Query psy936
Match_columns 344
No_of_seqs 189 out of 1865
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 17:07:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy936.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/936hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1054|consensus 100.0 1.4E-41 2.9E-46 335.8 7.0 234 83-342 441-694 (897)
2 KOG1052|consensus 100.0 1.9E-33 4.1E-38 295.0 20.8 255 44-330 204-471 (656)
3 KOG4440|consensus 100.0 7.3E-31 1.6E-35 261.0 16.7 231 85-338 460-722 (993)
4 KOG1053|consensus 100.0 2.1E-30 4.4E-35 265.5 17.2 229 85-336 463-713 (1258)
5 PF00060 Lig_chan: Ligand-gate 99.6 2.5E-18 5.5E-23 146.6 -4.9 109 204-312 1-115 (148)
6 PF00497 SBP_bac_3: Bacterial 99.2 1.6E-10 3.4E-15 102.9 10.8 95 56-191 1-95 (225)
7 PRK11917 bifunctional adhesin/ 98.8 1.5E-08 3.3E-13 94.9 10.1 101 52-192 36-139 (259)
8 PRK15010 ABC transporter lysin 98.8 1.8E-08 3.8E-13 94.0 9.7 100 53-193 25-124 (260)
9 PRK15437 histidine ABC transpo 98.8 3.4E-08 7.4E-13 92.0 9.3 100 52-192 24-123 (259)
10 PRK10797 glutamate and asparta 98.7 2.9E-08 6.3E-13 95.3 8.7 99 53-192 39-144 (302)
11 PRK15007 putative ABC transpor 98.7 4.8E-08 1E-12 89.5 9.3 97 53-190 20-116 (243)
12 PRK09495 glnH glutamine ABC tr 98.7 5.1E-08 1.1E-12 90.0 9.5 98 53-192 24-121 (247)
13 PRK11260 cystine transporter s 98.7 1.2E-07 2.5E-12 88.8 9.8 105 46-191 32-137 (266)
14 PF10613 Lig_chan-Glu_bd: Liga 98.6 1.4E-08 3.1E-13 75.5 2.4 48 82-129 13-65 (65)
15 TIGR02995 ectoine_ehuB ectoine 98.6 9.2E-08 2E-12 90.0 8.6 103 48-192 26-130 (275)
16 TIGR01096 3A0103s03R lysine-ar 98.6 1.4E-07 3E-12 86.6 9.3 101 51-192 21-121 (250)
17 TIGR03870 ABC_MoxJ methanol ox 98.4 7.1E-07 1.5E-11 82.8 8.5 89 55-192 1-92 (246)
18 PRK10859 membrane-bound lytic 98.4 7.2E-07 1.6E-11 91.1 7.6 99 51-191 40-138 (482)
19 PRK09959 hybrid sensory histid 98.2 2.1E-06 4.6E-11 96.2 7.2 106 48-192 49-155 (1197)
20 PRK09959 hybrid sensory histid 98.2 3.4E-06 7.4E-11 94.6 8.2 97 54-191 302-398 (1197)
21 cd00134 PBPb Bacterial peripla 98.1 1.5E-05 3.2E-10 69.2 8.7 94 66-194 5-98 (218)
22 TIGR03871 ABC_peri_MoxJ_2 quin 98.1 7.9E-06 1.7E-10 74.3 7.2 90 55-191 1-90 (232)
23 TIGR02285 conserved hypothetic 98.1 1E-05 2.2E-10 75.8 7.6 96 53-191 17-114 (268)
24 smart00062 PBPb Bacterial peri 98.0 3.1E-05 6.7E-10 66.9 8.3 98 55-193 1-98 (219)
25 COG0834 HisJ ABC-type amino ac 97.9 4.4E-05 9.5E-10 70.5 8.5 103 52-194 32-137 (275)
26 COG4623 Predicted soluble lyti 97.2 0.00037 8E-09 68.2 4.5 101 53-195 22-122 (473)
27 PF07885 Ion_trans_2: Ion chan 95.7 0.034 7.4E-07 42.4 6.2 56 239-294 22-78 (79)
28 TIGR01098 3A0109s03R phosphate 93.9 0.13 2.9E-06 47.1 6.1 47 89-141 49-95 (254)
29 PRK00489 hisG ATP phosphoribos 84.4 1.5 3.2E-05 41.8 4.8 51 121-194 54-106 (287)
30 KOG3713|consensus 75.4 4.6 0.0001 41.2 5.0 46 239-284 375-421 (477)
31 KOG1419|consensus 74.5 6.7 0.00015 40.8 5.9 90 206-296 235-325 (654)
32 PLN03192 Voltage-dependent pot 73.6 7.6 0.00016 42.6 6.6 52 244-295 253-305 (823)
33 TIGR03431 PhnD phosphonate ABC 71.8 8.1 0.00018 36.2 5.6 41 93-139 48-88 (288)
34 cd08468 PBP2_Pa0477 The C-term 61.2 18 0.0004 30.7 5.3 74 89-193 13-87 (202)
35 cd08459 PBP2_DntR_NahR_LinR_li 57.4 31 0.00066 29.0 6.0 70 89-192 13-83 (201)
36 cd08420 PBP2_CysL_like C-termi 57.4 25 0.00054 29.1 5.3 71 89-193 13-84 (201)
37 cd08463 PBP2_DntR_like_4 The C 57.3 32 0.00069 29.5 6.2 72 89-193 13-85 (203)
38 cd08450 PBP2_HcaR The C-termin 57.1 27 0.00058 29.1 5.5 70 89-192 13-83 (196)
39 cd08425 PBP2_CynR The C-termin 57.0 26 0.00055 29.3 5.4 69 90-192 15-84 (197)
40 PF03466 LysR_substrate: LysR 56.6 18 0.00039 30.6 4.5 70 89-192 19-89 (209)
41 cd05466 PBP2_LTTR_substrate Th 56.4 25 0.00055 28.5 5.2 70 89-192 13-83 (197)
42 cd08466 PBP2_LeuO The C-termin 56.1 26 0.00056 29.4 5.3 71 89-193 13-84 (200)
43 cd08438 PBP2_CidR The C-termin 55.7 32 0.00069 28.5 5.8 70 89-192 13-83 (197)
44 cd08415 PBP2_LysR_opines_like 55.3 31 0.00068 28.6 5.7 70 89-192 13-83 (196)
45 PRK10537 voltage-gated potassi 55.2 22 0.00047 35.7 5.3 52 239-290 166-218 (393)
46 cd08461 PBP2_DntR_like_3 The C 55.1 32 0.00069 28.8 5.7 70 89-192 13-83 (198)
47 cd08440 PBP2_LTTR_like_4 TThe 53.7 32 0.0007 28.3 5.5 70 89-192 13-83 (197)
48 cd08412 PBP2_PAO1_like The C-t 52.8 28 0.0006 29.0 4.9 70 89-192 13-83 (198)
49 cd08426 PBP2_LTTR_like_5 The C 52.6 28 0.00062 29.0 5.0 70 89-192 13-83 (199)
50 cd08451 PBP2_BudR The C-termin 52.5 29 0.00063 28.9 5.0 70 90-192 15-85 (199)
51 cd08421 PBP2_LTTR_like_1 The C 52.2 37 0.00081 28.2 5.7 70 89-192 13-83 (198)
52 cd08434 PBP2_GltC_like The sub 51.8 28 0.00061 28.7 4.8 70 89-192 13-83 (195)
53 cd08467 PBP2_SyrM The C-termin 51.8 37 0.0008 28.7 5.6 70 89-192 13-83 (200)
54 cd08448 PBP2_LTTR_aromatics_li 51.7 37 0.0008 28.1 5.5 70 89-192 13-83 (197)
55 cd08462 PBP2_NodD The C-termin 51.4 39 0.00085 28.5 5.7 70 89-193 13-83 (200)
56 cd08465 PBP2_ToxR The C-termin 51.3 32 0.00069 29.2 5.1 69 89-191 13-82 (200)
57 cd08442 PBP2_YofA_SoxR_like Th 50.1 42 0.0009 27.7 5.6 70 89-192 13-83 (193)
58 cd08446 PBP2_Chlorocatechol Th 50.0 39 0.00084 28.2 5.4 70 89-192 14-84 (198)
59 cd08456 PBP2_LysR The C-termin 49.9 34 0.00074 28.4 5.0 70 89-192 13-83 (196)
60 cd08460 PBP2_DntR_like_1 The C 49.5 44 0.00095 28.1 5.7 70 89-193 13-83 (200)
61 cd08445 PBP2_BenM_CatM_CatR Th 48.6 38 0.00082 28.6 5.2 70 89-192 14-84 (203)
62 cd08414 PBP2_LTTR_aromatics_li 48.5 39 0.00085 27.9 5.2 69 90-192 14-83 (197)
63 cd08433 PBP2_Nac The C-teminal 47.9 46 0.001 27.7 5.6 70 89-192 13-83 (198)
64 cd08419 PBP2_CbbR_RubisCO_like 47.8 38 0.00083 28.0 5.0 70 89-192 12-82 (197)
65 cd08464 PBP2_DntR_like_2 The C 47.1 53 0.0012 27.3 5.8 69 89-191 13-82 (200)
66 cd08452 PBP2_AlsR The C-termin 45.8 53 0.0011 27.6 5.6 70 89-192 13-83 (197)
67 cd08486 PBP2_CbnR The C-termin 45.2 39 0.00084 28.7 4.7 70 89-192 14-84 (198)
68 PRK03601 transcriptional regul 45.2 38 0.00082 31.4 4.9 71 89-193 102-173 (275)
69 cd08469 PBP2_PnbR The C-termin 45.1 52 0.0011 28.3 5.6 70 89-192 13-83 (221)
70 cd08430 PBP2_IlvY The C-termin 44.0 55 0.0012 27.1 5.4 44 89-139 13-57 (199)
71 cd08436 PBP2_LTTR_like_3 The C 44.0 47 0.001 27.3 5.0 71 89-192 13-84 (194)
72 cd08416 PBP2_MdcR The C-termin 43.5 56 0.0012 27.1 5.4 72 89-192 13-85 (199)
73 PRK09508 leuO leucine transcri 42.0 56 0.0012 30.8 5.7 71 89-193 125-196 (314)
74 cd08485 PBP2_ClcR The C-termin 41.5 48 0.001 28.0 4.7 44 89-139 14-58 (198)
75 cd08417 PBP2_Nitroaromatics_li 41.0 32 0.00069 28.7 3.5 70 89-192 13-83 (200)
76 PRK11242 DNA-binding transcrip 40.8 52 0.0011 30.4 5.2 71 89-193 104-175 (296)
77 cd08411 PBP2_OxyR The C-termin 40.7 62 0.0013 27.0 5.3 70 89-192 14-84 (200)
78 cd08458 PBP2_NocR The C-termin 40.5 64 0.0014 27.0 5.3 70 89-192 13-83 (196)
79 cd08427 PBP2_LTTR_like_2 The C 40.1 75 0.0016 26.2 5.6 72 89-192 13-85 (195)
80 cd08457 PBP2_OccR The C-termin 39.6 72 0.0016 26.6 5.5 44 89-139 13-57 (196)
81 cd08435 PBP2_GbpR The C-termin 39.3 67 0.0014 26.6 5.2 73 89-193 13-86 (201)
82 TIGR03339 phn_lysR aminoethylp 39.2 58 0.0013 29.6 5.2 70 90-193 98-168 (279)
83 PRK11151 DNA-binding transcrip 39.1 51 0.0011 30.8 4.9 70 89-192 104-174 (305)
84 PF01007 IRK: Inward rectifier 38.8 95 0.0021 30.5 6.7 60 240-299 83-145 (336)
85 PF12273 RCR: Chitin synthesis 38.3 24 0.00051 29.5 2.2 12 206-217 3-14 (130)
86 cd08441 PBP2_MetR The C-termin 38.1 81 0.0017 26.3 5.6 43 90-139 14-57 (198)
87 PF15050 SCIMP: SCIMP protein 38.0 77 0.0017 26.5 5.0 21 206-226 7-27 (133)
88 PRK11553 alkanesulfonate trans 36.9 57 0.0012 30.9 4.8 41 92-138 43-84 (314)
89 cd08413 PBP2_CysB_like The C-t 36.8 67 0.0015 27.0 4.9 72 89-193 13-85 (198)
90 cd08444 PBP2_Cbl The C-termina 36.6 63 0.0014 27.2 4.7 72 89-193 13-85 (198)
91 cd08418 PBP2_TdcA The C-termin 36.5 67 0.0014 26.7 4.8 72 89-192 13-85 (201)
92 cd08449 PBP2_XapR The C-termin 36.0 76 0.0017 26.2 5.0 72 89-192 13-85 (197)
93 cd08437 PBP2_MleR The substrat 35.9 78 0.0017 26.3 5.1 73 89-193 13-86 (198)
94 PF12273 RCR: Chitin synthesis 35.1 40 0.00087 28.1 3.1 26 208-233 2-27 (130)
95 PRK09906 DNA-binding transcrip 34.9 84 0.0018 29.1 5.6 69 90-192 104-173 (296)
96 cd08431 PBP2_HupR The C-termin 34.5 1.1E+02 0.0023 25.4 5.7 43 89-138 13-56 (195)
97 cd08439 PBP2_LrhA_like The C-t 34.4 79 0.0017 26.2 4.9 42 90-138 14-56 (185)
98 KOG1418|consensus 32.9 23 0.00051 34.4 1.5 58 238-295 112-170 (433)
99 TIGR02122 TRAP_TAXI TRAP trans 32.1 37 0.00081 31.9 2.7 42 92-139 48-90 (320)
100 KOG0498|consensus 31.9 42 0.00091 36.4 3.2 88 242-329 295-403 (727)
101 cd08453 PBP2_IlvR The C-termin 31.3 1.3E+02 0.0029 25.0 5.8 73 89-192 13-86 (200)
102 cd08447 PBP2_LTTR_aromatics_li 31.2 91 0.002 25.8 4.7 44 89-139 13-57 (198)
103 PF12974 Phosphonate-bd: ABC t 30.6 1E+02 0.0022 27.9 5.3 43 91-139 16-58 (243)
104 KOG3684|consensus 30.1 1.2E+02 0.0027 31.0 5.9 48 240-287 286-334 (489)
105 TIGR02136 ptsS_2 phosphate bin 29.8 77 0.0017 29.9 4.4 78 89-191 48-127 (287)
106 TIGR01729 taurine_ABC_bnd taur 29.0 1.1E+02 0.0024 28.7 5.3 38 97-140 20-57 (300)
107 PRK11482 putative DNA-binding 28.9 1.2E+02 0.0026 28.8 5.6 69 89-193 130-199 (317)
108 cd08443 PBP2_CysB The C-termin 28.8 1.2E+02 0.0025 25.6 5.0 71 89-192 13-84 (198)
109 PF10661 EssA: WXG100 protein 28.5 79 0.0017 27.2 3.8 29 200-228 114-142 (145)
110 cd08423 PBP2_LTTR_like_6 The C 28.5 1.5E+02 0.0033 24.3 5.7 73 89-192 13-88 (200)
111 KOG4390|consensus 27.6 29 0.00062 34.8 1.1 46 239-284 354-400 (632)
112 PRK10837 putative DNA-binding 27.6 1.1E+02 0.0025 28.0 5.1 70 90-193 103-173 (290)
113 PRK07377 hypothetical protein; 27.5 71 0.0015 28.7 3.4 45 89-139 93-137 (184)
114 PRK11233 nitrogen assimilation 26.0 1.5E+02 0.0032 27.8 5.6 68 90-191 106-174 (305)
115 PF13531 SBP_bac_11: Bacterial 26.0 73 0.0016 28.4 3.4 87 89-202 11-102 (230)
116 COG1638 DctP TRAP-type C4-dica 25.9 1E+02 0.0022 30.2 4.5 49 92-141 47-95 (332)
117 PF09084 NMT1: NMT1/THI5 like; 25.6 1.8E+02 0.0039 25.4 5.8 38 98-141 15-52 (216)
118 cd08428 PBP2_IciA_ArgP The C-t 25.3 1.6E+02 0.0036 24.3 5.3 40 92-138 16-55 (195)
119 PRK10341 DNA-binding transcrip 25.0 1.5E+02 0.0034 27.8 5.6 71 90-192 111-182 (312)
120 PRK15421 DNA-binding transcrip 24.5 1.6E+02 0.0035 27.9 5.6 69 91-193 104-173 (317)
121 TIGR01256 modA molybdenum ABC 23.4 1.7E+02 0.0037 25.7 5.3 41 92-139 9-50 (216)
122 COG4762 Uncharacterized protei 23.0 68 0.0015 28.0 2.3 53 5-59 81-134 (168)
123 TIGR02424 TF_pcaQ pca operon t 22.9 2E+02 0.0043 26.6 5.8 72 90-193 107-179 (300)
124 TIGR03298 argP transcriptional 22.6 1.5E+02 0.0033 27.3 5.0 65 93-191 107-171 (292)
125 PRK11013 DNA-binding transcrip 22.4 1.8E+02 0.0039 27.2 5.5 44 89-139 107-151 (309)
126 TIGR02995 ectoine_ehuB ectoine 22.3 1.2E+02 0.0026 28.0 4.2 41 290-330 121-162 (275)
127 KOG1545|consensus 22.3 17 0.00036 36.2 -1.7 76 209-285 361-438 (507)
128 PRK09986 DNA-binding transcrip 21.7 1.6E+02 0.0035 27.0 4.9 71 90-192 111-182 (294)
129 PRK12682 transcriptional regul 21.6 1.7E+02 0.0036 27.5 5.0 72 89-193 106-178 (309)
130 PRK03635 chromosome replicatio 21.1 1.8E+02 0.0038 27.0 5.1 67 91-191 105-171 (294)
131 PHA02650 hypothetical protein; 20.6 2.4E+02 0.0052 21.8 4.6 31 200-230 44-74 (81)
132 cd08478 PBP2_CrgA The C-termin 20.5 1.7E+02 0.0037 24.2 4.5 66 89-191 16-82 (199)
133 cd08429 PBP2_NhaR The C-termin 20.4 2.2E+02 0.0047 24.4 5.2 44 89-139 13-57 (204)
134 PRK09791 putative DNA-binding 20.4 2.6E+02 0.0056 25.9 6.1 74 89-194 108-182 (302)
No 1
>KOG1054|consensus
Probab=100.00 E-value=1.4e-41 Score=335.75 Aligned_cols=234 Identities=23% Similarity=0.444 Sum_probs=217.4
Q ss_pred CceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCC------chhhhhhcccceecEEEeeccchhhhhHHHhhhhhhH
Q psy936 83 GKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ------DGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSE 156 (344)
Q Consensus 83 g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~------~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~ 156 (344)
|.-++.|+++|++.+||++.+.+|++....++.||.. |+||+|.|..|++|+++++++++.+|++
T Consensus 441 gn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~grAdiavApLTIt~~REe--------- 511 (897)
T KOG1054|consen 441 GNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYGRADIAVAPLTITLVREE--------- 511 (897)
T ss_pred CCcccceeHHHHHHHHHHhcCceEEEEEecCCcccccCCCcccccchhHHHhcCccceEEeeeeeehhhhh---------
Confidence 4445669999999999999999999999989889974 6799999999999999999999999999
Q ss_pred HHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCC-CcccccccchhhHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy936 157 EEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESA-TGSGLLAPFEIEVWFLILISLVLIGPIMHAIMRVRRWLSGT 235 (344)
Q Consensus 157 ~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~-~~~~~l~PF~~~vWl~il~~~i~~~~vl~~i~r~~~~~~~~ 235 (344)
.+|||.||+..++.+|.++|..+. ..++|+.|...++|+|++.+++.++++++++.|++|++|+.
