-HHHHHHHCS----HTCC
T ss_pred HHHHHHHcCccceEEEE-C---CChHHhhHHHHHHhCCC---CCCC
Confidence 57889999999999999 5 59999999999999999 6666
No 6
>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=98.37 E-value=6.2e-07 Score=70.11 Aligned_cols=43 Identities=14% Similarity=0.163 Sum_probs=39.8
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCC-ccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYN-RAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs-~~EliG~ 73 (95)
.++++++.++++++++|.. +.|++||++|++++||+ +++++|+
T Consensus 253 ~~~~l~e~~~d~I~v~D~~---G~I~~~N~a~~~l~G~~~~~~l~G~ 296 (442)
T TIGR02040 253 NLARLYHEAPDAIVFSDAD---GTIRGANEAFLELTDSSSLEAVRGR 296 (442)
T ss_pred HHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCChHHHcCC
Confidence 5889999999999999987 79999999999999997 5789999
No 7
>PRK13559 hypothetical protein; Provisional
Probab=98.31 E-value=1.1e-06 Score=66.17 Aligned_cols=53 Identities=25% Similarity=0.412 Sum_probs=45.8
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
.++++++.++++++++|....++.|+++|++|++++||+.+|++|+ ++.++..
T Consensus 44 ~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~~~e~iG~----~~~~l~~ 96 (361)
T PRK13559 44 LFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYAAEEVVGR----NCRFLQG 96 (361)
T ss_pred HHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCCHHHHcCC----ChhhhcC
Confidence 4566899999999999987667899999999999999999999999 6555543
No 8
>PRK13560 hypothetical protein; Provisional
Probab=98.19 E-value=4.5e-06 Score=67.97 Aligned_cols=62 Identities=11% Similarity=0.095 Sum_probs=48.0
Q ss_pred ccee-ecccchhhhhhhh----HHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 9 GWRK-NTAPEVELVRRTY----MYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 9 ~~~~-~~~~~~~~~~~~~----~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
++.| ..+++.+...+.. ...++.+++..++++++.|.. +.|+++|++|++++||+++|++|+
T Consensus 181 ~~~g~~~DIT~rk~ae~~l~~~~~~l~~l~e~~~~~i~~~d~~---g~i~~~N~~~~~~~G~~~~e~~g~ 247 (807)
T PRK13560 181 QVDGFAEDITERKRAEERIDEALHFLQQLLDNIADPAFWKDED---AKVFGCNDAACLACGFRREEIIGM 247 (807)
T ss_pred EEEEEEEccchHHHHHHHHHHHHHHHHHHHhhCCCeEEEEcCC---CCEEEEhHHHHHHhCCCHHHHcCC
Confidence 4555 4455543322222 234678999999999999987 799999999999999999999999
No 9
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=98.12 E-value=5.2e-06 Score=60.25 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=43.3
Q ss_pred hhHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 24 TYMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 24 ~~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.....++.+++..+++++++|.. +.|+|+|++|++++||+++|++|+
T Consensus 3 ~~~~~l~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~g~ 49 (333)
T TIGR02966 3 ALLSRFRAAAQALPDAVVVLDEE---GQIEWCNPAAERLLGLRWPDDLGQ 49 (333)
T ss_pred hHHHHHHHHHHhCcCcEEEECCC---CcEEEEcHHHHHHhCCChHHHcCC
Confidence 35567899999999999999988 689999999999999999999998
No 10
>PRK10060 RNase II stability modulator; Provisional
Probab=98.00 E-value=8.6e-06 Score=67.59 Aligned_cols=45 Identities=13% Similarity=0.115 Sum_probs=41.2
Q ss_pred HHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 26 MYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 26 ~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
....+++++.++++++++|.. +.|+|+|++|++++||+.+|++|+
T Consensus 110 ~~~~~~v~~~~~~gI~i~D~~---g~I~~~N~a~~~l~Gy~~~eliG~ 154 (663)
T PRK10060 110 LSFAEQVVSEANSVIVILDSR---GNIQRFNRLCEEYTGLKEHDVIGQ 154 (663)
T ss_pred HHHHHHHHhhCCceEEEEeCC---CCEEEEcHHHHHHHCcCHHHHcCC
Confidence 345577899999999999998 799999999999999999999999
No 11
>PRK09776 putative diguanylate cyclase; Provisional
Probab=98.00 E-value=1.3e-05 Score=68.09 Aligned_cols=69 Identities=9% Similarity=0.016 Sum_probs=51.9
Q ss_pred CcCCccccee-ecccchhhhhhhhH----HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCC
Q psy17885 3 EMGNKRGWRK-NTAPEVELVRRTYM----YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDY 74 (95)
Q Consensus 3 ~~~~~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~ 74 (95)
+.|...+.+| ..+++.+...+..+ +.++.+++..+++++++|.. +.|+++|++|++++||+.+|++|++
T Consensus 507 ~~G~~~~~ig~~~DITerk~~e~~L~~~~~~l~~~l~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~e~iG~~ 580 (1092)
T PRK09776 507 KDGEVERLLGINMDMTEVRQLNEALFQEKERLHITLDSIGEAVVCTDMA---MKVTFMNPVAEKMTGWTQEEALGVP 580 (1092)
T ss_pred CCCCEEEEEeeeeehhHHHHHHHHHHHHHHHHHHHHhccccEEEEECCC---CeEEEEcHHHHHHhCCCHHHHcCCC
Confidence 4455556666 55555443332222 24567889999999999987 7999999999999999999999993
No 12
>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=97.90 E-value=6.2e-06 Score=50.95 Aligned_cols=38 Identities=16% Similarity=0.255 Sum_probs=34.6
Q ss_pred hCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 33 NGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 33 ~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+++++++++++|++ +.|+++|+++.++.|++.++++|+
