Query 043549
Match_columns 162
No_of_seqs 147 out of 1499
Neff 10.2
Searched_HMMs 46136
Date Fri Mar 29 06:08:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043549hhsearch_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 99.5 1.3E-13 2.8E-18 85.2 8.0 82 1-85 23-104 (104)
2 PRK13559 hypothetical protein; 99.2 3.9E-10 8.4E-15 84.8 13.3 88 1-91 78-165 (361)
3 PF08448 PAS_4: PAS fold; Int 99.2 6.2E-11 1.3E-15 73.9 6.3 83 2-88 28-110 (110)
4 PRK13557 histidine kinase; Pro 99.2 9.2E-10 2E-14 86.6 13.0 89 1-92 65-153 (540)
5 PRK13558 bacterio-opsin activa 99.1 1.8E-09 3.8E-14 87.5 12.1 91 1-94 183-273 (665)
6 PRK10060 RNase II stability mo 99.1 5.3E-10 1.2E-14 90.5 8.6 110 1-114 143-259 (663)
7 PRK11091 aerobic respiration c 99.0 2.4E-09 5.1E-14 88.2 8.4 90 1-93 187-276 (779)
8 PRK13560 hypothetical protein; 99.0 3.5E-09 7.6E-14 87.0 9.1 92 1-93 506-598 (807)
9 PF08447 PAS_3: PAS fold; Int 98.9 3E-09 6.6E-14 64.3 4.8 79 1-80 11-91 (91)
10 PRK09776 putative diguanylate 98.9 8.9E-09 1.9E-13 87.4 9.2 109 1-112 568-685 (1092)
11 PF00989 PAS: PAS fold; Inter 98.9 6.3E-09 1.4E-13 65.0 5.5 80 1-83 33-113 (113)
12 TIGR02938 nifL_nitrog nitrogen 98.8 5.1E-09 1.1E-13 81.3 5.8 89 1-92 36-124 (494)
13 PRK13560 hypothetical protein; 98.7 5.4E-08 1.2E-12 80.1 8.7 90 1-93 236-327 (807)
14 KOG0501 K+-channel KCNQ [Inorg 98.7 6.6E-08 1.4E-12 75.2 7.8 88 1-89 52-139 (971)
15 PRK11359 cyclic-di-GMP phospho 98.7 8.5E-08 1.8E-12 79.1 7.6 88 1-91 168-256 (799)
16 PRK09776 putative diguanylate 98.6 4.9E-08 1.1E-12 83.0 6.1 92 1-95 315-407 (1092)
17 PF14598 PAS_11: PAS domain; P 98.5 1.1E-06 2.3E-11 55.5 8.0 82 2-86 26-109 (111)
18 TIGR00229 sensory_box PAS doma 98.4 1.2E-06 2.5E-11 53.0 6.9 86 1-90 35-121 (124)
19 TIGR02040 PpsR-CrtJ transcript 98.4 1.7E-06 3.7E-11 67.1 8.3 83 1-90 284-368 (442)
20 cd00130 PAS PAS domain; PAS mo 98.3 1E-05 2.2E-10 46.5 9.1 80 1-83 24-103 (103)
21 TIGR02040 PpsR-CrtJ transcript 98.0 1.3E-05 2.9E-10 62.1 6.1 82 1-89 28-110 (442)
22 PRK11359 cyclic-di-GMP phospho 98.0 1.5E-05 3.4E-10 65.9 6.8 88 1-93 44-135 (799)
23 PRK11360 sensory histidine kin 98.0 0.00011 2.5E-09 58.4 11.1 87 1-93 294-381 (607)
24 PRK11073 glnL nitrogen regulat 97.8 8.8E-05 1.9E-09 55.5 6.8 82 1-92 39-120 (348)
25 smart00086 PAC Motif C-termina 97.6 0.00082 1.8E-08 31.8 7.1 41 46-86 3-43 (43)
26 PF13596 PAS_10: PAS domain; P 97.5 0.001 2.2E-08 41.2 7.8 71 7-84 36-106 (106)
27 COG5002 VicK Signal transducti 97.5 0.0018 3.9E-08 48.4 9.9 86 1-96 143-228 (459)
28 TIGR02966 phoR_proteo phosphat 97.3 0.003 6.4E-08 46.5 8.8 76 1-92 38-113 (333)
29 KOG1229 3'5'-cyclic nucleotide 96.8 0.00067 1.5E-08 51.9 2.1 76 1-79 189-265 (775)
30 TIGR02938 nifL_nitrog nitrogen 96.7 0.00071 1.5E-08 52.6 1.0 47 48-94 203-259 (494)
31 KOG3558 Hypoxia-inducible fact 96.6 0.0018 4E-08 51.9 3.1 83 1-86 296-379 (768)
32 PF12860 PAS_7: PAS fold 96.5 0.013 2.8E-07 36.7 6.0 34 50-90 81-114 (115)
33 COG2461 Uncharacterized conser 95.4 0.031 6.6E-07 42.4 4.6 79 8-93 327-405 (409)
34 COG5000 NtrY Signal transducti 95.1 0.1 2.2E-06 42.1 6.7 63 50-135 443-506 (712)
35 COG2202 AtoS FOG: PAS/PAC doma 94.7 0.27 5.8E-06 31.9 7.3 84 1-88 144-230 (232)
36 KOG3560 Aryl-hydrocarbon recep 94.5 0.16 3.4E-06 40.3 6.2 81 1-85 305-385 (712)
37 PF07310 PAS_5: PAS domain; I 94.0 0.39 8.5E-06 31.2 6.6 70 8-80 67-136 (137)
38 PRK11086 sensory histidine kin 92.7 0.93 2E-05 36.0 8.3 37 53-92 296-332 (542)
39 PF08348 PAS_6: YheO-like PAS 92.1 0.87 1.9E-05 28.9 6.0 47 41-89 66-112 (118)
40 PRK11006 phoR phosphate regulo 92.0 0.95 2.1E-05 35.1 7.3 74 1-92 130-203 (430)
41 COG3829 RocR Transcriptional r 91.7 0.042 9E-07 43.6 -0.5 148 1-160 149-308 (560)
42 PF08670 MEKHLA: MEKHLA domain 91.5 1.3 2.8E-05 29.4 6.4 79 1-82 65-144 (148)
43 PRK10820 DNA-binding transcrip 89.1 1.1 2.4E-05 36.0 5.4 75 1-88 112-190 (520)
44 KOG3559 Transcriptional regula 78.7 2 4.3E-05 33.2 2.5 69 1-72 247-315 (598)
45 PF09884 DUF2111: Uncharacteri 78.3 9.2 0.0002 22.6 4.7 47 33-84 37-83 (84)
46 PRK09959 hybrid sensory histid 76.9 22 0.00048 31.6 8.8 23 70-92 675-697 (1197)
47 PRK11388 DNA-binding transcrip 74.2 9.2 0.0002 31.6 5.5 77 1-88 235-311 (638)
48 COG3852 NtrB Signal transducti 67.8 33 0.00072 26.0 6.5 89 29-134 62-151 (363)
49 COG3290 CitA Signal transducti 66.2 68 0.0015 26.1 8.3 74 2-89 248-323 (537)
50 PRK10841 hybrid sensory kinase 52.3 70 0.0015 28.0 6.9 19 75-93 415-433 (924)
51 KOG3753 Circadian clock protei 50.8 39 0.00085 29.2 4.9 65 1-68 353-420 (1114)
52 PF10934 DUF2634: Protein of u 45.4 65 0.0014 20.2 4.4 59 3-67 50-109 (112)
53 COG0093 RplN Ribosomal protein 42.6 33 0.00072 21.8 2.7 27 49-75 69-95 (122)
54 PRK15053 dpiB sensor histidine 41.3 67 0.0014 25.7 5.0 32 59-91 299-330 (545)
55 PF14827 Cache_3: Sensory doma 41.1 65 0.0014 20.0 4.0 26 58-83 88-113 (116)
56 COG2964 Uncharacterized protei 38.8 66 0.0014 22.9 4.0 36 51-88 86-121 (220)
57 COG5388 Uncharacterized protei 38.2 69 0.0015 22.4 3.8 74 7-83 86-159 (209)
58 PF02743 Cache_1: Cache domain 37.0 73 0.0016 18.1 3.5 29 57-85 12-40 (81)
59 TIGR02373 photo_yellow photoac 33.4 1.3E+02 0.0029 19.3 7.2 40 1-42 48-87 (124)
60 PF08275 Toprim_N: DNA primase 32.9 53 0.0012 21.0 2.6 20 62-83 79-98 (128)
61 COG4191 Signal transduction hi 28.9 41 0.00088 27.7 1.8 25 109-133 377-402 (603)
62 COG4048 Uncharacterized protei 25.6 1.8E+02 0.0039 18.3 4.6 34 52-87 70-103 (123)
63 PRK08571 rpl14p 50S ribosomal 23.7 1.3E+02 0.0029 19.6 3.2 29 48-76 79-107 (132)
64 PF01724 DUF29: Domain of unkn 23.4 1E+02 0.0023 20.1 2.8 17 146-162 43-59 (139)
65 PTZ00054 60S ribosomal protein 22.9 1.5E+02 0.0032 19.6 3.3 28 48-75 86-113 (139)
66 PF13953 PapC_C: PapC C-termin 21.2 1E+02 0.0022 17.1 2.1 26 49-77 3-28 (68)
67 KOG3561 Aryl-hydrocarbon recep 21.2 1.4E+02 0.003 25.9 3.6 81 1-84 394-476 (803)
68 TIGR03673 rpl14p_arch 50S ribo 21.1 1.6E+02 0.0034 19.2 3.1 29 48-76 78-106 (131)
69 PF00512 HisKA: His Kinase A ( 20.7 95 0.0021 16.7 1.9 12 137-148 10-21 (68)
70 COG2205 KdpD Osmosensitive K+ 20.0 2.1E+02 0.0046 25.0 4.3 25 131-155 662-686 (890)
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=99.50 E-value=1.3e-13 Score=85.24 Aligned_cols=82 Identities=27% Similarity=0.469 Sum_probs=74.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||++++++|++ +..+.++.........+.+.+..+..+..+....+++|+.+|+.+++.|+.+++|++.++++++
T Consensus 23 ~~g~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~i~~~~g~~~~~i~~~ 99 (104)
T PF13426_consen 23 LFGYSREELIGKS---ISDFFPEEDRPEFEEQIERALEEGGSWSGEVRLRRKDGETFWVEVSASPIRDEDGEITGIIGIF 99 (104)
T ss_dssp HHTS-HHHHTTSB---GGGGCSTTSCHHHHHHHHHHHHHTSSEEEEEEEEETTSEEEEEEEEEEEEEETTSSEEEEEEEE
T ss_pred HHCcCHHHHcCCC---cccccCcccchhhHHHHHHHHhcCCceeEEEEEEcCCCCEEEEEEEEEEEECCCCCEEEEEEEE
Confidence 4799999999999 8778877777778888999999999999999999999999999999999999999999999999
Q ss_pred eeccc
Q 043549 81 VEVSK 85 (162)
Q Consensus 81 ~DITe 85 (162)
+||||
T Consensus 100 ~DiTe 104 (104)
T PF13426_consen 100 RDITE 104 (104)
T ss_dssp EEEHH
T ss_pred EECCC
Confidence 99996
No 2
>PRK13559 hypothetical protein; Provisional
Probab=99.23 E-value=3.9e-10 Score=84.83 Aligned_cols=88 Identities=36% Similarity=0.644 Sum_probs=75.2
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||+.++++|++ +..+..+.........+...+..+..+..+....+++|..+|+.....|+.+.+|.+.+++++.