T Consensus 512 --------------viDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYEwh~ 577 (897)
T KOG1054|consen 512 --------------VIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHT 577 (897)
T ss_pred --------------hhccccchhhcCeEEEEeCcccCCCCeeeecchhHHHHHHHHHHHHhcceEEEEEEeccCchheec
Confidence 999999999999999999998765 77899999999999999999999999999999999988864
Q ss_pred C------------CCCcCchhHHHHHHHHHHcCCCCCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeecCCCCCCCC
Q psy936 236 Q------------SELYPISACTWFVYGALMKQGSTLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQFTLPIH 303 (344)
Q Consensus 236 ~------------~~~~~i~~~~~~~~~~ll~qg~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~I~ 303 (344)
+ .+.+++.+|+|++++++|+||.+..||+.|+||+.++||+|+||++++|||||+++||..++.+||+
T Consensus 578 Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvsPIE 657 (897)
T KOG1054|consen 578 EEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIE 657 (897)
T ss_pred cccccCCCCCCCCCccchhhHHHHHHHHHHHhcCCCCCccccccceeccchhhhhhhhhhhhhhHHHHHHhHHhhcCcch
Confidence 2 2367899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHhCCC-CcEEEEcCchhhHhhhhccCCCcccccccc
Q psy936 304 SVEDIANPT-NTWCAEAGGAVEYSIKLYRFQTPEHFTIFW 342 (344)
Q Consensus 304 TledL~~s~-~~~g~~~~~~~e~~l~~~~~~~~~~~~~~~ 342 (344)
|.|||++++ +.||+..++++..|++. .+...|+|+|
T Consensus 658 SaEDLAkQteIaYGt~~~GSTkeFFr~---Skiavy~kMW 694 (897)
T KOG1054|consen 658 SAEDLAKQTEIAYGTLDSGSTKEFFRR---SKIAVYEKMW 694 (897)
T ss_pred hHHHHhhcceeeeeecCCCchHHHHhh---hhHHHHHHHH
Confidence 999999987 79999999999999988 5566777777
No 2
>KOG1052|consensus
Probab=100.00 E-value=1.9e-33 Score=294.97 Aligned_cols=255 Identities=27% Similarity=0.504 Sum_probs=223.9
Q ss_pred CCCccccC--CCceEEEEecCCCcccccCCCceeeeec--CCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCC
Q psy936 44 LPDSWLII--EQLRLPIEPTIPSFLFQDQKPMSWVTTN--NKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ 119 (344)
Q Consensus 44 ~p~~~~~l--~g~~L~v~~~~P~~~~~~~~P~~~~~~~--~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~ 119 (344)
.+++...+ +|++++|+ + ...+||.....+ ..++.-.+.|+++||++++++++||+++++.++++. |..
T Consensus 204 ~~~~~~~~~~~~~~l~v~------~-~~~~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~-g~~ 275 (656)
T KOG1052|consen 204 FVPKGWFFPTNGKPLRVG------V-VTEPPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGS-GSR 275 (656)
T ss_pred cCcCCccccCCCceEEEE------E-eccCCceeeeecccccCCCCccceEEehHHHHHHHhCCCceEEEEcCCCC-CCC
Confidence 33444444 69999999 6 566676655543 223444677999999999999999999999998876 654
Q ss_pred -----chhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCC
Q psy936 120 -----DGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESA 194 (344)
Q Consensus 120 -----~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~ 194 (344)
|+|+++++.+|++|++ ++++++.+|.+ .+|||.|+.+.+.++++++++...
T Consensus 276 ~~~g~~~g~v~~l~~~~advg-~~~tit~~R~~-----------------------~vdfT~p~~~~~~~i~~~~~~~~~ 331 (656)
T KOG1052|consen 276 DPNGNWDGLVGQLVDGEADVG-ADITITPERSK-----------------------YVDFTIPYLQFGIVIIVRKPDSRS 331 (656)
T ss_pred CCCCChhHHHHHHhcCccccc-cceEEeecccc-----------------------cEEeccceEeccEEEEEEecCCcc
Confidence 4599999999999999 99999999999 999999999999999999998877
Q ss_pred CcccccccchhhHHHHHHHHHHHHHHHHHHHHHHhhcccCCC---CCCcCchhHHHHHHHHHHcCCCCCCCCCcchhHHH
Q psy936 195 TGSGLLAPFEIEVWFLILISLVLIGPIMHAIMRVRRWLSGTQ---SELYPISACTWFVYGALMKQGSTLNPRTDSTRIMF 271 (344)
Q Consensus 195 ~~~~~l~PF~~~vWl~il~~~i~~~~vl~~i~r~~~~~~~~~---~~~~~i~~~~~~~~~~ll~qg~~~~p~s~s~Ril~ 271 (344)
..+.+++||++.+|++++++++++++++|++.|+.+..+..+ ...++..+++|.+++++++|++...|++.++|++.
T Consensus 332 ~~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~ 411 (656)
T KOG1052|consen 332 KLWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYELPPRQIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLL 411 (656)
T ss_pred cceEEecCCcHHHHHHHHHHHHHHHHHHHHHhccccccCCccccceeEeecccchhhhhHHHhccCCCccccchhhhHHH
Confidence 788999999999999999999999999999999887776111 12456778999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcccceeeeeecCCCCCCCCCHHHHhC-CCCcEEEEcCchhhHhhhhc
Q psy936 272 ASWWIFIMILTAFYTANLTAFLTLSQFTLPIHSVEDIAN-PTNTWCAEAGGAVEYSIKLY 330 (344)
Q Consensus 272 ~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~I~TledL~~-s~~~~g~~~~~~~e~~l~~~ 330 (344)
++||+++++++++|||+|+|+||.++..+||++++||++ ++..+|...+++...++++.
T Consensus 412 ~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~~~dL~~~~~~~~g~~~~~~~~~~~~~~ 471 (656)
T KOG1052|consen 412 GAWWLFVLILISSYTANLTAFLTVPRLRSPIDSLDDLADQSNIPYGTQRGSFTRIYLEES 471 (656)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCCcccCHHHHHHhcCCeEEEEecchHHHHHHHH
Confidence 999999999999999999999999999999999999995 88999999999999999876
No 3
>KOG4440|consensus
Probab=99.97 E-value=7.3e-31 Score=260.96 Aligned_cols=231 Identities=22% Similarity=0.377 Sum_probs=207.5
Q ss_pred eEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCC-------------chhhhhhcccceecEEEeeccchhhhhHHHhh
Q psy936 85 LEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ-------------DGSIMNILKTGEVDMVAAFVPVLNIKKNKMAA 151 (344)
Q Consensus 85 ~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~-------------~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~ 151 (344)
.+..|+++|++-.|++++||+|+.....+.++|.+ |+|++|.|.+|++||+++++++++||.+
T Consensus 460 fCC~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~---- 535 (993)
T KOG4440|consen 460 FCCYGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQ---- 535 (993)
T ss_pred hhhhHHHHHHHHHHHHhhcceEEEEEeecccccceeeeecccccccceehhhhhhhhCCccceEeeceeeChhhhh----
Confidence 35579999999999999999999999999888874 4599999999999999999999999999
Q ss_pred hhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCCCcccccccchhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy936 152 LVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESATGSGLLAPFEIEVWFLILISLVLIGPIMHAIMRVRRW 231 (344)
Q Consensus 152 ~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vWl~il~~~i~~~~vl~~i~r~~~~ 231 (344)
.++||.|+-..++.++.+++...++..+|++||+.++|+++.+++.+++++++++.|+++.
T Consensus 536 -------------------yieFskPfkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPF 596 (993)
T KOG4440|consen 536 -------------------YIEFSKPFKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPF 596 (993)
T ss_pred -------------------heeccCcccccceEEEeeCCCCCchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 9999999999999999999999999999999999999999999999999999999999874
Q ss_pred ccC-------CCCCCcCchhHHHHHHHHHHcCCC-CCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeecCCCCCCCC
Q psy936 232 LSG-------TQSELYPISACTWFVYGALMKQGS-TLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQFTLPIH 303 (344)
Q Consensus 232 ~~~-------~~~~~~~i~~~~~~~~~~ll~qg~-~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~I~ 303 (344)
... +.+....++..+|++|+++++.|. +..||+.|.|++-++|.=|+||+.++|||||+++|...+.+..+.
T Consensus 597 gRFk~~ds~~~ee~alnlssAmWF~WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~lt 676 (993)
T KOG4440|consen 597 GRFKVNDSEEEEEDALNLSSAMWFSWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLT 676 (993)
T ss_pred cceeeccCccchhhhcchhhhHHHHhHhhhccccCCCCCcchhHHHHHHHHhhhheeeehhhhhhhhhheeecCcccccc
Confidence 332 123467899999999999999995 579999999999999999999999999999999999999998888
Q ss_pred CHHHHhC----CCCcEEEEcCchhhHhhhh-------ccCCCcccc
Q psy936 304 SVEDIAN----PTNTWCAEAGGAVEYSIKL-------YRFQTPEHF 338 (344)
Q Consensus 304 TledL~~----s~~~~g~~~~~~~e~~l~~-------~~~~~~~~~ 338 (344)
-+.|-.- .++.+++..+++++.|++. |+.|-+.++
T Consensus 677 GinDpRLRNps~nf~~aTVk~SsVd~YFrRqVELS~MyR~ME~hNy 722 (993)
T KOG4440|consen 677 GINDPRLRNPSDNFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNY 722 (993)
T ss_pred CCCCccccCcccceeEEEecCccHHHHHHHHhHHHHHHHhhhhcch
Confidence 8877543 3579999999999999987 666666554
No 4
>KOG1053|consensus
Probab=99.97 E-value=2.1e-30 Score=265.49 Aligned_cols=229 Identities=18% Similarity=0.341 Sum_probs=201.3
Q ss_pred eEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCC----chhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHH
Q psy936 85 LEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ----DGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEEL 160 (344)
Q Consensus 85 ~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~----~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~ 160 (344)
.+..||++||++.||+.+||+|+++.+.++++|.. |+|++|++..+++||++++++++.+|.+
T Consensus 463 kCCkGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSe------------- 529 (1258)
T KOG1053|consen 463 KCCKGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSE------------- 529 (1258)
T ss_pred hhhhhhhHHHHHHHHhhcCcceEEEEecCCcccceecCcchhhHHHHHhhhhheeeeeeEechhhhc-------------
Confidence 45689999999999999999999999999999985 6799999999999999999999999999
Q ss_pred HHHhhhccccEEEeceeeccceeEEEEeCCCCCCCcccccccchhhHHHHHHHHHHHHHHHH-HHHHHHhhcccCC----
Q psy936 161 KLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESATGSGLLAPFEIEVWFLILISLVLIGPIM-HAIMRVRRWLSGT---- 235 (344)
Q Consensus 161 ~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~~~~~~l~PF~~~vWl~il~~~i~~~~vl-~~i~r~~~~~~~~---- 235 (344)
.||||.||..+++.+||++.+...+-..|+.||++.+|++++++++.++.+. ++++++++.....
T Consensus 530 ----------vVDFSvPFveTgIsVmV~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~ 599 (1258)
T KOG1053|consen 530 ----------VVDFSVPFVETGISVMVARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLAN 599 (1258)
T ss_pred ----------cccccccccccceEEEEEecCCccCchhhcCCcchHHHHHHHHHHHHHHHHHHHHHhhcCcccccccccC
Confidence 9999999999999999999998888888999999999999988887665554 4677777643321
Q ss_pred ----CCCCcCchhHHHHHHHHHHcCCCC-CCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeecCCCCCCCCCHHHHhC
Q psy936 236 ----QSELYPISACTWFVYGALMKQGST-LNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQFTLPIHSVEDIAN 310 (344)
Q Consensus 236 ----~~~~~~i~~~~~~~~~~ll~qg~~-~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~~~I~TledL~~ 310 (344)
....|+|+.++|..++.+++.+.+ ..|+...+||+..+|.+|++++.++|||||+++|....+...+.-+.|=.-
T Consensus 600 gkkpggp~FtigkaiwllwaLvFnnsVpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~Kf 679 (1258)
T KOG1053|consen 600 GKKPGGPSFTIGKAIWLLWALVFNNSVPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKF 679 (1258)
T ss_pred CCCCCCcceehhhHHHHHHHHHhCCCcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccc
Confidence 123688999999999999999877 589999999999999999999999999999999999998887777766542
Q ss_pred -----C--CCcEEEEcCchhhHhhhh-ccCCCcc
Q psy936 311 -----P--TNTWCAEAGGAVEYSIKL-YRFQTPE 336 (344)
Q Consensus 311 -----s--~~~~g~~~~~~~e~~l~~-~~~~~~~ 336 (344)
+ ++++|+..++++|.++++ |..||..
T Consensus 680 qrP~dq~PpFRFGTVpngSTE~niR~Nyp~MHeY 713 (1258)
T KOG1053|consen 680 QRPHDQYPPFRFGTVPNGSTERNIRSNYPEMHEY 713 (1258)
T ss_pred cCccccCCCcccccCCCCchhhhHHhccHHHHHH
Confidence 2 589999999999999988 7777654
No 5
>PF00060 Lig_chan: Ligand-gated ion channel; InterPro: IPR001320 The ability of synapses to modify their synaptic strength in response to activity is a fundamental property of the nervous system and may be an essential component of learning and memory. There are three classes of ionotropic glutamate receptor, namely NMDA (N-methyl-D-aspartate), AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole-4-propionic acid) and kainate receptors. They are believed to play critical roles in synaptic plasticity. At many synapses in the brain, transient activation of NMDA receptors leads to a persistent modification in the strength of synaptic transmission mediated by AMPA receptors and kainate receptors can act as the induction trigger for long-term changes in synaptic transmission [].; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 3FAT_A 3KFM_A 3KEI_A 3EN3_A 3EPE_B 3FAS_A 2F34_A 3C34_B 3S2V_A 3GBB_B ....
Probab=99.65 E-value=2.5e-18 Score=146.63 Aligned_cols=109 Identities=39% Similarity=0.774 Sum_probs=84.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhhcccCC------CCCCcCchhHHHHHHHHHHcCCCCCCCCCcchhHHHHHHHHH
Q psy936 204 EIEVWFLILISLVLIGPIMHAIMRVRRWLSGT------QSELYPISACTWFVYGALMKQGSTLNPRTDSTRIMFASWWIF 277 (344)
Q Consensus 204 ~~~vWl~il~~~i~~~~vl~~i~r~~~~~~~~------~~~~~~i~~~~~~~~~~ll~qg~~~~p~s~s~Ril~~~w~l~ 277 (344)
++++|+++++++++++++++++.|+.+..++. .+...++.+++|++++.+++|+....|++.++|++.++|+++
T Consensus 1 s~~vW~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~s~s~Ril~~~w~l~ 80 (148)
T PF00060_consen 1 SWSVWLLILLSILLVSLVLWLFERFSPYEWRKNQSSPPRRWRFSLSNSFWYTFGTLLQQGSSIRPRSWSGRILLAFWWLF 80 (148)
T ss_dssp -HHHHHHHHHHHHHHHTTGGGT------------------HHHHHHHHHHHCCCCCHHHHH------HHHHHHHHHHHHH
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccccCcccHHHHHHHHHHhhccccccccccchHHHHHHHHHHHH
Confidence 57899999999999999999999987765544 112456889999999999999999999999999999999999
Q ss_pred HHHHHhhcccceeeeeecCCCCCCCCCHHHHhCCC
Q psy936 278 IMILTAFYTANLTAFLTLSQFTLPIHSVEDIANPT 312 (344)
Q Consensus 278 ~lil~~~Yta~L~s~Lt~~~~~~~I~TledL~~s~ 312 (344)
++++.++|+|+|+|+||.|+.+++|+|+|||++++
T Consensus 81 ~lil~~~Yta~L~s~Lt~~~~~~~i~sl~dL~~~~ 115 (148)
T PF00060_consen 81 SLILIASYTANLTSFLTVPKYEPPIDSLEDLANSG 115 (148)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHTSS-SSHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHhcccCcCCCCCCHHHHHHCC
Confidence 99999999999999999999999999999999988
No 6
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=99.18 E-value=1.6e-10 Score=102.90 Aligned_cols=95 Identities=17% Similarity=0.399 Sum_probs=81.4
Q ss_pred EEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEE
Q psy936 56 LPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMV 135 (344)
Q Consensus 56 L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~ 135 (344)
|||| +..+.+||.+.. ++|+. .|+++|+++.+++++|++++++..+ +.+++..+.+|++|++
T Consensus 1 l~V~------~~~~~~P~~~~~---~~~~~--~G~~~dl~~~i~~~~g~~~~~~~~~-------~~~~~~~l~~g~~D~~ 62 (225)
T PF00497_consen 1 LRVG------VDEDYPPFSYID---EDGEP--SGIDVDLLRAIAKRLGIKIEFVPMP-------WSRLLEMLENGKADII 62 (225)
T ss_dssp EEEE------EESEBTTTBEEE---TTSEE--ESHHHHHHHHHHHHHTCEEEEEEEE-------GGGHHHHHHTTSSSEE
T ss_pred CEEE------EcCCCCCeEEEC---CCCCE--EEEhHHHHHHHHhhcccccceeecc-------cccccccccccccccc
Confidence 6788 546789999764 46755 4999999999999999999998842 3478999999999999
Q ss_pred EeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCC
Q psy936 136 AAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 136 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
++++..+.+|.+ .++||.|+.....++++++.+
T Consensus 63 ~~~~~~~~~r~~-----------------------~~~~s~p~~~~~~~~~~~~~~ 95 (225)
T PF00497_consen 63 IGGLSITPERAK-----------------------KFDFSDPYYSSPYVLVVRKGD 95 (225)
T ss_dssp ESSEB-BHHHHT-----------------------TEEEESESEEEEEEEEEETTS
T ss_pred cccccccccccc-----------------------cccccccccchhheeeecccc
Confidence 999999999988 999999999999999999744
No 7
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=98.84 E-value=1.5e-08 Score=94.87 Aligned_cols=101 Identities=14% Similarity=0.215 Sum_probs=81.0
Q ss_pred CCceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHC-CC--cEEEEeeCCCCCCCCchhhhhhcc
Q psy936 52 EQLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKY-EF--SYEIILPSRKTLLDQDGSIMNILK 128 (344)
Q Consensus 52 ~g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~l-nf--t~~~~~~~~~~~G~~~~g~~~~l~ 128 (344)
+..+|+|| +..+.|||.+.+ +++|++. |+++|+++++++++ |. +++++..+. .....++.
T Consensus 36 ~~g~l~vg------~~~~~pP~~~~~--~~~g~~~--G~~vdl~~~ia~~llg~~~~~~~~~~~~-------~~~~~~l~ 98 (259)
T PRK11917 36 SKGQLIVG------VKNDVPHYALLD--QATGEIK--GFEIDVAKLLAKSILGDDKKIKLVAVNA-------KTRGPLLD 98 (259)
T ss_pred hCCEEEEE------ECCCCCCceeee--CCCCcee--EeeHHHHHHHHHHhcCCCccEEEEEcCh-------hhHHHHHH
Confidence 35889999 656789998643 3467655 99999999999995 64 455544321 23557899
Q ss_pred cceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 129 TGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 129 ~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
+|++|+++++++++.+|.+ .++||.|++.++..+++++.+.
T Consensus 99 ~g~~D~~~~~~~~t~eR~~-----------------------~~~fs~py~~~~~~lvv~~~~~ 139 (259)
T PRK11917 99 NGSVDAVIATFTITPERKR-----------------------IYNFSEPYYQDAIGLLVLKEKN 139 (259)
T ss_pred CCCccEEEecccCChhhhh-----------------------eeeeccCceeeceEEEEECCCC
Confidence 9999999999999999999 9999999999999999998754
No 8
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=98.82 E-value=1.8e-08 Score=93.99 Aligned_cols=100 Identities=10% Similarity=0.171 Sum_probs=83.8
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhccccee
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEV 132 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~ 132 (344)
..+|+|+ +..+.+||++.+ ++|+.. |+++||++.++++++.+++++..+ |+.++.++.+|++
T Consensus 25 ~~~l~v~------~~~~~pPf~~~~---~~g~~~--G~~vdl~~~ia~~lg~~~~~~~~~-------~~~~~~~l~~g~~ 86 (260)
T PRK15010 25 PETVRIG------TDTTYAPFSSKD---AKGDFV--GFDIDLGNEMCKRMQVKCTWVASD-------FDALIPSLKAKKI 86 (260)
T ss_pred CCeEEEE------ecCCcCCceeEC---CCCCEE--eeeHHHHHHHHHHhCCceEEEeCC-------HHHHHHHHHCCCC
Confidence 4778999 634689999753 467654 999999999999999999987532 3469999999999
Q ss_pred cEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCC
Q psy936 133 DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 133 Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
|++++.+..+.+|.+ .++||.|++.+..++++++....