T Consensus 1 l~~~p~~i~v~D~~---~~i~~~N~~~~~~~~~~~~~~~G~ 38 (110)
T PF08448_consen 1 LDSSPDGIFVIDPD---GRIVYANQAAAELFGVSPEELIGR 38 (110)
T ss_dssp HHHCSSEEEEEETT---SBEEEE-HHHHHHHTSTHHHHTTS
T ss_pred CCCCCceeEEECCC---CEEEEEHHHHHHHhCCCHHHHhhc
Confidence 45689999999988 899999999999999999999999
No 13
>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=97.87 E-value=3.5e-05 Score=44.13 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=39.1
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.++.+++..+.+++++|.. +.|+++|++|+++.|++..+++|+
T Consensus 4 ~~~~~~~~~~~~~~~~d~~---~~i~~~n~~~~~~~g~~~~~~~~~ 46 (124)
T TIGR00229 4 RYRAIFESSPDAIIVIDLE---GNILYVNPAFEEIFGYSAEELIGR 46 (124)
T ss_pred HHHHHHhhCCceEEEEcCC---CcEEEEchHHHHHhCCChHHhcCc
Confidence 4567888999999999987 699999999999999999999998
No 14
>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=97.85 E-value=2e-05 Score=61.59 Aligned_cols=44 Identities=16% Similarity=0.053 Sum_probs=40.1
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.++.+++.+++++++.|... +.|+++|++|++++||+.+|++|+
T Consensus 134 r~~~l~e~~~~~i~~~d~~~--g~i~~~N~a~~~l~G~~~~el~g~ 177 (442)
T TIGR02040 134 RYRVVLEVSSDAVLLVDMST--GRIVEANSAAAALLGGVGQSLVGR 177 (442)
T ss_pred HHHHHHhhCCceEEEEECCC--CEEEEEcHHHHHHhCcCHHHHcCC
Confidence 56788999999999999732 799999999999999999999999
No 15
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=97.84 E-value=1.4e-05 Score=59.68 Aligned_cols=45 Identities=18% Similarity=0.163 Sum_probs=41.9
Q ss_pred HHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 26 MYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 26 ~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.+.+.++++..+++++++|.+ +.|+++|++|++++||+.++++|+
T Consensus 6 ~~~~~~il~~~~~gi~~~d~~---~~i~~~N~a~~~~~g~~~~~~~g~ 50 (348)
T PRK11073 6 LPDAGQILNSLINSILLLDDD---LAIHYANPAAQQLLAQSSRKLFGT 50 (348)
T ss_pred cchHHHHHhcCcCeEEEECCC---CeEeeEcHHHHHHhCCCHHHHcCC
Confidence 456789999999999999987 799999999999999999999999
No 16
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.76 E-value=2.9e-05 Score=60.30 Aligned_cols=44 Identities=16% Similarity=0.209 Sum_probs=40.7
Q ss_pred HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 27 ~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
..++.++++.+++++++|.. +.|++||++|++++||+.+|++|+
T Consensus 98 ~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~a~~l~g~~~~~~~g~ 141 (430)
T PRK11006 98 KRFRSGAESLPDAVVLTTEE---GNIFWCNGLAQQLLGFRWPEDNGQ 141 (430)
T ss_pred HHHHHHHHhCCCeEEEEcCC---CceeHHHHHHHHHhCCCChHhCCC
Confidence 35678899999999999987 799999999999999999999999
No 17
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=97.67 E-value=5.4e-05 Score=63.02 Aligned_cols=43 Identities=12% Similarity=0.033 Sum_probs=40.2
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.++.+++..++++++.|.. +.|+++|++|++++||+++|++|+
T Consensus 156 ~l~~il~~~~~~i~~~D~~---g~i~~~N~a~~~l~G~~~~eliG~ 198 (779)
T PRK11091 156 LLRSFLDASPDLVYYRNED---GEFSGCNRAMELLTGKSEKQLIGL 198 (779)
T ss_pred HHHHHHhcCcceEEEECCC---CcEEeEcHHHHHHhCcCHHHHcCC
Confidence 4577899999999999987 799999999999999999999999
No 18
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=97.67 E-value=9.1e-05 Score=61.03 Aligned_cols=58 Identities=21% Similarity=0.311 Sum_probs=48.0
Q ss_pred ecccchhhhhhhhHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 13 NTAPEVELVRRTYMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
..+++.+...+........+++..++++++.|.. +.|+++|++|++++||+.+|++|+
T Consensus 122 ~~DiT~~~~~~~~~~~~~~~~~~~~~~i~~~d~~---g~i~~~N~~~~~l~G~~~~e~~g~ 179 (799)
T PRK11359 122 VRDASVEMAQKEQTRQLIIAVDHLDRPVIVLDPE---RRIVQCNRAFTEMFGYCISEASGM 179 (799)
T ss_pred EeeccchhhhHHHHHHHHHHHhcCCCcEEEEcCC---CcEEEEChhhHhhhCCCHHHHCCC
Confidence 4455555555555566677889999999999987 799999999999999999999999
No 19
>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=97.64 E-value=5.4e-05 Score=57.76 Aligned_cols=44 Identities=23% Similarity=0.456 Sum_probs=41.1
Q ss_pred HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 27 ~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+.++.+++..++++++.|.. +.++|+|++|++++||++++++|+
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~---g~~~~~N~~~~~~~G~~~~~~~g~ 47 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLK---ANILYANDAFTRITGYTKEEIIGK 47 (494)
T ss_pred HHHHHHHHhCCceEEEECCC---CcEEEEchhheeecCCCHHHHhCC
Confidence 46788999999999999987 689999999999999999999999
No 20
>PRK13558 bacterio-opsin activator; Provisional
Probab=97.59 E-value=0.00011 Score=60.09 Aligned_cols=53 Identities=26% Similarity=0.484 Sum_probs=45.4
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
..+++++..+.++++.|....++.|+|+|++|++++||+.+|++|+ ++..+..