T Consensus 78 l~G~~~~e~iG~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~G~~~~~v~~~ 154 (361)
T PRK13559 78 LTGYAAEEVVGRN---CRFLQGAATDPIAVAKIRAAIAAEREIVVELLNYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQ 154 (361)
T ss_pred HhCCCHHHHcCCC---hhhhcCCCCCHHHHHHHHHHhccCCceEEEEEEEcCCCCEEEEEEEEEEEEcCCCCEEEeeeee
Confidence 5899999999999 7766655555555666777788888888888889999999999999999999999999999999
Q ss_pred eeccccchhhh
Q 043549 81 VEVSKYTEGVN 91 (162)
Q Consensus 81 ~DITe~k~~e~ 91 (162)
+|||++|+.++
T Consensus 155 ~DITerk~~e~ 165 (361)
T PRK13559 155 WDVTDIRAVRA 165 (361)
T ss_pred eehhcchhhHH
Confidence 99999998654
No 3
>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=99.19 E-value=6.2e-11 Score=73.87 Aligned_cols=83 Identities=20% Similarity=0.315 Sum_probs=69.8
Q ss_pred CCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEee
Q 043549 2 SDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQV 81 (162)
Q Consensus 2 ~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~ 81 (162)
+|++.++++|++ +..+.++.........+.+.+.++.....+..... +|...|+.+.+.|+.|.+|.+.+++++++
T Consensus 28 ~~~~~~~~~G~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~Pi~~~~g~~~g~~~~~~ 103 (110)
T PF08448_consen 28 FGVSPEELIGRS---LFDLLPPEDREEFQAALRRALAGGEPVFFEEILLR-DGEERWFEVSISPIFDEDGEVVGVLVIIR 103 (110)
T ss_dssp HTSTHHHHTTSB---HHHHSCCGCHHHHHHHHHHHHHHTSEEEEEEEECT-TSCEEEEEEEEEEEECTTTCEEEEEEEEE
T ss_pred hCCCHHHHhhcc---chhccccchhhhhHHHHHHhhccCceEEEEEEEee-cCCcEEEEEEEEEeEcCCCCEEEEEEEEE
Confidence 588899999999 77777776666667778888888777766655544 89999999999999999999999999999
Q ss_pred eccccch
Q 043549 82 EVSKYTE 88 (162)
Q Consensus 82 DITe~k~ 88 (162)
|||++|+
T Consensus 104 DiT~~rr 110 (110)
T PF08448_consen 104 DITERRR 110 (110)
T ss_dssp EECCHHH
T ss_pred ECchhhC
Confidence 9999885
No 4
>PRK13557 histidine kinase; Provisional
Probab=99.16 E-value=9.2e-10 Score=86.55 Aligned_cols=89 Identities=40% Similarity=0.785 Sum_probs=77.6
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||+.+|++|++ +..+.++.........++..+..+..+..+....+++|+.+|+...+.|+.+.+|.+.+++++.
T Consensus 65 ~~G~~~~e~~g~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~i~~~~g~~~~~~~~~ 141 (540)
T PRK13557 65 MTGYAAEEIIGNN---CRFLQGPETDRATVAEVRDAIAERREIATEILNYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQ 141 (540)
T ss_pred HhCCCHHHhcCCC---hHhhcCCCCCHHHHHHHHHHHHcCCCceEEEEEEeCCCCEEEEEEEEEEeECCCCCEEEEEEEe
Confidence 5899999999999 7777777666666777788888888888888889999999999999999999999999999999
Q ss_pred eeccccchhhhh
Q 043549 81 VEVSKYTEGVND 92 (162)
Q Consensus 81 ~DITe~k~~e~e 92 (162)
+|||++++.+++
T Consensus 142 ~dit~~~~~e~~ 153 (540)
T PRK13557 142 LDVSRRRDAEDA 153 (540)
T ss_pred cChHHHHHHHHH
Confidence 999999986543
No 5
>PRK13558 bacterio-opsin activator; Provisional
Probab=99.09 E-value=1.8e-09 Score=87.51 Aligned_cols=91 Identities=31% Similarity=0.652 Sum_probs=77.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||++++++|++ +..+.++.........+...+..+..+..+.+..+++|..+|+.+...|+.+.+|.+.+++++.
T Consensus 183 l~G~~~eel~g~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~pi~d~~G~~~~~vgi~ 259 (665)
T PRK13558 183 ITGYSPDEVLGRN---CRFLQGEDTNEERVAELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRDEDGTVTHYVGFQ 259 (665)
T ss_pred HhCcCHHHHcCCC---HHHhcCCCccHHHHHHHHHHHhcCCCeEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEE
Confidence 5799999999999 7767666655555566777778888888999999999999999999999999999999999999
Q ss_pred eeccccchhhhhhh
Q 043549 81 VEVSKYTEGVNDKA 94 (162)
Q Consensus 81 ~DITe~k~~e~e~~ 94 (162)
+|||++|++|++.+
T Consensus 260 ~DITerk~~E~~L~ 273 (665)
T PRK13558 260 TDVTERKEAELALQ 273 (665)
T ss_pred EeCcHHHHHHHHHH
Confidence 99999999766543
No 6
>PRK10060 RNase II stability modulator; Provisional
Probab=99.08 E-value=5.3e-10 Score=90.51 Aligned_cols=110 Identities=14% Similarity=0.157 Sum_probs=80.5
Q ss_pred CCCCCcccccCCCCCCccc-ccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCC-eEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRF-LQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGK-TIKFIG 78 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~-~~~~v~ 78 (162)
++||+.++++|++ +.. +.++.........++..+..+..|..+.+..+++|..+|+..... +.+..|. ...+++
T Consensus 143 l~Gy~~~eliG~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~-~~~~~g~~~~~~i~ 218 (663)
T PRK10060 143 YTGLKEHDVIGQS---VFKLFMSRREAAASRRNIRGFFRSGNAYEVERWIKTRKGQRLFLFRNKF-VHSGSGKNEIFLIC 218 (663)
T ss_pred HHCcCHHHHcCCC---HHHHhCChhhHHHHHHHHHHHHhcCCceEEEEEEEeCCCCEEEEEeeeE-EEcCCCCceEEEEE
Confidence 5899999999999 544 444444444556667778888889999999999999888765544 4444444 456888
Q ss_pred Eeeeccccchhhhhhhccc-----CCchhhhhhhchhhHHH
Q 043549 79 MQVEVSKYTEGVNDKALRP-----NGLSKSLIRYDARQKEK 114 (162)
Q Consensus 79 ~~~DITe~k~~e~e~~~~~-----~~l~~~~~~~d~~~~~~ 114 (162)
+.+|||++++.+++..... |+|||+..+.+......
T Consensus 219 ~~~DITe~k~~e~~l~~~a~~D~LTGL~NR~~f~~~l~~~l 259 (663)
T PRK10060 219 SGTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAI 259 (663)
T ss_pred EEEechHHHHHHHHHHHHhhcCccCCCcCHHHHHHHHHHHH
Confidence 9999999999766544432 89999998877665443
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.97 E-value=2.4e-09 Score=88.20 Aligned_cols=90 Identities=19% Similarity=0.222 Sum_probs=75.0
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||+.++++|++ +..+.++.............+..+..+..+.+...++|..+|+.++..|+.+.+|.+.++++++
T Consensus 187 l~G~~~~eliG~~---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~v~~~ 263 (779)
T PRK11091 187 LTGKSEKQLIGLT---PKDVYSPEAAEKVIETDEKVFRHNVSLTYEQWLDYPDGRKACFELRKVPFYDRVGKRHGLMGFG 263 (779)
T ss_pred HhCcCHHHHcCCC---hHHhCCHHHHHHHHHHHHHHHhcCCCeEEEEEEEcCCCCEEEEEEEeeeEEcCCCCEEEEEEEE
Confidence 4799999999999 7767666544444555566677778888899999999999999999999999999999999999
Q ss_pred eeccccchhhhhh
Q 043549 81 VEVSKYTEGVNDK 93 (162)
Q Consensus 81 ~DITe~k~~e~e~ 93 (162)
+|||++|+++++.
T Consensus 264 ~DITe~k~~e~~l 276 (779)
T PRK11091 264 RDITERKRYQDAL 276 (779)
T ss_pred eehhHHHHHHHHH
Confidence 9999999976543
No 8
>PRK13560 hypothetical protein; Provisional
Probab=98.96 E-value=3.5e-09 Score=87.00 Aligned_cols=92 Identities=13% Similarity=0.162 Sum_probs=69.3
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcC-CceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNG-KSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||+++++++... .+..+.+|++.......+......+ ..+..+++..+++|..+|+.....|++|.+|.+.+++++
T Consensus 506 ~~G~~~~e~~~~~~-~~~~~~~p~d~~~~~~~~~~~~~~g~~~~~~e~r~~~~dG~~~w~~~~~~~~~d~~G~~~~~~g~ 584 (807)
T PRK13560 506 QFGYEPDEFISGKR-MFAAIIHPADLEQVAAEVAEFAAQGVDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGI 584 (807)
T ss_pred hcCCCHHHhhcccc-hHhhhcChhhHHHHHHHHHHHHhcCCccceeEEEEEcCCCCEEEEEecceeeeCCCCCEEEEEEE
Confidence 36899888876330 0333455555444445555555444 457788999999999999999999999999999999999
Q ss_pred eeeccccchhhhhh
Q 043549 80 QVEVSKYTEGVNDK 93 (162)
Q Consensus 80 ~~DITe~k~~e~e~ 93 (162)
.+|||++|++|++.
