Query psy8548
Match_columns 102
No_of_seqs 114 out of 1113
Neff 9.5
Searched_HMMs 46136
Date Fri Aug 16 21:40:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8548hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13426 PAS_9: PAS domain; PD 99.6 1.9E-13 4.2E-18 77.6 10.6 79 2-86 1-79 (104)
2 PF00989 PAS: PAS fold; Inter 99.2 2.3E-10 5.1E-15 65.7 8.9 80 1-86 10-90 (113)
3 PRK13557 histidine kinase; Pro 99.0 3.7E-09 8.1E-14 75.3 10.0 81 2-85 40-120 (540)
4 PRK10060 RNase II stability mo 98.9 8E-09 1.7E-13 76.4 8.8 79 2-86 121-200 (663)
5 PF08448 PAS_4: PAS fold; Int 98.9 2E-08 4.4E-13 57.3 8.5 78 1-85 4-81 (110)
6 PF08447 PAS_3: PAS fold; Int 98.9 7.3E-09 1.6E-13 57.8 6.4 70 18-88 1-73 (91)
7 PRK13559 hypothetical protein; 98.9 3.3E-08 7.1E-13 67.8 10.1 81 2-85 53-133 (361)
8 cd00130 PAS PAS domain; PAS mo 98.8 3.5E-07 7.5E-12 48.0 9.6 80 1-86 1-80 (103)
9 PRK13560 hypothetical protein; 98.7 1.4E-07 3.1E-12 70.1 9.3 79 2-86 214-292 (807)
10 TIGR02938 nifL_nitrog nitrogen 98.6 1.2E-07 2.6E-12 66.6 6.6 78 2-85 14-91 (494)
11 TIGR02040 PpsR-CrtJ transcript 98.6 2.4E-07 5.2E-12 65.5 8.1 78 1-86 261-340 (442)
12 PRK13558 bacterio-opsin activa 98.6 8.6E-07 1.9E-11 65.5 10.0 81 3-86 159-239 (665)
13 PRK11091 aerobic respiration c 98.6 3.6E-07 7.9E-12 68.5 8.1 79 1-85 164-242 (779)
14 PF14598 PAS_11: PAS domain; P 98.6 1.8E-06 3.8E-11 50.7 9.2 76 7-88 7-84 (111)
15 KOG0501|consensus 98.5 2.2E-07 4.7E-12 67.6 5.9 83 3-86 28-110 (971)
16 TIGR02040 PpsR-CrtJ transcript 98.4 3.3E-07 7.1E-12 64.8 3.8 78 2-85 6-84 (442)
17 PRK11073 glnL nitrogen regulat 98.4 2.6E-06 5.7E-11 58.0 7.9 76 1-84 16-91 (348)
18 TIGR00229 sensory_box PAS doma 98.4 8.2E-06 1.8E-10 44.6 8.4 78 2-85 13-91 (124)
19 PRK11359 cyclic-di-GMP phospho 98.3 2.9E-06 6.3E-11 63.5 8.0 79 2-86 146-225 (799)
20 PRK11359 cyclic-di-GMP phospho 98.3 1.9E-06 4.2E-11 64.5 6.9 79 2-86 22-104 (799)
21 PRK09776 putative diguanylate 98.3 4.4E-06 9.5E-11 64.5 8.5 79 2-86 293-372 (1092)
22 TIGR02966 phoR_proteo phosphat 98.0 3E-05 6.4E-10 51.9 6.6 40 1-46 15-54 (333)
23 PF13188 PAS_8: PAS domain; PD 98.0 2.1E-05 4.6E-10 41.2 4.6 31 1-39 10-40 (64)
24 KOG1229|consensus 98.0 1.5E-06 3.1E-11 61.7 -0.2 74 3-82 168-242 (775)
25 PF12860 PAS_7: PAS fold 97.9 0.00015 3.2E-09 42.2 7.6 35 1-39 4-39 (115)
26 PRK09776 putative diguanylate 97.8 0.00014 2.9E-09 56.4 7.9 79 2-86 546-628 (1092)
27 PRK10820 DNA-binding transcrip 97.3 0.00068 1.5E-08 49.5 5.6 42 1-48 89-130 (520)
28 PRK11360 sensory histidine kin 97.3 0.0023 4.9E-08 46.1 8.2 58 1-66 271-328 (607)
29 PF13596 PAS_10: PAS domain; P 97.2 0.0012 2.7E-08 37.7 5.2 74 1-83 8-81 (106)
30 PRK11006 phoR phosphate regulo 97.2 0.0025 5.4E-08 45.0 7.3 35 1-39 107-141 (430)
31 smart00091 PAS PAS domain. PAS 97.2 0.0026 5.7E-08 30.2 5.6 34 2-39 11-44 (67)
32 PRK13560 hypothetical protein; 97.1 0.0025 5.4E-08 47.8 6.6 34 2-39 342-376 (807)
33 COG2202 AtoS FOG: PAS/PAC doma 97.0 0.012 2.7E-07 34.7 8.4 79 2-86 122-203 (232)
34 KOG3558|consensus 97.0 0.00076 1.7E-08 50.2 3.0 71 16-88 284-354 (768)
35 PRK11388 DNA-binding transcrip 96.9 0.005 1.1E-07 45.9 7.0 41 1-47 212-252 (638)
36 PF08670 MEKHLA: MEKHLA domain 96.6 0.021 4.5E-07 35.2 6.8 80 4-87 43-122 (148)
37 TIGR02373 photo_yellow photoac 96.1 0.07 1.5E-06 31.9 7.0 59 2-66 26-85 (124)
38 PRK15053 dpiB sensor histidine 95.7 0.014 3E-07 42.3 3.5 35 1-39 231-267 (545)
39 COG3829 RocR Transcriptional r 95.1 0.072 1.6E-06 39.3 5.4 40 1-46 126-165 (560)
40 COG3852 NtrB Signal transducti 94.9 0.14 3E-06 35.5 6.1 59 3-69 18-76 (363)
41 PRK11086 sensory histidine kin 94.4 0.049 1.1E-06 39.2 3.3 35 1-39 230-267 (542)
42 COG5002 VicK Signal transducti 94.4 0.06 1.3E-06 37.9 3.5 36 1-40 120-155 (459)
43 TIGR02938 nifL_nitrog nitrogen 94.1 0.071 1.5E-06 37.6 3.5 34 2-39 140-173 (494)
44 KOG3559|consensus 93.2 0.07 1.5E-06 38.1 2.2 31 5-39 228-258 (598)
45 KOG3560|consensus 92.8 0.46 1E-05 35.3 5.8 70 16-87 293-362 (712)
46 PF08446 PAS_2: PAS fold; Int 92.6 0.33 7.2E-06 28.2 4.2 41 4-49 17-60 (110)
47 COG3283 TyrR Transcriptional r 92.5 0.26 5.7E-06 35.1 4.2 35 1-39 89-123 (511)
48 COG3290 CitA Signal transducti 91.8 0.21 4.6E-06 36.8 3.2 42 2-49 225-268 (537)
49 PRK09959 hybrid sensory histid 91.3 1.1 2.4E-05 35.9 6.9 31 1-35 585-615 (1197)
50 KOG3561|consensus 91.1 0.26 5.7E-06 38.0 3.3 40 3-47 106-145 (803)
51 PF06785 UPF0242: Uncharacteri 90.3 0.37 8.1E-06 33.6 3.1 71 4-83 299-369 (401)
52 KOG3558|consensus 89.8 0.61 1.3E-05 35.5 4.0 50 3-58 130-179 (768)
53 PF07310 PAS_5: PAS domain; I 87.5 4.5 9.7E-05 24.3 6.7 75 4-83 39-113 (137)
54 KOG3560|consensus 84.3 1.3 2.9E-05 33.0 3.1 43 1-48 120-162 (712)
55 COG5000 NtrY Signal transducti 83.2 1.9 4E-05 32.8 3.6 34 2-39 380-413 (712)
56 KOG3753|consensus 73.9 12 0.00026 29.9 5.4 71 16-88 341-414 (1114)
57 KOG3559|consensus 64.8 5.3 0.00012 29.0 1.9 42 2-48 89-130 (598)
58 PRK10618 phosphotransfer inter 49.8 28 0.0006 27.8 3.8 29 1-32 352-380 (894)
59 KOG3753|consensus 49.7 20 0.00044 28.7 2.9 24 16-39 202-225 (1114)
60 PF02084 Bindin: Bindin; Inte 49.7 3.6 7.9E-05 27.2 -0.8 6 34-39 110-115 (238)
61 PRK14538 putative bifunctional 46.5 31 0.00068 27.4 3.6 32 1-39 111-143 (838)
62 KOG3561|consensus 34.2 40 0.00087 26.7 2.5 70 16-87 382-452 (803)
63 PRK08402 replication factor A; 26.3 2.2E+02 0.0048 20.3 4.9 22 16-37 258-279 (355)
64 PF09695 YtfJ_HI0045: Bacteria 20.5 1.2E+02 0.0026 19.1 2.4 17 3-23 126-142 (160)
No 1
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=99.55 E-value=1.9e-13 Score=77.61 Aligned_cols=79 Identities=24% Similarity=0.331 Sum_probs=67.5
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
+.+++++|.+ ++|+++|++|++++|++.++++|+ +...+..+.........+.+.+..+..+..++.+++++|+
T Consensus 1 p~~i~i~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~ 74 (104)
T PF13426_consen 1 PDGIFILDPD----GRILYVNPAFERLFGYSREELIGK--SISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGE 74 (104)
T ss_dssp -SEEEEEETT----SBEEEE-HHHHHHHTS-HHHHTTS--BGGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSE
T ss_pred CEEEEEECCc----CcEEehhHHHHHHHCcCHHHHcCC--CcccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCC
Confidence 3689999998 999999999999999999999999 6666666666778888889999988889999999999999
Q ss_pred eeeec
Q psy8548 82 HEEEE 86 (102)
Q Consensus 82 ~~~~~ 86 (102)
.+|+.