T Consensus 149 ~~~~~~~~~~~gi~~~d~~~~dg~i~~~N~~~~~l~G~~~eel~g~----~~~~l~~ 201 (665)
T PRK13558 149 LKERALDEAPVGITIADATLPDEPLIYINDAFERITGYSPDEVLGR----NCRFLQG 201 (665)
T ss_pred HHHHHHhcCCccEEEEcCCCCCCcEEEEcHHHHHHhCcCHHHHcCC----CHHHhcC
Confidence 3467899999999999977677899999999999999999999999 6554443
No 21
>PRK13560 hypothetical protein; Provisional
Probab=97.53 E-value=0.00021 Score=58.30 Aligned_cols=69 Identities=14% Similarity=0.017 Sum_probs=49.9
Q ss_pred CcCCccccee-ecccchhhhhhhhH----HHHHHHhCCCCCeEEEEecCCCCCcEEEE-chHHHHhhCCCccccCCCC
Q psy17885 3 EMGNKRGWRK-NTAPEVELVRRTYM----YDERQKNGHPDSSFLLANAQIVDFPIVYC-NESFCKISGYNRAEVPSDY 74 (95)
Q Consensus 3 ~~~~~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~gi~I~d~~~~~~~I~yv-N~aF~~mtGYs~~EliG~~ 74 (95)
+.|...|+++ ..+++.+...+..+ ..++.+++.++.++++.|.. +.|+++ |+++++++||+.+|++|++
T Consensus 303 ~~g~~~g~~~~~~DITerk~~e~~L~~se~~l~~l~~~~~~~i~~~d~~---g~i~~~nn~~~~~~~G~~~~e~~g~~ 377 (807)
T PRK13560 303 KENHCAGLVGAITDISGRRAAERELLEKEDMLRAIIEAAPIAAIGLDAD---GNICFVNNNAAERMLGWSAAEVMGKP 377 (807)
T ss_pred CCCCEEEEEEEEEechHHHHHHHHHHHHHHHHHHHHHhCcccEEEEcCC---CCEEEecCHHHHHHhCCCHHHHcCCC
Confidence 3344455555 55555443332222 24578899999999999987 688887 6888889999999999983
No 22
>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=97.46 E-value=0.00022 Score=54.43 Aligned_cols=68 Identities=12% Similarity=0.094 Sum_probs=48.8
Q ss_pred CcCCccccee-ecccchhhhhhhhH----HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 3 EMGNKRGWRK-NTAPEVELVRRTYM----YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 3 ~~~~~~~~~~-~~~~~~~~~~~~~~----~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+.|+..|+++ ..+++.....++.+ ..++.+++.++.++++.|.. +.|+++|++|++++|+...+..+.
T Consensus 101 ~~g~~~~~~~~~~DIt~~k~~e~~l~~~~~~~~~~~~~~~~~i~~~d~~---~~i~~~N~~~~~~~g~~~~~~~~~ 173 (494)
T TIGR02938 101 EAGETTHFLGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPT---GRVILDNQEYKKLATDLRVKEPAH 173 (494)
T ss_pred CCCCEEEEEEehhhhhHHHHHHHHHHHHHHHHHHHHhcccceEEEEcCC---CCEEEechhHHHhhchhhhhHHHH
Confidence 4455556666 45555433322222 24578899999999999976 799999999999999998876654
No 23
>PRK09776 putative diguanylate cyclase; Provisional
Probab=97.44 E-value=0.00016 Score=61.59 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=40.9
Q ss_pred HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 27 ~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+.++.+++..+.++++.|.+ +.|+++|++|++++||+.+|++|+
T Consensus 283 ~r~~~l~e~~~~~i~~~d~d---G~i~~~N~~~~~l~G~~~~el~g~ 326 (1092)
T PRK09776 283 TRFRNAMEYSAIGMALVGTE---GQWLQVNKALCQFLGYSQEELRGL 326 (1092)
T ss_pred HHHHHHHHhCCceEEEEcCC---CcEEehhHHHHHHhCCCHHHHccC
Confidence 45688999999999999987 799999999999999999999999
No 24
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=97.39 E-value=0.00016 Score=59.64 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=39.2
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
....+++..+.++++.|.. +.|+++|++|++++||+.+|++|+
T Consensus 13 ~~~~~le~~~~~i~~~d~~---g~i~~~N~~~~~l~G~s~eeliG~ 55 (799)
T PRK11359 13 IFFPALEQNMMGAVLINEN---DEVLFFNPAAEKLWGYKREEVIGN 55 (799)
T ss_pred hHHHHHHhhcCcEEEEcCC---CeEEEEcHHHHHHhCCCHHHHcCC
Confidence 4467888899999999977 799999999999999999999999
No 25
>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=97.36 E-value=0.00033 Score=37.84 Aligned_cols=34 Identities=18% Similarity=0.325 Sum_probs=30.8
Q ss_pred CCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 37 ~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+.++++.|.. +.++++|++|+++.|++.++++|+
T Consensus 2 ~~~i~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~ 35 (103)
T cd00130 2 PDGVIVLDLD---GRILYANPAAEQLLGYSPEELIGK 35 (103)
T ss_pred CceEEEECCC---CcEEEECHHHHHHhCCCHHHHcCc
Confidence 5678888877 699999999999999999999998
No 26
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.12 E-value=0.00043 Score=56.59 Aligned_cols=49 Identities=8% Similarity=0.042 Sum_probs=43.9
Q ss_pred hhhhHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 22 RRTYMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 22 ~~~~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.+..-..+..++++.+++++++|.. +.|+++|++++++.|++.++++|+
T Consensus 75 ~e~e~~~L~aIL~sm~eGVi~vD~~---G~I~~iN~aA~~Llg~~~eel~Gk 123 (520)
T PRK10820 75 SEREHRALSALLEALPEPVLSIDMK---GKVELANPASCQLFGQSEEKLRNH 123 (520)
T ss_pred HHHHHHHHHHHHHhCCCcEEEECCC---CeeeHhHHHHHHHHCcCHHHHCCC
Confidence 3345566788999999999999998 799999999999999999999999
No 27
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=97.11 E-value=0.0013 Score=33.20 Aligned_cols=42 Identities=17% Similarity=0.209 Sum_probs=36.5
Q ss_pred HHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 29 ERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 29 ~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
++.+++..+.++++.+.. +.+.++|+.+.++.|+...++.|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~ 44 (67)
T smart00091 3 LRAILESLPDGIFVLDLD---GRILYANPAAEELLGYSPEELIGK 44 (67)
T ss_pred HHHHHhhCCceEEEEcCC---CeEEEECHHHHHHhCCCHHHHcCC
Confidence 355677888999999876 689999999999999999999887
No 28
>PF12860 PAS_7: PAS fold
Probab=96.98 E-value=0.00086 Score=43.24 Aligned_cols=38 Identities=13% Similarity=0.220 Sum_probs=34.9
Q ss_pred hCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCcccc-CCC
Q psy17885 33 NGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV-PSD 73 (95)
Q Consensus 33 ~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~El-iG~ 73 (95)
+++.+.|++|.|+. ++++++|++|.+|.|++.+.+ .|.