T Consensus 585 ~~DITerK~aE~~L 598 (807)
T PRK13560 585 VIDISERKHAEEKI 598 (807)
T ss_pred EechHHHHHHHHHH
Confidence 99999999976543
No 9
>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=98.89 E-value=3e-09 Score=64.29 Aligned_cols=79 Identities=24% Similarity=0.282 Sum_probs=60.0
Q ss_pred CCCCCcccccCCCC-CCcccccCCCCCHHHHHHHHH-HHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEE
Q 043549 1 MSDPTGKELIGCCL-LCSRFLQGPETDKNEVEKIRD-AVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIG 78 (162)
Q Consensus 1 l~G~~~~e~~g~~~-~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~ 78 (162)
++||+++++ +.+- ..+..+.+|++.......+.+ ....+..+..+++.++++|+..|+...+.++.|++|++..++|
T Consensus 11 i~G~~~~~~-~~~~~~~~~~~ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~~~G 89 (91)
T PF08447_consen 11 IFGYSPEEI-GKPDFEEWLERIHPDDRERVRQAIQQAALQNGEPFEIEYRIRRKDGEYRWIEVRGRPIFDENGKPIRIIG 89 (91)
T ss_dssp HHTS-HHHH-TCBEHHHHHHHB-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGTTSTEEEEEEEEEEEETTTS-EEEEEE
T ss_pred HhCCCHHHh-ccCCHHHHHhhcCHHHHHHHHHHHHHHhhccCcceEEEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEE
Confidence 479999888 4320 002235667777777777888 6778889999999999999999999999999999999999998
Q ss_pred Ee
Q 043549 79 MQ 80 (162)
Q Consensus 79 ~~ 80 (162)
++
T Consensus 90 v~ 91 (91)
T PF08447_consen 90 VI 91 (91)
T ss_dssp EE
T ss_pred EC
Confidence 74
No 10
>PRK09776 putative diguanylate cyclase; Provisional
Probab=98.89 E-value=8.9e-09 Score=87.43 Aligned_cols=109 Identities=12% Similarity=0.092 Sum_probs=79.7
Q ss_pred CCCCCcccccCCCCCCcccccCCCC--CHHHHHHHHHHHHcCCc--eEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPET--DKNEVEKIRDAVRNGKS--YCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKF 76 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~~--~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~ 76 (162)
++||+.+|++|++ ...+..... .......+......... +..+....+++|..+|+.....|+.+.+|.+.++
T Consensus 568 l~G~~~~e~iG~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~pi~~~~g~~~g~ 644 (1092)
T PRK09776 568 MTGWTQEEALGVP---LLTVLHITFGDNGPLMENIYSCLTSRSAAYLEQDVVLHCRSGGSYDVHYSITPLSTLDGENIGS 644 (1092)
T ss_pred HhCCCHHHHcCCC---HHHHcccccCCcchhhHHHHHHHhcCCCccccceEEEEeCCCcEEEEEEEeeeeecCCCCEEEE
Confidence 4799999999998 654443221 11222234444444433 4567778899999999999999999999999999
Q ss_pred EEEeeeccccchhhhhhhccc-----CCchhhhhhhchhhH
Q 043549 77 IGMQVEVSKYTEGVNDKALRP-----NGLSKSLIRYDARQK 112 (162)
Q Consensus 77 v~~~~DITe~k~~e~e~~~~~-----~~l~~~~~~~d~~~~ 112 (162)
+++++|||++|+.+++..... |+|+|+..+.+...+
T Consensus 645 v~~~~DITe~k~~e~~L~~~a~~D~lTgl~nr~~f~~~l~~ 685 (1092)
T PRK09776 645 VLVIQDVTESRKMLRQLSYSASHDALTHLANRASFEKQLRR 685 (1092)
T ss_pred EEEEEecchHHHHHHHHHhhcCCCcccCCccHHHHHHHHHH
Confidence 999999999999776654433 799998877665433
No 11
>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=98.86 E-value=6.3e-09 Score=64.96 Aligned_cols=80 Identities=25% Similarity=0.409 Sum_probs=61.5
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEE-EEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCG-RLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||++++++|++ +..+.++.+.......+.+.+..++.... +.....++|+.+|+.+...|+.+.+|.+.+++++
T Consensus 33 l~g~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~ 109 (113)
T PF00989_consen 33 LLGYSREELIGKS---LFDLIHPEDRRELRERLRQALSQGESGESFEVRFRLRDGRPRWVEVRASPVRDEDGQIIGILVI 109 (113)
T ss_dssp HHSS-HHHHTTSB---GGGGCSGGGHHHHHHHHHHHHHHCCHECEEEEEEEETTSCEEEEEEEEEEEEETTEEEEEEEEE
T ss_pred HHccCHHHHcCCc---HHHhcCchhhHHHHHHHHHHHHcCCCceeEEEEEEecCCcEEEEEEEEEEEEeCCCCEEEEEEE
Confidence 4799999999999 66666555444466677777777765544 4444446999999999999999999999999999
Q ss_pred eeec
Q 043549 80 QVEV 83 (162)
Q Consensus 80 ~~DI 83 (162)
++||
T Consensus 110 ~~DI 113 (113)
T PF00989_consen 110 FRDI 113 (113)
T ss_dssp EEE-
T ss_pred EEeC
Confidence 9997
No 12
>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=98.85 E-value=5.1e-09 Score=81.27 Aligned_cols=89 Identities=26% Similarity=0.459 Sum_probs=74.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||++++++|++ ...+..+.........+++.+..+..+..+....+++|..+|+.....|+.+.+|.+.+++++.
T Consensus 36 ~~G~~~~~~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~ 112 (494)
T TIGR02938 36 ITGYTKEEIIGKN---ESVLSNHTTPPEVYQALWGSLAEQKPWAGKLLNRRKDGELYLAELTVAPVLNEAGETTHFLGMH 112 (494)
T ss_pred ecCCCHHHHhCCC---chhhcCCCCCHHHHHHHHHHHHhCCcccceeeccCCCccchhhheeeEEEECCCCCEEEEEEeh
Confidence 5899999999988 6656555555556667777777888888888888999999999999999999999999999999
Q ss_pred eeccccchhhhh
Q 043549 81 VEVSKYTEGVND 92 (162)
Q Consensus 81 ~DITe~k~~e~e 92 (162)
+|||++|+.+++
T Consensus 113 ~DIt~~k~~e~~ 124 (494)
T TIGR02938 113 RDITELHRLEQV 124 (494)
T ss_pred hhhhHHHHHHHH
Confidence 999999987654
No 13
>PRK13560 hypothetical protein; Provisional
Probab=98.74 E-value=5.4e-08 Score=80.07 Aligned_cols=90 Identities=12% Similarity=0.043 Sum_probs=69.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEe--eeeeCCCCCeEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTV--TPIKDDSGKTIKFIG 78 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~--~~i~d~~g~~~~~v~ 78 (162)
++||++++++|++ +..+.++..........+..+..++....+.+..++||..+|+.+.. .|+.+.+|.+.++++
T Consensus 236 ~~G~~~~e~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~~~g~~~g~~~ 312 (807)
T PRK13560 236 ACGFRREEIIGMS---IHDFAPAQPADDYQEADAAKFDADGSQIIEAEFQNKDGRTRPVDVIFNHAEFDDKENHCAGLVG 312 (807)
T ss_pred HhCCCHHHHcCCc---chhcCCcchhHHHHHHHHHHhccCCceEEEEEEEcCCCCEEEEEEEecceEEEcCCCCEEEEEE
Confidence 5899999999999 76666554433333444555666777778888999999999776654 566788899999999
Q ss_pred Eeeeccccchhhhhh
Q 043549 79 MQVEVSKYTEGVNDK 93 (162)
Q Consensus 79 ~~~DITe~k~~e~e~ 93 (162)
+.+|||++|++|.+.
T Consensus 313 ~~~DITerk~~e~~L 327 (807)
T PRK13560 313 AITDISGRRAAEREL 327 (807)
T ss_pred EEEechHHHHHHHHH
Confidence 999999999976543
No 14
>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]
Probab=98.71 E-value=6.6e-08 Score=75.22 Aligned_cols=88 Identities=26% Similarity=0.469 Sum_probs=79.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
+.||.+.|++.++ |-+.++..+..++...+.+.+.+.+.+..++|+.+.+|+.+++|+.+.+.|++++...++.|++.+
T Consensus 52 lsGY~RAevMQKs-~tc~FMyGEltdk~ti~k~~~t~eN~~~~qfEillyKKN~TPvW~~vqiAPIrNe~d~VVLfLctF 130 (971)
T KOG0501|consen 52 LSGYHRAEVMQKS-CTCSFMYGELTDKGTIEKVRQTLENYETNQFEILLYKKNRTPVWLLVQIAPIRNEKDKVVLFLCTF 130 (971)
T ss_pred ccCccHHHHhccc-ceeeeeeccccchhhHHHHHHHHHhhhhcceeeEeeecCCCceEEEEEeecccCCCceEEEEEeec
Confidence 4699999999987 345667777778888899999999999999999999999999999999999999999999999999
Q ss_pred eeccccchh
Q 043549 81 VEVSKYTEG 89 (162)
Q Consensus 81 ~DITe~k~~ 89 (162)
+|||..|+-
T Consensus 131 kDIT~~KQP 139 (971)
T KOG0501|consen 131 KDITALKQP 139 (971)
T ss_pred ccchhhcCC
Confidence 999999985
No 15
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.66 E-value=8.5e-08 Score=79.09 Aligned_cols=88 Identities=13% Similarity=0.138 Sum_probs=71.7
Q ss_pred CCCCCcccccCCCCCCcccc-cCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFL-QGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||+.++++|++ ...+ .++.........+...+..+..+..+.+..+++|..+|+.....|+.+.+|.+.+++++
T Consensus 168 l~G~~~~e~~g~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~v~d~~g~~~~~~~~ 244 (799)
T PRK11359 168 MFGYCISEASGMQ---PDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQNLVMT 244 (799)
T ss_pred hhCCCHHHHCCCC---hHHhcCCCCCcHHHHHHHHHhhccCCCCcceeEEeCCCCCEEEEEeeeeeeecCCCceeEEEEE
Confidence 4799999999998 5544 34444445555666777777777888888999999999999999999999999999999
Q ss_pred eeeccccchhhh
Q 043549 80 QVEVSKYTEGVN 91 (162)
Q Consensus 80 ~~DITe~k~~e~ 91 (162)
.+|||++|+.++
T Consensus 245 ~~DITerk~~e~ 256 (799)
T PRK11359 245 FSDITEERQIRQ 256 (799)
T ss_pred eehhhhHHHHHH
Confidence 999999998654
No 16
>PRK09776 putative diguanylate cyclase; Provisional
Probab=98.65 E-value=4.9e-08 Score=83.00 Aligned_cols=92 Identities=21% Similarity=0.369 Sum_probs=72.2
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcC-CceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNG-KSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||+.+|++|++ +..+.+|++.......+.+...+. ..+..+.+..++||+.+|+.....|+.+.+|.+.+++++
T Consensus 315 l~G~~~~el~g~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~~~~~~g~~~~~i~~ 391 (1092)
T PRK09776 315 FLGYSQEELRGLT---FQQLTWPEDLNKDLQQVEKLLSGEINSYSMEKRYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQ 391 (1092)
T ss_pred HhCCCHHHHccCC---ceeccCcchhHhHHHHHHHHHcCCccceeeeeEEEcCCCCEEEEEEEEEEEECCCCCEeeehhh
Confidence 5899999999999 766666665444444444444332 346778889999999999999999999999999999999
Q ss_pred eeeccccchhhhhhhc
Q 043549 80 QVEVSKYTEGVNDKAL 95 (162)
Q Consensus 80 ~~DITe~k~~e~e~~~ 95 (162)
.+|||++|++|++.+.
T Consensus 392 ~~DITerk~~e~~l~~ 407 (1092)
T PRK09776 392 IEDINELKRTEQVNER 407 (1092)
T ss_pred HHhhHHHHHHHHHHHH
Confidence 9999999997665433
No 17
>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=98.52 E-value=1.1e-06 Score=55.48 Aligned_cols=82 Identities=16% Similarity=0.118 Sum_probs=64.1
Q ss_pred CCCCcccccCCCCCCcccccCCCCCHH-HHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCC-CCeEEEEEE
Q 043549 2 SDPTGKELIGCCLLCSRFLQGPETDKN-EVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDS-GKTIKFIGM 79 (162)
Q Consensus 2 ~G~~~~e~~g~~~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~-g~~~~~v~~ 79 (162)
+||.++|++|++ +..+.+|++... ......+.+..|.....-+++..++|..+|+...+.++.++. +++..++++
T Consensus 26 lgy~~~eLvG~s---~y~~~H~~D~~~~~~~~~~~~~~~g~~~~~~yR~~~k~g~~vwvqt~~~~~~n~~~~~~~~Iv~~ 102 (111)
T PF14598_consen 26 LGYLPEELVGRS---IYDFVHPDDLQRVLKQHHREVLQKGQSVSPYYRFRTKNGGYVWVQTKATLFYNPWTSKPEFIVCT 102 (111)
T ss_dssp HSS-HHHHTTSB---GGGGBSCCTHHHHHHHHHHHHHHHSSEEEEEEEEE-TTSSEEEEEEEEEEEEETTTTCEEEEEEE
T ss_pred cCCCcHHHcCCc---hHHhCCHhhhhhHHHHHHHHHhhCCCcCcceEEEEecCCcEEEEEEEEEEEECCCCCCccEEEEE
Confidence 599999999999 777777877665 556677778888887778999999999999999999998754 566677777
Q ss_pred eeecccc
Q 043549 80 QVEVSKY 86 (162)
Q Consensus 80 ~~DITe~ 86 (162)
.+=|++.