T Consensus 87 Di~~~~~~~t~eR~~-----------------------~~~fs~p~~~~~~~~~~~~~~~~ 124 (260)
T PRK15010 87 DAIISSLSITDKRQQ-----------------------EIAFSDKLYAADSRLIAAKGSPI 124 (260)
T ss_pred CEEEecCcCCHHHHh-----------------------hcccccceEeccEEEEEECCCCC
Confidence 999998989999988 99999999999999999887543
No 9
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=98.75 E-value=3.4e-08 Score=91.98 Aligned_cols=100 Identities=11% Similarity=0.195 Sum_probs=84.2
Q ss_pred CCceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccce
Q psy936 52 EQLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGE 131 (344)
Q Consensus 52 ~g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~ 131 (344)
...+|+|+ +..+.+||++. +++|+.. |+++|++++++++++.+++++..+ |+.++.++.+|+
T Consensus 24 ~~~~l~v~------~~~~~~P~~~~---~~~g~~~--G~~vdi~~~ia~~lg~~i~~~~~p-------w~~~~~~l~~g~ 85 (259)
T PRK15437 24 IPQNIRIG------TDPTYAPFESK---NSQGELV--GFDIDLAKELCKRINTQCTFVENP-------LDALIPSLKAKK 85 (259)
T ss_pred cCCeEEEE------eCCCCCCccee---CCCCCEE--eeeHHHHHHHHHHcCCceEEEeCC-------HHHHHHHHHCCC
Confidence 35788999 63357999864 2567655 999999999999999999987632 457899999999
Q ss_pred ecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 132 VDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 132 ~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
+|++++++..+.+|.. .++|+.|+..++..+++++...
T Consensus 86 ~D~~~~~~~~t~eR~~-----------------------~~~fs~p~~~~~~~~~~~~~~~ 123 (259)
T PRK15437 86 IDAIMSSLSITEKRQQ-----------------------EIAFTDKLYAADSRLVVAKNSD 123 (259)
T ss_pred CCEEEecCCCCHHHhh-----------------------hccccchhhcCceEEEEECCCC
Confidence 9999999999999988 9999999999999999988654
No 10
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=98.75 E-value=2.9e-08 Score=95.28 Aligned_cols=99 Identities=11% Similarity=0.143 Sum_probs=79.4
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHH----HC---CCcEEEEeeCCCCCCCCchhhhh
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSA----KY---EFSYEIILPSRKTLLDQDGSIMN 125 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~----~l---nft~~~~~~~~~~~G~~~~g~~~ 125 (344)
...|+|| +..+++||++.. ++|+.. |+++|+++.+++ ++ +.+++++..+ +..++.
T Consensus 39 ~g~L~Vg------~~~~~pP~~f~~---~~g~~~--G~didl~~~ia~~l~~~lg~~~~~~~~v~~~-------~~~~i~ 100 (302)
T PRK10797 39 NGVIVVG------HRESSVPFSYYD---NQQKVV--GYSQDYSNAIVEAVKKKLNKPDLQVKLIPIT-------SQNRIP 100 (302)
T ss_pred CCeEEEE------EcCCCCCcceEC---CCCCEe--eecHHHHHHHHHHHHHhhCCCCceEEEEEcC-------hHhHHH
Confidence 4679999 656789999742 456554 999997777766 55 4677776643 125789
Q ss_pred hcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 126 ILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 126 ~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+|++|+++++++++.+|.. .++||.||+.++..+++++.+.
T Consensus 101 ~L~~G~~Di~~~~~~~t~eR~~-----------------------~~~fS~Py~~~~~~lv~r~~~~ 144 (302)
T PRK10797 101 LLQNGTFDFECGSTTNNLERQK-----------------------QAAFSDTIFVVGTRLLTKKGGD 144 (302)
T ss_pred HHHCCCccEEecCCccCcchhh-----------------------cceecccEeeccEEEEEECCCC
Confidence 9999999999999999999998 9999999999999999998653
No 11
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=98.73 E-value=4.8e-08 Score=89.52 Aligned_cols=97 Identities=9% Similarity=0.104 Sum_probs=80.6
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhccccee
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEV 132 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~ 132 (344)
..+|+|+ +..+.+||++.+ .+|+.. |+++|+++.+++++|.+++++..+ |+.++..+.+|++
T Consensus 20 ~~~l~v~------~~~~~~P~~~~~---~~g~~~--G~~~dl~~~i~~~lg~~~~~~~~~-------~~~~~~~l~~g~~ 81 (243)
T PRK15007 20 AETIRFA------TEASYPPFESID---ANNQIV--GFDVDLAQALCKEIDATCTFSNQA-------FDSLIPSLKFRRV 81 (243)
T ss_pred CCcEEEE------eCCCCCCceeeC---CCCCEE--eeeHHHHHHHHHHhCCcEEEEeCC-------HHHHhHHHhCCCc
Confidence 4589999 644789999653 467654 999999999999999999987532 3468899999999
Q ss_pred cEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCC
Q psy936 133 DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRP 190 (344)
Q Consensus 133 Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~ 190 (344)
|++++++..+.+|.+ .++||.|++....+++.+..
T Consensus 82 D~~~~~~~~~~~r~~-----------------------~~~fs~p~~~~~~~~v~~~~ 116 (243)
T PRK15007 82 EAVMAGMDITPEREK-----------------------QVLFTTPYYDNSALFVGQQG 116 (243)
T ss_pred CEEEEcCccCHHHhc-----------------------ccceecCccccceEEEEeCC
Confidence 999888888899988 99999999998888887754
No 12
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=98.73 E-value=5.1e-08 Score=89.98 Aligned_cols=98 Identities=16% Similarity=0.253 Sum_probs=82.2
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhccccee
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEV 132 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~ 132 (344)
..+|+|+ +..+.+||.+. ++|+. .|+++|+++.+++++|.+++++..+ |.+++..+.+|++
T Consensus 24 ~~~l~v~------~~~~~~P~~~~----~~g~~--~G~~vdl~~~ia~~lg~~~~~~~~~-------~~~~~~~l~~G~v 84 (247)
T PRK09495 24 DKKLVVA------TDTAFVPFEFK----QGDKY--VGFDIDLWAAIAKELKLDYTLKPMD-------FSGIIPALQTKNV 84 (247)
T ss_pred CCeEEEE------eCCCCCCeeec----CCCce--EEEeHHHHHHHHHHhCCceEEEeCC-------HHHHHHHHhCCCc
Confidence 4689999 64578999863 35655 4999999999999999999987532 4578999999999
Q ss_pred cEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 133 DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 133 Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
|+++++++.+.+|.+ .++|+.|+..+.+.+++++...
T Consensus 85 Di~~~~~~~t~~R~~-----------------------~~~fs~p~~~~~~~~~~~~~~~ 121 (247)
T PRK09495 85 DLALAGITITDERKK-----------------------AIDFSDGYYKSGLLVMVKANNN 121 (247)
T ss_pred CEEEecCccCHHHHh-----------------------hccccchheecceEEEEECCCC
Confidence 999888888999988 8999999999999999986543
No 13
>PRK11260 cystine transporter subunit; Provisional
Probab=98.66 E-value=1.2e-07 Score=88.75 Aligned_cols=105 Identities=17% Similarity=0.248 Sum_probs=85.7
Q ss_pred CccccCC-CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhh
Q psy936 46 DSWLIIE-QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIM 124 (344)
Q Consensus 46 ~~~~~l~-g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~ 124 (344)
+....++ ..+|+|+ +..+.+||.+. +++|+.. |+.+|+++.+++++|.+++++..+ |..+.
T Consensus 32 ~~l~~i~~~~~l~v~------~~~~~~P~~~~---~~~g~~~--G~~~dl~~~i~~~lg~~~e~~~~~-------~~~~~ 93 (266)
T PRK11260 32 GLLNKVKERGTLLVG------LEGTYPPFSFQ---GEDGKLT--GFEVEFAEALAKHLGVKASLKPTK-------WDGML 93 (266)
T ss_pred ccHHHhhcCCeEEEE------eCCCcCCceEE---CCCCCEE--EehHHHHHHHHHHHCCeEEEEeCC-------HHHHH
Confidence 3344443 4789999 64578999853 3567554 999999999999999999997742 34789
Q ss_pred hhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCC
Q psy936 125 NILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 125 ~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.++.+|++|+++++...+.+|.. .+.||.|+...+..+++++.+
T Consensus 94 ~~l~~G~~D~~~~~~~~~~~r~~-----------------------~~~fs~p~~~~~~~~~~~~~~ 137 (266)
T PRK11260 94 ASLDSKRIDVVINQVTISDERKK-----------------------KYDFSTPYTVSGIQALVKKGN 137 (266)
T ss_pred HHHhcCCCCEEEeccccCHHHHh-----------------------ccccCCceeecceEEEEEcCC
Confidence 99999999999988888899988 999999999999999998754
No 14
>PF10613 Lig_chan-Glu_bd: Ligated ion channel L-glutamate- and glycine-binding site; InterPro: IPR019594 This entry, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and binds L-glutamate and glycine [, ]. It is found in association with IPR001320 from INTERPRO. ; GO: 0004970 ionotropic glutamate receptor activity, 0005234 extracellular-glutamate-gated ion channel activity, 0016020 membrane; PDB: 4E0W_A 3S9E_A 3QXM_B 2F34_A 3C34_B 3S2V_A 3GBB_B 2F36_D 4E0X_A 1TXF_A ....
Probab=98.64 E-value=1.4e-08 Score=75.54 Aligned_cols=48 Identities=23% Similarity=0.347 Sum_probs=38.3
Q ss_pred CCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCC-----chhhhhhccc
Q psy936 82 TGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQ-----DGSIMNILKT 129 (344)
Q Consensus 82 ~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~-----~~g~~~~l~~ 129 (344)
+|..++.|+++||++.||+.+||+++++.+++++||.. |+|++++|.+
T Consensus 13 ~g~~~~eGyciDll~~la~~l~F~y~i~~~~Dg~yG~~~~~g~W~GmiGeli~ 65 (65)
T PF10613_consen 13 TGNDRYEGYCIDLLEELAEELNFTYEIYLVPDGKYGSKNPNGSWNGMIGELIR 65 (65)
T ss_dssp BGGGGEESHHHHHHHHHHHHHT-EEEEEE-TTS--EEBETTSEBEHHHHHHHT
T ss_pred CCCccEEEEHHHHHHHHHHHcCCeEEEEECCCCCCcCcCCCCcCcCHHHHhcC
Confidence 45567789999999999999999999999999999985 5699998864
No 15
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=98.64 E-value=9.2e-08 Score=90.04 Aligned_cols=103 Identities=15% Similarity=0.224 Sum_probs=83.5
Q ss_pred cccCC-CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCc-EEEEeeCCCCCCCCchhhhh
Q psy936 48 WLIIE-QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFS-YEIILPSRKTLLDQDGSIMN 125 (344)
Q Consensus 48 ~~~l~-g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft-~~~~~~~~~~~G~~~~g~~~ 125 (344)
+.++. ..+|+|+ + .+.+||++.+ ++|+.. |+++|+++++++++|.+ +++... .|+.++.
T Consensus 26 ~~~i~~~~~l~v~------~-~~~pP~~~~~---~~g~~~--G~~~dl~~~i~~~lg~~~~~~~~~-------~w~~~~~ 86 (275)
T TIGR02995 26 LEELKEQGFARIA------I-ANEPPFTYVG---ADGKVS--GAAPDVARAIFKRLGIADVNASIT-------EYGALIP 86 (275)
T ss_pred HHHHHhCCcEEEE------c-cCCCCceeEC---CCCcee--cchHHHHHHHHHHhCCCceeeccC-------CHHHHHH
Confidence 34444 3779999 7 5789999753 567654 99999999999999986 454432 2457899
Q ss_pred hcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 126 ILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 126 ~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+|++|+++.+++.+.+|.. .++||.|++.+...+++++.+.
T Consensus 87 ~l~~G~~Di~~~~~~~t~eR~~-----------------------~~~fs~py~~~~~~~~~~~~~~ 130 (275)
T TIGR02995 87 GLQAGRFDAIAAGLFIKPERCK-----------------------QVAFTQPILCDAEALLVKKGNP 130 (275)
T ss_pred HHHCCCcCEEeecccCCHHHHh-----------------------ccccccceeecceeEEEECCCC
Confidence 9999999999888888999988 9999999999999999988653
No 16
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=98.63 E-value=1.4e-07 Score=86.56 Aligned_cols=101 Identities=13% Similarity=0.184 Sum_probs=83.6
Q ss_pred CCCceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccc
Q psy936 51 IEQLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTG 130 (344)
Q Consensus 51 l~g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g 130 (344)
.++.+|+|+ +..+.+||.+.. ++|+. .|+++|+++.+++++|.+++++..+ +..++.++.+|
T Consensus 21 ~~~~~l~v~------~~~~~~P~~~~~---~~g~~--~G~~~dl~~~i~~~lg~~~~~~~~~-------~~~~~~~l~~G 82 (250)
T TIGR01096 21 AKEGSVRIG------TETGYPPFESKD---ANGKL--VGFDVDLAKALCKRMKAKCKFVEQN-------FDGLIPSLKAK 82 (250)
T ss_pred hhCCeEEEE------ECCCCCCceEEC---CCCCE--EeehHHHHHHHHHHhCCeEEEEeCC-------HHHHHHHHhCC
Confidence 444789999 645789998653 46655 5999999999999999999987632 34788999999
Q ss_pred eecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 131 EVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 131 ~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
++|++++++..+.+|.. .+.|+.|++.....+++++.+.
T Consensus 83 ~~D~~~~~~~~~~~r~~-----------------------~~~~s~p~~~~~~~~~~~~~~~ 121 (250)
T TIGR01096 83 KVDAIMATMSITPKRQK-----------------------QIDFSDPYYATGQGFVVKKGSD 121 (250)
T ss_pred CcCEEEecCccCHHHhh-----------------------ccccccchhcCCeEEEEECCCC
Confidence 99999887878888877 8999999999999999987654
No 17
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=98.44 E-value=7.1e-07 Score=82.81 Aligned_cols=89 Identities=17% Similarity=0.125 Sum_probs=70.5
Q ss_pred eEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhh---hhcccce
Q psy936 55 RLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIM---NILKTGE 131 (344)
Q Consensus 55 ~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~---~~l~~g~ 131 (344)
+|+|| +..+.|||++. ++ .|+++||++++|+++|.+++++..+ | .+++ ..|.+|+
T Consensus 1 ~l~vg------~~~~~pPf~~~-----~~----~Gfdvdl~~~ia~~lg~~~~~~~~~---~----~~~~~~~~~L~~g~ 58 (246)
T TIGR03870 1 TLRVC------AATKEAPYSTK-----DG----SGFENKIAAALAAAMGRKVVFVWLA---K----PAIYLVRDGLDKKL 58 (246)
T ss_pred CeEEE------eCCCCCCCccC-----CC----CcchHHHHHHHHHHhCCCeEEEEec---c----chhhHHHHHHhcCC
Confidence 47899 76788999963 22 4999999999999999999998643 2 2333 6899999
Q ss_pred ecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 132 VDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 132 ~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
+|+++ ++.++.+| +.||.||..++.++++++.+.
T Consensus 59 ~Dii~-~~~~t~~r--------------------------~~fS~PY~~~~~~~v~~k~~~ 92 (246)
T TIGR03870 59 CDVVL-GLDTGDPR--------------------------VLTTKPYYRSSYVFLTRKDRN 92 (246)
T ss_pred ccEEE-eCCCChHH--------------------------HhcccCcEEeeeEEEEeCCCC
Confidence 99998 47666544 358999999999999997753
No 18
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=98.38 E-value=7.2e-07 Score=91.13 Aligned_cols=99 Identities=14% Similarity=0.279 Sum_probs=80.1
Q ss_pred CCCceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccc
Q psy936 51 IEQLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTG 130 (344)
Q Consensus 51 l~g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g 130 (344)
-+..+|+|+ + . .+|+.+.. .+++ . .|+++|+++.+++++|.+++++...+ +..++..|.+|
T Consensus 40 ~~~g~LrVg------~-~-~~P~~~~~--~~~~-~--~G~~~DLl~~ia~~LGv~~e~v~~~~------~~~ll~aL~~G 100 (482)
T PRK10859 40 QERGELRVG------T-I-NSPLTYYI--GNDG-P--TGFEYELAKRFADYLGVKLEIKVRDN------ISQLFDALDKG 100 (482)
T ss_pred HhCCEEEEE------E-e-cCCCeeEe--cCCC-c--ccHHHHHHHHHHHHhCCcEEEEecCC------HHHHHHHHhCC
Confidence 345789999 5 2 35666433 2333 2 59999999999999999999885432 34799999999
Q ss_pred eecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCC
Q psy936 131 EVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 131 ~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
++|+++++++++.+|.+ .++||.|+......+++++.+
T Consensus 101 ~iDi~~~~lt~T~eR~~-----------------------~~~FS~Py~~~~~~lv~r~~~ 138 (482)
T PRK10859 101 KADLAAAGLTYTPERLK-----------------------QFRFGPPYYSVSQQLVYRKGQ 138 (482)
T ss_pred CCCEEeccCcCChhhhc-----------------------cCcccCCceeeeEEEEEeCCC
Confidence 99999999999999998 999999999999999998764
No 19
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=98.21 E-value=2.1e-06 Score=96.21 Aligned_cols=106 Identities=16% Similarity=0.142 Sum_probs=84.5
Q ss_pred cccCC-CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhh
Q psy936 48 WLIIE-QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNI 126 (344)
Q Consensus 48 ~~~l~-g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~ 126 (344)
+..++ ..+|+|| +..+.+|+.+.. +++|+.. |+++|+++.+++++|.+++++..++ |.+++++
T Consensus 49 ~~~l~~~~~l~vg------v~~~~~p~~~~~--~~~g~~~--G~~~D~l~~ia~~lG~~~e~v~~~~------~~~~l~~ 112 (1197)
T PRK09959 49 LRWLASKKNLVIA------VHKSQTATLLHT--DSQQRVR--GINADYLNLLKRALNIKLTLREYAD------HQKAMDA 112 (1197)
T ss_pred HHHHhhCCeEEEE------ecCCCCCCceee--cCCCccc--eecHHHHHHHHHhcCCceEEEeCCC------HHHHHHH
Confidence 44443 4679999 645555654332 3677665 9999999999999999999987543 4589999
Q ss_pred cccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCC
Q psy936 127 LKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 127 l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
+.+|++|++.+.+..+.+|.. .++||.||+.+..++++++...
T Consensus 113 l~~g~iDl~~~~~~~~~~r~~-----------------------~~~fs~py~~~~~~~v~~~~~~ 155 (1197)
T PRK09959 113 LEEGEVDIVLSHLVASPPLND-----------------------DIAATKPLIITFPALVTTLHDS 155 (1197)
T ss_pred HHcCCCcEecCcccccccccc-----------------------chhcCCCccCCCceEEEeCCCC
Confidence 999999999888888999988 9999999999988888887543
No 20
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=98.19 E-value=3.4e-06 Score=94.58 Aligned_cols=97 Identities=18% Similarity=0.223 Sum_probs=79.0
Q ss_pred ceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceec
Q psy936 54 LRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVD 133 (344)
Q Consensus 54 ~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~D 133 (344)
.+|+|+ +..+.|||.+.+ ++|+.. |+++|+++.+++++|.+++++.... +......+.+|++|
T Consensus 302 ~~l~v~------~~~~~pP~~~~d---~~g~~~--G~~~Dll~~i~~~~g~~~~~v~~~~------~~~~~~~l~~g~~D 364 (1197)
T PRK09959 302 PDLKVL------ENPYSPPYSMTD---ENGSVR--GVMGDILNIITLQTGLNFSPITVSH------NIHAGTQLNPGGWD 364 (1197)
T ss_pred CceEEE------cCCCCCCeeEEC---CCCcEe--eehHHHHHHHHHHHCCeEEEEecCC------HHHHHHHHHCCCce
Confidence 579999 656789999763 567655 9999999999999999998877542 22466789999999
Q ss_pred EEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCC
Q psy936 134 MVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 134 i~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
++.+. ..+.+|.+ .++||.||..+.+++++++..