T Consensus 75 ~~~~~ 79 (104)
T PF13426_consen 75 TFWVE 79 (104)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 98875
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=99.21 E-value=2.3e-10 Score=65.73 Aligned_cols=80 Identities=21% Similarity=0.282 Sum_probs=57.9
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEE-EEEEEecC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKL-EVIFYKKN 79 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~-e~~~~~~~ 79 (102)
++++++++|.+ |+|+++|+++++++|++.++++|+ +...+..+.........+...+..+..... ......++
T Consensus 10 ~~~~i~~~d~~----g~I~~~N~a~~~l~g~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (113)
T PF00989_consen 10 SPDGIFVIDED----GRILYVNQAAEELLGYSREELIGK--SLFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRD 83 (113)
T ss_dssp SSSEEEEEETT----SBEEEECHHHHHHHSS-HHHHTTS--BGGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETT
T ss_pred CCceEEEEeCc----CeEEEECHHHHHHHccCHHHHcCC--cHHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecC
Confidence 46799999987 999999999999999999999999 554444443333466677777776665443 44444458
Q ss_pred CCeeeec
Q psy8548 80 GYHEEEE 86 (102)
Q Consensus 80 G~~~~~~ 86 (102)
|..+|+.
T Consensus 84 g~~~~~~ 90 (113)
T PF00989_consen 84 GRPRWVE 90 (113)
T ss_dssp SCEEEEE
T ss_pred CcEEEEE
Confidence 8877764
No 3
>PRK13557 histidine kinase; Provisional
Probab=99.03 E-value=3.7e-09 Score=75.27 Aligned_cols=81 Identities=26% Similarity=0.611 Sum_probs=64.9
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
..+|++.|....+ ++|+|+|++|++++||+.++++|+ +...+.++.........++..+..+..+..++...+++|+
T Consensus 40 ~~~i~v~d~~~~~-g~i~~~N~a~~~~~G~~~~e~~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~ 116 (540)
T PRK13557 40 RMPMIVTDPNQPD-NPIVFANRAFLEMTGYAAEEIIGN--NCRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGS 116 (540)
T ss_pred cCcEEEEcCCCCC-CCEEEEcHHHHHHhCCCHHHhcCC--ChHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEEeCCCC
Confidence 3578888874334 899999999999999999999998 6666666666666677777788888778888888888998
Q ss_pred eeee
Q psy8548 82 HEEE 85 (102)
Q Consensus 82 ~~~~ 85 (102)
.+|+
T Consensus 117 ~~~~ 120 (540)
T PRK13557 117 SFWN 120 (540)
T ss_pred EEEE
Confidence 8775
No 4
>PRK10060 RNase II stability modulator; Provisional
Probab=98.93 E-value=8e-09 Score=76.44 Aligned_cols=79 Identities=14% Similarity=0.139 Sum_probs=62.6
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCc-ccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCAC-KFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~-~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
+++|+++|.+ |+|+++|++|++++||+.++++|+ +. .++.++.........+...+..+..|..+...++++|
T Consensus 121 ~~gI~i~D~~----g~I~~~N~a~~~l~Gy~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G 194 (663)
T PRK10060 121 NSVIVILDSR----GNIQRFNRLCEEYTGLKEHDVIGQ--SVFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKTRKG 194 (663)
T ss_pred CceEEEEeCC----CCEEEEcHHHHHHHCcCHHHHcCC--CHHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCC
Confidence 5789999998 899999999999999999999998 54 3343443334445566677778888999999999999
Q ss_pred Ceeeec
Q psy8548 81 YHEEEE 86 (102)
Q Consensus 81 ~~~~~~ 86 (102)
..+|+.
T Consensus 195 ~~~~~~ 200 (663)
T PRK10060 195 QRLFLF 200 (663)
T ss_pred CEEEEE
Confidence 877653
No 5
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=98.92 E-value=2e-08 Score=57.27 Aligned_cols=78 Identities=19% Similarity=0.284 Sum_probs=59.4
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
++.+++++|.+ ++++++|+++++++|++.++++|+ ....+.++.........+.+.+..+.....+..... +|
T Consensus 4 ~p~~i~v~D~~----~~i~~~N~~~~~~~~~~~~~~~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 76 (110)
T PF08448_consen 4 SPDGIFVIDPD----GRIVYANQAAAELFGVSPEELIGR--SLFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DG 76 (110)
T ss_dssp CSSEEEEEETT----SBEEEE-HHHHHHHTSTHHHHTTS--BHHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TS
T ss_pred CCceeEEECCC----CEEEEEHHHHHHHhCCCHHHHhhc--cchhccccchhhhhHHHHHHhhccCceEEEEEEEee-cC
Confidence 46789999998 999999999999999999999999 655566655566677777788877777666555544 66
Q ss_pred Ceeee
Q psy8548 81 YHEEE 85 (102)
Q Consensus 81 ~~~~~ 85 (102)
..+|.
T Consensus 77 ~~~~~ 81 (110)
T PF08448_consen 77 EERWF 81 (110)
T ss_dssp CEEEE
T ss_pred CcEEE
Confidence 55554
No 6
>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=98.91 E-value=7.3e-09 Score=57.85 Aligned_cols=70 Identities=27% Similarity=0.356 Sum_probs=50.9
Q ss_pred EEEecHHHHHhhCCChhhhcCCCCC--cccccCCCCCHHHHHHHHH-HHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548 18 IVYCSDGFCELSGFARAQIMQKGCA--CKFLYGPDTSEEHKTQIEK-ALESKTELKLEVIFYKKNGYHEEEEEE 88 (102)
Q Consensus 18 i~~~N~~~~~i~G~~~~ei~g~~~~--~~~l~~~~~~~~~~~~i~~-~l~~~~~~~~e~~~~~~~G~~~~~~~~ 88 (102)
|+++|+.|++++||+.+++ +.+.. ...+..|++.....+.+.. ....+..+..++++++++|+.+|++.-
T Consensus 1 ~i~~s~~~~~i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~ 73 (91)
T PF08447_consen 1 IIYWSDNFYEIFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVR 73 (91)
T ss_dssp -EEE-THHHHHHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEE
T ss_pred CEEEeHHHHHHhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEE
Confidence 5899999999999999999 54101 2233456667777777777 677788999999999999999998753
No 7
>PRK13559 hypothetical protein; Provisional
Probab=98.88 E-value=3.3e-08 Score=67.78 Aligned_cols=81 Identities=25% Similarity=0.531 Sum_probs=62.8
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
..+|+++|..... +.++++|++|++++||+.++++|+ ....+..+.........+...+..+..+..+...++++|.
T Consensus 53 ~~~i~i~D~~~~~-g~i~~~N~a~~~l~G~~~~e~iG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~ 129 (361)
T PRK13559 53 RMAMCITDPHQPD-LPIVLANQAFLDLTGYAAEEVVGR--NCRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGE 129 (361)
T ss_pred CCcEEEecCCCCC-CcEEEEchHHHHHhCCCHHHHcCC--ChhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEEcCCCC
Confidence 4578899975333 789999999999999999999998 6555655555556666677777777777788887888888
Q ss_pred eeee
Q psy8548 82 HEEE 85 (102)
Q Consensus 82 ~~~~ 85 (102)
.+|+
T Consensus 130 ~~~~ 133 (361)
T PRK13559 130 PFWN 133 (361)
T ss_pred EEEE
Confidence 7765
No 8
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=98.76 E-value=3.5e-07 Score=48.03 Aligned_cols=80 Identities=20% Similarity=0.284 Sum_probs=56.0
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
++.+++++|.. +.++++|++++.++|++..+++|+ ....+..+.........+......+..+..+......+|
T Consensus 1 ~~~~i~~~d~~----~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (103)
T cd00130 1 LPDGVIVLDLD----GRILYANPAAEQLLGYSPEELIGK--SLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDG 74 (103)
T ss_pred CCceEEEECCC----CcEEEECHHHHHHhCCCHHHHcCc--cHHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCC
Confidence 35688899987 899999999999999999999987 543344444444444444444544555666777777777
Q ss_pred Ceeeec
Q psy8548 81 YHEEEE 86 (102)
Q Consensus 81 ~~~~~~ 86 (102)
..+|+.