T Consensus 103 n~vlse~ 109 (111)
T PF14598_consen 103 NTVLSEE 109 (111)
T ss_dssp EEEESCE
T ss_pred EEEeccC
Confidence 6666653
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=98.44 E-value=1.2e-06 Score=53.00 Aligned_cols=86 Identities=20% Similarity=0.335 Sum_probs=59.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcC-CceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNG-KSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++|++.++++|.+ ...+.++.........+...+..+ .....+......+|...|+.....|+. .+|...+++++
T Consensus 35 ~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 110 (124)
T TIGR00229 35 IFGYSAEELIGRN---VLELIPEEDREEVRERIERLLEGEREPVSEERRVRRKDGSEIWVEVSVSPIR-TNGGELGVVGI 110 (124)
T ss_pred HhCCChHHhcCcc---hhhhcChhhhHHHHHHHHHHHcCCCCCcceEeeeEcCCCCEEEEEEEEeehh-hCCCeeEEEEE
Confidence 3678888888887 555555444333333444444433 223344444578899999999999988 77888899999
Q ss_pred eeeccccchhh
Q 043549 80 QVEVSKYTEGV 90 (162)
Q Consensus 80 ~~DITe~k~~e 90 (162)
..|||++++.+
T Consensus 111 ~~dit~~~~~~ 121 (124)
T TIGR00229 111 VRDITERKQAE 121 (124)
T ss_pred eeehhHHHHHH
Confidence 99999998854
No 19
>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=98.40 E-value=1.7e-06 Score=67.08 Aligned_cols=83 Identities=10% Similarity=-0.026 Sum_probs=57.1
Q ss_pred CCCCC-cccccCCCCCCcccccCCCCCHHHHHHHHHHH-HcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEE
Q 043549 1 MSDPT-GKELIGCCLLCSRFLQGPETDKNEVEKIRDAV-RNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIG 78 (162)
Q Consensus 1 l~G~~-~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~-~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~ 78 (162)
++||+ .++++|++ +..+..+... .. ..+...+ ..+.....+....+++|+.+|+.+++.|+.+.++ ..+++
T Consensus 284 l~G~~~~~~l~G~~---~~~~~~~~~~-~~-~~~~~~~~~~g~~~~~~~~~~~~~G~~~~ve~s~~~i~~~~~--~~~~~ 356 (442)
T TIGR02040 284 LTDSSSLEAVRGRT---LDRWLGRGGV-DL-RVLLSNVRRTGQVRLYATTLTGEFGAQTEVEISAAWVDQGER--PLIVL 356 (442)
T ss_pred HhCCCChHHHcCCC---HHHHhCCCcc-cH-HHHHHHHhhcCceEEEEEEEEcCCCCEEEEEEEEEEeccCCc--eEEEE
Confidence 57997 57799999 6544432221 11 2222333 3344444667778999999999999999976544 46888
Q ss_pred Eeeeccccchhh
Q 043549 79 MQVEVSKYTEGV 90 (162)
Q Consensus 79 ~~~DITe~k~~e 90 (162)
+++|||++++.+
T Consensus 357 v~rDITeR~~~~ 368 (442)
T TIGR02040 357 VIRDISRRLTMR 368 (442)
T ss_pred EEecchhhccCC
Confidence 999999999864
No 20
>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=98.35 E-value=1e-05 Score=46.45 Aligned_cols=80 Identities=26% Similarity=0.476 Sum_probs=60.7
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++|++.++++|.. ...+.++.........+......+..+..+......+|...|+.....++.+..|...+++++.
T Consensus 24 ~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (103)
T cd00130 24 LLGYSPEELIGKS---LLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLVSLTPIRDEGGEVIGLLGVV 100 (103)
T ss_pred HhCCCHHHHcCcc---HHHhcCCccchHHHHHHHHHHhcCcCeEEEEEEEccCCCEEEEEEEEEEEecCCCCEEEEEEEE
Confidence 3688888889988 5555555555444455555555556667777888888999999999999988888888899988
Q ss_pred eec
Q 043549 81 VEV 83 (162)
Q Consensus 81 ~DI 83 (162)
+||
T Consensus 101 ~di 103 (103)
T cd00130 101 RDI 103 (103)
T ss_pred ecC
Confidence 886
No 21
>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=98.03 E-value=1.3e-05 Score=62.15 Aligned_cols=82 Identities=11% Similarity=0.011 Sum_probs=54.0
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCC-ceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGK-SYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||+.+|++|++ +..+++++........+.+....+. .+..+.....++|..+|+.++..++.+ + .+++++
T Consensus 28 ~~g~~~~el~G~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~g~~~~~~~~~~~~~~--~--~~~~~i 100 (442)
T TIGR02040 28 PSFEQLSEWEGRR---WEEIVTAESVEKFELRLSEALRTGRGAVRVELNHIDPSSFELPMRFILVRLGA--D--RGVLAL 100 (442)
T ss_pred ccccccccCCCCc---HhHhhCcchHHHHHHHHHHHhccCCCcceEeeccCCCCCCccCeEEEEEEeCC--C--CeEEEE
Confidence 5799999999999 7777666554333344444454443 455565555666767777776666544 2 256788
Q ss_pred eeeccccchh
Q 043549 80 QVEVSKYTEG 89 (162)
Q Consensus 80 ~~DITe~k~~ 89 (162)
.+|||++++.
T Consensus 101 ~rDi~~~~~~ 110 (442)
T TIGR02040 101 GRDLRAVAEL 110 (442)
T ss_pred ecccHHHHHH
Confidence 8999986653
No 22
>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional
Probab=98.03 E-value=1.5e-05 Score=65.88 Aligned_cols=88 Identities=19% Similarity=0.299 Sum_probs=61.7
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcC----CceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNG----KSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKF 76 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~----~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~ 76 (162)
++||+++|++|++ ...+.++.........+......+ ..+..+.+..++||+.+|+.....|+. .+|. ..+
T Consensus 44 l~G~s~eeliG~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~~~~-~~g~-~~~ 118 (799)
T PRK11359 44 LWGYKREEVIGNN---IDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVS-AEGK-VYY 118 (799)
T ss_pred HhCCCHHHHcCCC---HHHhcCccccccchHHHhhhhccCCccccccceeeEEecCCcCEEEEEEEeeeec-cCCc-eEE
Confidence 5899999999999 666666654433333333333332 234458888999999999999888873 3454 467
Q ss_pred EEEeeeccccchhhhhh
Q 043549 77 IGMQVEVSKYTEGVNDK 93 (162)
Q Consensus 77 v~~~~DITe~k~~e~e~ 93 (162)
+++.+|||++++.+++.
T Consensus 119 ~~~~~DiT~~~~~~~~~ 135 (799)
T PRK11359 119 LALVRDASVEMAQKEQT 135 (799)
T ss_pred EEEEeeccchhhhHHHH
Confidence 88899999988865543
No 23
>PRK11360 sensory histidine kinase AtoS; Provisional
Probab=98.00 E-value=0.00011 Score=58.39 Aligned_cols=87 Identities=14% Similarity=0.088 Sum_probs=63.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCce-EEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSY-CGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
++||++++++|++ +..+.++.. .....+.+.+..+... ..+.....++|... +.+...|+.+++|.+.+++++
T Consensus 294 l~g~~~~~~~g~~---~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~g~~~~~i~~ 367 (607)
T PRK11360 294 ITGLQRHELVGKP---YSELFPPNT--PFASPLLDTLEHGTEHVDLEISFPGRDRTIE-LSVSTSLLHNTHGEMIGALVI 367 (607)
T ss_pred HhCCChHHhcCCc---HHHHcCCch--hHHHHHHHHHhcCCCccceEEEEEcCCCcEE-EEEEEeeEEcCCCCEEEEEEE
Confidence 4789999999999 766665432 2233444555554433 34566667777765 888999999999999999999
Q ss_pred eeeccccchhhhhh
Q 043549 80 QVEVSKYTEGVNDK 93 (162)
Q Consensus 80 ~~DITe~k~~e~e~ 93 (162)
.+|||++++.+.+.
T Consensus 368 ~~Dite~~~~e~~l 381 (607)
T PRK11360 368 FSDLTERKRLQRRV 381 (607)
T ss_pred EeechHHHHHHHHH
Confidence 99999999976544
No 24
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=97.79 E-value=8.8e-05 Score=55.51 Aligned_cols=82 Identities=12% Similarity=0.133 Sum_probs=56.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||+.++++|++ ++.+.+... .....+.+.+..+..+..+.....++|..+|+.++..|+. . ..++..+
T Consensus 39 ~~g~~~~~~~g~~---~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~--~---~~~~~~~ 108 (348)
T PRK11073 39 LLAQSSRKLFGTP---LPELLSYFS--LNIELMRESLQAGQGFTDNEVTLVIDGRSHILSLTAQRLP--E---GMILLEM 108 (348)
T ss_pred HhCCCHHHHcCCC---HHHHcCcch--hhHHHHHHHHHcCCcccccceEEEECCceEEEEEEEEEcc--C---ceeEEEE
Confidence 5799999999999 776654332 1223444555555555444455567999999999999986 2 2456678
Q ss_pred eeccccchhhhh
Q 043549 81 VEVSKYTEGVND 92 (162)
Q Consensus 81 ~DITe~k~~e~e 92 (162)
+|||++++.+.+
T Consensus 109 ~dit~~~~~~~~ 120 (348)
T PRK11073 109 APMDNQRRLSQE 120 (348)
T ss_pred echhHHHHHHHH
Confidence 999998885443
No 25
>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.
Probab=97.64 E-value=0.00082 Score=31.79 Aligned_cols=41 Identities=24% Similarity=0.588 Sum_probs=34.2
Q ss_pred EEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeecccc
Q 043549 46 RLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKY 86 (162)
Q Consensus 46 e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~ 86 (162)
+......+|..+|+.....++.+..|.+.+++++..|||++
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~ 43 (43)
T smart00086 3 EYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43 (43)
T ss_pred EEEEEecCCCEEEEEEEeEEEECCCCCEEEEEEEEEeccCC
Confidence 34566788999999988899988888888999999999863
No 26
>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.
Probab=97.52 E-value=0.001 Score=41.20 Aligned_cols=71 Identities=21% Similarity=0.276 Sum_probs=44.2
Q ss_pred ccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeecc
Q 043549 7 KELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVS 84 (162)
Q Consensus 7 ~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DIT 84 (162)
...+|++ ...+.++. .......+.+.+..++....+... ..+| .|+.+...|+++++|...|++.++.|||
T Consensus 36 ~~~iGr~---l~~~~~~~-~~~~l~~~i~~~~~~~~~~~~~~~-~~~~--~~~~~~~~P~~~~~g~~~G~v~~~~DIT 106 (106)
T PF13596_consen 36 PSDIGRP---LFDIHPPL-SYPNLKKIIEQVRSGKEEEFEIVI-PNGG--RWYLVRYRPYRDEDGEYAGAVITFQDIT 106 (106)
T ss_dssp GGGTTSB---CCCSS-HH-HHHHHHHHHHHHHTTSBSEEEEEE-EETT--EEEEEEEEEEE-TTS-EEEEEEEEEE-G
T ss_pred hHHCCCC---HHHcCCcc-chHHHHHHHHHHHcCCCceEEEEe-cCCC--EEEEEEEEEEECCCCCEEEEEEEEEecC
Confidence 3557888 66565442 223334455666666654444333 3455 4667789999999999999999999998
No 27
>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=97.51 E-value=0.0018 Score=48.42 Aligned_cols=86 Identities=14% Similarity=0.094 Sum_probs=55.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++|.+.++++|++ .-.+..-.+. -.+.+......+...+. ...+..+..++..+.+..+.|-+.+++++.
T Consensus 143 ~L~~~~E~~~~~~---i~elL~i~d~----y~~~dL~e~~~s~lld~---~~~~E~~~lrv~Fs~i~rEsGfisGlIaVl 212 (459)
T COG5002 143 MLGVSKEDALGRS---ILELLKIEDT----YTFEDLVEKNDSLLLDS---SDEEEGYVLRVNFSVIQRESGFISGLIAVL 212 (459)
T ss_pred HhCcCHHHHhccc---HHHHhCCccc----eeHHHHHhcCCcEEEee---cCCCccEEEEEEEEEEeecccccceeEEEE
Confidence 3577778888887 3323222211 12233333333333332 236777888888888988999999999999
Q ss_pred eeccccchhhhhhhcc
Q 043549 81 VEVSKYTEGVNDKALR 96 (162)
Q Consensus 81 ~DITe~k~~e~e~~~~ 96 (162)
+|+||+.+.|.|.+..