T Consensus 365 ~i~~~-~~t~~r~~-----------------------~~~fs~py~~~~~~~v~~~~~ 398 (1197)
T PRK09959 365 IIPGA-IYSEDREN-----------------------NVLFAEAFITTPYVFVMQKAP 398 (1197)
T ss_pred Eeecc-cCCccccc-----------------------cceeccccccCCEEEEEecCC
Confidence 87554 46888888 999999999999999987653
No 21
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=98.10 E-value=1.5e-05 Score=69.23 Aligned_cols=94 Identities=16% Similarity=0.282 Sum_probs=76.6
Q ss_pred ccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhh
Q psy936 66 LFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIK 145 (344)
Q Consensus 66 ~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r 145 (344)
+..+.+||.+. +++|+. .|+..++++.++++++.+++++..+ +..+...+.+|++|+++.....+.+|
T Consensus 5 ~~~~~~p~~~~---~~~g~~--~G~~~~~~~~~~~~~g~~~~~~~~~-------~~~~~~~l~~g~~D~~~~~~~~~~~~ 72 (218)
T cd00134 5 TAGTYPPFSFR---DANGEL--TGFDVDLAKAIAKELGVKVKFVEVD-------WDGLITALKSGKVDLIAAGMTITPER 72 (218)
T ss_pred cCCCCCCeeEE---CCCCCE--EeeeHHHHHHHHHHhCCeEEEEeCC-------HHHHHHHHhcCCcCEEeecCcCCHHH
Confidence 43667899854 356655 4999999999999999998888754 24789999999999998877667777
Q ss_pred hHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCC
Q psy936 146 KNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESA 194 (344)
Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~ 194 (344)
.. .+.|+.|+.....++++++.+...
T Consensus 73 ~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~ 98 (218)
T cd00134 73 AK-----------------------QVDFSDPYYKSGQVILVKKGSPIK 98 (218)
T ss_pred Hh-----------------------hccCcccceeccEEEEEECCCCCC
Confidence 77 788999999999999999876544
No 22
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=98.09 E-value=7.9e-06 Score=74.25 Aligned_cols=90 Identities=19% Similarity=0.222 Sum_probs=69.6
Q ss_pred eEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecE
Q psy936 55 RLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDM 134 (344)
Q Consensus 55 ~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di 134 (344)
.|+|+ +..+.+||++ .++ .|+++||++.+++++|.+++++..+.. + +-++..+.+|++|+
T Consensus 1 ~l~v~------~~~~~~P~~~-----~~~----~G~~~el~~~i~~~~g~~i~~~~~~~~-~----~~~~~~l~~g~~Di 60 (232)
T TIGR03871 1 ALRVC------ADPNNLPFSN-----EKG----EGFENKIAQLLADDLGLPLEYTWFPQR-R----GFVRNTLNAGRCDV 60 (232)
T ss_pred CeEEE------eCCCCCCccC-----CCC----CchHHHHHHHHHHHcCCceEEEecCcc-h----hhHHHHHhcCCccE
Confidence 37888 6566789984 122 499999999999999999998764321 1 12567899999999
Q ss_pred EEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCC
Q psy936 135 VAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 135 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
+++ +.+|.+ .++||.||...++++++++.+
T Consensus 61 ~~~----~~~r~~-----------------------~~~fs~py~~~~~~lv~~~~~ 90 (232)
T TIGR03871 61 VIG----VPAGYE-----------------------MVLTTRPYYRSTYVFVTRKDS 90 (232)
T ss_pred EEe----ccCccc-----------------------cccccCCcEeeeEEEEEeCCC
Confidence 876 355666 789999999999999998774
No 23
>TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown.
Probab=98.07 E-value=1e-05 Score=75.79 Aligned_cols=96 Identities=8% Similarity=0.051 Sum_probs=76.1
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccce
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGE 131 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~ 131 (344)
..+|+++ + .++|||.+.. .+|+. .|+..++++++++++ ++++++... .|.+++..+ +|+
T Consensus 17 ~~~l~~~------~-~~~pPf~~~~---~~~~~--~G~~~~i~~~i~~~~~~~~~~~~~~-------pw~r~l~~l-~~~ 76 (268)
T TIGR02285 17 KEAITWI------V-NDFPPFFIFS---GPSKG--RGVFDVILQEIRRALPQYEHRFVRV-------SFARSLKEL-QGK 76 (268)
T ss_pred cceeEEE------e-cccCCeeEeC---CCCCC--CChHHHHHHHHHHHcCCCceeEEEC-------CHHHHHHHH-hcC
Confidence 4688888 7 6889998652 34443 499899999999998 888887653 356788999 788
Q ss_pred ecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeecc-ceeEEEEeCCC
Q psy936 132 VDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQ-SQYVVMMKRPH 191 (344)
Q Consensus 132 ~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~-~~~~~~v~~~~ 191 (344)
.|.++.+++.+.+|.. .++||.|+.. ...++++++.+
T Consensus 77 ~d~~~~~~~~t~eR~~-----------------------~~~Fs~P~~~~~~~~~~~~~~~ 114 (268)
T TIGR02285 77 GGVCTVNLLRTPEREK-----------------------FLIFSDPTLRALPVGLVLRKEL 114 (268)
T ss_pred CCeEEeeccCCcchhh-----------------------ceeecCCccccCCceEEEccch
Confidence 8888888999999998 9999999875 56788887653
No 24
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=97.97 E-value=3.1e-05 Score=66.92 Aligned_cols=98 Identities=17% Similarity=0.308 Sum_probs=78.1
Q ss_pred eEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecE
Q psy936 55 RLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDM 134 (344)
Q Consensus 55 ~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di 134 (344)
+|+|+ +..+.+|+... +.+|. ..|+..|+++.++++++.++++...+ +..+...+.+|++|+
T Consensus 1 ~l~v~------~~~~~~p~~~~---~~~g~--~~G~~~~~~~~~~~~~g~~~~~~~~~-------~~~~~~~l~~g~~D~ 62 (219)
T smart00062 1 TLRVG------TNGDYPPFSFA---DEDGE--LTGFDVDLAKAIAKELGLKVEFVEVS-------FDNLLTALKSGKIDV 62 (219)
T ss_pred CEEEE------ecCCCCCcEEE---CCCCC--cccchHHHHHHHHHHhCCeEEEEecc-------HHHHHHHHHCCcccE
Confidence 47888 43567898853 24565 45999999999999999999887742 247889999999999
Q ss_pred EEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCC
Q psy936 135 VAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 135 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
++.....+.+|.. .+.++.|+......+++++....
T Consensus 63 ~~~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~ 98 (219)
T smart00062 63 VAAGMTITPERAK-----------------------QVDFSDPYYKSGQVILVRKDSPI 98 (219)
T ss_pred EeccccCCHHHHh-----------------------heeeccceeeceeEEEEecCCCC
Confidence 9887766667766 78999999999999999877653
No 25
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=97.90 E-value=4.4e-05 Score=70.53 Aligned_cols=103 Identities=18% Similarity=0.277 Sum_probs=79.8
Q ss_pred CCceEEEEecCCCccccc-CCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcE--EEEeeCCCCCCCCchhhhhhcc
Q psy936 52 EQLRLPIEPTIPSFLFQD-QKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSY--EIILPSRKTLLDQDGSIMNILK 128 (344)
Q Consensus 52 ~g~~L~v~~~~P~~~~~~-~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~--~~~~~~~~~~G~~~~g~~~~l~ 128 (344)
....++|+ +... .+|+.+... ..|+. .|+++|+++.++++++... ++... .+.+++..+.
T Consensus 32 ~~~~~~v~------~~~~~~~p~~~~~~--~~~~~--~G~dvdl~~~ia~~l~~~~~~~~~~~-------~~~~~~~~l~ 94 (275)
T COG0834 32 ARGKLRVG------TEATYAPPFEFLDA--KGGKL--VGFDVDLAKAIAKRLGGDKKVEFVPV-------AWDGLIPALK 94 (275)
T ss_pred hcCeEEEE------ecCCCCCCcccccC--CCCeE--EeeeHHHHHHHHHHhCCcceeEEecc-------chhhhhHHHh
Confidence 55778888 5323 459986542 22444 5999999999999988763 43332 2358999999
Q ss_pred cceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCC
Q psy936 129 TGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESA 194 (344)
Q Consensus 129 ~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~ 194 (344)
.|++|+.+..++++.+|.+ .++||.||+..+..+++++.+...
T Consensus 95 ~g~~D~~~~~~~~t~er~~-----------------------~~~fs~py~~~~~~~~~~~~~~~~ 137 (275)
T COG0834 95 AGKVDIIIAGMTITPERKK-----------------------KVDFSDPYYYSGQVLLVKKDSDIG 137 (275)
T ss_pred cCCcCEEEeccccCHHHhc-----------------------cccccccccccCeEEEEECCCCcC
Confidence 9999999999999998877 899999999999999998776653
No 26
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=97.20 E-value=0.00037 Score=68.19 Aligned_cols=101 Identities=15% Similarity=0.254 Sum_probs=79.3
Q ss_pred CceEEEEecCCCcccccCCCceeeeecCCCCceEEeeehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhccccee
Q psy936 53 QLRLPIEPTIPSFLFQDQKPMSWVTTNNKTGKLEGHGIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEV 132 (344)
Q Consensus 53 g~~L~v~~~~P~~~~~~~~P~~~~~~~~~~g~~~~~G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~ 132 (344)
-..|||+ + . ..|.++.. +++|+ . |+++++.+.+|+.+|.+++++..++. +.++.+|.+|++
T Consensus 22 rGvLrV~------t-i-nsp~sy~~--~~~~p-~--G~eYelak~Fa~yLgV~Lki~~~~n~------dqLf~aL~ng~~ 82 (473)
T COG4623 22 RGVLRVS------T-I-NSPLSYFE--DKGGP-T--GLEYELAKAFADYLGVKLKIIPADNI------DQLFDALDNGNA 82 (473)
T ss_pred cCeEEEE------e-e-cCccceec--cCCCc-c--chhHHHHHHHHHHhCCeEEEEecCCH------HHHHHHHhCCCc
Confidence 4789999 5 3 35665322 34443 3 99999999999999999999886542 279999999999
Q ss_pred cEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEeceeeccceeEEEEeCCCCCCC
Q psy936 133 DMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIELGQSQYVVMMKRPHESAT 195 (344)
Q Consensus 133 Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p~~~~~~~~~v~~~~~~~~ 195 (344)
|+++++.....+|.+ .+..+..+++..+.++.++.+..++
T Consensus 83 DL~Aagl~~~~~~l~-----------------------~~~~gP~y~svs~qlVyRkG~~Rp~ 122 (473)
T COG4623 83 DLAAAGLLYNSERLK-----------------------NFQPGPTYYSVSQQLVYRKGQYRPR 122 (473)
T ss_pred ceecccccCChhHhc-----------------------ccCCCCceecccHHHHhhcCCCCCC
Confidence 999999998888866 6666767888888888888776664
No 27
>PF07885 Ion_trans_2: Ion channel; InterPro: IPR013099 This entry includes the two membrane helix type ion channels found in bacteria []. ; PDB: 1KKD_A 2A0L_A 1ORQ_C 3UKM_C 1LNQ_E 3OUS_A 3LDC_A 3LDD_A 3RBZ_A 3LDE_A ....
Probab=95.74 E-value=0.034 Score=42.37 Aligned_cols=56 Identities=20% Similarity=0.387 Sum_probs=47.9
Q ss_pred CcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeee
Q psy936 239 LYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLT 294 (344)
Q Consensus 239 ~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt 294 (344)
..++.+++|+++.++...| ++..|.+..+|++...+.+.++.+.+...+.+++.++
T Consensus 22 ~~~~~da~yfs~~t~tTvGyGDi~p~t~~gr~~~~~~~~~G~~~~~~~~~~~~~~l~ 78 (79)
T PF07885_consen 22 KWSFIDALYFSFVTITTVGYGDIVPQTPAGRIFTIIYMLIGIFLFALFLSVLASVLT 78 (79)
T ss_dssp TTSHHHHHHHHHHHHTT---SSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhcccCCCccCCccchHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5679999999999999888 6689999999999999999999999998888876654
No 28
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=93.90 E-value=0.13 Score=47.08 Aligned_cols=47 Identities=11% Similarity=0.125 Sum_probs=37.0
Q ss_pred eehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccc
Q psy936 89 GIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPV 141 (344)
Q Consensus 89 G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~ 141 (344)
+...++.+.+++++|.+++++...+ +..++..+.+|++|+++.+...
T Consensus 49 ~~~~~l~~~l~~~~g~~v~~~~~~~------~~~~~~~l~~g~~Di~~~~~~~ 95 (254)
T TIGR01098 49 RRWEPLADYLEKKLGIKVQLFVATD------YSAVIEAMRFGRVDIAWFGPSS 95 (254)
T ss_pred HHHHHHHHHHHHHhCCcEEEEeCCC------HHHHHHHHHcCCccEEEECcHH
Confidence 4456899999999999999876432 2368899999999999866543
No 29
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=84.41 E-value=1.5 Score=41.81 Aligned_cols=51 Identities=14% Similarity=0.146 Sum_probs=42.4
Q ss_pred hhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEEEecee--eccceeEEEEeCCCCCC
Q psy936 121 GSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKWKWGIE--LGQSQYVVMMKRPHESA 194 (344)
Q Consensus 121 ~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v~fs~p--~~~~~~~~~v~~~~~~~ 194 (344)
.++...|.+|++|+++.+...+.+|.. .++++.+ |.....+++++..+...
T Consensus 54 ~~i~~~L~sG~vDlgi~g~~~~~er~~-----------------------~v~~~~~l~~~~~~lvvvvp~~~~i~ 106 (287)
T PRK00489 54 DDIPGYVADGVVDLGITGEDLLEESGA-----------------------DVEELLDLGFGKCRLVLAVPEDSDWQ 106 (287)
T ss_pred HHHHHHHHcCCCCEEEcchHHHHHCCC-----------------------CceEeeeccCCceEEEEEEECCCCCC
Confidence 489999999999999999988888877 7788886 77788888888765443
No 30
>KOG3713|consensus
Probab=75.35 E-value=4.6 Score=41.21 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=39.4
Q ss_pred CcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhh
Q psy936 239 LYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAF 284 (344)
Q Consensus 239 ~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~ 284 (344)
-.+|-.++|+..-+|...| ++..|++.++|++...-.++++++.+.
T Consensus 375 FtSIPa~~WWaiVTMTTVGYGDm~P~T~~Gklvas~cil~GVLvlAl 421 (477)
T KOG3713|consen 375 FTSIPAGFWWAVVTMTTVGYGDMVPVTVLGKLVASLCILCGVLVLAL 421 (477)
T ss_pred CccccchhheeeEEEeeecccCccccccchHHHHHHHHHHhHHHhhc
Confidence 3468899998888887777 679999999999999999999888776
No 31
>KOG1419|consensus
Probab=74.50 E-value=6.7 Score=40.75 Aligned_cols=90 Identities=14% Similarity=0.206 Sum_probs=66.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhh
Q psy936 206 EVWFLILISLVLIGPIMHAIMRVRRWLSGTQSELYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAF 284 (344)
Q Consensus 206 ~vWl~il~~~i~~~~vl~~i~r~~~~~~~~~~~~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~ 284 (344)
..|..-++.+++.+.+.|+.++-...+.. +...-+..+++|+-.-+++..| ++..|.++.+|++...+.++++-+-+.
T Consensus 235 Tt~YIGFL~LIfsSflVYLaEKd~~~e~~-n~~F~TyADALWWG~ITltTIGYGDk~P~TWlGr~laa~fsligiSFFAL 313 (654)
T KOG1419|consen 235 TTWYIGFLVLIFSSFLVYLAEKDAQGEGT-NDEFPTYADALWWGVITLTTIGYGDKTPQTWLGRLLAACFSLIGISFFAL 313 (654)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcccccccc-cccchhHHHHHHhhheeEEeeccCCcCcccchhHHHHHHHHHHHHHHHhc
Confidence 45776677777777777777755333211 1112357889998666666666 578999999999999999999999999
Q ss_pred cccceeeeeecC
Q psy936 285 YTANLTAFLTLS 296 (344)
Q Consensus 285 Yta~L~s~Lt~~ 296 (344)
=.+.|.|-++..
T Consensus 314 PAGILGSGfALK 325 (654)
T KOG1419|consen 314 PAGILGSGFALK 325 (654)
T ss_pred ccccccchhhhh
Confidence 999998877764
No 32
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=73.61 E-value=7.6 Score=42.57 Aligned_cols=52 Identities=17% Similarity=0.321 Sum_probs=45.9
Q ss_pred hHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeec
Q psy936 244 ACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTL 295 (344)
Q Consensus 244 ~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~ 295 (344)
.++++++.++...| ++..|.+..+|++.++++++++.+.++..+++++.+..
T Consensus 253 ~slYwai~TmtTVGYGDi~p~t~~E~i~~i~~ml~g~~~~a~~ig~i~~li~~ 305 (823)
T PLN03192 253 SAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVE 305 (823)
T ss_pred HHHHHHHHHHhhccCCCcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47888888888887 57889999999999999999999999999999887654
No 33
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=71.81 E-value=8.1 Score=36.19 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=32.3
Q ss_pred HHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 93 EILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 93 ~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+.+.+++++|.++++....+ +..++..+.+|++|+++.+.
T Consensus 48 ~l~~~l~~~~g~~v~~~~~~~------~~~~~~al~~g~~D~~~~~~ 88 (288)
T TIGR03431 48 PLADYLSKKLGVKVKLFFATD------YAGVIEGMRFGKVDIAWYGP 88 (288)
T ss_pred HHHHHHHHHhCCcEEEEeCCC------HHHHHHHHHcCCccEEEECh
Confidence 477899999999998765432 23688999999999998653
No 34
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=61.17 E-value=18 Score=30.66 Aligned_cols=74 Identities=14% Similarity=0.203 Sum_probs=48.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.+++++.... ..+++.+.+|++|+++........-..
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~~~~~~~-------~~~~~~l~~g~~Dl~i~~~~~~~~~~~-------------------- 65 (202)
T cd08468 13 AVMPRLMARLEELAPSVRLNLVHAEQ-------KLPLDALLAGEIDFALGYSHDDGAEPR-------------------- 65 (202)
T ss_pred HHhHHHHHHHHhhCCCCEEEEEECCh-------HhHHHHHHCCCccEEEecccccccCCC--------------------
Confidence 45568888898887 67777765321 268999999999999875432100011
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+.. .++.....++++++.+..
T Consensus 66 ---~~~~-~~l~~~~~~~~~~~~hpl 87 (202)
T cd08468 66 ---LIEE-RDWWEDTYVVIASRDHPR 87 (202)
T ss_pred ---CEEE-EEEecCcEEEEEeCCCCC
Confidence 3333 467777888888877653
No 35
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=57.40 E-value=31 Score=29.01 Aligned_cols=70 Identities=19% Similarity=0.311 Sum_probs=47.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.+++++.... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~v~v~i~~~~~-------~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (201)
T cd08459 13 YFLPRLLAALREVAPGVRIETVRLPV-------DELEEALESGEIDLAIGYLPDL---GA-------------------- 62 (201)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEecCc-------cCHHHHhhCCCceEEEEcCCCC---cc--------------------
Confidence 44567888888877 56676654221 2578899999999998654321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~l~-~~~l~~~~~~~v~~~~~~ 83 (201)
T cd08459 63 ---GFF-QQRLFRERYVCLVRKDHP 83 (201)
T ss_pred ---cce-EEEeecCceEEEEcCCCc
Confidence 333 357888888888887654
No 36
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=57.35 E-value=25 Score=29.13 Aligned_cols=71 Identities=15% Similarity=0.205 Sum_probs=47.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++.... ...+.+++.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~~~l~~~~~~-------~~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (201)
T cd08420 13 YLLPRLLARFRKRYPEVRVSLTIGN-------TEEIAERVLDGEIDLGLVEGPVD---HP-------------------- 62 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEEeCC-------cHHHHHHHHCCCccEEEecCCCC---Cc--------------------
Confidence 44567888888876 5667765422 13578899999999998754322 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. +.++....+++++++.+..
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~~~~ 84 (201)
T cd08420 63 ---DLI-VEPFAEDELVLVVPPDHPL 84 (201)
T ss_pred ---ceE-EEeecCccEEEEecCCCCc
Confidence 222 2477888888888766543
No 37
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=57.28 E-value=32 Score=29.52 Aligned_cols=72 Identities=19% Similarity=0.150 Sum_probs=48.3
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +..+++..... +..+.+.|.+|++|+++....... .
T Consensus 13 ~~~~~~l~~~~~~~P~~~v~~~~~~~------~~~l~~~L~~g~lDl~i~~~~~~~---~-------------------- 63 (203)
T cd08463 13 LFLPELVARFRREAPGARLEIHPLGP------DFDYERALASGELDLVIGNWPEPP---E-------------------- 63 (203)
T ss_pred HHhHHHHHHHHHHCCCCEEEEEeCCc------chhHHHHHhcCCeeEEEeccccCC---C--------------------
Confidence 45668888888877 56777654211 126899999999999987432211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+++ .++.+...++++++.+..