T Consensus 75 ~~~~~~ 80 (103)
T cd00130 75 SVIWVL 80 (103)
T ss_pred CEEEEE
Confidence 766643
No 9
>PRK13560 hypothetical protein; Provisional
Probab=98.71 E-value=1.4e-07 Score=70.10 Aligned_cols=79 Identities=14% Similarity=0.254 Sum_probs=58.6
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
++++++.|.+ ++++++|++++.++||+.++++|+ +...+.++.............+..+.....+....+++|+
T Consensus 214 ~~~i~~~d~~----g~i~~~N~~~~~~~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~ 287 (807)
T PRK13560 214 ADPAFWKDED----AKVFGCNDAACLACGFRREEIIGM--SIHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKDGR 287 (807)
T ss_pred CCeEEEEcCC----CCEEEEhHHHHHHhCCCHHHHcCC--cchhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCCCC
Confidence 5688899987 899999999999999999999998 5554554433333323334445566666778888899999
Q ss_pred eeeec
Q psy8548 82 HEEEE 86 (102)
Q Consensus 82 ~~~~~ 86 (102)
.+|++
T Consensus 288 ~~~~~ 292 (807)
T PRK13560 288 TRPVD 292 (807)
T ss_pred EEEEE
Confidence 88553
No 10
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=98.63 E-value=1.2e-07 Score=66.59 Aligned_cols=78 Identities=17% Similarity=0.251 Sum_probs=60.1
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
+.++++.|.+ ++++++|++++.++|++.++++|+ ....+..+.........+...+..+..+..++...+++|+
T Consensus 14 ~~~i~~~d~~----g~~~~~N~~~~~~~G~~~~~~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 87 (494)
T TIGR02938 14 PLAISITDLK----ANILYANDAFTRITGYTKEEIIGK--NESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRRKDGE 87 (494)
T ss_pred CceEEEECCC----CcEEEEchhheeecCCCHHHHhCC--CchhhcCCCCCHHHHHHHHHHHHhCCcccceeeccCCCcc
Confidence 4678899987 899999999999999999999998 5554554445555666666777777777777777777777
Q ss_pred eeee
Q psy8548 82 HEEE 85 (102)
Q Consensus 82 ~~~~ 85 (102)
.+|+
T Consensus 88 ~~~~ 91 (494)
T TIGR02938 88 LYLA 91 (494)
T ss_pred chhh
Confidence 6664
No 11
>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=98.63 E-value=2.4e-07 Score=65.46 Aligned_cols=78 Identities=13% Similarity=0.106 Sum_probs=52.5
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCC-hhhhcCCCCCcccccCCCCCHHHHHHHHHHHH-hCCcEEEEEEEEec
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFA-RAQIMQKGCACKFLYGPDTSEEHKTQIEKALE-SKTELKLEVIFYKK 78 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~-~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~-~~~~~~~e~~~~~~ 78 (102)
+.++|+++|.+ |+|+++|++|++++||+ .++++|+ +...+..+.. .. ...+...+. .+.....+....++
T Consensus 261 ~~d~I~v~D~~----G~I~~~N~a~~~l~G~~~~~~l~G~--~~~~~~~~~~-~~-~~~~~~~~~~~g~~~~~~~~~~~~ 332 (442)
T TIGR02040 261 APDAIVFSDAD----GTIRGANEAFLELTDSSSLEAVRGR--TLDRWLGRGG-VD-LRVLLSNVRRTGQVRLYATTLTGE 332 (442)
T ss_pred CCceEEEEcCC----CcEEehhHHHHHHhCCCChHHHcCC--CHHHHhCCCc-cc-HHHHHHHHhhcCceEEEEEEEEcC
Confidence 35789999987 89999999999999997 5789998 5433332211 11 122233333 33333456667789
Q ss_pred CCCeeeec
Q psy8548 79 NGYHEEEE 86 (102)
Q Consensus 79 ~G~~~~~~ 86 (102)
+|+.+|++
T Consensus 333 ~G~~~~ve 340 (442)
T TIGR02040 333 FGAQTEVE 340 (442)
T ss_pred CCCEEEEE
Confidence 99988885
No 12
>PRK13558 bacterio-opsin activator; Provisional
Probab=98.57 E-value=8.6e-07 Score=65.49 Aligned_cols=81 Identities=25% Similarity=0.599 Sum_probs=63.0
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH 82 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~ 82 (102)
.++++.|...+. +.++++|++|++++||+.++++|+ ....+.++.........+...+..+..+..+++.++++|..
T Consensus 159 ~gi~~~d~~~~d-g~i~~~N~~~~~l~G~~~eel~g~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~ 235 (665)
T PRK13558 159 VGITIADATLPD-EPLIYINDAFERITGYSPDEVLGR--NCRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGST 235 (665)
T ss_pred ccEEEEcCCCCC-CcEEEEcHHHHHHhCcCHHHHcCC--CHHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEECCCCCE
Confidence 467777753334 899999999999999999999998 65555555555555566677777788888898999999988
Q ss_pred eeec
Q psy8548 83 EEEE 86 (102)
Q Consensus 83 ~~~~ 86 (102)
+|+.
T Consensus 236 ~~~~ 239 (665)
T PRK13558 236 FWNQ 239 (665)
T ss_pred EEEE
Confidence 8763
No 13
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.57 E-value=3.6e-07 Score=68.51 Aligned_cols=79 Identities=18% Similarity=0.168 Sum_probs=57.7
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
++++|++.|.+ |+++++|++++.++|++.++++|+ ....+.++.............+..+..+..+....+++|
T Consensus 164 ~~~~i~~~D~~----g~i~~~N~a~~~l~G~~~~eliG~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G 237 (779)
T PRK11091 164 SPDLVYYRNED----GEFSGCNRAMELLTGKSEKQLIGL--TPKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDG 237 (779)
T ss_pred CcceEEEECCC----CcEEeEcHHHHHHhCcCHHHHcCC--ChHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCC
Confidence 46789999987 999999999999999999999998 544444443333344444455566667777777777777
Q ss_pred Ceeee
Q psy8548 81 YHEEE 85 (102)
Q Consensus 81 ~~~~~ 85 (102)
..+|+
T Consensus 238 ~~~~~ 242 (779)
T PRK11091 238 RKACF 242 (779)
T ss_pred CEEEE
Confidence 76554
No 14
>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=98.55 E-value=1.8e-06 Score=50.70 Aligned_cols=76 Identities=16% Similarity=0.163 Sum_probs=57.8
Q ss_pred EEeCCCCCCCCEEEecHH-HHHhhCCChhhhcCCCCCcccccCCCCCHH-HHHHHHHHHHhCCcEEEEEEEEecCCCeee
Q psy8548 7 LGNAQVPSLYPIVYCSDG-FCELSGFARAQIMQKGCACKFLYGPDTSEE-HKTQIEKALESKTELKLEVIFYKKNGYHEE 84 (102)
Q Consensus 7 i~d~~~~~~~~i~~~N~~-~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~-~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~ 84 (102)
-.+.+ +.|+++.+. ...++||..++++|+ ....+.++.+-.. ..+.....+..|.....-+++..++|..+|
T Consensus 7 rhs~d----gki~~~d~~~v~~~lgy~~~eLvG~--s~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vw 80 (111)
T PF14598_consen 7 RHSLD----GKITYVDSRAVSSLLGYLPEELVGR--SIYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVW 80 (111)
T ss_dssp EEETT----SBEEEEETTHHHHHHSS-HHHHTTS--BGGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEE
T ss_pred EECCC----cEEEEEcCccChhhcCCCcHHHcCC--chHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEE
Confidence 44555 899999999 699999999999999 4444444545443 556777788888887788999999999999
Q ss_pred ecch
Q psy8548 85 EEEE 88 (102)
Q Consensus 85 ~~~~ 88 (102)
+.+.