T Consensus 1 Ld~l~~Gv~v~D~~---~rl~~~N~~~~~l~~~~~~~~~~G~ 39 (115)
T PF12860_consen 1 LDSLPQGVAVFDSD---GRLVFWNQRFRELFGLPPEMLRPGA 39 (115)
T ss_pred CCCcCceEEEEcCC---CeEEeEcHHHHHHhCCCHHHhcCCC
Confidence 47789999999988 799999999999999999998 777
No 29
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=96.98 E-value=0.0013 Score=51.27 Aligned_cols=43 Identities=16% Similarity=0.055 Sum_probs=39.2
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
..+.+++..+++++++|.. +.|+++|++|++++||+.++++|+
T Consensus 263 ~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~l~g~~~~~~~g~ 305 (607)
T PRK11360 263 LNELILESIADGVIAIDRQ---GKITTMNPAAEVITGLQRHELVGK 305 (607)
T ss_pred HHHHHHHhccCeEEEEcCC---CCEEEECHHHHHHhCCChHHhcCC
Confidence 3467788999999999977 799999999999999999999999
No 30
>KOG1229|consensus
Probab=96.97 E-value=0.00025 Score=58.66 Aligned_cols=42 Identities=17% Similarity=0.249 Sum_probs=37.0
Q ss_pred HHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCC
Q psy17885 30 RQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDY 74 (95)
Q Consensus 30 ~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~ 74 (95)
=.+++...+++=|+|.+ ..|.|||+||++|+||.+.|++|++
T Consensus 160 FaaLD~c~eAiEI~~dd---hViQYVNpAfE~mmG~hkgEliGke 201 (775)
T KOG1229|consen 160 FAALDECDEAIEICDDD---HVIQYVNPAFENMMGCHKGELIGKE 201 (775)
T ss_pred HHHHhhhhhhheeccch---hHHHHhcHHHHhhhcchhhhhcCCc
Confidence 35677888889898877 7899999999999999999999994
No 31
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=96.90 E-value=0.0015 Score=54.51 Aligned_cols=70 Identities=20% Similarity=0.252 Sum_probs=56.7
Q ss_pred CCCcCCccccee-ecccch--hhhhhh---hHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 1 MNEMGNKRGWRK-NTAPEV--ELVRRT---YMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 1 ~~~~~~~~~~~~-~~~~~~--~~~~~~---~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
|+|++...|+.+ +.+.+. +..++. ....+..+++.+.++++++|.. +.++++|.+..++.|++.++++|+
T Consensus 85 ~~~~~~~~g~~~~~~~~~e~~~~~~~~l~~~~~~l~~il~~~~~~l~vvD~~---G~~i~~N~~~~~~~gl~~e~~~gk 160 (560)
T COG3829 85 VDEQGRVVGVLEVFLDISEALELIEENLRQLRQRLEAILDSIDDGLLVVDED---GIIIYYNKAYAKLLGLSPEEVLGK 160 (560)
T ss_pred eecCCceeeeehhhhhhHHHHHHHHHHHHHHHHHHHHHHhhccCceEEEcCC---CcEEEEcHHHHHHhCCCHHHHcCC
Confidence 468888999988 555553 222333 2345678899999999999999 799999999999999999999999
No 32
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=96.61 E-value=0.0074 Score=37.20 Aligned_cols=42 Identities=17% Similarity=0.181 Sum_probs=38.1
Q ss_pred HHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 29 ERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 29 ~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+..+++..+.++++.|.. +.+.++|++|++++||+..+.+++
T Consensus 114 ~~~~~~~~~~~~~~~d~~---~~~~~~n~~~~~~~g~~~~~~~~~ 155 (232)
T COG2202 114 LRALLEASPDGIWVLDED---GRILYANPAAEELLGYSPEEELGR 155 (232)
T ss_pred HHHHHhhCCceEEEEeCC---CCEEEeCHHHHHHhCCChHHhcCC
Confidence 567899999999999985 799999999999999998888877
No 33
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=96.44 E-value=0.0036 Score=51.89 Aligned_cols=41 Identities=7% Similarity=0.041 Sum_probs=38.3
Q ss_pred HHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 30 RQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 30 ~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
..+++..+++++++|+. +.|+++|++++++.|++.++++|+
T Consensus 206 ~~il~~~~~gVl~vD~~---G~I~~~N~aa~~llg~s~~~l~G~ 246 (638)
T PRK11388 206 NALLESMDDGVIAWDEQ---GNLQFLNAQAARLLRLDATASQGR 246 (638)
T ss_pred HHHHhccCCcEEEECCC---CeEehhhHHHHHHhCcCHHHHCCC
Confidence 45888899999999998 799999999999999999999999
No 34
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=95.94 E-value=0.015 Score=46.24 Aligned_cols=43 Identities=9% Similarity=0.020 Sum_probs=37.6
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCc--cccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNR--AEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~--~EliG~ 73 (95)
....+++...++++++|.+ +.|+++|+++++++|+.. ++++|+
T Consensus 223 ~~~~il~~~~egii~~D~~---g~I~~~N~~a~~ll~~~~~~~~~~g~ 267 (545)
T PRK15053 223 QQEALFSSVYEGLIAVDPH---GYITAINRNARKMLGLSSPGRQWLGK 267 (545)
T ss_pred HHHHHHHHhCceEEEECCC---CeEEeecHHHHHHhCCCCcchhhcCC
Confidence 3456788899999999998 799999999999999976 469998
No 35
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=95.81 E-value=0.018 Score=45.16 Aligned_cols=44 Identities=5% Similarity=0.053 Sum_probs=37.0
Q ss_pred HHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCC---ccccCCC
Q psy17885 27 YDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYN---RAEVPSD 73 (95)
Q Consensus 27 ~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs---~~EliG~ 73 (95)
+....++++.+++++++|.. ++|+++|+++++++|++ ..+.+|+
T Consensus 221 ~~~~~il~~~~~gIi~~D~~---g~I~~~N~~a~~llg~~~~~~~~~~~~ 267 (542)
T PRK11086 221 EQRQAMLQSIKEGVIAVDDR---GEVTLINDEAKRLFNYKKGLEDDPLGT 267 (542)
T ss_pred HHHHHHHHHhcCcEEEECCC---CeEEEEhHHHHHHhCCCcCCcccccCC
Confidence 44578899999999999988 79999999999999876 3466666
No 36
>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=95.36 E-value=0.0076 Score=36.49 Aligned_cols=21 Identities=33% Similarity=0.782 Sum_probs=16.9
Q ss_pred EEEEchHHHHhhCCCccccCCC
Q psy17885 52 IVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 52 I~yvN~aF~~mtGYs~~EliG~ 73 (95)
|+|+|+.|++|+||+.+++ +.