T Consensus 213 hDvTEqek~e~ErRef 228 (459)
T COG5002 213 HDVTEQEKVERERREF 228 (459)
T ss_pred ecccHHHHHHHHHHHH
Confidence 9999999977665443
No 28
>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=97.26 E-value=0.003 Score=46.54 Aligned_cols=76 Identities=8% Similarity=-0.029 Sum_probs=50.5
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||++++.+|++ +..+..+ . .+.+.+..+.. ........++|..+|+.+...|+.+.. ++++.
T Consensus 38 ~~g~~~~~~~g~~---~~~~~~~---~----~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~p~~~~~-----~~~~~ 101 (333)
T TIGR02966 38 LLGLRWPDDLGQR---ITNLIRH---P----EFVEYLAAGRF-SEPLELPSPINSERVLEIRIAPYGEEQ-----KLLVA 101 (333)
T ss_pred HhCCChHHHcCCc---HHHHccC---H----HHHHHHHhccc-CCCeEeecCCCCceEEEEEEEEcCCCc-----eEEEE
Confidence 5799999999998 6555432 1 22333333222 223444557888899999999987642 67788
Q ss_pred eeccccchhhhh
Q 043549 81 VEVSKYTEGVND 92 (162)
Q Consensus 81 ~DITe~k~~e~e 92 (162)
+|||++++.+..
T Consensus 102 ~dit~~~~~~~~ 113 (333)
T TIGR02966 102 RDVTRLRRLEQM 113 (333)
T ss_pred eCchHHHHHHHH
Confidence 999999886543
No 29
>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]
Probab=96.85 E-value=0.00067 Score=51.93 Aligned_cols=76 Identities=22% Similarity=0.320 Sum_probs=63.9
Q ss_pred CCCCCcccccCCCCCCcccccCCCC-CHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPET-DKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
|+||-+.|++|++ ...+...+. .......+..+++.|+.|+++...+++.|......+...|+.+..|++.+|+..
T Consensus 189 mmG~hkgEliGke---~adlpkkdknradlldtintcikkgke~qG~~~aRRksgdS~dqh~~itP~~gqggkirhfvsl 265 (775)
T KOG1229|consen 189 MMGCHKGELIGKE---EADLPKKDKNRADLLDTINTCIKKGKEAQGEEEARRKSGDSCDQHFIITPFAGQGGKIRHFVSL 265 (775)
T ss_pred hhcchhhhhcCCc---hhhccccccchhhhhhhhhHhhhcCccccchHHHhhccCCcccceEEEeeecCCCCceeeehhh
Confidence 5799999999999 776655443 346778899999999999999999999998888888999999988888888643
No 30
>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=96.65 E-value=0.00071 Score=52.62 Aligned_cols=47 Identities=15% Similarity=0.067 Sum_probs=31.4
Q ss_pred EEEecCCc-eEEEEEEeeeeeCCCCCe---------EEEEEEeeeccccchhhhhhh
Q 043549 48 LNYKKDGT-PFWNLLTVTPIKDDSGKT---------IKFIGMQVEVSKYTEGVNDKA 94 (162)
Q Consensus 48 ~~~~~dG~-~~~~~~~~~~i~d~~g~~---------~~~v~~~~DITe~k~~e~e~~ 94 (162)
.....+|. .+|+.....++.+..|.. .+++++++|||++|++|++.+
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~DITe~k~~ee~l~ 259 (494)
T TIGR02938 203 RFDRGGGRPARWLSCTGSVIGMESDCADSFFCAAEQPYLLLTIADISNLREEQERAR 259 (494)
T ss_pred eeccCCCceeeEEEecCceEEeecchhhheeccCCCchheehHHHHHHHHHHHHHHH
Confidence 33344444 688888887876655543 345668899999999765443
No 31
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=96.62 E-value=0.0018 Score=51.91 Aligned_cols=83 Identities=17% Similarity=0.173 Sum_probs=66.7
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCC-CCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDS-GKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~-g~~~~~v~~ 79 (162)
++||+++|++|+. +-.++++.+...........+..|....+.++...++|...|+....+.+.+.. ++...+|++
T Consensus 296 lm~y~PeeLvGrS---~Ye~~Ha~Ds~~v~KSh~dL~~KGQv~TgyYR~lak~GGyvWlQTqATVi~~tkn~q~q~IicV 372 (768)
T KOG3558|consen 296 LMDYEPEELVGRS---CYEFVHALDSDRVRKSHHDLLTKGQVVTGYYRLLAKNGGYVWLQTQATVIYNTKNPQEQNIICV 372 (768)
T ss_pred HhcCCHHHhhchh---HHHhhhHhhhhHHHHHHHHHHhcCccchhHHHHHHhcCCeEEEEeeeEEEecCCCCCcceEEEE
Confidence 4699999999999 666777777666777788888889999999999999999999999998887643 455667777
Q ss_pred eeecccc
Q 043549 80 QVEVSKY 86 (162)
Q Consensus 80 ~~DITe~ 86 (162)
.-=|+..
T Consensus 373 nYVlS~~ 379 (768)
T KOG3558|consen 373 NYVLSNI 379 (768)
T ss_pred Eeeeccc
Confidence 6666655
No 32
>PF12860 PAS_7: PAS fold
Probab=96.50 E-value=0.013 Score=36.74 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=25.3
Q ss_pred EecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccchhh
Q 043549 50 YKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTEGV 90 (162)
Q Consensus 50 ~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~e 90 (162)
...||. |+.+...|..+ | +++.+++|||+++++|
T Consensus 81 ~~~dgr--~l~~~~~~~~~--G---g~v~~~~DVT~~~~~E 114 (115)
T PF12860_consen 81 RLPDGR--WLEVRAQPLPD--G---GFVLTFTDVTERRRAE 114 (115)
T ss_pred ECCCCE--EEEEEeEECCC--C---CEEEEEEeCCHHHHhc
Confidence 456774 66777788754 5 5778889999999965
No 33
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=95.44 E-value=0.031 Score=42.37 Aligned_cols=79 Identities=18% Similarity=0.280 Sum_probs=59.5
Q ss_pred cccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccc
Q 043549 8 ELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYT 87 (162)
Q Consensus 8 e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k 87 (162)
.++|++ ...-+|| ........+.+.+.+|.....++|. .+|. ..+.++..+++|++|.-.+++.+.+|||.-+
T Consensus 327 sviGr~---v~~chpP-ksv~iv~ki~~~fksG~kd~~efw~--~~~~-~~i~i~Y~av~de~ge~~g~le~~qdi~~i~ 399 (409)
T COG2461 327 SVIGRR---VQLCHPP-KSVHIVEKILKDFKSGEKDFAEFWI--NMGD-KFIHIRYFAVKDEEGEYLGTLEVVQDITRIK 399 (409)
T ss_pred HhhCCc---ccCCCCC-chHHHHHHHHHHhhcCCcchHHHhc--cCCC-ceEEEEEEEEEcCCCceeeeehhhhhhHHHH
Confidence 467888 5544444 3456678888999999888888883 2232 2556778899999999999999999999998
Q ss_pred hhhhhh
Q 043549 88 EGVNDK 93 (162)
Q Consensus 88 ~~e~e~ 93 (162)
+.+-+.
T Consensus 400 ~l~gek 405 (409)
T COG2461 400 ELEGEK 405 (409)
T ss_pred hccchh
Confidence 865544
No 34
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=95.10 E-value=0.1 Score=42.13 Aligned_cols=63 Identities=13% Similarity=0.191 Sum_probs=41.2
Q ss_pred EecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccchhhhhhhcccCCchhhhhhhchhhHHHHhhhH-HHHHHHhcc
Q 043549 50 YKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTEGVNDKALRPNGLSKSLIRYDARQKEKALGSI-TEVIQTVKR 128 (162)
Q Consensus 50 ~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~e~e~~~~~~~l~~~~~~~d~~~~~~~~~~~-~~~~~~~~~ 128 (162)
....|+...+.+..+....+ .-.++|.++.|||+... +||..+++.. ....|++++
T Consensus 443 ~~r~g~~rtl~Vq~t~~~~d--~~~gyVvt~DDITdLV~---------------------AQRs~AW~dVArRIAHEIKN 499 (712)
T COG5000 443 LAREGEERTLNVQATREPED--NGNGYVVTFDDITDLVI---------------------AQRSAAWGDVARRIAHEIKN 499 (712)
T ss_pred cccCCCceeeeeeeeecccc--cCCceEEEecchHHHHH---------------------HHHHHHHHHHHHHHHHHhcC
Confidence 34456666777666655332 22368889999999888 3445555555 346688888
Q ss_pred chhhccc
Q 043549 129 SQSHIRA 135 (162)
Q Consensus 129 ~~~~~~~ 135 (162)
|.+++..
T Consensus 500 PLTPIQL 506 (712)
T COG5000 500 PLTPIQL 506 (712)
T ss_pred CCchhhh
Confidence 8877753
No 35
>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]
Probab=94.71 E-value=0.27 Score=31.92 Aligned_cols=84 Identities=21% Similarity=0.360 Sum_probs=51.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHH-HHHHHHHH-HHcCCceEEEEEEEecCCce-EEEEEEeeeeeCCCCCeEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKN-EVEKIRDA-VRNGKSYCGRLLNYKKDGTP-FWNLLTVTPIKDDSGKTIKFI 77 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~-~~~~~~~~-~~~~~~~~~e~~~~~~dG~~-~~~~~~~~~i~d~~g~~~~~v 77 (162)
++||+..+..+.. ...+........ ........ .........+.....++|.. .+......+... .|.+..+.
T Consensus 144 ~~g~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~-~~~~~~~~ 219 (232)
T COG2202 144 LLGYSPEEELGRG---LSDLIHPEDEERRELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRD-DGEIVGVV 219 (232)
T ss_pred HhCCChHHhcCCC---hhheEecCCCchhhHHHHHHhhccCCCCcceEEEEEecCCCEEEEEEeeeeEecC-CCceEEEE
Confidence 4678766666666 433332222211 11122222 22233466788888899996 777777766654 68888888
Q ss_pred EEeeeccccch
Q 043549 78 GMQVEVSKYTE 88 (162)
Q Consensus 78 ~~~~DITe~k~ 88 (162)
....|++++++
T Consensus 220 ~~~~d~~~~~~ 230 (232)
T COG2202 220 GIARDITERKQ 230 (232)
T ss_pred EEEechHHHhh
Confidence 99999998876
No 36
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=94.46 E-value=0.16 Score=40.31 Aligned_cols=81 Identities=17% Similarity=0.088 Sum_probs=59.5
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||...|+.|.+ --.+++.++..-..+.-.+.+++|++.-.-++..+|+|.+.|+..+...+. .+|++-.++..-
T Consensus 305 ~lgy~eaEL~~m~---gY~lvH~~D~~y~Aeah~e~iktgeSGmlvyR~qtk~grw~wvqssarlly-kngkPD~vi~th 380 (712)
T KOG3560|consen 305 TLGYCEAELHGMP---GYNLVHVEDKVYMAEAHSEGIKTGESGMLVYREQTKAGRWAWVQSSARLLY-KNGKPDLVIDTH 380 (712)
T ss_pred hhccchhhccCCC---ccceeehhhhhhhhHHHHHHhhcCCcceEEEEEeecCCcEEEeeccceeee-ecCCCCEEEecC
Confidence 4789999999877 433444444333345666788888887778888999999999988777665 467887777777
Q ss_pred eeccc
Q 043549 81 VEVSK 85 (162)
Q Consensus 81 ~DITe 85 (162)
+-+++
T Consensus 381 r~l~D 385 (712)
T KOG3560|consen 381 RGLGD 385 (712)
T ss_pred CCccc
Confidence 77776
No 37
>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long.
Probab=93.96 E-value=0.39 Score=31.24 Aligned_cols=70 Identities=20% Similarity=0.192 Sum_probs=54.1
Q ss_pred cccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 8 ELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 8 e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
|+.|++ +..+..+.........+...+...............+|....++....|+.+++|.+..++|..