T Consensus 81 vqt~ 84 (111)
T PF14598_consen 81 VQTK 84 (111)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 9764
No 15
>KOG0501|consensus
Probab=98.54 E-value=2.2e-07 Score=67.62 Aligned_cols=83 Identities=42% Similarity=0.835 Sum_probs=73.0
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCe
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYH 82 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~ 82 (102)
..+++.+++.-+ ..|+|+|+.||++.||.+.+++.+++.+.+.++...+......+++.+.+.+.-++|+..+.++..+
T Consensus 28 tsFlL~NAQiVD-~PiVY~NdgFcKlsGY~RAevMQKs~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TP 106 (971)
T KOG0501|consen 28 TSFLLANAQIVD-WPIVYCNDGFCKLSGYHRAEVMQKSCTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTP 106 (971)
T ss_pred cceeeccceeec-cceEEecCcchhccCccHHHHhcccceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCc
Confidence 356777776666 8999999999999999999999996667888999889999999999999998888999999999999
Q ss_pred eeec
Q psy8548 83 EEEE 86 (102)
Q Consensus 83 ~~~~ 86 (102)
+|.-
T Consensus 107 vW~~ 110 (971)
T KOG0501|consen 107 VWLL 110 (971)
T ss_pred eEEE
Confidence 8864
No 16
>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=98.39 E-value=3.3e-07 Score=64.77 Aligned_cols=78 Identities=9% Similarity=0.038 Sum_probs=51.3
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCC-cEEEEEEEEecCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKT-ELKLEVIFYKKNG 80 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~-~~~~e~~~~~~~G 80 (102)
+++++++|.+ |+|+++|++++.++||+.++++|+ +...+.++.........+...+..+. .+..+.....++|
T Consensus 6 ~d~~~~~d~~----g~i~~~n~~~~~~~g~~~~el~G~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g 79 (442)
T TIGR02040 6 ADVTLLLDAE----GVVREVAANPHHPSFEQLSEWEGR--RWEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPSS 79 (442)
T ss_pred CcEEEEECCC----CcEEEEEECCCcccccccccCCCC--cHhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCCC
Confidence 5789999988 999999999999999999999999 65444444433333344444444433 3444444444455
Q ss_pred Ceeee
Q psy8548 81 YHEEE 85 (102)
Q Consensus 81 ~~~~~ 85 (102)
..+|+
T Consensus 80 ~~~~~ 84 (442)
T TIGR02040 80 FELPM 84 (442)
T ss_pred CccCe
Confidence 44443
No 17
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=98.38 E-value=2.6e-06 Score=58.04 Aligned_cols=76 Identities=9% Similarity=0.074 Sum_probs=49.9
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
++++++++|.+ ++|+++|+++++++|++..+++|+ +...+.+... .....+...+..+..+.........+|
T Consensus 16 ~~~gi~~~d~~----~~i~~~N~a~~~~~g~~~~~~~g~--~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~g 87 (348)
T PRK11073 16 LINSILLLDDD----LAIHYANPAAQQLLAQSSRKLFGT--PLPELLSYFS--LNIELMRESLQAGQGFTDNEVTLVIDG 87 (348)
T ss_pred CcCeEEEECCC----CeEeeEcHHHHHHhCCCHHHHcCC--CHHHHcCcch--hhHHHHHHHHHcCCcccccceEEEECC
Confidence 46789999987 899999999999999999999998 6554443321 122333444544444333333334466
Q ss_pred Ceee
Q psy8548 81 YHEE 84 (102)
Q Consensus 81 ~~~~ 84 (102)
+.+|
T Consensus 88 ~~~~ 91 (348)
T PRK11073 88 RSHI 91 (348)
T ss_pred ceEE
Confidence 5555
No 18
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=98.36 E-value=8.2e-06 Score=44.60 Aligned_cols=78 Identities=19% Similarity=0.286 Sum_probs=48.5
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-CcEEEEEEEEecCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TELKLEVIFYKKNG 80 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~~~~e~~~~~~~G 80 (102)
+.+++++|.. +.++++|++++.++|++..+++|+ ....+.++.........+...+... ............+|
T Consensus 13 ~~~~~~~d~~----~~i~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (124)
T TIGR00229 13 PDAIIVIDLE----GNILYVNPAFEEIFGYSAEELIGR--NVLELIPEEDREEVRERIERLLEGEREPVSEERRVRRKDG 86 (124)
T ss_pred CceEEEEcCC----CcEEEEchHHHHHhCCChHHhcCc--chhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeEcCCC
Confidence 4578888887 899999999999999999999987 4433333333333333344444322 22333444445566
Q ss_pred Ceeee
Q psy8548 81 YHEEE 85 (102)
Q Consensus 81 ~~~~~ 85 (102)
..+|+
T Consensus 87 ~~~~~ 91 (124)
T TIGR00229 87 SEIWV 91 (124)
T ss_pred CEEEE
Confidence 65554
No 19
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.34 E-value=2.9e-06 Score=63.50 Aligned_cols=79 Identities=14% Similarity=0.254 Sum_probs=59.6
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcc-cccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACK-FLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~-~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
+.+++++|.+ ++++++|+++++++|++.++++|+ ... ++..+.........+...+..+..+..+++..+++|
T Consensus 146 ~~~i~~~d~~----g~i~~~N~~~~~l~G~~~~e~~g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG 219 (799)
T PRK11359 146 DRPVIVLDPE----RRIVQCNRAFTEMFGYCISEASGM--QPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTG 219 (799)
T ss_pred CCcEEEEcCC----CcEEEEChhhHhhhCCCHHHHCCC--ChHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCC
Confidence 4578888887 899999999999999999999998 433 344444455555556666666666777777888888
Q ss_pred Ceeeec
Q psy8548 81 YHEEEE 86 (102)
Q Consensus 81 ~~~~~~ 86 (102)
+.+|+.
T Consensus 220 ~~~~~~ 225 (799)
T PRK11359 220 EKIWIK 225 (799)
T ss_pred CEEEEE
Confidence 877763
No 20
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.34 E-value=1.9e-06 Score=64.47 Aligned_cols=79 Identities=19% Similarity=0.218 Sum_probs=53.6
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC----CcEEEEEEEEe
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK----TELKLEVIFYK 77 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~----~~~~~e~~~~~ 77 (102)
..+++++|.+ ++++++|+++++++||+.++++|+ +...+.++.........+......+ ..+..+.+.++
T Consensus 22 ~~~i~~~d~~----g~i~~~N~~~~~l~G~s~eeliG~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 95 (799)
T PRK11359 22 MMGAVLINEN----DEVLFFNPAAEKLWGYKREEVIGN--NIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEK 95 (799)
T ss_pred cCcEEEEcCC----CeEEEEcHHHHHHhCCCHHHHcCC--CHHHhcCccccccchHHHhhhhccCCccccccceeeEEec
Confidence 3567888887 899999999999999999999998 5444444433322222333333322 23445777888
Q ss_pred cCCCeeeec
Q psy8548 78 KNGYHEEEE 86 (102)
Q Consensus 78 ~~G~~~~~~ 86 (102)
++|+.+|+.
T Consensus 96 ~dG~~~~v~ 104 (799)
T PRK11359 96 KDGSKIWTR 104 (799)
T ss_pred CCcCEEEEE
Confidence 899877764
No 21
>PRK09776 putative diguanylate cyclase; Provisional
Probab=98.31 E-value=4.4e-06 Score=64.48 Aligned_cols=79 Identities=15% Similarity=0.287 Sum_probs=57.1
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-CcEEEEEEEEecCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TELKLEVIFYKKNG 80 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~~~~e~~~~~~~G 80 (102)
..+|++.|.+ |+++++|+++++++||+.++++|+ ....+..+.........+...+... ..+..+.+..+++|
T Consensus 293 ~~~i~~~d~d----G~i~~~N~~~~~l~G~~~~el~g~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG 366 (1092)
T PRK09776 293 AIGMALVGTE----GQWLQVNKALCQFLGYSQEELRGL--TFQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYYRRDG 366 (1092)
T ss_pred CceEEEEcCC----CcEEehhHHHHHHhCCCHHHHccC--CceeccCcchhHhHHHHHHHHHcCCccceeeeeEEEcCCC
Confidence 3578889987 899999999999999999999998 5444444444333434444333322 34677888889999
Q ss_pred Ceeeec
Q psy8548 81 YHEEEE 86 (102)
Q Consensus 81 ~~~~~~ 86 (102)
+.+|+.
T Consensus 367 ~~~~~~ 372 (1092)
T PRK09776 367 EVVWAL 372 (1092)
T ss_pred CEEEEE
Confidence 888764
No 22
>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=98.00 E-value=3e-05 Score=51.94 Aligned_cols=40 Identities=15% Similarity=0.206 Sum_probs=34.6
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccc
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFL 46 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l 46 (102)
+..+|+++|.+ ++++++|++|++++|++.++.+|+ +...+
T Consensus 15 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~~~g~--~~~~~ 54 (333)
T TIGR02966 15 LPDAVVVLDEE----GQIEWCNPAAERLLGLRWPDDLGQ--RITNL 54 (333)
T ss_pred CcCcEEEECCC----CcEEEEcHHHHHHhCCChHHHcCC--cHHHH
Confidence 45789999998 899999999999999999999998 54433
No 23
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=97.98 E-value=2.1e-05 Score=41.16 Aligned_cols=31 Identities=19% Similarity=0.369 Sum_probs=24.8
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
++.+|+++| . ++|+++|+++++++||+ ..|+
T Consensus 10 ~~~~i~i~d-~----~~i~~~N~~~~~l~g~~---~~~~ 40 (64)
T PF13188_consen 10 SPDGILIID-G----GRIIYVNPAFEELFGYS---LEGE 40 (64)
T ss_dssp SSSEEEEEE-T----SBEEEE-HHHHHHHCS----HTCC
T ss_pred CccceEEEE-C----CChHHhhHHHHHHhCCC---CCCC
Confidence 467899999 7 79999999999999998 4554
No 24
>KOG1229|consensus
Probab=97.96 E-value=1.5e-06 Score=61.73 Aligned_cols=74 Identities=16% Similarity=0.188 Sum_probs=58.0
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCC-CHHHHHHHHHHHHhCCcEEEEEEEEecCCC
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDT-SEEHKTQIEKALESKTELKLEVIFYKKNGY 81 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~-~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~ 81 (102)
++|=|+|.+ ..|+|+||+|+.|+|+-+.+++|+ +...++..+. ....+..+...++.|..|++++..+++.|.