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~ 21 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GK 21 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TC
T ss_pred CEEEeHHHHHHhCCCHHHh-cc
Confidence 6899999999999999999 65
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=93.93 E-value=0.038 Score=36.46 Aligned_cols=38 Identities=24% Similarity=0.370 Sum_probs=31.5
Q ss_pred CCCcEEEEchH-HHHhhCCCccccCCCCCCCCcccccCCCCC
Q psy17885 48 VDFPIVYCNES-FCKISGYNRAEVPSDYDIPTYNLLVGSYLQ 88 (95)
Q Consensus 48 ~~~~I~yvN~a-F~~mtGYs~~EliG~~~~~~~~~L~g~~~~ 88 (95)
.++.|+||.+. ...+.||..+||+|++ -+.|+++++..
T Consensus 10 ~dgki~~~d~~~v~~~lgy~~~eLvG~s---~y~~~H~~D~~ 48 (111)
T PF14598_consen 10 LDGKITYVDSRAVSSLLGYLPEELVGRS---IYDFVHPDDLQ 48 (111)
T ss_dssp TTSBEEEEETTHHHHHHSS-HHHHTTSB---GGGGBSCCTHH
T ss_pred CCcEEEEEcCccChhhcCCCcHHHcCCc---hHHhCCHhhhh
Confidence 46899999999 8999999999999994 57888776654
No 38
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=92.63 E-value=0.24 Score=43.38 Aligned_cols=41 Identities=10% Similarity=-0.036 Sum_probs=34.7
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVP 71 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~Eli 71 (95)
..+.++++.+.++++.|.. +.|+++|++|++++|++..+..
T Consensus 577 ~~~~i~~~~~~~i~~~d~~---g~i~~~N~~~~~~~g~~~~~~~ 617 (1197)
T PRK09959 577 FRKALSDSLPNPTYVVNWQ---GNVISHNSAFEHYFTADYYKNA 617 (1197)
T ss_pred HHHHHHhhCCCcEEEEcCC---CcEEEehHHHHHHhCccccccc
Confidence 3467889999999999987 7999999999999998754433
No 39
>KOG3561|consensus
Probab=90.67 E-value=0.17 Score=44.24 Aligned_cols=57 Identities=19% Similarity=0.181 Sum_probs=42.3
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccCCCCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYLQS 89 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g~~~~~ 89 (95)
.+..++-.+-|||+++=..+ +.|+||++.-..+.||.-+||+|++ =+.+|+....+.
T Consensus 95 eL~~LmLeAlDGF~fvV~cd--G~IvyVSeSVT~~L~y~QsDL~~qS---ly~ilhp~d~~~ 151 (803)
T KOG3561|consen 95 ELTHLILEALDGFLFVVNCD--GRIVYVSESVTSVLGYLQSDLMGQS---LYDILHPLDNDK 151 (803)
T ss_pred HHHHHHHHHhcCeEEEEecC--ceEEEEecchHHhhCcCHHHHhcch---HHHhcCccccCc
Confidence 45555555566776555444 8999999999999999999999993 477776655443
No 40
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=90.59 E-value=0.21 Score=39.75 Aligned_cols=41 Identities=12% Similarity=0.150 Sum_probs=37.7
Q ss_pred HHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 30 RQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 30 ~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
...++.....+++.|.. +.|.|+|++++.+.|.+..-+.|+
T Consensus 10 ~~~Ln~~~~pVl~vd~~---~~i~yaN~aAe~~~~~Sa~~L~~~ 50 (363)
T COG3852 10 GAILNNLINPVLLVDDE---LAIHYANPAAEQLLAVSARRLAGT 50 (363)
T ss_pred HhHHhccCCceEEEcCC---CcEEecCHHHHHHHHHHHHHHhcC
Confidence 46788899999999997 799999999999999999999998
No 41
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=89.93 E-value=0.23 Score=31.31 Aligned_cols=41 Identities=7% Similarity=0.071 Sum_probs=30.8
Q ss_pred HHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 29 ERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 29 ~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
+..++++.+.+++++|.. ..|.|.|++..++.+.. ...+|+
T Consensus 1 L~~il~s~~~~i~~vD~~---~~I~~~n~~a~~~f~~~-~~~iGr 41 (106)
T PF13596_consen 1 LNNILDSMPIGIIFVDRN---LRIRYFNPAAARLFNLS-PSDIGR 41 (106)
T ss_dssp HHHHHHHSSSEEEEEETT---SBEEEE-SCGC-SS----GGGTTS
T ss_pred ChHHHhcCCCCEEEEcCC---CeEEEeChhHhhhcCCC-hHHCCC
Confidence 356788889999999999 69999999999999866 455799
No 42
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=89.57 E-value=0.6 Score=38.34 Aligned_cols=46 Identities=9% Similarity=0.047 Sum_probs=40.4
Q ss_pred hHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 25 YMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 25 ~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.--.+...+++.++.++-+|-. +.+..+|+||++++|-+.+++.|+
T Consensus 78 ~hl~L~aLL~al~~pVlsvd~k---g~v~~aNpAa~~l~~~~~~~~~g~ 123 (511)
T COG3283 78 EHLALSALLEALPEPVLSVDMK---GKVDMANPAACQLFGRKEDRLRGH 123 (511)
T ss_pred HhHHHHHHHHhCCCceEEeccc---CceeecCHHHHHHhCCChhhhcCc
Confidence 3345667888899999998877 799999999999999999999999
No 43
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=88.73 E-value=0.83 Score=38.37 Aligned_cols=43 Identities=9% Similarity=0.089 Sum_probs=38.0
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCcc--ccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRA--EVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~--EliG~ 73 (95)
+...++++..+|++.+|+. +.|+.+|.+-++|.|+... +++|+
T Consensus 216 er~A~l~si~EGviAvd~~---G~It~~N~~A~~ll~~~~~~~~~ig~ 260 (537)