T Consensus 67 d~tG~~---~~el~~~~~~~~~~~~~~~v~~~~~p~~~~~~~~~~~g~~~~~e~l~LPL~~~~~~v~rilG~~ 136 (137)
T PF07310_consen 67 DLTGRR---LSELFPPEDRERVRRAYRAVVERPAPVRARGRAEDADGRYLEYERLLLPLRSDGGTVDRILGAL 136 (137)
T ss_pred CCCCCC---HHHhcChHhHHHHHHHHHHHHcCCceEEEEEEEecCCCCeeEEEEEEcccCCCCCCccEEEEec
Confidence 566777 6656666655556667777777778877777777888988888888999999889888888863
No 38
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=92.74 E-value=0.93 Score=35.98 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=28.3
Q ss_pred CCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccchhhhh
Q 043549 53 DGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTEGVND 92 (162)
Q Consensus 53 dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~e~e 92 (162)
+|. ++.....|+.+ +|.+.+++.+++|+|+.++.+.+
T Consensus 296 ~g~--~~~~~~~pi~~-~g~~~g~v~~~rDite~~~l~~~ 332 (542)
T PRK11086 296 NGR--LLLTNTVPVRV-NGEIIGAIATFRDKTEVRQLAQR 332 (542)
T ss_pred CCE--EEEEEEEEEeE-CCEEEEEEEEEEEchHHHHHHHH
Confidence 454 34456779987 78899999999999998875443
No 39
>PF08348 PAS_6: YheO-like PAS domain; InterPro: IPR013559 This domain is found in various hypothetical bacterial proteins that are similar to the Escherichia coli protein YheO (P64624 from SWISSPROT). Their function is unknown, but a few members are annotated as being HTH-containing proteins and putative DNA-binding proteins.
Probab=92.14 E-value=0.87 Score=28.95 Aligned_cols=47 Identities=21% Similarity=0.282 Sum_probs=37.1
Q ss_pred CceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccchh
Q 043549 41 KSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTEG 89 (162)
Q Consensus 41 ~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~ 89 (162)
..+...+....++|. .++.+...++|++|++++.+++..|+|....+
T Consensus 66 ~~~~~nY~~~~~~Gk--~lrSsT~~Ird~~g~~iG~LCIN~D~s~~~~~ 112 (118)
T PF08348_consen 66 EDYIINYKTKTKDGK--ILRSSTFFIRDENGKLIGALCINFDISALEQA 112 (118)
T ss_pred CCccccccccCCCCC--EEEEEEEEEECCCCCEEEEEEEEeccHHHHHH
Confidence 344455666778885 45667888999999999999999999987774
No 40
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=91.96 E-value=0.95 Score=35.09 Aligned_cols=74 Identities=12% Similarity=0.069 Sum_probs=39.8
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++||+.++..|++ ...+..+. .....+ ... ...........+|. ++.+...|..+ + .++.+.
T Consensus 130 l~g~~~~~~~g~~---~~~~~~~~---~~~~~~----~~~-~~~~~~~~~~~~~~--~~~~~~~~~~~--~---~~~~~~ 191 (430)
T PRK11006 130 LLGFRWPEDNGQN---ILNLLRYP---EFTQYL----KTR-DFSRPLTLVLNNGR--HLEIRVMPYTE--G---QLLMVA 191 (430)
T ss_pred HhCCCChHhCCCc---HHHHhcCH---HHHHHH----Hhc-ccCCCeEEEcCCCC--EEEEEEEEcCC--C---cEEEEE
Confidence 4789989999998 55444321 121111 111 11122223344554 44455556543 3 256778
Q ss_pred eeccccchhhhh
Q 043549 81 VEVSKYTEGVND 92 (162)
Q Consensus 81 ~DITe~k~~e~e 92 (162)
+|||++++.+..
T Consensus 192 ~dit~~~~~e~~ 203 (430)
T PRK11006 192 RDVTQMHQLEGA 203 (430)
T ss_pred ehhhHHHHHHHH
Confidence 999999886543
No 41
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=91.68 E-value=0.042 Score=43.59 Aligned_cols=148 Identities=14% Similarity=0.225 Sum_probs=76.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++|++.++++|++ ...+...... ....+.+..+++.......+..+. . -....|+. .+|.+.+.++++
T Consensus 149 ~~gl~~e~~~gk~---~~~v~~~~~~----s~~l~vl~~~kp~~~~~~~~~~~~--~--i~~~~pv~-~~g~l~G~v~~~ 216 (560)
T COG3829 149 LLGLSPEEVLGKH---LLDVVSAGED----STLLEVLRTGKPIRDVVQTYNGNK--I--IVNVAPVY-ADGQLIGVVGIS 216 (560)
T ss_pred HhCCCHHHHcCCc---HHHHHhccCC----ceehhhhhcCCcceeeeeeecCCc--e--eEeeccEe-cCCcEEEEEEee
Confidence 3688889999998 5444311111 123455566666554443332222 1 23445554 456899999999
Q ss_pred eeccccchhhhhhhcccCC--chhhhhhhchhhHHHHhhhHHHHHHHhccchhhcc----------ccchhHHHHHHHHH
Q 043549 81 VEVSKYTEGVNDKALRPNG--LSKSLIRYDARQKEKALGSITEVIQTVKRSQSHIR----------ALSLDTTNKLEEKR 148 (162)
Q Consensus 81 ~DITe~k~~e~e~~~~~~~--l~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~l~~~~~~~~ 148 (162)
+|+++......+....... ++..--+.+-..+...+-+.-.....+........ .+++...+...|-.
T Consensus 217 ~~~~~l~~l~~~~~~~~~~~~~~a~y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~ 296 (560)
T COG3829 217 KDVSELERLTRELEESEGLLRLKAKYTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRAN 296 (560)
T ss_pred cchHHHHHHHHHHHHHhhhhccccccchhhhccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccC
Confidence 9999988765443333311 11111222223333332222222222222211111 24455556677777
Q ss_pred hhHHHHHHHhhh
Q 043549 149 SSILIVLCLHLL 160 (162)
Q Consensus 149 ~~~~~~~~~~~~ 160 (162)
.+++.++|.+++
T Consensus 297 ~PFIaiNCaAiP 308 (560)
T COG3829 297 GPFIAINCAAIP 308 (560)
T ss_pred CCeEEEecccCC
Confidence 888888888765
No 42
>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=91.54 E-value=1.3 Score=29.40 Aligned_cols=79 Identities=18% Similarity=0.139 Sum_probs=51.1
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEE-eeeeeCCCCCeEEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLT-VTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~-~~~i~d~~g~~~~~v~~ 79 (162)
|++++-+++.+.| ...-..+...+.....+.+....|-.....-..+.+.|..|+++-. +=-+.|++|...+--.+
T Consensus 65 l~e~~w~el~~lP---sr~sae~~~r~er~~lL~~v~~qG~~~~y~GiRiss~Grrf~ie~a~vW~l~D~~g~~~GqAa~ 141 (148)
T PF08670_consen 65 LFETTWDELVGLP---SRLSAEEPERKERQSLLAQVMQQGYIDNYSGIRISSTGRRFRIERATVWNLIDEDGNYCGQAAM 141 (148)
T ss_pred HhcCCHHHHhcCc---HhhccChhhHHHHHHHHHHHHHhCCccCCCeEEEcCCCCeEEEeceEEEEEEcCCCCEEEEEEE
Confidence 4677888888888 7765555444555566666666665444445667889998887643 33456778877665554
Q ss_pred eee
Q 043549 80 QVE 82 (162)
Q Consensus 80 ~~D 82 (162)
+.+
T Consensus 142 F~~ 144 (148)
T PF08670_consen 142 FSN 144 (148)
T ss_pred Eee
Confidence 443
No 43
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=89.10 E-value=1.1 Score=36.02 Aligned_cols=75 Identities=11% Similarity=0.132 Sum_probs=45.0
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeee--CCCCCe--EEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIK--DDSGKT--IKF 76 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~--d~~g~~--~~~ 76 (162)
++|++.++++|++ +..+.+... +.+.+..+...... .....+|..++ +...|+. +++|.. .+.
T Consensus 112 Llg~~~eel~Gk~---i~eli~~~~-------l~~~le~~~~~~~~-~~v~~~g~~~~--v~~~PI~~~d~~g~~~~~Ga 178 (520)
T PRK10820 112 LFGQSEEKLRNHT---AAQLINGFN-------FLRWLESEPQDSHN-EHVVINGQDFL--MEITPVYLQDENDQHVLVGA 178 (520)
T ss_pred HHCcCHHHHCCCc---HHHHcCcch-------HHHHHHcCCCccce-EEEEECCEEEE--EEEEeeeecCCCCceeEEEE
Confidence 4788888999999 666654321 22333333321111 22344576555 4567776 656653 789
Q ss_pred EEEeeeccccch
Q 043549 77 IGMQVEVSKYTE 88 (162)
Q Consensus 77 v~~~~DITe~k~ 88 (162)
|.+++|+++..+
T Consensus 179 Vivlrd~~~l~~ 190 (520)
T PRK10820 179 VVMLRSTARMGR 190 (520)
T ss_pred EEEeccHHHHHH
Confidence 999999997643
No 44
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=78.72 E-value=2 Score=33.17 Aligned_cols=69 Identities=10% Similarity=-0.051 Sum_probs=41.0
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCC
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGK 72 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~ 72 (162)
++||++.+++|+. +-..++..+.......-...+..|..-.--+++..+.|.+.|+.-....+.+....
T Consensus 247 ltgYepqdliekt---LY~~ih~~D~~~lr~~H~~ll~kGqvtTkYYR~l~k~ggwvwvqsyat~vHnSrSS 315 (598)
T KOG3559|consen 247 LTGYEPQDLIEKT---LYHHIHGCDSFHLRCAHHLLLVKGQVTTKYYRFLLKQGGWVWVQSYATFVHNSRSS 315 (598)
T ss_pred hhCCCchhhhhHH---HHHHhhhhhHHHHHHHHHHHHhccccccHHHHHHHcCCceEEEEEeeEEEeccccC
Confidence 4799999999998 44344443333333333333444433333456667888888887777666655443
No 45
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=78.32 E-value=9.2 Score=22.58 Aligned_cols=47 Identities=28% Similarity=0.433 Sum_probs=32.3
Q ss_pred HHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeecc
Q 043549 33 IRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVS 84 (162)
Q Consensus 33 ~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DIT 84 (162)
+.+.+..++... .....|...-+.+.+.|+++.+|.++.-+|+ -|+|
T Consensus 37 Le~vl~~g~v~r----~~P~~G~Y~G~PViV~PI~~~~g~viaAiGv-VD~t 83 (84)
T PF09884_consen 37 LEEVLETGKVIR----VTPIEGPYKGVPVIVAPIKDEDGEVIAAIGV-VDLT 83 (84)
T ss_pred HHHHHHcCCEEE----eccCCcccCCeeEEEEEEEcCCCCEEEEEEE-EEcc
Confidence 445565554432 2334565556677899999999999999986 6776
No 46
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=76.90 E-value=22 Score=31.62 Aligned_cols=23 Identities=4% Similarity=0.108 Sum_probs=16.8
Q ss_pred CCCeEEEEEEeeeccccchhhhh
Q 043549 70 SGKTIKFIGMQVEVSKYTEGVND 92 (162)
Q Consensus 70 ~g~~~~~v~~~~DITe~k~~e~e 92 (162)
.+...++++.++|||++++.+.+
T Consensus 675 ~~~~~~~~~~~~dite~~~~~~~ 697 (1197)
T PRK09959 675 ASDHAVYICGWQDITETRDLIHA 697 (1197)
T ss_pred CCCceEEEEEEEehhHHHHHHHH
Confidence 34455678888999999886543
No 47
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=74.16 E-value=9.2 Score=31.61 Aligned_cols=77 Identities=14% Similarity=0.197 Sum_probs=45.4
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEe
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQ 80 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~ 80 (162)
++|++.++++|++ ...+.+.. ..+.+.+..+..+.........+|..+++.+.+.|+.+..|. +++.+.