T Consensus 168 eAiEI~~dd----hViQYVNpAfE~mmG~hkgEliGk--e~adlpkkdknradlldtintcikkgke~qG~~~aRRksgd 241 (775)
T KOG1229|consen 168 EAIEICDDD----HVIQYVNPAFENMMGCHKGELIGK--EEADLPKKDKNRADLLDTINTCIKKGKEAQGEEEARRKSGD 241 (775)
T ss_pred hhheeccch----hHHHHhcHHHHhhhcchhhhhcCC--chhhccccccchhhhhhhhhHhhhcCccccchHHHhhccCC
Confidence 345566665 788999999999999999999999 6555554433 446777888889999999998888887775
Q ss_pred e
Q psy8548 82 H 82 (102)
Q Consensus 82 ~ 82 (102)
.
T Consensus 242 S 242 (775)
T KOG1229|consen 242 S 242 (775)
T ss_pred c
Confidence 3
No 25
>PF12860 PAS_7: PAS fold
Probab=97.90 E-value=0.00015 Score=42.24 Aligned_cols=35 Identities=14% Similarity=0.243 Sum_probs=31.6
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhh-cCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQI-MQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei-~g~ 39 (102)
|++||++.|.+ ++++++|++|..++|++...+ .|.
T Consensus 4 l~~Gv~v~D~~----~rl~~~N~~~~~l~~~~~~~~~~G~ 39 (115)
T PF12860_consen 4 LPQGVAVFDSD----GRLVFWNQRFRELFGLPPEMLRPGA 39 (115)
T ss_pred cCceEEEEcCC----CeEEeEcHHHHHHhCCCHHHhcCCC
Confidence 67899999998 899999999999999999887 555
No 26
>PRK09776 putative diguanylate cyclase; Provisional
Probab=97.79 E-value=0.00014 Score=56.42 Aligned_cols=79 Identities=10% Similarity=0.151 Sum_probs=51.1
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCC--CCCHHHHHHHHHHHHhCCc--EEEEEEEEe
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGP--DTSEEHKTQIEKALESKTE--LKLEVIFYK 77 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~--~~~~~~~~~i~~~l~~~~~--~~~e~~~~~ 77 (102)
+++|+++|.+ ++++++|+++++++||+.++++|+ +...+... .........+......... +..+....+
T Consensus 546 ~~~i~~~D~~----g~i~~~N~a~~~l~G~~~~e~iG~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 619 (1092)
T PRK09776 546 GEAVVCTDMA----MKVTFMNPVAEKMTGWTQEEALGV--PLLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHC 619 (1092)
T ss_pred ccEEEEECCC----CeEEEEcHHHHHHhCCCHHHHcCC--CHHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEe
Confidence 4678889987 899999999999999999999998 53333221 1111222224444433333 445666677
Q ss_pred cCCCeeeec
Q psy8548 78 KNGYHEEEE 86 (102)
Q Consensus 78 ~~G~~~~~~ 86 (102)
++|..+|+.
T Consensus 620 ~~G~~~~~~ 628 (1092)
T PRK09776 620 RSGGSYDVH 628 (1092)
T ss_pred CCCcEEEEE
Confidence 788776653
No 27
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=97.30 E-value=0.00068 Score=49.46 Aligned_cols=42 Identities=10% Similarity=0.162 Sum_probs=36.4
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG 48 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~ 48 (102)
|.++|+++|.+ |+|+++|+++++++|++.++++|+ +...+.+
T Consensus 89 m~eGVi~vD~~----G~I~~iN~aA~~Llg~~~eel~Gk--~i~eli~ 130 (520)
T PRK10820 89 LPEPVLSIDMK----GKVELANPASCQLFGQSEEKLRNH--TAAQLIN 130 (520)
T ss_pred CCCcEEEECCC----CeeeHhHHHHHHHHCcCHHHHCCC--cHHHHcC
Confidence 67899999998 999999999999999999999998 6554443
No 28
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=97.30 E-value=0.0023 Score=46.11 Aligned_cols=58 Identities=16% Similarity=0.236 Sum_probs=41.5
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK 66 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~ 66 (102)
++++++++|.+ ++++++|+++++++|++.++++|+ +...+.++. ......+...+..+
T Consensus 271 ~~~~i~~~d~~----g~i~~~N~~~~~l~g~~~~~~~g~--~~~~~~~~~--~~~~~~~~~~~~~~ 328 (607)
T PRK11360 271 IADGVIAIDRQ----GKITTMNPAAEVITGLQRHELVGK--PYSELFPPN--TPFASPLLDTLEHG 328 (607)
T ss_pred ccCeEEEEcCC----CCEEEECHHHHHHhCCChHHhcCC--cHHHHcCCc--hhHHHHHHHHHhcC
Confidence 35688999987 899999999999999999999998 655454432 22233444444443
No 29
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.22 E-value=0.0012 Score=37.74 Aligned_cols=74 Identities=14% Similarity=0.180 Sum_probs=42.0
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNG 80 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G 80 (102)
|+.+++++|.+ ++|++.|++..+++++.... +|+ +...+.++.. ......+.+.+..+..-..+... ..+|
T Consensus 8 ~~~~i~~vD~~----~~I~~~n~~a~~~f~~~~~~-iGr--~l~~~~~~~~-~~~l~~~i~~~~~~~~~~~~~~~-~~~~ 78 (106)
T PF13596_consen 8 MPIGIIFVDRN----LRIRYFNPAAARLFNLSPSD-IGR--PLFDIHPPLS-YPNLKKIIEQVRSGKEEEFEIVI-PNGG 78 (106)
T ss_dssp SSSEEEEEETT----SBEEEE-SCGC-SS---GGG-TTS--BCCCSS-HHH-HHHHHHHHHHHHTTSBSEEEEEE-EETT
T ss_pred CCCCEEEEcCC----CeEEEeChhHhhhcCCChHH-CCC--CHHHcCCccc-hHHHHHHHHHHHcCCCceEEEEe-cCCC
Confidence 56789999998 89999999999999976544 788 6555554422 22333444555556543333333 2455
Q ss_pred Cee
Q psy8548 81 YHE 83 (102)
Q Consensus 81 ~~~ 83 (102)
+.+
T Consensus 79 ~~~ 81 (106)
T PF13596_consen 79 RWY 81 (106)
T ss_dssp EEE
T ss_pred EEE
Confidence 543
No 30
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=97.19 E-value=0.0025 Score=45.00 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=32.4
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
++++|+++|.+ |+|+++|+++++++|++.+++.|+
T Consensus 107 ~~~~i~~~d~~----g~i~~~N~~a~~l~g~~~~~~~g~ 141 (430)
T PRK11006 107 LPDAVVLTTEE----GNIFWCNGLAQQLLGFRWPEDNGQ 141 (430)
T ss_pred CCCeEEEEcCC----CceeHHHHHHHHHhCCCChHhCCC
Confidence 46789999987 899999999999999999999988
No 31
>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=97.18 E-value=0.0026 Score=30.17 Aligned_cols=34 Identities=18% Similarity=0.311 Sum_probs=29.0
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
+.++++++.. +.++++|+.+..++|++..++.+.
T Consensus 11 ~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 44 (67)
T smart00091 11 PDGIFVLDLD----GRILYANPAAEELLGYSPEELIGK 44 (67)
T ss_pred CceEEEEcCC----CeEEEECHHHHHHhCCCHHHHcCC
Confidence 4567778876 899999999999999999888876
No 32
>PRK13560 hypothetical protein; Provisional
Probab=97.06 E-value=0.0025 Score=47.77 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=29.5
Q ss_pred CceEEEEeCCCCCCCCEEEe-cHHHHHhhCCChhhhcCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYC-SDGFCELSGFARAQIMQK 39 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~-N~~~~~i~G~~~~ei~g~ 39 (102)
+.+|+++|.+ +.++++ |+++++++||+.++++|+
T Consensus 342 ~~~i~~~d~~----g~i~~~nn~~~~~~~G~~~~e~~g~ 376 (807)
T PRK13560 342 PIAAIGLDAD----GNICFVNNNAAERMLGWSAAEVMGK 376 (807)
T ss_pred cccEEEEcCC----CCEEEecCHHHHHHhCCCHHHHcCC
Confidence 4678899987 899987 678888999999999998
No 33
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=97.02 E-value=0.012 Score=34.65 Aligned_cols=79 Identities=16% Similarity=0.141 Sum_probs=48.2
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHH-HHHH-HHHHHHhCCcEEEEEEEEecC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEE-HKTQ-IEKALESKTELKLEVIFYKKN 79 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~-~~~~-i~~~l~~~~~~~~e~~~~~~~ 79 (102)
..++++.|.. +.++++|++++.++|++..+.++. ....+........ .... ..........+..+......+
T Consensus 122 ~~~~~~~d~~----~~~~~~n~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (232)
T COG2202 122 PDGIWVLDED----GRILYANPAAEELLGYSPEEELGR--GLSDLIHPEDEERRELELARALAEGRGGPLEIEYRVRRKD 195 (232)
T ss_pred CceEEEEeCC----CCEEEeCHHHHHHhCCChHHhcCC--ChhheEecCCCchhhHHHHHHhhccCCCCcceEEEEEecC
Confidence 3567788876 899999999999999998877766 3332222211111 1111 111222334466777878888
Q ss_pred CCe-eeec
Q psy8548 80 GYH-EEEE 86 (102)
Q Consensus 80 G~~-~~~~ 86 (102)
|.. .+..