T COG3290 216 ERQAMLQSIKEGVIAVDKK---GVITLINQAAQKLLGLRQPSGDPIGR 260 (537)
T ss_pred HHHHHHHHhhceEEEECCC---CeEeehhHHHHHHhcccCcCcccccc
Confidence 3356788899999999998 7999999999999999987 69998
No 44
>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=87.35 E-value=0.64 Score=32.13 Aligned_cols=40 Identities=13% Similarity=0.034 Sum_probs=37.4
Q ss_pred HHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 31 QKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 31 ~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.-++..+-|++=+|.. +.|+.-|.+=.+++|++++.++|+
T Consensus 20 eelD~lpFGvI~lD~~---G~V~~YN~aE~~~sg~~p~~vlGr 59 (124)
T TIGR02373 20 AQFDALPFGAIQLDGS---GVILRYNAAEGRITGRDPERVIGR 59 (124)
T ss_pred hHhhcCCcceEEECCC---CEEEEEecchhhhcCCChhhhhch
Confidence 4588899999999998 799999999999999999999999
No 45
>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=86.10 E-value=0.79 Score=30.12 Aligned_cols=42 Identities=21% Similarity=0.379 Sum_probs=31.6
Q ss_pred CCeEEEEecCCCCCcEEEEchHHHHhhCCC---ccccCCCCCCCCcccccC
Q psy17885 37 DSSFLLANAQIVDFPIVYCNESFCKISGYN---RAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 37 ~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs---~~EliG~~~~~~~~~L~g 84 (95)
+...+.+|.. ++.|++|++....+.|.+ .++++|+ +..-+.+
T Consensus 15 hG~LLa~d~~--~~~I~~~S~N~~~~lg~~~~~~~~llG~----~l~~ll~ 59 (110)
T PF08446_consen 15 HGALLALDPD--DLRIVQASENIAELLGIPPELPEELLGR----PLSELLG 59 (110)
T ss_dssp TSEEEEEETT--TTBEEEEETTHHHHHSS----HHHHTTC----BHHHHSC
T ss_pred CEEEEEEECC--CCEEEEEcCCHHHHhCCccccchhhccc----CHHHHhC
Confidence 3445566655 389999999999999999 9999999 6554444
No 46
>KOG3558|consensus
Probab=80.73 E-value=0.89 Score=39.44 Aligned_cols=37 Identities=19% Similarity=0.507 Sum_probs=30.5
Q ss_pred cCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 45 AQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 45 ~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
....|-+|+||.+.|..+.||+.+||+|++ -+.|.+.
T Consensus 279 Rhs~DmkityCedRisdlm~y~PeeLvGrS---~Ye~~Ha 315 (768)
T KOG3558|consen 279 RHSLDMKITYCEDRISDLMDYEPEELVGRS---CYEFVHA 315 (768)
T ss_pred eeecceeEEEEchhHHHHhcCCHHHhhchh---HHHhhhH
Confidence 333578999999999999999999999994 4666554
No 47
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=79.16 E-value=2.3 Score=34.72 Aligned_cols=52 Identities=12% Similarity=0.070 Sum_probs=41.9
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGS 85 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g~ 85 (95)
.+..++....+|++-+|.+ +.|+.+|..-.+|.|.+.++++|++ -..+|...
T Consensus 112 kL~SvlayMtDGViATdRr---G~iI~iN~~A~k~L~~~~E~~~~~~---i~elL~i~ 163 (459)
T COG5002 112 KLDSVLAYMTDGVIATDRR---GKIILINKPALKMLGVSKEDALGRS---ILELLKIE 163 (459)
T ss_pred HHHHHHHHHcCceEeecCC---CcEEEeccHHHHHhCcCHHHHhccc---HHHHhCCc
Confidence 3445566778999999998 7999999999999999999999993 34445433
No 48
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=77.49 E-value=0.89 Score=36.54 Aligned_cols=50 Identities=16% Similarity=0.272 Sum_probs=39.3
Q ss_pred hhhhHHHHHHHhCCC----CCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 22 RRTYMYDERQKNGHP----DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 22 ~~~~~~~~~~~~~~~----~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
-+.|+-++++++|.. ...++|-.+.. .+.+|+|.-|...+||+.++.+-.
T Consensus 278 vhnysLdcRrLfDsLreEnlgmlfVYs~k~--qRllFAN~~fk~wtGy~~edFl~~ 331 (401)
T PF06785_consen 278 VHNYSLDCRRLFDSLREENLGMLFVYSPKS--QRLLFANSQFKTWTGYSSEDFLKD 331 (401)
T ss_pred cccchHHHHHHHhhhcccccceEEEecchh--hHHHHhHHHHHHHhccCHHHHHhc
Confidence 345777889999875 33455666554 789999999999999999988876
No 49
>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=75.00 E-value=5.7 Score=28.00 Aligned_cols=44 Identities=11% Similarity=0.047 Sum_probs=32.5
Q ss_pred HHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCC
Q psy17885 29 ERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDY 74 (95)
Q Consensus 29 ~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~ 74 (95)
.+.++. .+.+++ .-...++-..+|+|.+-.+|.+|+-+|+.+.|
T Consensus 34 ~~~L~~-ap~ail-sh~~~~dP~f~yaN~aaL~l~e~~w~el~~lP 77 (148)
T PF08670_consen 34 AKALWH-APFAIL-SHGTKADPIFIYANQAALDLFETTWDELVGLP 77 (148)
T ss_pred HHHHHc-CCCEEE-EcCCCCCCEEEehhHHHHHHhcCCHHHHhcCc
Confidence 344444 566654 33444566788999999999999999999994
No 50
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=73.98 E-value=6.9 Score=34.53 Aligned_cols=37 Identities=8% Similarity=-0.111 Sum_probs=32.2
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYN 66 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs 66 (95)
..+.+++..+.|+++.|... +.|+++|++++++.|+.