T Consensus 64 ---~l~~-~~l~~~~~~lv~~~~h~l 85 (203)
T cd08463 64 ---HLHL-SPLFSDEIVCLMRADHPL 85 (203)
T ss_pred ---CcEE-eEeecCceEEEEeCCCCc
Confidence 2233 477888889998877654
No 38
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=57.06 E-value=27 Score=29.11 Aligned_cols=70 Identities=14% Similarity=0.127 Sum_probs=46.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++....... .
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~~-------~~~~~~l~~~~~Dl~i~~~~~~~---~-------------------- 62 (196)
T cd08450 13 QWLPEVLPILREEHPDLDVELSSLFS-------PQLAEALMRGKLDVAFMRPEIQS---D-------------------- 62 (196)
T ss_pred hhHHHHHHHHHhhCCCcEEEEEecCh-------HHHHHHHhcCCccEEEEeCCCCC---C--------------------
Confidence 45568888888876 66777765221 26788999999999986443211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~~~~~~~p 83 (196)
T cd08450 63 ---GID-YQLLLKEPLIVVLPADHR 83 (196)
T ss_pred ---CcE-EEEEEccceEEEecCCCC
Confidence 222 346777888888877654
No 39
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=56.96 E-value=26 Score=29.32 Aligned_cols=69 Identities=16% Similarity=0.252 Sum_probs=45.0
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+...++..+.++. +.++++.... ...+...+.+|++|+++....... .
T Consensus 15 ~l~~~l~~~~~~~P~v~i~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~---~--------------------- 63 (197)
T cd08425 15 LIGPLIDRFHARYPGIALSLREMP-------QERIEAALADDRLDLGIAFAPVRS---P--------------------- 63 (197)
T ss_pred hhHHHHHHHHHHCCCcEEEEEECc-------HHHHHHHHHcCCccEEEEecCCCC---C---------------------
Confidence 3457788888776 5666665422 126788999999999986543221 1
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 64 --~~~-~~~l~~~~~~~v~~~~~p 84 (197)
T cd08425 64 --DID-AQPLFDERLALVVGATHP 84 (197)
T ss_pred --CcE-EEEeccccEEEEecCCCc
Confidence 222 246777888888877654
No 40
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=56.59 E-value=18 Score=30.58 Aligned_cols=70 Identities=19% Similarity=0.323 Sum_probs=48.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.|.+|++|+++........
T Consensus 19 ~~l~~~l~~~~~~~P~i~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~~----------------------- 68 (209)
T PF03466_consen 19 SLLPPLLAEFRERHPNIRIEIREGD-------SDELIEALRSGELDLAITFGPPPPP----------------------- 68 (209)
T ss_dssp HTHHHHHHHHHHHSTTEEEEEEEES-------HHHHHHHHHTTSSSEEEESSSSSST-----------------------
T ss_pred HHHHHHHHHHHHHCCCcEEEEEecc-------chhhhHHHhcccccEEEEEeecccc-----------------------
Confidence 34457788887776 5566665532 1368899999999999987765222
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.++
T Consensus 69 ---~~~-~~~l~~~~~~~~~~~~~p 89 (209)
T PF03466_consen 69 ---GLE-SEPLGEEPLVLVVSPDHP 89 (209)
T ss_dssp ---TEE-EEEEEEEEEEEEEETTSG
T ss_pred ---ccc-cccccceeeeeeeecccc
Confidence 233 347888899999998763
No 41
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA bin
Probab=56.44 E-value=25 Score=28.53 Aligned_cols=70 Identities=16% Similarity=0.271 Sum_probs=45.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+...+.+|++|+++...... ..
T Consensus 13 ~~l~~~i~~~~~~~p~i~i~~~~~~-------~~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (197)
T cd05466 13 YLLPPLLAAFRQRYPGVELSLVEGG-------SSELLEALLEGELDLAIVALPVD---DP-------------------- 62 (197)
T ss_pred HHhHHHHHHHHHHCCCCEEEEEECC-------hHHHHHHHHcCCceEEEEcCCCC---CC--------------------
Confidence 34457777777766 4566665432 12578899999999998765431 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.++ ..++.....++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~~~~~~~~ 83 (197)
T cd05466 63 ---GLE-SEPLFEEPLVLVVPPDHP 83 (197)
T ss_pred ---cce-EeeeeccceEEEecCCCC
Confidence 233 336677788888887654
No 42
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=56.11 E-value=26 Score=29.37 Aligned_cols=71 Identities=21% Similarity=0.272 Sum_probs=47.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 62 (200)
T cd08466 13 LLLPRLLARLKQLAPNISLRESPSS-------EEDLFEDLRLQEVDLVIDYVPFR---DP-------------------- 62 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEecCc-------hHhHHHHHHcCCccEEEecccCC---CC--------------------
Confidence 44567888888876 6677765422 12578999999999998643221 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. +.++....+++++++.+..
T Consensus 63 ---~~~-~~~l~~~~~~lv~~~~~~~ 84 (200)
T cd08466 63 ---SFK-SELLFEDELVCVARKDHPR 84 (200)
T ss_pred ---Cce-eeeecccceEEEEeCCCCC
Confidence 222 3477888889998876643
No 43
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=55.71 E-value=32 Score=28.49 Aligned_cols=70 Identities=17% Similarity=0.317 Sum_probs=45.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +..+++.... ...+.+.|.+|++|+++....... .
T Consensus 13 ~~l~~~l~~~~~~~p~v~i~i~~~~-------~~~~~~~L~~~~~Dl~i~~~~~~~---~-------------------- 62 (197)
T cd08438 13 LLFAPLLAAFRQRYPNIELELVEYG-------GKKVEQAVLNGELDVGITVLPVDE---E-------------------- 62 (197)
T ss_pred hhcHHHHHHHHHHCcCeEEEEEEcC-------cHHHHHHHHcCCCCEEEEeccccc---C--------------------
Confidence 34557888888876 4555554421 126789999999999987543211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~~~ 83 (197)
T cd08438 63 ---EFD-SQPLCNEPLVAVLPRGHP 83 (197)
T ss_pred ---Cce-eEEeccccEEEEecCCCC
Confidence 222 236778888888887654
No 44
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=55.31 E-value=31 Score=28.58 Aligned_cols=70 Identities=13% Similarity=0.180 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~~-------~~~~~~l~~~~~Dl~i~~~~~~---~~-------------------- 62 (196)
T cd08415 13 SLLPRAIARFRARHPDVRISLHTLSS-------STVVEAVLSGQADLGLASLPLD---HP-------------------- 62 (196)
T ss_pred cccHHHHHHHHHHCCCcEEEEEecch-------HHHHHHHHcCCccEEEEeCCCC---CC--------------------
Confidence 44567888888876 66777655321 2578899999999998754322 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+ .+.++.....++++++.+.
T Consensus 63 ---~~-~~~~l~~~~~~~v~~~~~~ 83 (196)
T cd08415 63 ---GL-ESEPLASGRAVCVLPPGHP 83 (196)
T ss_pred ---cc-eeeeecccceEEEEcCCCC
Confidence 22 2347777888888876543
No 45
>PRK10537 voltage-gated potassium channel; Provisional
Probab=55.16 E-value=22 Score=35.70 Aligned_cols=52 Identities=17% Similarity=0.241 Sum_probs=39.8
Q ss_pred CcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhccccee
Q psy936 239 LYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFYTANLT 290 (344)
Q Consensus 239 ~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~ 290 (344)
..++.+++|+++.++...| ++..|.+..+|++...+.++++.+..+..+.++
T Consensus 166 ~~s~~dA~y~svvt~tTvGyGdi~p~t~~grl~~i~~ii~Gi~vf~~~is~i~ 218 (393)
T PRK10537 166 IESLSTAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIF 218 (393)
T ss_pred CCCHHHHHHhhheeeecccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999888777666 457899999999999999888776555444443
No 46
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=55.15 E-value=32 Score=28.76 Aligned_cols=70 Identities=20% Similarity=0.221 Sum_probs=46.3
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++..... ..+...+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~f~~~~P~v~i~i~~~~~-------~~~~~~l~~~~~Di~i~~~~~~---~~-------------------- 62 (198)
T cd08461 13 AILPPLLAALRQEAPGVRVAIRDLES-------DNLEAQLERGEVDLALTTPEYA---PD-------------------- 62 (198)
T ss_pred HHhHHHHHHHHHHCCCcEEEEeeCCc-------ccHHHHHhcCCCcEEEecCccC---Cc--------------------
Confidence 44567888888877 67777754321 2578899999999998643221 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~lv~~~~~p 83 (198)
T cd08461 63 ---GLR-SRPLFEERYVCVTRRGHP 83 (198)
T ss_pred ---cce-eeeeecCcEEEEEcCCCh
Confidence 222 347777888888877654
No 47
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=53.73 E-value=32 Score=28.29 Aligned_cols=70 Identities=14% Similarity=0.233 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~p~v~i~i~~~~-------~~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (197)
T cd08440 13 TLLPPVLAAFRRRHPGIRVRLRDVS-------AEQVIEAVRSGEVDFGIGSEPEA---DP-------------------- 62 (197)
T ss_pred hHHHHHHHHHHHhCCCcEEEEEeCC-------hHHHHHHHHcCCccEEEEeCCCC---CC--------------------
Confidence 45568888888776 5667665422 12688899999999998754321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.. .++.....++++++.+.
T Consensus 63 ---~~~~-~~l~~~~~~~~~~~~~p 83 (197)
T cd08440 63 ---DLEF-EPLLRDPFVLVCPKDHP 83 (197)
T ss_pred ---CeeE-EEeecccEEEEecCCCC
Confidence 2222 36777888888876654
No 48
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=52.77 E-value=28 Score=28.99 Aligned_cols=70 Identities=14% Similarity=0.151 Sum_probs=47.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~~~~D~~i~~~~~~---~~-------------------- 62 (198)
T cd08412 13 YYLPGLLRRFREAYPGVEVRVVEGN-------QEELEEGLRSGELDLALTYDLDL---PE-------------------- 62 (198)
T ss_pred hhhHHHHHHHHHHCCCcEEEEEECC-------HHHHHHHHHcCCCcEEEEcCCCC---Cc--------------------
Confidence 55678888888887 6777776522 12678899999999998754321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~~~~~~~~ 83 (198)
T cd08412 63 ---DIA-FEPLARLPPYVWLPADHP 83 (198)
T ss_pred ---ccc-eeeeeccceEEEecCCCC
Confidence 222 357777788888876654
No 49
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=52.64 E-value=28 Score=29.01 Aligned_cols=70 Identities=13% Similarity=0.224 Sum_probs=45.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~~~~D~~i~~~~~~---~~-------------------- 62 (199)
T cd08426 13 ELLPSLIARFRQRYPGVFFTVDVAS-------TADVLEAVLSGEADIGLAFSPPP---EP-------------------- 62 (199)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEeCC-------cHHHHHHHHCCCccEEEecCCCC---CC--------------------
Confidence 34557777787775 5666665421 13688999999999998644321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++.....++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~hp 83 (199)
T cd08426 63 ---GIR-VHSRQPAPIGAVVPPGHP 83 (199)
T ss_pred ---CeE-EEeeccCcEEEEecCCCC
Confidence 233 347788888888887654
No 50
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=52.50 E-value=29 Score=28.88 Aligned_cols=70 Identities=13% Similarity=0.216 Sum_probs=46.1
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ...
T Consensus 15 ~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~--~~~--------------------- 64 (199)
T cd08451 15 LVPGLIRRFREAYPDVELTLEEAN-------TAELLEALREGRLDAAFVRPPVA--RSD--------------------- 64 (199)
T ss_pred ccHHHHHHHHHHCCCcEEEEecCC-------hHHHHHHHHCCCccEEEEecCCC--CCC---------------------
Confidence 4567888888887 5677766532 12678899999999998654321 011
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+ -+.++.....++++++.+.
T Consensus 65 --~~-~~~~l~~~~~~~v~~~~~~ 85 (199)
T cd08451 65 --GL-VLELLLEEPMLVALPAGHP 85 (199)
T ss_pred --ce-eEEEeecccEEEEecCCCC
Confidence 22 2357777888888876553
No 51
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=52.16 E-value=37 Score=28.23 Aligned_cols=70 Identities=16% Similarity=0.106 Sum_probs=47.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~~-------~~~~~~l~~~~~D~~i~~~~~~---~~-------------------- 62 (198)
T cd08421 13 EFLPEDLASFLAAHPDVRIDLEERLS-------ADIVRAVAEGRADLGIVAGNVD---AA-------------------- 62 (198)
T ss_pred hhhHHHHHHHHHHCCCceEEEEecCc-------HHHHHHHhcCCceEEEEecCCC---CC--------------------
Confidence 34457888888876 66676654221 2678999999999998654321 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+ .++....+++++++.+.
T Consensus 63 ---~~~~-~~l~~~~~~~v~~~~~p 83 (198)
T cd08421 63 ---GLET-RPYRTDRLVVVVPRDHP 83 (198)
T ss_pred ---CcEE-EEeecCcEEEEeCCCCC
Confidence 3333 47788888888887654
No 52
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity,
Probab=51.78 E-value=28 Score=28.69 Aligned_cols=70 Identities=19% Similarity=0.394 Sum_probs=46.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-..++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~---~~-------------------- 62 (195)
T cd08434 13 SLVPDLIRAFRKEYPNVTFELHQGS-------TDELLDDLKNGELDLALCSPVPD---EP-------------------- 62 (195)
T ss_pred hhhHHHHHHHHHhCCCeEEEEecCc-------HHHHHHHHHcCCccEEEEccCCC---CC--------------------
Confidence 34457778888876 6666665421 12678899999999998654321 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+ .++....+++++++.+.
T Consensus 63 ---~l~~-~~l~~~~~~~v~~~~~~ 83 (195)
T cd08434 63 ---DIEW-IPLFTEELVLVVPKDHP 83 (195)
T ss_pred ---CeeE-EEeecceEEEEecCCCc
Confidence 3333 47778888888877654
No 53
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=51.75 E-value=37 Score=28.74 Aligned_cols=70 Identities=10% Similarity=0.120 Sum_probs=45.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~~~-------~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (200)
T cd08467 13 ALLPRLAPRLRERAPGLDLRLCPIGD-------DLAERGLEQGTIDLAVGRFAVP---PD-------------------- 62 (200)
T ss_pred HHHHHHHHHHHhhCCCCEEEEecCCc-------ccHHHHhhCCCcCEEEecCCCC---Cc--------------------
Confidence 45567888888776 56666654221 2578999999999998643211 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~h~ 83 (200)
T cd08467 63 ---GLV-VRRLYDDGFACLVRHGHP 83 (200)
T ss_pred ---cce-eEEeeeccEEEEEcCCCc
Confidence 222 247778888888876654
No 54
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=51.70 E-value=37 Score=28.10 Aligned_cols=70 Identities=19% Similarity=0.175 Sum_probs=46.6
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.+++++... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~i~~~~-------~~~~~~~l~~~~~Di~i~~~~~~---~~-------------------- 62 (197)
T cd08448 13 RGLPRILRAFRAEYPGIEVALHEMS-------SAEQIEALLRGELDLGFVHSRRL---PA-------------------- 62 (197)
T ss_pred HHHHHHHHHHHHHCCCCeEEEEeCC-------HHHHHHHHHcCCcceEEEeCCCC---Cc--------------------
Confidence 45568888888877 6777776422 12678899999999998643221 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....++++++..+.
T Consensus 63 ---~~~-~~~l~~~~~~~~~~~~hp 83 (197)
T cd08448 63 ---GLS-ARLLHREPFVCCLPAGHP 83 (197)
T ss_pred ---Cce-EEEEecCcEEEEeeCCCC
Confidence 222 246777888888877653
No 55
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=51.41 E-value=39 Score=28.52 Aligned_cols=70 Identities=16% Similarity=0.274 Sum_probs=46.2
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-..++..+.+++ +.++++.... . .+++.+.+|++|+++..-.... .
T Consensus 13 ~~l~~~i~~~~~~~P~i~l~i~~~~-------~-~~~~~l~~g~~D~~i~~~~~~~---~-------------------- 61 (200)
T cd08462 13 VLLPPVIERVAREAPGVRFELLPPD-------D-QPHELLERGEVDLLIAPERFMS---D-------------------- 61 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEecCC-------h-hHHHHHhcCCeeEEEecCCCCC---C--------------------
Confidence 34457777787776 5667765421 1 5899999999999986432211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++.....++++++.+..
T Consensus 62 ---~~~-~~~l~~~~~~~v~~~~hpl 83 (200)
T cd08462 62 ---GHP-SEPLFEEEFVCVVWADNPL 83 (200)
T ss_pred ---Cce-eeeeeccceEEEEcCCCCc
Confidence 222 2377788888888877654
No 56
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=51.29 E-value=32 Score=29.24 Aligned_cols=69 Identities=16% Similarity=0.269 Sum_probs=45.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+.+.|.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~f~~~~P~i~l~i~~~~-------~~~~~~~L~~g~~Dl~i~~~~~~---~~-------------------- 62 (200)
T cd08465 13 LVLPALMRQLRAEAPGIDLAVSQAS-------REAMLAQVADGEIDLALGVFPEL---PE-------------------- 62 (200)
T ss_pred HhhhHHHHHHHHHCCCcEEEEecCC-------hHhHHHHHHCCCccEEEeccccC---Cc--------------------
Confidence 45567788887765 5666655421 13689999999999998643221 12
Q ss_pred cccEEEeceeeccceeEEEEeCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.+.. .++.+...++++++.+
T Consensus 63 ---~~~~-~~l~~~~~~lv~~~~h 82 (200)
T cd08465 63 ---ELHA-ETLFEERFVCLADRAT 82 (200)
T ss_pred ---CeeE-EEeeeccEEEEEeCCC
Confidence 3333 3677778888888765
No 57
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=50.12 E-value=42 Score=27.73 Aligned_cols=70 Identities=16% Similarity=0.213 Sum_probs=46.7
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~~-------~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 62 (193)
T cd08442 13 VRLPPLLAAYHARYPKVDLSLSTGTT-------GALIQAVLEGRLDGAFVAGPVE---HP-------------------- 62 (193)
T ss_pred hhhHHHHHHHHHHCCCceEEEEeCCc-------HHHHHHHHCCCccEEEEeCCCC---CC--------------------
Confidence 44568888888877 67777765321 2688899999999998653321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~~~ 83 (193)
T cd08442 63 ---RLE-QEPVFQEELVLVSPKGHP 83 (193)
T ss_pred ---CcE-EEEeecCcEEEEecCCCc
Confidence 222 346777888888887654
No 58
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=49.95 E-value=39 Score=28.21 Aligned_cols=70 Identities=7% Similarity=0.110 Sum_probs=44.7
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 14 ~~l~~~i~~~~~~~P~v~l~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~---~~-------------------- 63 (198)
T cd08446 14 DTVPRLLRAFLTARPDVTVSLHNMT-------KDEQIEALRAGRIHIGFGRFYPV---EP-------------------- 63 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEeeCC-------HHHHHHHHHCCCccEEEEecCCC---CC--------------------
Confidence 34567788888776 5666665421 12578899999999998644321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++.....++++++.+.
T Consensus 64 ---~~~-~~~l~~~~~~~v~~~~~p 84 (198)
T cd08446 64 ---DIA-VENVAQERLYLAVPKSHP 84 (198)
T ss_pred ---Cce-eEEeeeccEEEEEeCCCC
Confidence 221 336677788888877654
No 59
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=49.90 E-value=34 Score=28.44 Aligned_cols=70 Identities=9% Similarity=0.022 Sum_probs=45.7
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~~~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 62 (196)
T cd08456 13 SFLPRAIKAFLQRHPDVTISIHTRD-------SPTVEQWLSAQQCDLGLVSTLHE---PP-------------------- 62 (196)
T ss_pred hhHHHHHHHHHHHCCCcEEEEEeCC-------HHHHHHHHHcCCccEEEEecCCC---CC--------------------
Confidence 45568888888887 6677765522 12577889999999998643221 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~~~~~~~~~ 83 (196)
T cd08456 63 ---GIE-RERLLRIDGVCVLPPGHR 83 (196)
T ss_pred ---Cee-EEEeeccCeEEEecCCCc
Confidence 222 346777788888876543
No 60
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=49.51 E-value=44 Score=28.12 Aligned_cols=70 Identities=14% Similarity=0.217 Sum_probs=46.5
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... . ...+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~v~v~l~~~~-------~-~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 61 (200)
T cd08460 13 AFGPALLAAVAAEAPGVRLRFVPES-------D-KDVDALREGRIDLEIGVLGPT---GP-------------------- 61 (200)
T ss_pred HHHHHHHHHHHHHCCCCEEEEecCc-------h-hHHHHHHCCCccEEEecCCCC---Cc--------------------
Confidence 55668888888877 5666664321 1 467899999999998743321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++....+++++++.+..