T Consensus 196 g~~~~~~~ 203 (232)
T COG2202 196 GERVRWIL 203 (232)
T ss_pred CCEEEEEE
Confidence 885 4443
No 34
>KOG3558|consensus
Probab=96.96 E-value=0.00076 Score=50.22 Aligned_cols=71 Identities=15% Similarity=0.221 Sum_probs=57.1
Q ss_pred CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecch
Q psy8548 16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEEE 88 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~~ 88 (102)
-+|+||.+.+..++||..++++|+ -+-.+.+..+...+.+.....+..|...++-++...++|-.+|+.+.
T Consensus 284 mkityCedRisdlm~y~PeeLvGr--S~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTq 354 (768)
T KOG3558|consen 284 MKITYCEDRISDLMDYEPEELVGR--SCYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQ 354 (768)
T ss_pred eeEEEEchhHHHHhcCCHHHhhch--hHHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEee
Confidence 799999999999999999999999 44334444455556666677788888888888888889998898875
No 35
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=96.91 E-value=0.005 Score=45.94 Aligned_cols=41 Identities=12% Similarity=0.094 Sum_probs=34.9
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccccc
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLY 47 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~ 47 (102)
++++|+++|.+ |+|+++|+++++++|++..+++|+ +...+.
T Consensus 212 ~~~gVl~vD~~----G~I~~~N~aa~~llg~s~~~l~G~--~i~~l~ 252 (638)
T PRK11388 212 MDDGVIAWDEQ----GNLQFLNAQAARLLRLDATASQGR--AITELL 252 (638)
T ss_pred cCCcEEEECCC----CeEehhhHHHHHHhCcCHHHHCCC--cHHHHh
Confidence 35789999998 999999999999999999999998 544333
No 36
>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=96.55 E-value=0.021 Score=35.25 Aligned_cols=80 Identities=8% Similarity=0.071 Sum_probs=48.2
Q ss_pred eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548 4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE 83 (102)
Q Consensus 4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~ 83 (102)
+|+-.+.. ++ -.++|.|++...|++++-+++.+- +.+.-..+.......+.+.+...+|-.....=....+.|+++
T Consensus 43 ailsh~~~-~d-P~f~yaN~aaL~l~e~~w~el~~l--Psr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRiss~Grrf 118 (148)
T PF08670_consen 43 AILSHGTK-AD-PIFIYANQAALDLFETTWDELVGL--PSRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRISSTGRRF 118 (148)
T ss_pred EEEEcCCC-CC-CEEEehhHHHHHHhcCCHHHHhcC--cHhhccChhhHHHHHHHHHHHHHhCCccCCCeEEEcCCCCeE
Confidence 34444433 23 689999999999999999999977 666444443344444444444444421111113346778887
Q ss_pred eecc
Q psy8548 84 EEEE 87 (102)
Q Consensus 84 ~~~~ 87 (102)
+++.
T Consensus 119 ~ie~ 122 (148)
T PF08670_consen 119 RIER 122 (148)
T ss_pred EEec
Confidence 7654
No 37
>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=96.07 E-value=0.07 Score=31.95 Aligned_cols=59 Identities=10% Similarity=0.026 Sum_probs=43.0
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCC-CHHHHHHHHHHHHhC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDT-SEEHKTQIEKALESK 66 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~-~~~~~~~i~~~l~~~ 66 (102)
+-|++-+|.+ |.|+..|.+=..++|++++.++|+ +...=..|+. ...+...+...+.++
T Consensus 26 pFGvI~lD~~----G~V~~YN~aE~~~sg~~p~~vlGr--~FF~eVAPC~~~~~f~gRF~~g~~~g 85 (124)
T TIGR02373 26 PFGAIQLDGS----GVILRYNAAEGRITGRDPERVIGR--NFFKEVAPCTDIPEFSGRFMEGVASG 85 (124)
T ss_pred CcceEEECCC----CEEEEEecchhhhcCCChhhhhch--hhhhhcccccCCHHHHHHHHhhhhcC
Confidence 4578888887 999999999999999999999999 5332233444 344555666655555
No 38
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=95.67 E-value=0.014 Score=42.30 Aligned_cols=35 Identities=11% Similarity=0.115 Sum_probs=30.8
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCCh--hhhcCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFAR--AQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~--~ei~g~ 39 (102)
|.++++++|.+ |+|+++|+++++++|++. .+++|+
T Consensus 231 ~~egii~~D~~----g~I~~~N~~a~~ll~~~~~~~~~~g~ 267 (545)
T PRK15053 231 VYEGLIAVDPH----GYITAINRNARKMLGLSSPGRQWLGK 267 (545)
T ss_pred hCceEEEECCC----CeEEeecHHHHHHhCCCCcchhhcCC
Confidence 46899999998 999999999999999865 468887
No 39
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=95.05 E-value=0.072 Score=39.27 Aligned_cols=40 Identities=13% Similarity=0.342 Sum_probs=34.8
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccc
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFL 46 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l 46 (102)
+.++++++|.. |+++++|++...++|.+.++++|+ +...+
T Consensus 126 ~~~~l~vvD~~----G~~i~~N~~~~~~~gl~~e~~~gk--~~~~v 165 (560)
T COG3829 126 IDDGLLVVDED----GIIIYYNKAYAKLLGLSPEEVLGK--HLLDV 165 (560)
T ss_pred ccCceEEEcCC----CcEEEEcHHHHHHhCCCHHHHcCC--cHHHH
Confidence 35788999998 999999999999999999999999 64444
No 40
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=94.92 E-value=0.14 Score=35.51 Aligned_cols=59 Identities=12% Similarity=0.116 Sum_probs=39.6
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcE
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTEL 69 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~ 69 (102)
..+++.|.+ +.|.|+|++++.++|.+...+.+. ....+.+. .......+.+...++..+
T Consensus 18 ~pVl~vd~~----~~i~yaN~aAe~~~~~Sa~~L~~~--~l~~l~~~--gs~ll~ll~q~~~~~~~~ 76 (363)
T COG3852 18 NPVLLVDDE----LAIHYANPAAEQLLAVSARRLAGT--RLSELLPF--GSLLLSLLDQVLERGQPV 76 (363)
T ss_pred CceEEEcCC----CcEEecCHHHHHHHHHHHHHHhcC--ChHHHcCC--CcHHHHHHHHHHHhcCCc
Confidence 356777776 899999999999999999998887 43333332 123344455555555443
No 41
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=94.44 E-value=0.049 Score=39.22 Aligned_cols=35 Identities=6% Similarity=0.121 Sum_probs=28.3
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCCh---hhhcCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFAR---AQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~---~ei~g~ 39 (102)
|.++|+++|.+ ++|+++|+++++++|++. .+.+|+
T Consensus 230 ~~~gIi~~D~~----g~I~~~N~~a~~llg~~~~~~~~~~~~ 267 (542)
T PRK11086 230 IKEGVIAVDDR----GEVTLINDEAKRLFNYKKGLEDDPLGT 267 (542)
T ss_pred hcCcEEEECCC----CeEEEEhHHHHHHhCCCcCCcccccCC
Confidence 46799999998 899999999999998753 345554
No 42
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=94.41 E-value=0.06 Score=37.94 Aligned_cols=36 Identities=8% Similarity=0.229 Sum_probs=33.5
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKG 40 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~ 40 (102)
|.+|++.+|.. |.|+.+|....+++|.+.++++|++
T Consensus 120 MtDGViATdRr----G~iI~iN~~A~k~L~~~~E~~~~~~ 155 (459)
T COG5002 120 MTDGVIATDRR----GKIILINKPALKMLGVSKEDALGRS 155 (459)
T ss_pred HcCceEeecCC----CcEEEeccHHHHHhCcCHHHHhccc
Confidence 67899999988 9999999999999999999999983
No 43
>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=94.06 E-value=0.071 Score=37.57 Aligned_cols=34 Identities=15% Similarity=0.127 Sum_probs=28.4
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
+.+++++|.+ ++++++|++|+.++|+...+..+.