T Consensus 344 l~~~Ii~~lp~Gilv~D~~~--~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 344 LNEEIVSNLPLGLLVYDFES--NRTVISNKIADHLLPHL 380 (894)
T ss_pred HHHHHHHhCCceEEEEECCC--CeEEEEhHHHHHHhCcc
Confidence 45788999999999999664 79999999999999874
No 51
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=64.92 E-value=16 Score=32.38 Aligned_cols=41 Identities=10% Similarity=-0.094 Sum_probs=33.0
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
..+.++...|-++++.|... +.|+|+|+.|.++.| .+ ++|+
T Consensus 103 ~~~~~l~~~p~gi~~~~~~~--~~i~W~N~~~~~~~~--~~-~~g~ 143 (838)
T PRK14538 103 IGEEVLNELPIGIVLIDISS--KEIQWLNPYANFILK--NP-EINT 143 (838)
T ss_pred HHHHHHHhCCceEEEEeCCC--CEEEEECHHHHHHhC--cc-ccCC
Confidence 33677888899999999432 799999999999977 33 8888
No 52
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=56.22 E-value=15 Score=31.95 Aligned_cols=40 Identities=13% Similarity=-0.056 Sum_probs=36.4
Q ss_pred HHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCC
Q psy17885 31 QKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSD 73 (95)
Q Consensus 31 ~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~ 73 (95)
.+++....|++..|.+ +.|.-+|++-++|.|.+.++++|+
T Consensus 374 ~VLsgvtaGVi~~d~~---g~i~t~N~~ae~~l~~~~~~~~G~ 413 (712)
T COG5000 374 AVLSGLTAGVIGFDNR---GCITTVNPSAEQILGKPFDQLLGQ 413 (712)
T ss_pred HHHhcCceeEEEEcCC---CeeEeecchHHHHhcCChhHhhcc
Confidence 3677789999999988 789999999999999999999998
No 53
>COG4224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.84 E-value=29 Score=22.12 Aligned_cols=32 Identities=16% Similarity=0.157 Sum_probs=28.0
Q ss_pred hhhhhhhhHHHHHHHhCCCCCeEEEEecCCCC
Q psy17885 18 VELVRRTYMYDERQKNGHPDSSFLLANAQIVD 49 (95)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~~ 49 (95)
+...|+.|++.++..+-..-+.+-|+|+.+.|
T Consensus 29 Q~~LR~eYl~~fr~~vk~~l~~ikiiDp~GnD 60 (77)
T COG4224 29 QAKLRREYLESFRGQVKNQLENIKIIDPKGND 60 (77)
T ss_pred HHHHHHHHHHHHHHHHHHhhcceeeeCCCCCC
Confidence 56779999999999998889999999998654
No 54
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=43.72 E-value=30 Score=25.97 Aligned_cols=36 Identities=11% Similarity=-0.090 Sum_probs=29.8
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCC
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYN 66 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs 66 (95)
.+..+++..+..+.|=+.. +.++++|.+|.+...-+
T Consensus 20 ~~~~~i~~~~~P~CiR~~~---g~fi~~N~~F~~~f~~~ 55 (217)
T PRK13719 20 SLTAFIDDYSYPACIRNES---GKFIFYNTLFLKEFLGQ 55 (217)
T ss_pred HHHHHHHcCCCCeEEECCC---CCeeecchHHHHHHHhc
Confidence 4455788899999998888 79999999999977643
No 55
>KOG3558|consensus
Probab=38.75 E-value=38 Score=29.82 Aligned_cols=48 Identities=15% Similarity=0.220 Sum_probs=37.7
Q ss_pred CCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccCCCC
Q psy17885 35 HPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYL 87 (95)
Q Consensus 35 ~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g~~~ 87 (95)
.+-+||+++=..+ +.++|+++.-....|.+--||.|.+ -+.|++..++
T Consensus 126 qsLDGFVm~l~~d--G~~lYiSEtVS~yLGLSQvELTG~S---vFDfiHP~Dh 173 (768)
T KOG3558|consen 126 QSLDGFVMALTQD--GDFLYISETVSIYLGLSQVELTGSS---VFDFIHPCDH 173 (768)
T ss_pred hhccceEEEEccC--CCEEEEechhHhhhCccceeeecch---hhhccCccCH
Confidence 3456776554443 8999999999999999999999994 5778776654
No 56
>COG4170 SapD ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=37.39 E-value=19 Score=28.00 Aligned_cols=62 Identities=13% Similarity=0.106 Sum_probs=44.0
Q ss_pred CCcCCcccceeecccchhhhhhhhHHHHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcc
Q psy17885 2 NEMGNKRGWRKNTAPEVELVRRTYMYDERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYN 80 (95)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~ 80 (95)
|| ||..|.+|.-.-.- .++.+++......-|++.++ +..+-|-...+++--.|..++|+ +..
T Consensus 31 nE-GEi~GLVGESGSGK--------SLiAK~Ic~v~kdnW~vTAD----R~Rf~~idLL~L~Pr~RRk~ig~----~is 92 (330)
T COG4170 31 NE-GEIRGLVGESGSGK--------SLIAKAICGVNKDNWRVTAD----RMRFDDIDLLRLSPRERRKLVGH----NVS 92 (330)
T ss_pred cc-ceeeeeeccCCCch--------hHHHHHHhcccccceEEEhh----hcccccchhhcCChHHhhhhhcc----chh
Confidence 44 46667777554443 35666666666666777666 67788888999999999999999 655
No 57
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=36.91 E-value=77 Score=27.99 Aligned_cols=40 Identities=10% Similarity=-0.074 Sum_probs=33.1
Q ss_pred HHHHHhCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccc
Q psy17885 28 DERQKNGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAE 69 (95)
Q Consensus 28 ~~~~~~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~E 69 (95)
..+++++..+.++++.+..+ +.++++|+.+.++.|+...+
T Consensus 335 ~~r~iv~~~p~gi~i~~~~~--g~~~~~N~~a~~~~~l~~~~ 374 (924)
T PRK10841 335 FNRKIVASAPVGICILRTSD--GTNILSNELAHNYLNMLTHE 374 (924)
T ss_pred HHHHHHHhCCccEEEEEcCC--CcEEEehHHHHHHhccCChh
Confidence 44778999999999998664 79999999999999875443
No 58
>COG4863 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.34 E-value=29 Score=28.55 Aligned_cols=43 Identities=12% Similarity=0.346 Sum_probs=35.4
Q ss_pred CeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccC
Q psy17885 38 SSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVG 84 (95)
Q Consensus 38 ~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g 84 (95)
+|.-+++-......+.|.|+.+.+-+-|+..|+|-. +..|+.+
T Consensus 257 dg~svi~~n~~n~~~eY~nps~~etts~r~gelIq~----SfdFind 299 (439)
T COG4863 257 DGISVIDVNLSNRQVEYQNPSLVETTSYRTGELIQK----SFDFIND 299 (439)
T ss_pred CCceEEEecCCccEEEEeccchhccccccccccchh----hhhhhhc
Confidence 455677766667778899999999999999999999 7887764
No 59
>PRK01631 hypothetical protein; Provisional
Probab=30.56 E-value=51 Score=20.92 Aligned_cols=31 Identities=10% Similarity=0.052 Sum_probs=27.2
Q ss_pred hhhhhhhhHHHHHHHhCCCCCeEEEEecCCC
Q psy17885 18 VELVRRTYMYDERQKNGHPDSSFLLANAQIV 48 (95)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~ 48 (95)
+...|..|+..++..|.+.-+++-|.|+.+.