T Consensus 62 ---~~~-~~~l~~~~~~~v~~~~hpl 83 (200)
T cd08460 62 ---EIR-VQTLFRDRFVGVVRAGHPL 83 (200)
T ss_pred ---chh-eeeeeccceEEEEeCCCCC
Confidence 222 3577788888888877653
No 61
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=48.65 E-value=38 Score=28.60 Aligned_cols=70 Identities=19% Similarity=0.263 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+...+.+|++|++++...... .
T Consensus 14 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~~---~-------------------- 63 (203)
T cd08445 14 GLLPELIRRFRQAAPDVEIELIEMT-------TVQQIEALKEGRIDVGFGRLRIED---P-------------------- 63 (203)
T ss_pred hHHHHHHHHHHHHCCCeEEEEEeCC-------hHHHHHHHHcCCCcEEEecCCCCC---C--------------------
Confidence 45667888888876 6666665421 136889999999999986432211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....++++++.+.
T Consensus 64 ---~~~-~~~l~~~~~~~v~~~~hp 84 (203)
T cd08445 64 ---AIR-RIVLREEPLVVALPAGHP 84 (203)
T ss_pred ---Cce-eEEEEeccEEEEeeCCCC
Confidence 222 336777788888887554
No 62
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=48.53 E-value=39 Score=27.92 Aligned_cols=69 Identities=17% Similarity=0.223 Sum_probs=44.9
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+-..++..+.++. +.++++.... ...+...+.+|++|+++...... ..
T Consensus 14 ~l~~~l~~~~~~~p~i~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~---~~--------------------- 62 (197)
T cd08414 14 LLPRLLRRFRARYPDVELELREMT-------TAEQLEALRAGRLDVGFVRPPPD---PP--------------------- 62 (197)
T ss_pred HHHHHHHHHHHHCCCcEEEEecCC-------hHHHHHHHHcCCccEEEEcCCCC---CC---------------------
Confidence 4457777777776 5566655421 12688899999999998754322 11
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....++++++.+.
T Consensus 63 --~~~-~~~l~~~~~~~v~~~~~~ 83 (197)
T cd08414 63 --GLA-SRPLLREPLVVALPADHP 83 (197)
T ss_pred --Cee-EEEEeeccEEEEecCCCc
Confidence 222 246778888888877654
No 63
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=47.89 E-value=46 Score=27.71 Aligned_cols=70 Identities=14% Similarity=0.198 Sum_probs=46.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~~-------~~~~~~l~~~~~D~~i~~~~~~---~~-------------------- 62 (198)
T cd08433 13 VLAVPLLRAVRRRYPGIRLRIVEGLS-------GHLLEWLLNGRLDLALLYGPPP---IP-------------------- 62 (198)
T ss_pred hcchHHHHHHHHHCCCcEEEEEecCc-------HHHHHHHhCCCCcEEEEeCCCC---CC--------------------
Confidence 34557788888876 56677654221 2688899999999998644321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+ -..++....+++++++.+.
T Consensus 63 ---~~-~~~~l~~~~~~~~~~~~~~ 83 (198)
T cd08433 63 ---GL-STEPLLEEDLFLVGPADAP 83 (198)
T ss_pred ---Ce-eEEEeccccEEEEecCCCc
Confidence 22 2347778888888876654
No 64
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=47.83 E-value=38 Score=28.00 Aligned_cols=70 Identities=13% Similarity=0.105 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++.... ...+.+.+.+|++|+++....... .
T Consensus 12 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~---~-------------------- 61 (197)
T cd08419 12 YFAPRLLGAFCRRHPGVEVSLRVGN-------REQVLERLADNEDDLAIMGRPPED---L-------------------- 61 (197)
T ss_pred hHhhHHHHHHHHHCCCceEEEEECC-------HHHHHHHHhcCCccEEEecCCCCC---C--------------------
Confidence 34557788888876 6777776522 125788999999999986433211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....++++++..+.
T Consensus 62 ---~~~-~~~l~~~~~~~~~~~~~~ 82 (197)
T cd08419 62 ---DLV-AEPFLDNPLVVIAPPDHP 82 (197)
T ss_pred ---CeE-EEEeccCCEEEEecCCCC
Confidence 222 347778888888876654
No 65
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=47.08 E-value=53 Score=27.30 Aligned_cols=69 Identities=17% Similarity=0.154 Sum_probs=44.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++...++..+.+++ +.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~~~~~-------~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (200)
T cd08464 13 WLAPPLLAALRAEAPGVRLVFRQVDP-------FNVGDMLDRGEIDLAIGVFGEL---PA-------------------- 62 (200)
T ss_pred HHHHHHHHHHHHHCCCcEEEEecCCc-------ccHHHHHhcCcccEEEecCCCC---cc--------------------
Confidence 45567788888876 66777654221 2578899999999998644321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.+. ..++....++++++..+
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~~ 82 (200)
T cd08464 63 ---WLK-REVLYTEGYACLFDPQQ 82 (200)
T ss_pred ---cce-eeeecccceEEEEeCCC
Confidence 222 24777778888887654
No 66
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=45.85 E-value=53 Score=27.61 Aligned_cols=70 Identities=16% Similarity=0.175 Sum_probs=45.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ |.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~---~~-------------------- 62 (197)
T cd08452 13 EFLPPIVREYRKKFPSVKVELRELS-------SPDQVEELLKGRIDIGFLHPPIQ---HT-------------------- 62 (197)
T ss_pred hHHHHHHHHHHHHCCCcEEEEEecC-------hHHHHHHHHCCCccEEEeeCCCC---CC--------------------
Confidence 34467888888776 5666665421 12688999999999998643221 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++.....++++++.+.
T Consensus 63 ---~~~-~~~l~~~~~~lv~~~~hp 83 (197)
T cd08452 63 ---ALH-IETVQSSPCVLALPKQHP 83 (197)
T ss_pred ---Cee-EEEeeeccEEEEEeCCCc
Confidence 233 246777778888876554
No 67
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=45.22 E-value=39 Score=28.69 Aligned_cols=70 Identities=7% Similarity=0.037 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+++.+.+|++|+++..-.. ...
T Consensus 14 ~~l~~~l~~f~~~~P~v~i~i~~~~-------~~~l~~~l~~g~~D~~~~~~~~---~~~-------------------- 63 (198)
T cd08486 14 RSLPLLLRAFLTSTPTATVSLTHMT-------KDEQVEGLLAGTIHVGFSRFFP---RHP-------------------- 63 (198)
T ss_pred HHHHHHHHHHHHhCCCeEEEEEECC-------HHHHHHHHHcCCceEEEecCCC---CCC--------------------
Confidence 44567788887776 6667665422 2368999999999999864321 112
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.++ +.++.+..+++++++.+.
T Consensus 64 ---~~~-~~~l~~~~~~lv~~~~h~ 84 (198)
T cd08486 64 ---GIE-IVNIAQEDLYLAVHRSQS 84 (198)
T ss_pred ---ceE-EEEEeeccEEEEecCCCc
Confidence 233 346777788888887654
No 68
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=45.18 E-value=38 Score=31.41 Aligned_cols=71 Identities=13% Similarity=0.201 Sum_probs=47.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++..+++..+.+++ +..++++... ...+++.+.+|++|+++....... .
T Consensus 102 ~~l~~~l~~f~~~~P~v~v~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~---~-------------------- 151 (275)
T PRK03601 102 CMLTPWLGRLYQNQEALQFEARIAQ-------RQSLVKQLHERQLDLLITTEAPKM---D-------------------- 151 (275)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEECC-------hHHHHHHHHcCCCCEEEEcCCCcc---C--------------------
Confidence 45567788887765 6666655532 236899999999999997543321 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++....+++++++.++.
T Consensus 152 ---~l~-~~~l~~~~~~~v~~~~~~~ 173 (275)
T PRK03601 152 ---EFS-SQLLGHFTLALYTSAPSKK 173 (275)
T ss_pred ---Ccc-EEEecceeEEEEecCchhh
Confidence 222 3478888899999876653
No 69
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=45.06 E-value=52 Score=28.26 Aligned_cols=70 Identities=14% Similarity=0.215 Sum_probs=45.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++...+ ++.+.+.+.+|++|+++...... ..
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~~~~-------~~~~~~~l~~g~~Di~i~~~~~~---~~-------------------- 62 (221)
T cd08469 13 VLLPALVRRLETEAPGIDLRIRPVT-------RLDLAEQLDLGRIDLVIGIFEQI---PP-------------------- 62 (221)
T ss_pred HHHHHHHHHHHHHCCCcEEEEeeCC-------hhhHHHHHHCCCccEEEecCCCC---Cc--------------------
Confidence 34567777777766 5666665422 12588899999999998754321 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....++++++.+.
T Consensus 63 ---~l~-~~~l~~~~~~~v~~~~~p 83 (221)
T cd08469 63 ---RFR-RRTLFDEDEVWVMRKDHP 83 (221)
T ss_pred ---cce-eeeeeccceEEEEeCCCc
Confidence 333 347778888888887654
No 70
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=43.99 E-value=55 Score=27.14 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=32.7
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~~~~~~-------~~~~~~~l~~g~~Dl~i~~~ 57 (199)
T cd08430 13 SFLPPILERFRAQHPQVEIKLHTGD-------PADAIDKVLNGEADIAIAAR 57 (199)
T ss_pred eeccHHHHHHHHHCCCceEEEEeCC-------HHHHHHHHHCCCCCEEEEec
Confidence 44568888999988 6777776532 12578899999999998653
No 71
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=43.97 E-value=47 Score=27.33 Aligned_cols=71 Identities=13% Similarity=0.187 Sum_probs=46.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++..... ....
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~--~~~~-------------------- 63 (194)
T cd08436 13 VDLPELLARFHRRHPGVDIRLRQAG-------SDDLLAAVREGRLDLAFVGLPE--RRPP-------------------- 63 (194)
T ss_pred HHHHHHHHHHHHHCCCcEEEEecCC-------HHHHHHHHHcCCccEEEEecCC--CCCC--------------------
Confidence 45567788888776 5666665421 1257889999999999875432 1112
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....+++++..+.
T Consensus 64 ---~~~-~~~l~~~~~~~~~~~~~~ 84 (194)
T cd08436 64 ---GLA-SRELAREPLVAVVAPDHP 84 (194)
T ss_pred ---CcE-EEEeecceEEEEecCCCc
Confidence 222 246777888888887654
No 72
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=43.54 E-value=56 Score=27.15 Aligned_cols=72 Identities=18% Similarity=0.251 Sum_probs=47.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ |.++++.... +..+.+.+.+|++|+++....... ...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~~-~~~-------------------- 64 (199)
T cd08416 13 NTVPRIIMGLKLRRPELDIELTLGS-------NKDLLKKLKDGELDAILVATPEGL-NDP-------------------- 64 (199)
T ss_pred hhhHHHHHHHHHhCCCeEEEEEEcC-------cHHHHHHHhCCCCCEEEEecCCcC-CCC--------------------
Confidence 45567888888887 6777776532 125788999999999987543200 111
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++....+++++++.+.
T Consensus 65 ---~l~-~~~l~~~~~~~v~~~~hp 85 (199)
T cd08416 65 ---DFE-VVPLFEDDIFLAVPATSP 85 (199)
T ss_pred ---CeE-EEEeecceEEEEECCCCc
Confidence 222 346777788888876554
No 73
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=42.03 E-value=56 Score=30.85 Aligned_cols=71 Identities=13% Similarity=0.172 Sum_probs=48.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++..... ..+.+.|.+|++|+++....... .
T Consensus 125 ~~l~~~l~~f~~~~P~i~l~i~~~~~-------~~~~~~l~~g~~Di~i~~~~~~~---~-------------------- 174 (314)
T PRK09508 125 RLTSQIYNRIEQIAPNIHVVFKSSLN-------QNIEHQLRYQETEFVISYEEFDR---P-------------------- 174 (314)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEeCcc-------hhHHHHHhcCCccEEEecCCCCc---c--------------------
Confidence 45678888888887 77888765322 25889999999999987543211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+.+ .++.....+++++..+..
T Consensus 175 ---~l~~-~~l~~~~~~lv~~~~hpl 196 (314)
T PRK09508 175 ---EFTS-VPLFKDELVLVASKNHPR 196 (314)
T ss_pred ---ccce-eeeecCceEEEEcCCCCc
Confidence 2232 367778888888876653
No 74
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=41.50 E-value=48 Score=28.03 Aligned_cols=44 Identities=14% Similarity=0.081 Sum_probs=31.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+-.+++..+.+++ |.+++++... .+.+.+++.+|++|+++...
T Consensus 14 ~~l~~~l~~~~~~~P~i~l~~~~~~-------~~~~~~~l~~~~~D~~i~~~ 58 (198)
T cd08485 14 HTLPLLLRQLLSVAPSATVSLTQMS-------KNRQIEALDAGTIDIGFGRF 58 (198)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEECC-------HHHHHHHHHcCCccEEEecC
Confidence 34567777777765 6777765421 13688999999999998653
No 75
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=40.98 E-value=32 Score=28.71 Aligned_cols=70 Identities=16% Similarity=0.283 Sum_probs=44.5
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 13 ~~~~~~i~~~~~~~P~i~l~~~~~~-------~~~~~~~l~~g~~D~~i~~~~~~---~~-------------------- 62 (200)
T cd08417 13 LLLPPLLARLRQEAPGVRLRFVPLD-------RDDLEEALESGEIDLAIGVFPEL---PP-------------------- 62 (200)
T ss_pred HHHHHHHHHHHhhCCCeEEEeccCC-------HHHHHHHHHcCCCCEEEeecccC---CC--------------------
Confidence 44557777777776 5566654321 12678899999999998754321 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....++++++..+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~~~ 83 (200)
T cd08417 63 ---GLR-SQPLFEDRFVCVARKDHP 83 (200)
T ss_pred ---ccc-hhhhhcCceEEEecCCCc
Confidence 221 246777788888876654
No 76
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=40.80 E-value=52 Score=30.40 Aligned_cols=71 Identities=21% Similarity=0.273 Sum_probs=46.3
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+..+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ..
T Consensus 104 ~~l~~~l~~~~~~~p~~~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 153 (296)
T PRK11242 104 YLIGPLIDAFHARYPGITLTIREMS-------QERIEALLADDELDVGIAFAPVH---SP-------------------- 153 (296)
T ss_pred hhhHHHHHHHHHHCCCCEEEEEeCC-------HHHHHHHHHCCCCcEEEEecCCC---Cc--------------------
Confidence 44567888888875 4455554321 12578899999999998654322 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. +.++....+++++++.++.
T Consensus 154 ---~l~-~~~l~~~~~~~~~~~~~pl 175 (296)
T PRK11242 154 ---EIE-AQPLFTETLALVVGRHHPL 175 (296)
T ss_pred ---cee-EEEeeeccEEEEEcCCCcc
Confidence 222 3577888899998886643
No 77
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=40.67 E-value=62 Score=26.96 Aligned_cols=70 Identities=16% Similarity=0.252 Sum_probs=44.6
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++....... .
T Consensus 14 ~~l~~~l~~~~~~~P~i~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~~---~-------------------- 63 (200)
T cd08411 14 YLLPRLLPALRQAYPKLRLYLREDQ-------TERLLEKLRSGELDAALLALPVDE---P-------------------- 63 (200)
T ss_pred hhhHHHHHHHHHHCCCcEEEEEeCc-------HHHHHHHHHcCCccEEEEeccCCC---C--------------------
Confidence 34567788888776 5666665421 126788999999999986543211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 64 ---~~~-~~~l~~~~~~~v~~~~~p 84 (200)
T cd08411 64 ---GLE-EEPLFDEPFLLAVPKDHP 84 (200)
T ss_pred ---Cce-EEEeeccceEEEecCCCC
Confidence 222 236777788888876654
No 78
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=40.48 E-value=64 Score=27.04 Aligned_cols=70 Identities=9% Similarity=0.077 Sum_probs=44.7
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++...+ ...+.+.+.+|++|+++....... .
T Consensus 13 ~~l~~~l~~f~~~~P~v~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~---~-------------------- 62 (196)
T cd08458 13 SFMSGVIQTFIADRPDVSVYLDTVP-------SQTVLELVSLQHYDLGISILAGDY---P-------------------- 62 (196)
T ss_pred hhhHHHHHHHHHHCCCcEEEEeccC-------hHHHHHHHHcCCCCEEEEeccCCC---C--------------------
Confidence 34457888888876 5566654421 125788999999999987543211 1
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. +.++.....+++++..+.
T Consensus 63 ---~~~-~~~l~~~~~~~v~~~~hp 83 (196)
T cd08458 63 ---GLT-TEPVPSFRAVCLLPPGHR 83 (196)
T ss_pred ---Cce-EEEeccCceEEEecCCCc
Confidence 222 246777788888876553
No 79
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=40.08 E-value=75 Score=26.17 Aligned_cols=72 Identities=14% Similarity=0.187 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++....... ...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~~~-------~~~~~~l~~g~~Dl~i~~~~~~~-~~~-------------------- 64 (195)
T cd08427 13 GLLPRALARLRRRHPDLEVHIVPGLS-------AELLARVDAGELDAAIVVEPPFP-LPK-------------------- 64 (195)
T ss_pred HHhHHHHHHHHHHCCCceEEEEeCCc-------HHHHHHHHCCCCCEEEEcCCCCc-ccc--------------------
Confidence 44567888888777 66777654221 26888999999999987542211 011
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....+++++++.+.
T Consensus 65 ---~~~-~~~l~~~~~~~v~~~~~p 85 (195)
T cd08427 65 ---DLV-WTPLVREPLVLIAPAELA 85 (195)
T ss_pred ---Cce-EEEcccCcEEEEECCCCC
Confidence 222 346777888888887654
No 80
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=39.56 E-value=72 Score=26.61 Aligned_cols=44 Identities=14% Similarity=0.167 Sum_probs=31.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~~~~~~~-------~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08457 13 GFLPRFLAAFLRLRPNLHLSLMGLSS-------SQVLEAVASGRADLGIADG 57 (196)
T ss_pred cccHHHHHHHHHHCCCeEEEEEecCc-------HHHHHHHHcCCccEEEecc
Confidence 44567888888877 56666654221 2578899999999998654
No 81
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=39.29 E-value=67 Score=26.58 Aligned_cols=73 Identities=15% Similarity=0.198 Sum_probs=45.2
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... .+..
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~-~~~~-------------------- 64 (201)
T cd08435 13 VLLPPAIARLLARHPRLTVRVVEGT-------SDELLEGLRAGELDLAIGRLADD-EQPP-------------------- 64 (201)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEeCC-------HHHHHHHHHcCCccEEEEecCcc-cCCC--------------------
Confidence 34457777777765 4555554321 12678899999999998653211 0111
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++....+++++++.+..
T Consensus 65 ---~~~-~~~l~~~~~~~~~~~~~~l 86 (201)
T cd08435 65 ---DLA-SEELADEPLVVVARPGHPL 86 (201)
T ss_pred ---CcE-EEEcccCcEEEEEeCCCcC
Confidence 222 2477788888888876543
No 82
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=39.20 E-value=58 Score=29.64 Aligned_cols=70 Identities=14% Similarity=0.317 Sum_probs=46.0
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+-.+++..+.+++ +.+++++... ...++..+.+|++|+++..-.... .
T Consensus 98 ~~~~~l~~~~~~~p~v~l~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~---~--------------------- 146 (279)
T TIGR03339 98 YVLDLVARFRQRYPGIEVSVRIGN-------SQEVLQALQSYRVDVAVSSEVVDD---P--------------------- 146 (279)
T ss_pred HHHHHHHHHHHHCCCcEEEEEECC-------HHHHHHHHHcCCCcEEEEecccCC---C---------------------
Confidence 3457777787776 4666665422 136889999999999986433221 1
Q ss_pred ccEEEeceeeccceeEEEEeCCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++....+++++++.++.
T Consensus 147 --~~~-~~~l~~~~~~lv~s~~~pl 168 (279)
T TIGR03339 147 --RLD-RVVLGNDPLVAVVHRQHPL 168 (279)
T ss_pred --ceE-EEEcCCceEEEEECCCCcc
Confidence 222 2477888899998876643
No 83
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=39.06 E-value=51 Score=30.83 Aligned_cols=70 Identities=10% Similarity=0.151 Sum_probs=45.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-..++..+.++. +.++++.... ...+.+++.+|++|+++...... ..