T Consensus 140 ~~~i~~~d~~----~~i~~~N~~~~~~~g~~~~~~~~~ 173 (494)
T TIGR02938 140 PVAFVLLDPT----GRVILDNQEYKKLATDLRVKEPAH 173 (494)
T ss_pred cceEEEEcCC----CCEEEechhHHHhhchhhhhHHHH
Confidence 4578899987 899999999999999887766543
No 44
>KOG3559|consensus
Probab=93.22 E-value=0.07 Score=38.11 Aligned_cols=31 Identities=10% Similarity=0.401 Sum_probs=26.6
Q ss_pred EEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 5 FVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 5 i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
+++...+ ..++|......+++||...+++++
T Consensus 228 mfraslD----lkliF~D~rv~qltgYepqdliek 258 (598)
T KOG3559|consen 228 MFRASLD----LKLIFLDSRVHQLTGYEPQDLIEK 258 (598)
T ss_pred EEEeecc----eEEEeehhhHHHhhCCCchhhhhH
Confidence 3455555 799999999999999999999988
No 45
>KOG3560|consensus
Probab=92.81 E-value=0.46 Score=35.29 Aligned_cols=70 Identities=9% Similarity=0.013 Sum_probs=51.6
Q ss_pred CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCeeeecc
Q psy8548 16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHEEEEE 87 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~~~~~ 87 (102)
+..+.+......++||...|+.|.+ .+.+++-. +-.-...+-.+.++.|++-..-++..+++|++.||-.
T Consensus 293 fa~vs~Dak~k~~lgy~eaEL~~m~-gY~lvH~~-D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqs 362 (712)
T KOG3560|consen 293 FALVSMDAKVKATLGYCEAELHGMP-GYNLVHVE-DKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQS 362 (712)
T ss_pred cceeccchhhhhhhccchhhccCCC-ccceeehh-hhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeec
Confidence 6778899999999999999999753 45554432 2222334445678888888888888999999999854
No 46
>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=92.61 E-value=0.33 Score=28.24 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=31.7
Q ss_pred eEEEEeCCCCCCCCEEEecHHHHHhhCCC---hhhhcCCCCCcccccCC
Q psy8548 4 NFVLGNAQVPSLYPIVYCSDGFCELSGFA---RAQIMQKGCACKFLYGP 49 (102)
Q Consensus 4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~---~~ei~g~~~~~~~l~~~ 49 (102)
..+.+|.. + ++|+.++.+...++|.+ .++++|+ +...+.+.
T Consensus 17 ~LLa~d~~--~-~~I~~~S~N~~~~lg~~~~~~~~llG~--~l~~ll~~ 60 (110)
T PF08446_consen 17 ALLALDPD--D-LRIVQASENIAELLGIPPELPEELLGR--PLSELLGA 60 (110)
T ss_dssp EEEEEETT--T-TBEEEEETTHHHHHSS----HHHHTTC--BHHHHSCC
T ss_pred EEEEEECC--C-CEEEEEcCCHHHHhCCccccchhhccc--CHHHHhCH
Confidence 34567764 4 89999999999999999 9999999 65555543
No 47
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=92.51 E-value=0.26 Score=35.14 Aligned_cols=35 Identities=9% Similarity=0.142 Sum_probs=31.7
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
|++.++.+|.. |.+..+|++++.++|.+.+.+.|.
T Consensus 89 l~~pVlsvd~k----g~v~~aNpAa~~l~~~~~~~~~g~ 123 (511)
T COG3283 89 LPEPVLSVDMK----GKVDMANPAACQLFGRKEDRLRGH 123 (511)
T ss_pred CCCceEEeccc----CceeecCHHHHHHhCCChhhhcCc
Confidence 56778888887 899999999999999999999987
No 48
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=91.77 E-value=0.21 Score=36.77 Aligned_cols=42 Identities=10% Similarity=0.127 Sum_probs=33.9
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChh--hhcCCCCCcccccCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARA--QIMQKGCACKFLYGP 49 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~--ei~g~~~~~~~l~~~ 49 (102)
.+|++.+|.. |.|+.+|.+.++|+|+... +++|+ ....+.+|
T Consensus 225 ~EGviAvd~~----G~It~~N~~A~~ll~~~~~~~~~ig~--~i~~v~~p 268 (537)
T COG3290 225 KEGVIAVDKK----GVITLINQAAQKLLGLRQPSGDPIGR--SIVEVLPP 268 (537)
T ss_pred hceEEEECCC----CeEeehhHHHHHHhcccCcCcccccc--cceEeecc
Confidence 5689999987 9999999999999998775 68887 55544443
No 49
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=91.26 E-value=1.1 Score=35.88 Aligned_cols=31 Identities=10% Similarity=-0.047 Sum_probs=26.5
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhh
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQ 35 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~e 35 (102)
|+.+|+++|.+ |+|+++|++++.++|++...
T Consensus 585 ~~~~i~~~d~~----g~i~~~N~~~~~~~g~~~~~ 615 (1197)
T PRK09959 585 LPNPTYVVNWQ----GNVISHNSAFEHYFTADYYK 615 (1197)
T ss_pred CCCcEEEEcCC----CcEEEehHHHHHHhCccccc
Confidence 46789999987 99999999999999976543
No 50
>KOG3561|consensus
Probab=91.15 E-value=0.26 Score=38.04 Aligned_cols=40 Identities=20% Similarity=0.350 Sum_probs=32.2
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCccccc
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLY 47 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~ 47 (102)
..+|++.-+ |+|+||+.....++||..++++|+. .+.+++
T Consensus 106 GF~fvV~cd----G~IvyVSeSVT~~L~y~QsDL~~qS-ly~ilh 145 (803)
T KOG3561|consen 106 GFLFVVNCD----GRIVYVSESVTSVLGYLQSDLMGQS-LYDILH 145 (803)
T ss_pred CeEEEEecC----ceEEEEecchHHhhCcCHHHHhcch-HHHhcC
Confidence 345677776 8999999999999999999999984 344443
No 51
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=90.26 E-value=0.37 Score=33.58 Aligned_cols=71 Identities=13% Similarity=0.178 Sum_probs=44.1
Q ss_pred eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548 4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE 83 (102)
Q Consensus 4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~ 83 (102)
++++-.+. + .+.+|+|..|...+||+.++++.. ..+++..+. ..|..-.... ......+.+.+++++|...
T Consensus 299 mlfVYs~k--~-qRllFAN~~fk~wtGy~~edFl~~--~~dIV~eGl---~qW~~dL~~~-s~~E~~grlviKTK~~g~i 369 (401)
T PF06785_consen 299 MLFVYSPK--S-QRLLFANSQFKTWTGYSSEDFLKD--FSDIVQEGL---AQWETDLQLL-SRQERSGRLVIKTKNGGNI 369 (401)
T ss_pred eEEEecch--h-hHHHHhHHHHHHHhccCHHHHHhc--chHHHHhhH---HHHHHHHHhh-hhhhhhceEEEEecCCCce
Confidence 45566665 3 799999999999999999999865 445444331 1222111122 2223356777778877644
No 52
>KOG3558|consensus
Probab=89.79 E-value=0.61 Score=35.51 Aligned_cols=50 Identities=14% Similarity=0.119 Sum_probs=37.2
Q ss_pred ceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHH
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQ 58 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~ 58 (102)
..|++++.+ |.++|++......+|++.=|+.|. ..+.+.++.+...+...
T Consensus 130 GFVm~l~~d----G~~lYiSEtVS~yLGLSQvELTG~--SvFDfiHP~DheE~~eq 179 (768)
T KOG3558|consen 130 GFVMALTQD----GDFLYISETVSIYLGLSQVELTGS--SVFDFIHPCDHEEIAEQ 179 (768)
T ss_pred ceEEEEccC----CCEEEEechhHhhhCccceeeecc--hhhhccCccCHHHHHHH
Confidence 345677776 999999999999999999999998 44445555554444433
No 53
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=87.46 E-value=4.5 Score=24.30 Aligned_cols=75 Identities=12% Similarity=0.149 Sum_probs=47.4
Q ss_pred eEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhCCcEEEEEEEEecCCCee
Q psy8548 4 NFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESKTELKLEVIFYKKNGYHE 83 (102)
Q Consensus 4 ~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~~~~~~e~~~~~~~G~~~ 83 (102)
.++|++...+...++..+=...+.++|+. +-|+ ....+..+.........+...+...............+|...
T Consensus 39 ~i~ile~~~~~~~r~RLaGt~i~~~~G~d---~tG~--~~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~ 113 (137)
T PF07310_consen 39 HIFILEVDDPGDFRYRLAGTRIVELFGRD---LTGR--RLSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYL 113 (137)
T ss_pred CeEEEEEeCCCceEEEEecHHHHHHhCCC---CCCC--CHHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCee
Confidence 35666654332256667888889999874 4455 544455555555566666777777777666666666666653
No 54
>KOG3560|consensus
Probab=84.30 E-value=1.3 Score=33.01 Aligned_cols=43 Identities=19% Similarity=0.340 Sum_probs=33.7
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG 48 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~ 48 (102)
||..++++..+ |.|.|++......+||...+++.++ .+++++.