T Consensus 235 llg~s~~~l~G~~---i~~l~~~~------~~l~~vl~~~~~~~~~~~~l~~~g~~~~~~v~~~Pi~~~~g~--~~v~~l 303 (638)
T PRK11388 235 LLRLDATASQGRA---ITELLTLP------AVLQQAIKQAHPLKHVEVTFESQGQFIDAVITLKPIIEGQGT--SFILLL 303 (638)
T ss_pred HhCcCHHHHCCCc---HHHHhccc------hHHHHHHhcCCceeeEEEEEecCCceEEEEEEEEeecccCce--EEEEEe
Confidence 4677778888888 55554321 123344555554443333334467777888888998654443 355556
Q ss_pred eeccccch
Q 043549 81 VEVSKYTE 88 (162)
Q Consensus 81 ~DITe~k~ 88 (162)
+|++..++
T Consensus 304 ~~~~~~~~ 311 (638)
T PRK11388 304 HPVEQMRQ 311 (638)
T ss_pred hhhHHHHH
Confidence 78776544
No 48
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=67.77 E-value=33 Score=25.96 Aligned_cols=89 Identities=13% Similarity=0.135 Sum_probs=46.4
Q ss_pred HHHHHHHHHHcCCceE-EEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccchhhhhhhcccCCchhhhhhh
Q 043549 29 EVEKIRDAVRNGKSYC-GRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTEGVNDKALRPNGLSKSLIRY 107 (162)
Q Consensus 29 ~~~~~~~~~~~~~~~~-~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~e~e~~~~~~~l~~~~~~~ 107 (162)
....+.+....+..+. .+.-.. .+|....+...+.|+....|.+ +..++-+....+...+...+
T Consensus 62 ll~ll~q~~~~~~~~~~~~v~l~-~~g~~~~v~~~v~~v~~~~G~v---lle~~~~~~~~ridre~~q~----------- 126 (363)
T COG3852 62 LLSLLDQVLERGQPVTEYEVTLV-ILGRSHIVDLTVAPVPEEPGSV---LLEFHPRDMQRRLDREQTQH----------- 126 (363)
T ss_pred HHHHHHHHHHhcCCcccceeeee-ecCccceEEEEEeeccCCCCeE---EEEechhHHHhHhhHHHHHH-----------
Confidence 3444555555554443 233333 7888889999999997766643 34344444433322221111
Q ss_pred chhhHHHHhhhHHHHHHHhccchhhcc
Q 043549 108 DARQKEKALGSITEVIQTVKRSQSHIR 134 (162)
Q Consensus 108 d~~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (162)
.+.....+-..+..++++++.+.+.
T Consensus 127 --a~~~a~~~L~r~LAHEIKNPL~GiR 151 (363)
T COG3852 127 --AQQRAVKGLVRGLAHEIKNPLGGIR 151 (363)
T ss_pred --HHHHHHHHHHHHHHHHhcCcccchh
Confidence 1111223344667777777765443
No 49
>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]
Probab=66.15 E-value=68 Score=26.13 Aligned_cols=74 Identities=15% Similarity=0.193 Sum_probs=44.1
Q ss_pred CCCCc--ccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEE
Q 043549 2 SDPTG--KELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGM 79 (162)
Q Consensus 2 ~G~~~--~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~ 79 (162)
+|++. .+++|++ ...+.+|+.. +.+.+..+++...+. .+-+|. ++-....|+.. +|++.+.+.+
T Consensus 248 l~~~~~~~~~ig~~---i~~v~~p~~~------l~~vl~~~~~~~~~e--~~~ng~--~~i~nr~pI~~-~~~~~GaI~t 313 (537)
T COG3290 248 LGLRQPSGDPIGRS---IVEVLPPDSD------LPEVLETGKPQHDEE--IRINGR--LLVANRVPIRS-GGQIVGAIIT 313 (537)
T ss_pred hcccCcCccccccc---ceEeeccccC------cHHHHhcCCcccchh--hhcCCe--EEEEEeccEEE-CCEEeEEEEE
Confidence 44443 3678888 6666665321 122234444433322 233444 44456677764 6789999999
Q ss_pred eeeccccchh
Q 043549 80 QVEVSKYTEG 89 (162)
Q Consensus 80 ~~DITe~k~~ 89 (162)
+||-||-++.
T Consensus 314 FRdktei~~L 323 (537)
T COG3290 314 FRDKTEIKKL 323 (537)
T ss_pred EecHHHHHHH
Confidence 9999998874
No 50
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=52.30 E-value=70 Score=27.99 Aligned_cols=19 Identities=21% Similarity=0.048 Sum_probs=14.8
Q ss_pred EEEEEeeeccccchhhhhh
Q 043549 75 KFIGMQVEVSKYTEGVNDK 93 (162)
Q Consensus 75 ~~v~~~~DITe~k~~e~e~ 93 (162)
..++++.|||++++.+++.
T Consensus 415 ~~i~~~~Dit~r~~~e~~L 433 (924)
T PRK10841 415 VAICVLVDVSARVKMEESL 433 (924)
T ss_pred EEEEEEEEhhHHHHHHHHH
Confidence 4678889999999966543
No 51
>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]
Probab=50.83 E-value=39 Score=29.21 Aligned_cols=65 Identities=12% Similarity=0.124 Sum_probs=40.2
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCce---EEEEEEEecCCceEEEEEEeeeeeC
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSY---CGRLLNYKKDGTPFWNLLTVTPIKD 68 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~~e~~~~~~dG~~~~~~~~~~~i~d 68 (162)
++||-+.+++|+++ +. ++++.+...........++.++.- ...+++...+|..+.+...+..+.+
T Consensus 353 ~LGyLPqDLIG~si--l~-f~H~eDr~vm~q~H~~v~q~~G~p~F~~sp~Rf~aqNG~yv~ldTeWSsFVN 420 (1114)
T KOG3753|consen 353 LLGYLPQDLIGTSI--LA-FVHPEDRHVMVQIHQKVLQSGGKPVFSHSPIRFCAQNGSYVRLDTEWSSFVN 420 (1114)
T ss_pred hhccCchhhhccch--hh-hhcCCchHHHHHHHHHHHHhCCCCcccccceeeeecCCcEEEEechhhhccC
Confidence 47999999999994 44 444555444444444455444322 3457777888987766655544444
No 52
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=45.36 E-value=65 Score=20.19 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=32.5
Q ss_pred CCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCce-EEEEEEEecCCceEEEEEEeeeee
Q 043549 3 DPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSY-CGRLLNYKKDGTPFWNLLTVTPIK 67 (162)
Q Consensus 3 G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~e~~~~~~dG~~~~~~~~~~~i~ 67 (162)
|..-++++|+. +..+.......+.+.+++...... ..+-.....+|....+.+.+..+.
T Consensus 50 G~ele~lig~~------~~~~~~~sEi~r~I~EaL~~d~rI~~V~~f~f~~~~~~l~v~f~V~ti~ 109 (112)
T PF10934_consen 50 GSELEDLIGKN------YPREYVESEIEREIEEALLQDPRITSVENFSFEWEGDSLYVSFTVTTIY 109 (112)
T ss_pred chhHHHHhcCC------CChHHHHHHHHHHHHHHHhcCCCcceEEEEEEEEECCEEEEEEEEEEec
Confidence 44455666664 111222334566777777665433 233344456677777777766653
No 53
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=42.61 E-value=33 Score=21.78 Aligned_cols=27 Identities=15% Similarity=0.026 Sum_probs=22.6
Q ss_pred EEecCCceEEEEEEeeeeeCCCCCeEE
Q 043549 49 NYKKDGTPFWNLLTVTPIKDDSGKTIK 75 (162)
Q Consensus 49 ~~~~dG~~~~~~~~~~~i~d~~g~~~~ 75 (162)
.+++||+.+.+.-....+.+++|.+.+
T Consensus 69 ~rR~DGs~i~FddNA~Viin~~g~P~G 95 (122)
T COG0093 69 VRRPDGSYIKFDDNAAVIINPDGEPRG 95 (122)
T ss_pred eEcCCCCEEEeCCceEEEECCCCCccc
Confidence 467899999888888888888888865
No 54
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=41.25 E-value=67 Score=25.72 Aligned_cols=32 Identities=6% Similarity=-0.081 Sum_probs=23.1
Q ss_pred EEEEeeeeeCCCCCeEEEEEEeeeccccchhhh
Q 043549 59 NLLTVTPIKDDSGKTIKFIGMQVEVSKYTEGVN 91 (162)
Q Consensus 59 ~~~~~~~i~d~~g~~~~~v~~~~DITe~k~~e~ 91 (162)
+.....|+.. +|.+.+.+.+++|+|+.++.+.
T Consensus 299 ~~~~~~~i~~-~~~~~G~v~~~~d~te~~~l~~ 330 (545)
T PRK15053 299 VIANREAIRS-GDDLLGAIISFRSKDEISTLNA 330 (545)
T ss_pred EEEEeeeEEE-CCeEEEEEEEEEchHHHHHHHH
Confidence 3355677764 4567799999999999877544
No 55
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=41.11 E-value=65 Score=19.98 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=18.1
Q ss_pred EEEEEeeeeeCCCCCeEEEEEEeeec
Q 043549 58 WNLLTVTPIKDDSGKTIKFIGMQVEV 83 (162)
Q Consensus 58 ~~~~~~~~i~d~~g~~~~~v~~~~DI 83 (162)
+......|+.|.+|++++++.+...+
T Consensus 88 ~~~~~~~PV~d~~g~viG~V~VG~~~ 113 (116)
T PF14827_consen 88 PSLRAFAPVYDSDGKVIGVVSVGVSL 113 (116)
T ss_dssp EEEEEEEEEE-TTS-EEEEEEEEEEH
T ss_pred eEEEEEEeeECCCCcEEEEEEEEEEc
Confidence 44456789999999999998876544
No 56
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.84 E-value=66 Score=22.91 Aligned_cols=36 Identities=19% Similarity=0.324 Sum_probs=27.6
Q ss_pred ecCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccch
Q 043549 51 KKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYTE 88 (162)
Q Consensus 51 ~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k~ 88 (162)
-+||. .++-+...++|..|++++.+|+.-|++-..-
T Consensus 86 ~~~g~--~ikSsS~~Irn~~g~~iGmLCIN~d~s~l~~ 121 (220)
T COG2964 86 AKDGR--LIKSSSIFIRNKEGRIIGMLCINMDLSLLVP 121 (220)
T ss_pred CCCCc--eeeeeEEEEEcCCCCEEEEEEEecchhhhhH
Confidence 34554 4556677889999999999999999995433
No 57
>COG5388 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.18 E-value=69 Score=22.39 Aligned_cols=74 Identities=15% Similarity=0.117 Sum_probs=47.6
Q ss_pred ccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCceEEEEEEEecCCceEEEEEEeeeeeCCCCCeEEEEEEeeec
Q 043549 7 KELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEV 83 (162)
Q Consensus 7 ~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DI 83 (162)
.|+-|.+ +..+..+.+.....+.+.........+..........|...-+++-..|+....|....++|...-+
T Consensus 86 RELr~~~---F~sLW~~~~~~~~~r~~~~v~~~~tPvl~~~dg~s~~G~sl~fEmLl~PL~~~~g~~~R~LGais~~ 159 (209)
T COG5388 86 RELRGRD---FLSLWAEADRLELKRAADGVRKRRTPVLVTADGRSHGGRSLGFEMLLAPLQGASGETDRFLGAISPI 159 (209)
T ss_pred hhhcCCc---hhHhccccchHHHHHHHHHHhhccCceEEecchhhccCcccceeeeeecccCCCCCccchhhhcccc
Confidence 3555555 4444445444444455555555555655555556677777888888999988888877788766544
No 58
>PF02743 Cache_1: Cache domain; InterPro: IPR004010 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions [].; GO: 0016020 membrane; PDB: 3C8C_A 3LIB_D 3LIA_A 3LI8_A 3LI9_A.