T Consensus 104 ~~~~~~l~~~~~~~P~v~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 153 (305)
T PRK11151 104 YLLPHIIPMLHQTFPKLEMYLHEAQ-------THQLLAQLDSGKLDCAILALVKE---SE-------------------- 153 (305)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEeCC-------HHHHHHHHHcCCccEEEEecCCC---CC--------------------
Confidence 34456676777654 5555554422 13788999999999998754322 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+ ...++....+++++++.++
T Consensus 154 ---~l-~~~~l~~~~~~~~~~~~hp 174 (305)
T PRK11151 154 ---AF-IEVPLFDEPMLLAVYEDHP 174 (305)
T ss_pred ---Ce-EEEEeccCcEEEEecCCCC
Confidence 22 2358888999999987664
No 84
>PF01007 IRK: Inward rectifier potassium channel; InterPro: IPR013521 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Inwardly-rectifying potassium channels (Kir) are the principal class of two-TM domain potassium channels. They are characterised by the property of inward-rectification, which is described as the ability to allow large inward currents and smaller outward currents. Inwardly rectifying potassium channels (Kir) are responsible for regulating diverse processes including: cellular excitability, vascular tone, heart rate, renal salt flow, and insulin release []. To date, around twenty members of this superfamily have been cloned, which can be grouped into six families by sequence similarity, and these are designated Kir1.x-6.x [, ]. Cloned Kir channel cDNAs encode proteins of between ~370-500 residues, both N- and C-termini are thought to be cytoplasmic, and the N terminus lacks a signal sequence. Kir channel alpha subunits possess only 2TM domains linked with a P-domain. Thus, Kir channels share similarity with the fifth and sixth domains, and P-domain of the other families. It is thought that four Kir subunits assemble to form a tetrameric channel complex, which may be hetero- or homomeric [].; PDB: 3AT9_A 3AUW_D 3SYA_A 3ATE_A 3SYQ_A 3SYO_A 3ATB_A 3SYC_A 3AT8_A 3ATA_A ....
Probab=38.77 E-value=95 Score=30.52 Aligned_cols=60 Identities=13% Similarity=0.103 Sum_probs=47.2
Q ss_pred cCchhHHHHHHHHHHcCCCC---CCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeecCCCC
Q psy936 240 YPISACTWFVYGALMKQGST---LNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQFT 299 (344)
Q Consensus 240 ~~i~~~~~~~~~~ll~qg~~---~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~~~ 299 (344)
.++..++++++.++...|.. ..|....+-+++..=.+.++++.++-+|.+.+-++.|+..
T Consensus 83 ~~f~~aF~FSveT~tTIGYG~~~~~~~c~~a~~l~~~q~~~g~l~~a~~~Glvfar~srP~~R 145 (336)
T PF01007_consen 83 NSFTSAFLFSVETQTTIGYGSRYPTPECPYAIFLVTIQSLVGLLLDAFMTGLVFARFSRPKKR 145 (336)
T ss_dssp TTHHHHHHHHHHHHTT---SSSEB-CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCCG
T ss_pred cchhhheeEEEEEEEEeccCCcccCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence 46889999999998877743 3566677778888888899999999999999999999754
No 85
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=38.29 E-value=24 Score=29.52 Aligned_cols=12 Identities=17% Similarity=0.656 Sum_probs=5.2
Q ss_pred hHHHHHHHHHHH
Q psy936 206 EVWFLILISLVL 217 (344)
Q Consensus 206 ~vWl~il~~~i~ 217 (344)
.+|++|++.+++
T Consensus 3 ~l~~iii~~i~l 14 (130)
T PF12273_consen 3 VLFAIIIVAILL 14 (130)
T ss_pred eeHHHHHHHHHH
Confidence 344444444333
No 86
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=38.13 E-value=81 Score=26.26 Aligned_cols=43 Identities=14% Similarity=0.229 Sum_probs=30.4
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
+-..++..+.+++ +.++++..... ..+.+.+.+|++|+++..-
T Consensus 14 ~~~~~l~~~~~~~P~i~i~i~~~~~-------~~~~~~l~~g~~Dl~i~~~ 57 (198)
T cd08441 14 WLMPVLDQFRERWPDVELDLSSGFH-------FDPLPALLRGELDLVITSD 57 (198)
T ss_pred hhHHHHHHHHHhCCCeEEEEEeCCc-------hhHHHHHHcCCceEEEecC
Confidence 3457788888877 56676654221 2578999999999998643
No 87
>PF15050 SCIMP: SCIMP protein
Probab=37.97 E-value=77 Score=26.52 Aligned_cols=21 Identities=14% Similarity=0.738 Sum_probs=13.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHH
Q psy936 206 EVWFLILISLVLIGPIMHAIM 226 (344)
Q Consensus 206 ~vWl~il~~~i~~~~vl~~i~ 226 (344)
..|+.++++++++++++-++.
T Consensus 7 nFWiiLAVaII~vS~~lglIl 27 (133)
T PF15050_consen 7 NFWIILAVAIILVSVVLGLIL 27 (133)
T ss_pred chHHHHHHHHHHHHHHHHHHH
Confidence 568888888776655444443
No 88
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=36.88 E-value=57 Score=30.86 Aligned_cols=41 Identities=10% Similarity=0.149 Sum_probs=28.0
Q ss_pred HHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEee
Q psy936 92 FEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAF 138 (344)
Q Consensus 92 ~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~ 138 (344)
.+....+.+++ +.+++++..+.. ..++..+.+|++|+++.+
T Consensus 43 ~~~~~~~~~~~p~v~ie~~~~~~~------~~~~~aL~~G~iDia~~~ 84 (314)
T PRK11553 43 AKSHQLLEKRFPQTKISWVEFPAG------PQMLEALNVGSIDLGSTG 84 (314)
T ss_pred HHhhCHHHHhCCCCeeEEEECCCc------HHHHHHHHcCCCCEEccC
Confidence 34444565555 677777664321 268899999999999765
No 89
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=36.77 E-value=67 Score=27.02 Aligned_cols=72 Identities=11% Similarity=0.150 Sum_probs=46.5
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++....... ..
T Consensus 13 ~~l~~~l~~~~~~~P~i~v~~~~~~-------~~~~~~~l~~g~~D~~i~~~~~~~--~~-------------------- 63 (198)
T cd08413 13 YVLPPVIAAFRKRYPKVKLSLHQGT-------PSQIAEMVLKGEADIAIATEALDD--HP-------------------- 63 (198)
T ss_pred hhccHHHHHHHHhCCceEEEEEeCC-------HHHHHHHHHcCCCCEEEEccCCCC--CC--------------------
Confidence 34457788888876 4566665421 136789999999999986432111 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. +.++.....++++++.+..
T Consensus 64 ---~~~-~~~l~~~~~~~v~~~~hpl 85 (198)
T cd08413 64 ---DLV-TLPCYRWNHCVIVPPGHPL 85 (198)
T ss_pred ---CcE-EEEeeeeeEEEEecCCCcc
Confidence 233 3577888888988876653
No 90
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=36.64 E-value=63 Score=27.23 Aligned_cols=72 Identities=10% Similarity=0.072 Sum_probs=47.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...... ...
T Consensus 13 ~~l~~~l~~~~~~~P~v~l~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~--~~~-------------------- 63 (198)
T cd08444 13 YALPWVVQAFKEQFPNVHLVLHQGS-------PEEIASMLANGQADIGIATEALE--NHP-------------------- 63 (198)
T ss_pred hhhhHHHHHHHHHCCCeEEEEEeCC-------HHHHHHHHHCCCccEEEeccccC--CCc--------------------
Confidence 45668888888886 6677765522 12578999999999998643211 111
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++....+++++++.+..
T Consensus 64 ---~~~-~~~l~~~~~~~~~~~~hpl 85 (198)
T cd08444 64 ---ELV-SFPYYDWHHHIIVPVGHPL 85 (198)
T ss_pred ---CcE-EeeccccceeEEecCCCcc
Confidence 222 3477778888888776543
No 91
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=36.53 E-value=67 Score=26.65 Aligned_cols=72 Identities=17% Similarity=0.250 Sum_probs=45.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-..++..+.+++ +.++++.... ...+...+.+|++|+++....... ...
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~-~~~-------------------- 64 (201)
T cd08418 13 TLMPAVINRFKEQFPDVQISIYEGQ-------LSSLLPELRDGRLDFAIGTLPDEM-YLK-------------------- 64 (201)
T ss_pred hhhHHHHHHHHHHCCCceEEEEeCc-------HHHHHHHHHcCCCcEEEEecCCCC-CCc--------------------
Confidence 44567788888776 5666665421 126789999999999997543211 011
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+ .++....+++++++.+.
T Consensus 65 ---~~~~-~~l~~~~~~~v~~~~~~ 85 (201)
T cd08418 65 ---ELIS-EPLFESDFVVVARKDHP 85 (201)
T ss_pred ---ceeE-EeecCCceEEEeCCCCc
Confidence 2222 46777888888876654
No 92
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=36.00 E-value=76 Score=26.18 Aligned_cols=72 Identities=14% Similarity=0.042 Sum_probs=44.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+...++..+.+++ +.++++.... .....+.+.+|++|+++....... +..
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~~-~~~-------------------- 64 (197)
T cd08449 13 GGLGPALRRFKRQYPNVTVRFHELS-------PEAQKAALLSKRIDLGFVRFADTL-NDP-------------------- 64 (197)
T ss_pred hhHHHHHHHHHHHCCCeEEEEEECC-------HHHHHHHHhCCCccEEEecccccC-CCC--------------------
Confidence 44567888888876 5566654321 126788999999999986443210 011
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++....++++++..+.
T Consensus 65 ---~~~-~~~l~~~~~~~v~~~~~~ 85 (197)
T cd08449 65 ---PLA-SELLWREPMVVALPEEHP 85 (197)
T ss_pred ---Cce-EEEEEEeeEEEEecCCCC
Confidence 222 246777888888876543
No 93
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=35.86 E-value=78 Score=26.34 Aligned_cols=73 Identities=7% Similarity=0.113 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++..... .....
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~-~~~~~-------------------- 64 (198)
T cd08437 13 YYFPKLAKDLIKTGLMIQIDTYEGG-------SAELLEQLLQGDLDIALLGSLT-PLENS-------------------- 64 (198)
T ss_pred HHhHHHHHHHHHhCCceEEEEEEcC-------HHHHHHHHHcCCCCEEEecCCC-CCCcc--------------------
Confidence 34567888888876 5666665422 1268889999999999864311 01112
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.++ ..++.....++++++.+..
T Consensus 65 ---~l~-~~~l~~~~~~~~~~~~hpl 86 (198)
T cd08437 65 ---ALH-SKIIKTQHFMIIVSKDHPL 86 (198)
T ss_pred ---cce-EEEeecceEEEEecCCCcc
Confidence 333 2477888888888876543
No 94
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=35.09 E-value=40 Score=28.12 Aligned_cols=26 Identities=23% Similarity=0.293 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhccc
Q psy936 208 WFLILISLVLIGPIMHAIMRVRRWLS 233 (344)
Q Consensus 208 Wl~il~~~i~~~~vl~~i~r~~~~~~ 233 (344)
|+++++.++++.+++.++.++..++.
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR~ 27 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRRR 27 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHh
Confidence 77777777776666666665554433
No 95
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=34.92 E-value=84 Score=29.09 Aligned_cols=69 Identities=19% Similarity=0.241 Sum_probs=45.9
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+..+++..+.+++ +.++++.... ..+++..+.+|++|+++..... ...
T Consensus 104 ~l~~~~~~~~~~~p~v~i~~~~~~-------~~~~~~~l~~~~~D~~i~~~~~---~~~--------------------- 152 (296)
T PRK09906 104 LLPKVLPMFRLRHPDTLIELVSLI-------TTQQEEKLRRGELDVGFMRHPV---YSD--------------------- 152 (296)
T ss_pred HHHHHHHHHHHHCCCeEEEEEeCC-------cHHHHHHHHcCCeeEEEecCCC---CCC---------------------
Confidence 3456777777775 4455544422 1368899999999999875543 112
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+++ .++.....++++++.+.
T Consensus 153 --~l~~-~~l~~~~~~~v~~~~~p 173 (296)
T PRK09906 153 --EIDY-LELLDEPLVVVLPVDHP 173 (296)
T ss_pred --CceE-EEEecccEEEEecCCCc
Confidence 3343 58888999999987654
No 96
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=34.49 E-value=1.1e+02 Score=25.44 Aligned_cols=43 Identities=12% Similarity=0.161 Sum_probs=32.1
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEee
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAF 138 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~ 138 (344)
++-.+++..+.+++ |.++++..... ..+..++.+|++|+++..
T Consensus 13 ~~l~~~l~~~~~~~P~v~i~i~~~~~-------~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 13 QPLYPLIAEFYQLNKATRIRLSEEVL-------GGTWDALASGRADLVIGA 56 (195)
T ss_pred HHHHHHHHHHHHHCCCCceEEEEecc-------chHHHHHhCCCCCEEEEe
Confidence 45678888888887 67777755322 257889999999999864
No 97
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=34.42 E-value=79 Score=26.19 Aligned_cols=42 Identities=26% Similarity=0.450 Sum_probs=30.0
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEee
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAF 138 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~ 138 (344)
+..+++..+.+++ +.++++..... ..+.+++.+|++|+++..
T Consensus 14 ~l~~~l~~~~~~~P~v~i~~~~~~~-------~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 14 ILPFLLNRFASVYPRLAIEVVCKRT-------PRLMEMLERGEVDLALIT 56 (185)
T ss_pred HHHHHHHHHHHHCCCeEEEEEECCh-------HHHHHHHHCCCCcEEEEe
Confidence 3457777777766 67777755321 267899999999999864
No 98
>KOG1418|consensus
Probab=32.95 E-value=23 Score=34.39 Aligned_cols=58 Identities=21% Similarity=0.347 Sum_probs=47.2
Q ss_pred CCcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeec
Q psy936 238 ELYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTL 295 (344)
Q Consensus 238 ~~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~ 295 (344)
..+++..++++++.++..-| +...|++..+|++.+++.++++-+.-..-+++..+|+.
T Consensus 112 ~~W~f~~al~fs~tv~TTIGYG~i~P~T~~Gr~~~i~YaliGIPl~li~l~~~g~~l~~ 170 (433)
T KOG1418|consen 112 QQWSFSSALLFSITVITTIGYGNIAPRTDAGRLFTILYALVGIPLMLLILADIGKFLAD 170 (433)
T ss_pred cceecchhHhhhhheeeeccCCcccCCcCcchhHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 36789999999999888877 45789999999999999999998877666666555544
No 99
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=32.08 E-value=37 Score=31.85 Aligned_cols=42 Identities=17% Similarity=0.182 Sum_probs=29.0
Q ss_pred HHHHHHHHHHCC-CcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 92 FEILNTLSAKYE-FSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 92 ~~ll~~la~~ln-ft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
..+.+.++++++ .+++++.... ....+..+.+|++|+++...
T Consensus 48 ~~la~~~~~~~~~i~v~~~~~~~------~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 48 GAIAQLINKKSGKLRVRVQSTGG------SVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred HHHHHHHhccCCCeeEEEEeCcc------hHHHHHHHhCCCCcEEEEcc
Confidence 356677777776 6666655221 12578899999999998764
No 100
>KOG0498|consensus
Probab=31.94 E-value=42 Score=36.44 Aligned_cols=88 Identities=17% Similarity=0.217 Sum_probs=63.8
Q ss_pred chhHHHHHHHHHHcCCC-CCCCCCcchhHHHHHHHHHHHHHHhhcccceeeeeecCC-----CCCCCCCHHHHhCC----
Q psy936 242 ISACTWFVYGALMKQGS-TLNPRTDSTRIMFASWWIFIMILTAFYTANLTAFLTLSQ-----FTLPIHSVEDIANP---- 311 (344)
Q Consensus 242 i~~~~~~~~~~ll~qg~-~~~p~s~s~Ril~~~w~l~~lil~~~Yta~L~s~Lt~~~-----~~~~I~TledL~~s---- 311 (344)
...|+|+.+..+...|. ...+.+.+..++.++.+++++++.+..-||+++++..-. +...++.+++-...
T Consensus 295 Y~~aLyw~l~tLstvG~g~~~s~~~~E~iFsi~~mi~GllL~A~lIGNmt~~iqs~tsR~~~~r~k~rd~e~~m~~~~LP 374 (727)
T KOG0498|consen 295 YVYALYWGLSTLSTVGYGLVHANNMGEKIFSIFIMLFGLLLFAYLIGNMTALLQSLTSRTEEMRDKMRDAEQWMSRRQLP 374 (727)
T ss_pred HHHHHHHHhhHhhhccCCccCCCCcHHHHHHHHHHHHhHHHHHHHHhhHHHhHHHHhHHHHHHHHHHHHHHHHHHhccCC
Confidence 44678888888877775 467888999999999999999999999999999887643 22334444444332
Q ss_pred -----------CCcEEEEcCchhhHhhhh
Q psy936 312 -----------TNTWCAEAGGAVEYSIKL 329 (344)
Q Consensus 312 -----------~~~~g~~~~~~~e~~l~~ 329 (344)
-++|-..+|-..|..+++
T Consensus 375 ~~LRqRi~~y~q~kw~~t~Gvdee~lL~~ 403 (727)
T KOG0498|consen 375 PDLRQRIRRYEQYKWLATRGVDEEELLQS 403 (727)
T ss_pred HHHHHHHHHHHHHHHhhccCcCHHHHHHh
Confidence 136666666666666665
No 101
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=31.25 E-value=1.3e+02 Score=24.95 Aligned_cols=73 Identities=12% Similarity=0.134 Sum_probs=46.3
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...........
T Consensus 13 ~~l~~~l~~~~~~~P~i~l~i~~~~-------~~~~~~~l~~g~~D~~i~~~~~~~~~~~-------------------- 65 (200)
T cd08453 13 SVLPELVRRFREAYPDVELQLREAT-------SDVQLEALLAGEIDAGIVIPPPGASAPP-------------------- 65 (200)
T ss_pred HHHHHHHHHHHHhCCCceEEEEeCC-------HHHHHHHHHcCCCCEEEEecCcccCCCc--------------------
Confidence 44567888888776 6677765421 1257899999999999864322110111
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.++ ..++....+++++++.+.
T Consensus 66 ---~~~-~~~l~~~~~~~v~~~~hp 86 (200)
T cd08453 66 ---ALA-YRPLLSEPLVLAVPAAWA 86 (200)
T ss_pred ---cee-EEEeeeCceEEEEECCCc
Confidence 222 346777888888887654
No 102
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=31.18 E-value=91 Score=25.80 Aligned_cols=44 Identities=11% Similarity=0.107 Sum_probs=31.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++...
T Consensus 13 ~~l~~~l~~~~~~~P~i~v~~~~~~-------~~~~~~~l~~g~~D~~i~~~ 57 (198)
T cd08447 13 SFLPRLLAAARAALPDVDLVLREMV-------TTDQIEALESGRIDLGLLRP 57 (198)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEeCC-------HHHHHHHHHcCCceEEEecC
Confidence 45567888887776 5666665421 12678899999999998643
No 103
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=30.61 E-value=1e+02 Score=27.87 Aligned_cols=43 Identities=16% Similarity=0.237 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 91 AFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 91 ~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.-.+.+.|++++|.+++++...+- ..+...+.+|++|+++.+-
T Consensus 16 ~~~l~~~L~~~~g~~v~~~~~~~~------~~~~~~l~~g~~D~~~~~~ 58 (243)
T PF12974_consen 16 WAPLADYLSKQLGVPVELVPADDY------AEFIEALRSGEIDLAFMGP 58 (243)
T ss_dssp HHHHHHHHHHHHTSEEEEE--SSH------HHHHHHHHTTS-SEEE--H
T ss_pred HHHHHHHHHHHhCCCEEEEEcCCH------HHHHHHHHcCCccEEEECc
Confidence 447889999999999998776532 3788999999999997654
No 104
>KOG3684|consensus
Probab=30.09 E-value=1.2e+02 Score=31.03 Aligned_cols=48 Identities=15% Similarity=0.098 Sum_probs=35.1
Q ss_pred cCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhccc
Q psy936 240 YPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFYTA 287 (344)
Q Consensus 240 ~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Yta 287 (344)
-.+.++.|+..-+++..| ++..|.+.-+|.+.+.--+.+-..++.-.|
T Consensus 286 ~~~~nsmWli~iTFlsiGYGDiVP~TycGr~v~l~tGivGa~~sallvA 334 (489)
T KOG3684|consen 286 INYLNSMWLIAITFLSIGYGDIVPNTYCGRGVALLTGIVGAGCSSLLVA 334 (489)
T ss_pred HHHHhhHHHHHHHHhhcccCcccCCccccchHHHHhhhhhhhHHHHHHH
Confidence 348899999999999888 568999999998866555444444444333
No 105
>TIGR02136 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975.