T Consensus 120 LnGF~lVvt~e----g~ifyAS~tIedYLGFhQSDV~HQs-VYdlIHs 162 (712)
T KOG3560|consen 120 LNGFALVVTAE----GEIFYASATIEDYLGFHQSDVMHQS-VYDLIHS 162 (712)
T ss_pred cCCeEEEEecC----ceEEEehhhHHhhhcccccchhhhh-HHHHhhh
Confidence 35556677776 8999999999999999999999883 3444444
No 55
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=83.16 E-value=1.9 Score=32.79 Aligned_cols=34 Identities=9% Similarity=0.008 Sum_probs=30.6
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
..+++..|.+ |++.-+|++.++|+|.+..+++|+
T Consensus 380 taGVi~~d~~----g~i~t~N~~ae~~l~~~~~~~~G~ 413 (712)
T COG5000 380 TAGVIGFDNR----GCITTVNPSAEQILGKPFDQLLGQ 413 (712)
T ss_pred ceeEEEEcCC----CeeEeecchHHHHhcCChhHhhcc
Confidence 4578888887 899999999999999999999998
No 56
>KOG3753|consensus
Probab=73.93 E-value=12 Score=29.87 Aligned_cols=71 Identities=14% Similarity=0.139 Sum_probs=48.4
Q ss_pred CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHHhC-Cc--EEEEEEEEecCCCeeeecch
Q psy8548 16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALESK-TE--LKLEVIFYKKNGYHEEEEEE 88 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~~~-~~--~~~e~~~~~~~G~~~~~~~~ 88 (102)
..++.|..+...++||=..++||+. ...++++. +...+.+.-...++.+ .. ....+++..++|..+...++
T Consensus 341 Clf~hVDeaAVp~LGyLPqDLIG~s-il~f~H~e-Dr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTe 414 (1114)
T KOG3753|consen 341 CLFQHVDEAAVPLLGYLPQDLIGTS-ILAFVHPE-DRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTE 414 (1114)
T ss_pred ceeeecchhhhhhhccCchhhhccc-hhhhhcCC-chHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEech
Confidence 7788899999999999999999994 44555543 3344443334444433 23 33577888889988777664
No 57
>KOG3559|consensus
Probab=64.81 E-value=5.3 Score=28.98 Aligned_cols=42 Identities=10% Similarity=0.183 Sum_probs=32.9
Q ss_pred CceEEEEeCCCCCCCCEEEecHHHHHhhCCChhhhcCCCCCcccccC
Q psy8548 2 NSNFVLGNAQVPSLYPIVYCSDGFCELSGFARAQIMQKGCACKFLYG 48 (102)
Q Consensus 2 ~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~ 48 (102)
+..|++++++ |.|.|++....-.+|++.=|+-|.. ...++++
T Consensus 89 DGF~fvva~d----GkimYISETaSvhLGLSQVElTGNs-i~eYIH~ 130 (598)
T KOG3559|consen 89 DGFIFVVAPD----GKIMYISETASVHLGLSQVELTGNS-IYEYIHP 130 (598)
T ss_pred cceEEEEeCC----CCEEEEecceeeeecceeeEeecch-hhhhhcc
Confidence 4567788988 9999999999999999998888873 3344443
No 58
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=49.76 E-value=28 Score=27.81 Aligned_cols=29 Identities=10% Similarity=-0.040 Sum_probs=23.9
Q ss_pred CCceEEEEeCCCCCCCCEEEecHHHHHhhCCC
Q psy8548 1 MNSNFVLGNAQVPSLYPIVYCSDGFCELSGFA 32 (102)
Q Consensus 1 ~~~~i~i~d~~~~~~~~i~~~N~~~~~i~G~~ 32 (102)
++.|+++.|.. + ++++++|+++..++|..
T Consensus 352 lp~Gilv~D~~--~-~~Ii~~N~aA~~ll~~~ 380 (894)
T PRK10618 352 LPLGLLVYDFE--S-NRTVISNKIADHLLPHL 380 (894)
T ss_pred CCceEEEEECC--C-CeEEEEhHHHHHHhCcc
Confidence 45789999965 3 89999999999999853
No 59
>KOG3753|consensus
Probab=49.73 E-value=20 Score=28.67 Aligned_cols=24 Identities=21% Similarity=0.239 Sum_probs=22.7
Q ss_pred CCEEEecHHHHHhhCCChhhhcCC
Q psy8548 16 YPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
|+|+|+.+.+..++|+.++-+.+.
T Consensus 202 G~iLyis~q~a~ilg~krDv~s~a 225 (1114)
T KOG3753|consen 202 GRILYISEQAALILGCKRDVLSSA 225 (1114)
T ss_pred CcEEEeechhhhhccCchhhhccc
Confidence 899999999999999999988876
No 60
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=49.67 E-value=3.6 Score=27.21 Aligned_cols=6 Identities=0% Similarity=0.218 Sum_probs=2.9
Q ss_pred hhhcCC
Q psy8548 34 AQIMQK 39 (102)
Q Consensus 34 ~ei~g~ 39 (102)
+.++|.
T Consensus 110 kavLga 115 (238)
T PF02084_consen 110 KAVLGA 115 (238)
T ss_pred HHHhcc
Confidence 345554
No 61
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=46.48 E-value=31 Score=27.41 Aligned_cols=32 Identities=9% Similarity=-0.004 Sum_probs=25.2
Q ss_pred CCceEEEEe-CCCCCCCCEEEecHHHHHhhCCChhhhcCC
Q psy8548 1 MNSNFVLGN-AQVPSLYPIVYCSDGFCELSGFARAQIMQK 39 (102)
Q Consensus 1 ~~~~i~i~d-~~~~~~~~i~~~N~~~~~i~G~~~~ei~g~ 39 (102)
|+-+++++| .+ +.|+|+|+.|..++| .+ ++|+
T Consensus 111 ~p~gi~~~~~~~----~~i~W~N~~~~~~~~--~~-~~g~ 143 (838)
T PRK14538 111 LPIGIVLIDISS----KEIQWLNPYANFILK--NP-EINT 143 (838)
T ss_pred CCceEEEEeCCC----CEEEEECHHHHHHhC--cc-ccCC
Confidence 455788888 45 899999999999887 22 7777
No 62
>KOG3561|consensus
Probab=34.17 E-value=40 Score=26.73 Aligned_cols=70 Identities=13% Similarity=0.180 Sum_probs=44.2
Q ss_pred CCEEEecHHHHHhhCCChhhhcCCCCCcccccCCCCCHHHHHHHHHHHH-hCCcEEEEEEEEecCCCeeeecc
Q psy8548 16 YPIVYCSDGFCELSGFARAQIMQKGCACKFLYGPDTSEEHKTQIEKALE-SKTELKLEVIFYKKNGYHEEEEE 87 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~g~~~~~~~l~~~~~~~~~~~~i~~~l~-~~~~~~~e~~~~~~~G~~~~~~~ 87 (102)
|.++++......+.||...+++|+ ...-..+..+.......+..... .......-++.+.++|...+...
T Consensus 382 g~~~~~dqr~~~i~~~~~~~~~g~--ss~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~~~~ 452 (803)
T KOG3561|consen 382 GSFTFVDQRASAILGYQPQELLGR--SSYESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIPNKS 452 (803)
T ss_pred CceeccccccccccccCchhhcCc--ccccccCccccchhhchHHHHHHhcccccccccccccCCCCcccccc
Confidence 899999999999999999999998 44333333333333333333332 22233445666777887766543
No 63
>PRK08402 replication factor A; Reviewed
Probab=26.25 E-value=2.2e+02 Score=20.33 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=19.2
Q ss_pred CCEEEecHHHHHhhCCChhhhc
Q psy8548 16 YPIVYCSDGFCELSGFARAQIM 37 (102)
Q Consensus 16 ~~i~~~N~~~~~i~G~~~~ei~ 37 (102)
-.++..+.....++|.+.+++.
T Consensus 258 ~~vt~f~e~ae~llG~sa~el~ 279 (355)
T PRK08402 258 IRVTLFGDDAAELLGVEPEEIA 279 (355)
T ss_pred EEEEEecHHHHHHhCCCHHHHH
Confidence 4677889999999999999886
No 64
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=20.49 E-value=1.2e+02 Score=19.13 Aligned_cols=17 Identities=12% Similarity=0.253 Sum_probs=12.5
Q ss_pred ceEEEEeCCCCCCCCEEEecH
Q psy8548 3 SNFVLGNAQVPSLYPIVYCSD 23 (102)
Q Consensus 3 ~~i~i~d~~~~~~~~i~~~N~ 23 (102)
++|+++|.+ |.++|+-.
T Consensus 126 SaiiVlDK~----G~V~F~k~ 142 (160)
T PF09695_consen 126 SAIIVLDKQ----GKVQFVKE 142 (160)
T ss_pred ceEEEEcCC----ccEEEEEC
Confidence 567788887 78888643
Done!