Probab=37.02 E-value=73 Score=18.06 Aligned_cols=29 Identities=28% Similarity=0.483 Sum_probs=21.8
Q ss_pred EEEEEEeeeeeCCCCCeEEEEEEeeeccc
Q 043549 57 FWNLLTVTPIKDDSGKTIKFIGMQVEVSK 85 (162)
Q Consensus 57 ~~~~~~~~~i~d~~g~~~~~v~~~~DITe 85 (162)
-++-....|+.+.+|++.+++++--++..
T Consensus 12 ~~vi~~s~pi~~~~g~~~Gvv~~di~l~~ 40 (81)
T PF02743_consen 12 QPVITISVPIYDDDGKIIGVVGIDISLDQ 40 (81)
T ss_dssp EEEEEEEEEEEETTTEEEEEEEEEEEHHH
T ss_pred cEEEEEEEEEECCCCCEEEEEEEEeccce
Confidence 35566789999988999999887555544
No 59
>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=33.38 E-value=1.3e+02 Score=19.32 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=25.1
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCCc
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGKS 42 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 42 (162)
+.|++++.++|++. +..+.|=...+.....+.+....+.-
T Consensus 48 ~sg~~p~~vlGr~F--F~eVAPC~~~~~f~gRF~~g~~~g~L 87 (124)
T TIGR02373 48 ITGRDPERVIGRNF--FKEVAPCTDIPEFSGRFMEGVASGTL 87 (124)
T ss_pred hcCCChhhhhchhh--hhhcccccCCHHHHHHHHhhhhcCCC
Confidence 35889999999992 33333322344566777776666543
No 60
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=32.92 E-value=53 Score=21.04 Aligned_cols=20 Identities=30% Similarity=0.707 Sum_probs=14.8
Q ss_pred EeeeeeCCCCCeEEEEEEeeec
Q 043549 62 TVTPIKDDSGKTIKFIGMQVEV 83 (162)
Q Consensus 62 ~~~~i~d~~g~~~~~v~~~~DI 83 (162)
.+.|+.|..|++++|-| |.+
T Consensus 79 iifPI~d~~G~vvgF~g--R~l 98 (128)
T PF08275_consen 79 IIFPIRDERGRVVGFGG--RRL 98 (128)
T ss_dssp EEEEEE-TTS-EEEEEE--EES
T ss_pred EEEEEEcCCCCEEEEec--ccC
Confidence 47899999999999988 455
No 61
>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]
Probab=28.91 E-value=41 Score=27.71 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=18.7
Q ss_pred hhhHHHHhhhH-HHHHHHhccchhhc
Q 043549 109 ARQKEKALGSI-TEVIQTVKRSQSHI 133 (162)
Q Consensus 109 ~~~~~~~~~~~-~~~~~~~~~~~~~~ 133 (162)
...|+..+|++ ++..|++|.|..-.
T Consensus 377 QA~kLA~LGQmSA~iaHElNQPLaai 402 (603)
T COG4191 377 QAGKLAALGQMSAGIAHELNQPLAAI 402 (603)
T ss_pred HHHHHHHHHHHHHHHHHHhcCcHHHH
Confidence 46788889998 56888888875433
No 62
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.64 E-value=1.8e+02 Score=18.29 Aligned_cols=34 Identities=32% Similarity=0.367 Sum_probs=23.0
Q ss_pred cCCceEEEEEEeeeeeCCCCCeEEEEEEeeeccccc
Q 043549 52 KDGTPFWNLLTVTPIKDDSGKTIKFIGMQVEVSKYT 87 (162)
Q Consensus 52 ~dG~~~~~~~~~~~i~d~~g~~~~~v~~~~DITe~k 87 (162)
..|-..-..+.+.|++ ++|+++.-+|+ .|+|.--
T Consensus 70 ~~GpY~G~pVVV~Pik-~~g~viaAiGi-VDlt~gi 103 (123)
T COG4048 70 IIGPYRGLPVVVAPIK-DEGEVIAAIGI-VDLTAGI 103 (123)
T ss_pred CCCccCCceEEEEEec-cCCeEEEEEEe-eehhhhh
Confidence 3444444556788998 57888888886 6777543
No 63
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=23.65 E-value=1.3e+02 Score=19.56 Aligned_cols=29 Identities=17% Similarity=-0.017 Sum_probs=22.7
Q ss_pred EEEecCCceEEEEEEeeeeeCCCCCeEEE
Q 043549 48 LNYKKDGTPFWNLLTVTPIKDDSGKTIKF 76 (162)
Q Consensus 48 ~~~~~dG~~~~~~~~~~~i~d~~g~~~~~ 76 (162)
...++||+.+.+.-....+.+.+|.+.+.
T Consensus 79 ~~~R~dGs~i~F~dNa~VLin~~~~p~GT 107 (132)
T PRK08571 79 EYRRPDGTRVKFEDNAAVIVTPEGTPKGT 107 (132)
T ss_pred ceEcCCCcEEEeCCcEEEEECCCCCEeee
Confidence 34678999888888888888888887653
No 64
>PF01724 DUF29: Domain of unknown function DUF29; InterPro: IPR002636 This entry is represented by Ralstonia phage RSS1, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family.; PDB: 3FCN_A.
Probab=23.36 E-value=1e+02 Score=20.11 Aligned_cols=17 Identities=47% Similarity=0.399 Sum_probs=12.9
Q ss_pred HHHhhHHHHHHHhhhcC
Q 043549 146 EKRSSILIVLCLHLLKM 162 (162)
Q Consensus 146 ~~~~~~~~~~~~~~~~~ 162 (162)
+.-.|...+++.||+|.
T Consensus 43 ~~l~s~L~~ll~HLLK~ 59 (139)
T PF01724_consen 43 RALESRLRVLLAHLLKW 59 (139)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44467888889999883
No 65
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=22.88 E-value=1.5e+02 Score=19.60 Aligned_cols=28 Identities=18% Similarity=0.093 Sum_probs=22.5
Q ss_pred EEEecCCceEEEEEEeeeeeCCCCCeEE
Q 043549 48 LNYKKDGTPFWNLLTVTPIKDDSGKTIK 75 (162)
Q Consensus 48 ~~~~~dG~~~~~~~~~~~i~d~~g~~~~ 75 (162)
...++||+.+.+.-....+.+.+|.+.+
T Consensus 86 ~~rR~dGs~i~F~dNA~VLin~~~~p~G 113 (139)
T PTZ00054 86 AWRRKDGVFIYFEDNAGVIVNPKGEMKG 113 (139)
T ss_pred ceEcCCCcEEEeCCcEEEEECCCCCEee
Confidence 3467899988888888888888888765
No 66
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=21.24 E-value=1e+02 Score=17.11 Aligned_cols=26 Identities=23% Similarity=0.396 Sum_probs=12.1
Q ss_pred EEecCCceEEEEEEeeeeeCCCCCeEEEE
Q 043549 49 NYKKDGTPFWNLLTVTPIKDDSGKTIKFI 77 (162)
Q Consensus 49 ~~~~dG~~~~~~~~~~~i~d~~g~~~~~v 77 (162)
....+|++.++- ..+.+++|..+++|
T Consensus 3 l~~~~G~~lPfG---A~v~~~~g~~~g~V 28 (68)
T PF13953_consen 3 LRDADGKPLPFG---ASVSDEDGNNIGIV 28 (68)
T ss_dssp EEETTSEE--TT----EEEETTSSEEEEB
T ss_pred EEcCCCCcCCCC---cEEEcCCCCEEEEE
Confidence 445677666542 22335556655554
No 67
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=21.20 E-value=1.4e+02 Score=25.88 Aligned_cols=81 Identities=12% Similarity=0.051 Sum_probs=52.2
Q ss_pred CCCCCcccccCCCCCCcccccCCCCCHHHHHHHHHHHHcCC-ceEEEEEEEecCCceEEEEEEeeeeeCCC-CCeEEEEE
Q 043549 1 MSDPTGKELIGCCLLCSRFLQGPETDKNEVEKIRDAVRNGK-SYCGRLLNYKKDGTPFWNLLTVTPIKDDS-GKTIKFIG 78 (162)
Q Consensus 1 l~G~~~~e~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~~dG~~~~~~~~~~~i~d~~-g~~~~~v~ 78 (162)
+.||...++.|+. +....++++.......+.......+ ....-++.+.++|...|....+....+.. ..+.++++
T Consensus 394 i~~~~~~~~~g~s---s~~s~h~~d~~~~~~s~~~~~~~s~~~~~~~yr~~~~n~~~~~~~~~~~~~~n~~s~~~~~~~~ 470 (803)
T KOG3561|consen 394 ILGYQPQELLGRS---SYESSHPADSSPLSESLKQVQALSEQRSTLLYRFRSKNGSSIPNKSSAYLFSNPGSDEVEYIVC 470 (803)
T ss_pred ccccCchhhcCcc---cccccCccccchhhchHHHHHHhcccccccccccccCCCCccccccccccccCCCccccceeee
Confidence 4688999999998 6666666666555555544433322 22344566788999888877766665533 34566777
Q ss_pred Eeeecc
Q 043549 79 MQVEVS 84 (162)
Q Consensus 79 ~~~DIT 84 (162)
...-+.
T Consensus 471 ~ns~~~ 476 (803)
T KOG3561|consen 471 TNSNVP 476 (803)
T ss_pred cccccc
Confidence 666665
No 68
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=21.07 E-value=1.6e+02 Score=19.21 Aligned_cols=29 Identities=17% Similarity=-0.008 Sum_probs=22.5
Q ss_pred EEEecCCceEEEEEEeeeeeCCCCCeEEE
Q 043549 48 LNYKKDGTPFWNLLTVTPIKDDSGKTIKF 76 (162)
Q Consensus 48 ~~~~~dG~~~~~~~~~~~i~d~~g~~~~~ 76 (162)
...++||+.+-+.-....+.+.++.+.+.
T Consensus 78 ~~~R~dGs~i~FddNa~VLin~~~~P~GT 106 (131)
T TIGR03673 78 EYRRPDGTRVKFEDNAVVIVTPDGEPKGT 106 (131)
T ss_pred ceecCCCcEEEeCCcEEEEECCCCCEeee
Confidence 34678999888888888888888887653
No 69
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=20.74 E-value=95 Score=16.72 Aligned_cols=12 Identities=33% Similarity=0.313 Sum_probs=4.9
Q ss_pred chhHHHHHHHHH
Q 043549 137 SLDTTNKLEEKR 148 (162)
Q Consensus 137 ~~~l~~~~~~~~ 148 (162)
+||+.+++..|.
T Consensus 10 sHelr~PL~~i~ 21 (68)
T PF00512_consen 10 SHELRNPLTAIR 21 (68)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHHHH
Confidence 344444444333
No 70
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=20.00 E-value=2.1e+02 Score=24.98 Aligned_cols=25 Identities=16% Similarity=0.161 Sum_probs=17.7
Q ss_pred hhccccchhHHHHHHHHHhhHHHHH
Q 043549 131 SHIRALSLDTTNKLEEKRSSILIVL 155 (162)
Q Consensus 131 ~~~~~~~~~l~~~~~~~~~~~~~~~ 155 (162)
+...+.||||++++.-|..+.-+..
T Consensus 662 aLL~sISHDLRTPLt~i~Gaa~tL~ 686 (890)
T COG2205 662 ALLASISHDLRTPLTAIMGAAETLL 686 (890)
T ss_pred HHHHHhhccccCcHHHHhhhHHHhh
Confidence 3556778999999888876655443
Done!