T Consensus 28 q~~LR~eYl~~fR~~~~~~L~~i~ivD~~G~ 58 (76)
T PRK01631 28 QQMLRQNYTQTFRGSLDSILLNTKIVDQNGL 58 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCceeECCCCC
Confidence 5566899999999999999999999999864
No 60
>PRK01546 hypothetical protein; Provisional
Probab=26.86 E-value=67 Score=20.51 Aligned_cols=31 Identities=19% Similarity=0.118 Sum_probs=26.7
Q ss_pred hhhhhhhhHHHHHHHhCCCCCeEEEEecCCC
Q psy17885 18 VELVRRTYMYDERQKNGHPDSSFLLANAQIV 48 (95)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~ 48 (95)
+...|..|+..++..|.+.-+++-|.|+.+.
T Consensus 30 q~~LR~eYl~~fR~~~~~~L~~i~vvD~~G~ 60 (79)
T PRK01546 30 RQSLREQYLKGFRQNMLNELKGIKVVNEQGT 60 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHhccceEECCCCC
Confidence 5566889999999999999999999998864
No 61
>KOG3560|consensus
Probab=24.83 E-value=61 Score=28.04 Aligned_cols=47 Identities=17% Similarity=0.283 Sum_probs=34.6
Q ss_pred hCCCCCeEEEEecCCCCCcEEEEchHHHHhhCCCccccCCCCCCCCcccccCC
Q psy17885 33 NGHPDSSFLLANAQIVDFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGS 85 (95)
Q Consensus 33 ~~~~~~gi~I~d~~~~~~~I~yvN~aF~~mtGYs~~EliG~~~~~~~~~L~g~ 85 (95)
+.+...=++|+++. +.|.|++...+...||.-.+++.++ -+.+++..
T Consensus 117 LqsLnGF~lVvt~e---g~ifyAS~tIedYLGFhQSDV~HQs---VYdlIHse 163 (712)
T KOG3560|consen 117 LQSLNGFALVVTAE---GEIFYASATIEDYLGFHQSDVMHQS---VYDLIHSE 163 (712)
T ss_pred HHhcCCeEEEEecC---ceEEEehhhHHhhhcccccchhhhh---HHHHhhhh
Confidence 34443334455555 7999999999999999999999994 46655543
No 62
>PF13992 YecR: YecR-like lipoprotein
Probab=23.62 E-value=66 Score=20.13 Aligned_cols=29 Identities=28% Similarity=0.230 Sum_probs=20.9
Q ss_pred HHHHhhCCCccccCCCCCCCCcccccCCCC
Q psy17885 58 SFCKISGYNRAEVPSDYDIPTYNLLVGSYL 87 (95)
Q Consensus 58 aF~~mtGYs~~EliG~~~~~~~~~L~g~~~ 87 (95)
.=|+-.||+..|.+|.| ..+|....|..+
T Consensus 35 ~rCq~wGY~~Ae~fG~~-~~~C~~~~g~~C 63 (74)
T PF13992_consen 35 KRCQQWGYKGAEPFGGP-VKTCSRYGGSGC 63 (74)
T ss_pred HHHHHhCcCcCEecCCC-CceeecCCCCce
Confidence 34788999999999985 234665555544
No 63
>PF14877 mIF3: Mitochondrial translation initiation factor
Probab=23.22 E-value=1.1e+02 Score=22.32 Aligned_cols=60 Identities=18% Similarity=0.215 Sum_probs=49.6
Q ss_pred cccceeecccchhhhhhhhHHHHHHHhCCCCCeEEEEecCCC----CCcEEEEchHHHHhhCCC
Q psy17885 7 KRGWRKNTAPEVELVRRTYMYDERQKNGHPDSSFLLANAQIV----DFPIVYCNESFCKISGYN 66 (95)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~----~~~I~yvN~aF~~mtGYs 66 (95)
+-|-+..+.|+.--.+...+..+..-+|-...|+.|++.... +-|++-..+....+-.|+
T Consensus 31 ~~g~Vk~inp~t~~Le~~~l~~~~~~lDL~~~Gl~iV~~~~~~~~~~lPLVK~v~~~~alk~YS 94 (181)
T PF14877_consen 31 PNGKVKFINPETNKLEESNLRDIAKGLDLSKHGLQIVNSEKDQKGRDLPLVKIVEVREALKQYS 94 (181)
T ss_pred CCCeEEEEcCCCCcceeeeHHHHHHhCCccccceEEecccccCCCCcCceEEEecHHHHHHHHH
Confidence 457788888887667788899999999999999999987654 458888888888888887
No 64
>PRK02539 hypothetical protein; Provisional
Probab=23.12 E-value=88 Score=20.27 Aligned_cols=30 Identities=13% Similarity=0.160 Sum_probs=26.4
Q ss_pred hhhhhhhhHHHHHHHhCCCCCeEEEEecCC
Q psy17885 18 VELVRRTYMYDERQKNGHPDSSFLLANAQI 47 (95)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~ 47 (95)
+...|..|+..++..|...-+++-|.|+.+
T Consensus 29 q~~LR~eYl~~fR~~~~~~L~~i~ivD~~G 58 (85)
T PRK02539 29 QAKLREEYIEGYRRSVRHHIEGIKIVDEEG 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHhccceEECCCC
Confidence 556689999999999999999999999885
No 65
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=22.27 E-value=26 Score=21.57 Aligned_cols=31 Identities=10% Similarity=0.071 Sum_probs=19.7
Q ss_pred hhhhhhhhHHHHHHHhCCCCCeEEEEecCCC
Q psy17885 18 VELVRRTYMYDERQKNGHPDSSFLLANAQIV 48 (95)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~gi~I~d~~~~ 48 (95)
+...|..|+..++..|...-+++-|.|+.+.
T Consensus 27 q~~LR~eYl~~fR~~~~~~L~~i~ivD~~G~ 57 (65)
T PF05979_consen 27 QAELRQEYLQNFRGNFRSQLENIKIVDPDGN 57 (65)
T ss_dssp HHHHHHHHHHTTHHHHHHCSSTT--------
T ss_pred HHHHHHHHHHHHHHHHHHHhcceeEECCCCC
Confidence 4556889999999999988999999998864
Done!