Probab=29.79 E-value=77 Score=29.88 Aligned_cols=78 Identities=14% Similarity=0.127 Sum_probs=46.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++.... .+.++..+.+|++|+++..-....+...+.
T Consensus 48 ~~lp~~l~~f~~~~P~i~v~i~~~~-------s~~l~~~L~~G~iDlai~~~~~~~~~~~~~------------------ 102 (287)
T TIGR02136 48 PLAEAAAEEFQKIHPGVSVTVQGAG-------SGTGIKALINGTVDIGNSSRPIKDEELQKD------------------ 102 (287)
T ss_pred HHHHHHHHHHHhhCCCceEEEccCC-------chHHHHHHHcCCCchhhccCCCCHHHHHHH------------------
Confidence 34567777887777 5666654422 237899999999999986543322221000
Q ss_pred cccEEEe-ceeeccceeEEEEeCCC
Q psy936 168 EAMKWKW-GIELGQSQYVVMMKRPH 191 (344)
Q Consensus 168 ~~~~v~f-s~p~~~~~~~~~v~~~~ 191 (344)
+....++ ..++....+++++++.+
T Consensus 103 ~~~~~~l~~~~l~~~~l~lvv~~~h 127 (287)
T TIGR02136 103 KQKGIKLIEHKVAVDGLAVVVNKKN 127 (287)
T ss_pred hhcCCCceEEEEEEeeEEEEECCCC
Confidence 0001122 23788888999988765
No 106
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=29.04 E-value=1.1e+02 Score=28.67 Aligned_cols=38 Identities=11% Similarity=0.002 Sum_probs=28.4
Q ss_pred HHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeecc
Q psy936 97 TLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVP 140 (344)
Q Consensus 97 ~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~ 140 (344)
.+++++|.+++++..+.. ..++..+..|++|+++.+..
T Consensus 20 ~~~k~~Gl~Ve~~~~~~~------~~~~~al~~G~iD~~~~~~~ 57 (300)
T TIGR01729 20 AAAKEAGATIDWRKFDSG------ADISTALASGNVPIGVIGSS 57 (300)
T ss_pred chHHhcCCeeEEEecCcH------HHHHHHHHcCCCCEeccCCC
Confidence 366778999998775321 26889999999999975543
No 107
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=28.89 E-value=1.2e+02 Score=28.79 Aligned_cols=69 Identities=13% Similarity=0.087 Sum_probs=45.5
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+...++..+.+.+ +.+++... ..+..+.|.+|++|+++...... ..
T Consensus 130 ~~l~~~l~~f~~~~P~i~i~~~~---------~~~~~~~l~~g~~Dl~i~~~~~~---~~-------------------- 177 (317)
T PRK11482 130 LVMPVIYQAIKTHYPQLLLRNIP---------ISDAENQLSQFQTDLIIDTHSCS---NR-------------------- 177 (317)
T ss_pred HHHHHHHHHHHHHCCCCEEEEec---------chhHHHHHHCCCcCEEEeccCCC---CC--------------------
Confidence 34567777787776 55543211 12578999999999998755422 12
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+.. .++....++++++..++.
T Consensus 178 ---~~~~-~~l~~~~~~lv~~~~hpl 199 (317)
T PRK11482 178 ---TIQH-HVLFTDNVVLVCRQGHPL 199 (317)
T ss_pred ---ceEE-EEEecCcEEEEEeCCCCc
Confidence 3333 478888899998877654
No 108
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=28.85 E-value=1.2e+02 Score=25.61 Aligned_cols=71 Identities=17% Similarity=0.207 Sum_probs=45.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++.... ...+.+.+.+|++|+++....... ..
T Consensus 13 ~~l~~~l~~f~~~~P~~~i~i~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~--~~-------------------- 63 (198)
T cd08443 13 YVLPPVIKGFIERYPRVSLQMHQGS-------PTQIAEMVSKGLVDFAIATEALHD--YD-------------------- 63 (198)
T ss_pred eECcHHHHHHHHHCCCeEEEEEeCC-------HHHHHHHHHCCCccEEEEeccccc--cC--------------------
Confidence 55668888888876 6667765422 126788999999999986432111 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..++.....+++++..+.
T Consensus 64 ---~~~-~~~l~~~~~~~v~~~~hp 84 (198)
T cd08443 64 ---DLI-TLPCYHWNRCVVVKRDHP 84 (198)
T ss_pred ---Cce-EeeeeeceEEEEEcCCCc
Confidence 222 346777788888876654
No 109
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=28.53 E-value=79 Score=27.24 Aligned_cols=29 Identities=17% Similarity=0.106 Sum_probs=20.7
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHH
Q psy936 200 LAPFEIEVWFLILISLVLIGPIMHAIMRV 228 (344)
Q Consensus 200 l~PF~~~vWl~il~~~i~~~~vl~~i~r~ 228 (344)
-.|..+.++++|++++++++.+++.+.|-
T Consensus 114 ~~~~~~~i~~~i~g~ll~i~~giy~~~r~ 142 (145)
T PF10661_consen 114 KKPISPTILLSIGGILLAICGGIYVVLRK 142 (145)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667777787877877777777777653
No 110
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=28.45 E-value=1.5e+02 Score=24.29 Aligned_cols=73 Identities=14% Similarity=0.165 Sum_probs=46.4
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccch--hhhhHHHhhhhhhHHHHHHHHhh
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVL--NIKKNKMAALVKSEEEELKLQLQ 165 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~--~~r~~~~~~~~~~~~~~~~~~~~ 165 (344)
.+-.+++..+.+++ +.++++...+ ...+.+.+.+|++|+++...... .....
T Consensus 13 ~~l~~~l~~~~~~~P~i~i~~~~~~-------~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~------------------ 67 (200)
T cd08423 13 ALLPPALAALRARHPGLEVRLREAE-------PPESLDALRAGELDLAVVFDYPVTPPPDDP------------------ 67 (200)
T ss_pred HhhhHHHHHHHHhCCCCeEEEEeCC-------HHHHHHHHhcCCccEEEEeccccccCCCCC------------------
Confidence 34557788888876 5677765422 12578999999999998643210 01111
Q ss_pred hccccEEEeceeeccceeEEEEeCCCC
Q psy936 166 QEEAMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 166 ~~~~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+ ...++.....++++++.+.
T Consensus 68 -----~~-~~~~l~~~~~~~~~~~~~p 88 (200)
T cd08423 68 -----GL-TRVPLLDDPLDLVLPADHP 88 (200)
T ss_pred -----Cc-EEEEeccCcEEEEecCCCC
Confidence 22 2457788888888876654
No 111
>KOG4390|consensus
Probab=27.61 E-value=29 Score=34.82 Aligned_cols=46 Identities=17% Similarity=0.288 Sum_probs=34.9
Q ss_pred CcCchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhh
Q psy936 239 LYPISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAF 284 (344)
Q Consensus 239 ~~~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~ 284 (344)
.-++-..+|+++-++...| +++.|.+..++|+-.+..+.++++++.
T Consensus 354 FTsIPaaFWYTIVTmTTLGYGDMVp~TIaGKIfGsiCSLSGVLVIAL 400 (632)
T KOG4390|consen 354 FTSIPAAFWYTIVTMTTLGYGDMVPSTIAGKIFGSICSLSGVLVIAL 400 (632)
T ss_pred cccCcHhHhhheeeeeeccccccchHHHHHHHhhhhhcccceEEEec
Confidence 3468899999998887777 568999999999887766655544443
No 112
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=27.57 E-value=1.1e+02 Score=28.00 Aligned_cols=70 Identities=13% Similarity=0.121 Sum_probs=45.3
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+..+++..+.+++ +.++++.... ...+...+.+|++|+++...... ..
T Consensus 103 ~~~~~l~~~~~~~P~i~i~v~~~~-------~~~~~~~l~~g~~Di~i~~~~~~---~~--------------------- 151 (290)
T PRK10837 103 ILPAMIARYRRDYPQLPLELSVGN-------SQDVINAVLDFRVDIGLIEGPCH---SP--------------------- 151 (290)
T ss_pred hhHHHHHHHHHHCCCceEEEEECC-------HHHHHHHHHhCCceEEEecCCCC---CC---------------------
Confidence 3457777777776 6677765422 12688899999999998643221 11
Q ss_pred ccEEEeceeeccceeEEEEeCCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+. ..++.....++++++.++.
T Consensus 152 --~~~-~~~l~~~~~~lv~~~~hpl 173 (290)
T PRK10837 152 --ELI-SEPWLEDELVVFAAPDSPL 173 (290)
T ss_pred --cee-EEEeecceEEEEEcCCChh
Confidence 222 2467778888888876653
No 113
>PRK07377 hypothetical protein; Provisional
Probab=27.48 E-value=71 Score=28.65 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=36.7
Q ss_pred eehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
+-.++.++.+.++++.+++++..++.. .+.+.+.+|++|++++.-
T Consensus 93 ~~l~~~l~~~~~~y~~rlElv~y~~~~------~l~~aL~~~eVh~~c~~~ 137 (184)
T PRK07377 93 DQLIDQLRTILDKYHLRLELVVYPDLQ------ALEQALRDKEVHAICLES 137 (184)
T ss_pred HHHHHHHHHHHHHhCceeeEEecCCHH------HHHHHHhcCCccEEecCC
Confidence 446788899999999999999866543 688899999999887644
No 114
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=25.98 E-value=1.5e+02 Score=27.80 Aligned_cols=68 Identities=12% Similarity=0.173 Sum_probs=43.9
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+...++..+.+++ +..+++...+. ..+...+.+|++|+++....... .
T Consensus 106 ~~~~~l~~~~~~~p~i~l~~~~~~~-------~~~~~~l~~g~~Di~i~~~~~~~---~--------------------- 154 (305)
T PRK11233 106 LTMPLLQAVRAEFPGIVLYLHENSG-------ATLNEKLMNGQLDMAVIYEHSPV---A--------------------- 154 (305)
T ss_pred HHHHHHHHHHHHCCCcEEEEEECCc-------HHHHHHHHCCCCCEEEEcCCcCC---C---------------------
Confidence 3446788888876 66666654221 25788999999999986432211 1
Q ss_pred ccEEEeceeeccceeEEEEeCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.++ ..++.+..+++++++.+
T Consensus 155 --~~~-~~~l~~~~~~lv~~~~~ 174 (305)
T PRK11233 155 --GLS-SQPLLKEDLFLVGTQDC 174 (305)
T ss_pred --CcE-EEEEeeeeEEEEEcCcc
Confidence 222 23777888888887654
No 115
>PF13531 SBP_bac_11: Bacterial extracellular solute-binding protein; PDB: 2HXW_B 3FJG_C 3FJM_B 3FJ7_B 3FIR_B 3AXF_C 1WOD_A 1AMF_A 3R26_A 1SBP_A ....
Probab=25.97 E-value=73 Score=28.43 Aligned_cols=87 Identities=13% Similarity=0.109 Sum_probs=54.0
Q ss_pred eehHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccc-eecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTG-EVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g-~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
+..-++++.++++.+++++++..+. +.+...+..| ++|+.+..-....++.. .+
T Consensus 11 ~~~~~l~~~f~~~~g~~v~v~~~~s-------~~~~~~l~~g~~~Dv~~~~~~~~~~~l~------------------~~ 65 (230)
T PF13531_consen 11 PALEELAEAFEKQPGIKVEVSFGGS-------GELVRRLQAGKKPDVFIPASSEWLERLA------------------AA 65 (230)
T ss_dssp HHHHHHHHHHHHHHCEEEEEEEECH-------HHHHHHHHTT-S-SEEEESSHHHHHHHH------------------HT
T ss_pred HHHHHHHHHHHhccCCeEEEEECCh-------HHHHHHHhcCCCceEEEECCHHHHHHHH------------------hc
Confidence 3445778888788888888776432 3577777765 89998776543333322 01
Q ss_pred cccEEE--eceeeccceeEEEEeCCCC--CCCccccccc
Q psy936 168 EAMKWK--WGIELGQSQYVVMMKRPHE--SATGSGLLAP 202 (344)
Q Consensus 168 ~~~~v~--fs~p~~~~~~~~~v~~~~~--~~~~~~~l~P 202 (344)
..++ -..|+..+.+++++++... ..+|..+..|
T Consensus 66 --g~~~~~~~~~~~~~~~vl~~~~~~~~~~~~~~dL~~~ 102 (230)
T PF13531_consen 66 --GLVDPGSPAPLARSPLVLAVPKGNPKGIRSWADLAQP 102 (230)
T ss_dssp --TTCSGGGEEEEEEEEEEEEEETTSTTSTTCHHHHCST
T ss_pred --ccccCCcccccccCceEEEeccCcccccCCHHHHhhc
Confidence 1223 4568888899999998873 3345555443
No 116
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=25.89 E-value=1e+02 Score=30.19 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=40.6
Q ss_pred HHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccc
Q psy936 92 FEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPV 141 (344)
Q Consensus 92 ~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~ 141 (344)
-.+-+++.++.|-.+++...++...|. ...+++.++.|.+|+...+...
T Consensus 47 ~~fa~~v~ekt~G~l~i~vfP~~qLG~-~~~~ie~l~~G~id~~~~s~~~ 95 (332)
T COG1638 47 KKFAELVEEKTGGRLKIEVFPNSQLGG-EAEMIEQLRSGTLDIGVVSLGF 95 (332)
T ss_pred HHHHHHHHHHhCCeEEEEECCCcccCc-HHHHHHHHhcCCeeEEeccchh
Confidence 467788899999999999998888773 4579999999999999776543
No 117
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=25.62 E-value=1.8e+02 Score=25.42 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=28.6
Q ss_pred HHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccc
Q psy936 98 LSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPV 141 (344)
Q Consensus 98 la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~ 141 (344)
+-++.|.+++++.... ....+..|..|++|++++....
T Consensus 15 ~f~~~gl~ve~~~~~~------~~~~~~~l~~G~~D~~~~~~~~ 52 (216)
T PF09084_consen 15 YFKEEGLDVEIVFFGG------GGDVLEALASGKADIAVAGPDA 52 (216)
T ss_dssp HHHHTTEEEEEEEESS------HHHHHHHHHTTSHSEEEEECHH
T ss_pred CCccCeEEEEEEEecC------hhHHHHHHhcCCceEEeccchH
Confidence 4456688888887632 2378899999999999887753
No 118
>cd08428 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-
Probab=25.26 E-value=1.6e+02 Score=24.30 Aligned_cols=40 Identities=15% Similarity=0.267 Sum_probs=26.4
Q ss_pred HHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEee
Q psy936 92 FEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAF 138 (344)
Q Consensus 92 ~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~ 138 (344)
..++..+.++.+.++++.... ...+.+.+.+|++|+++..
T Consensus 16 ~~~l~~f~~~~~v~l~l~~~~-------~~~~~~~l~~~~~D~~i~~ 55 (195)
T cd08428 16 LPALAPVLKRERILLDLIVDD-------EDRTHDLLRDGEVVGCIST 55 (195)
T ss_pred HHHHHHHHhCcCeEEEEEeCC-------chhHHHHHHcCcceEEEEe
Confidence 356777777765555554422 1257889999999988753
No 119
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=25.01 E-value=1.5e+02 Score=27.76 Aligned_cols=71 Identities=11% Similarity=0.197 Sum_probs=45.1
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+..+++..+.+.+ +.++++.... ...+++.+.+|++|+++....... ...
T Consensus 111 ~l~~~l~~~~~~~p~v~i~~~~~~-------~~~~~~~l~~g~~Dl~i~~~~~~~-~~~--------------------- 161 (312)
T PRK10341 111 FMSDMINKFKEVFPKAQVSMYEAQ-------LSSFLPAIRDGRLDFAIGTLSNEM-KLQ--------------------- 161 (312)
T ss_pred hHHHHHHHHHHhCCCCEEEEEeCC-------HHHHHHHHHcCCCcEEEecCCccc-ccC---------------------
Confidence 3457777777765 4556655422 136899999999999986542111 111
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+. ..|+.....++++++.++
T Consensus 162 --~l~-~~~l~~~~~~lv~~~~~p 182 (312)
T PRK10341 162 --DLH-VEPLFESEFVLVASKSRT 182 (312)
T ss_pred --Cee-EEEEecccEEEEEcCCCc
Confidence 222 347888888899887654
No 120
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=24.52 E-value=1.6e+02 Score=27.91 Aligned_cols=69 Identities=10% Similarity=0.109 Sum_probs=45.5
Q ss_pred hHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccc
Q psy936 91 AFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEA 169 (344)
Q Consensus 91 ~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~ 169 (344)
-.+++..+.+++ +..+++.... ...+...|.+|++|+++..-... ..
T Consensus 104 l~~~l~~~~~~~P~i~l~~~~~~-------~~~~~~~L~~g~~Dl~i~~~~~~---~~---------------------- 151 (317)
T PRK15421 104 LTPALENFHKNWPQVEMDFKSGV-------TFDPQPALQQGELDLVMTSDILP---RS---------------------- 151 (317)
T ss_pred HHHHHHHHHHHCCCceEEEEeCc-------cHHHHHHHHCCCcCEEEecCccc---CC----------------------
Confidence 456777777775 5666665422 12678999999999998643221 11
Q ss_pred cEEEeceeeccceeEEEEeCCCCC
Q psy936 170 MKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 170 ~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+.+ .++.....+++++..++.
T Consensus 152 -~~~~-~~l~~~~~~lv~~~~hpl 173 (317)
T PRK15421 152 -GLHY-SPMFDYEVRLVLAPDHPL 173 (317)
T ss_pred -CceE-EEeccceEEEEEcCCCCc
Confidence 3333 578888899998877643
No 121
>TIGR01256 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.
Probab=23.39 E-value=1.7e+02 Score=25.75 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=27.8
Q ss_pred HHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccc-eecEEEeec
Q psy936 92 FEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTG-EVDMVAAFV 139 (344)
Q Consensus 92 ~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g-~~Di~~~~~ 139 (344)
-++++.+.++.+.++++..-. .+.++..+.+| ++|+.++.-
T Consensus 9 ~~~~~~f~~~~gi~V~~~~~g-------s~~l~~~l~~~~~aDv~~~~~ 50 (216)
T TIGR01256 9 KEIAKQFEKRTGNKVVFSFGS-------SGTLYTQIENGAPADLFISAD 50 (216)
T ss_pred HHHHHHHHHhhCCeEEEEeCC-------hHHHHHHHHcCCCCcEEEECC
Confidence 467788888888887765422 13466777666 499998754
No 122
>COG4762 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.04 E-value=68 Score=27.97 Aligned_cols=53 Identities=17% Similarity=0.152 Sum_probs=33.2
Q ss_pred ccceeeeceeeeeecCCCceeeEE-eeccCCCCcccccCCCCCccccCCCceEEEE
Q psy936 5 QPLTIRSACQVYLIPDEHTRYQVD-LTLTGRPDQAYQQSGLPDSWLIIEQLRLPIE 59 (344)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~p~~~~~l~g~~L~v~ 59 (344)
.||+.|+.|+|.+..++.+++-+. -++.+...+.+. -|--.+.......+.|.
T Consensus 81 g~w~~r~~cRVL~l~d~~~~~gf~yGTL~ghv~rgeE--rflierda~d~V~~~i~ 134 (168)
T COG4762 81 GIWFLRAPCRVLYLIDEPDVRGFGYGTLPGHVVRGEE--RFLIERDAMDSVVFEIL 134 (168)
T ss_pred eeeeeecccEEEEEecCCceeEEeecccCCccccchh--heeEEecCCCcEEEEee
Confidence 589999999999999998888774 345443332222 23333334444556666
No 123
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=22.89 E-value=2e+02 Score=26.60 Aligned_cols=72 Identities=14% Similarity=0.242 Sum_probs=45.3
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+..+++..+.+++ +.++++..... ..++.++.+|++|++++...... ...
T Consensus 107 ~~~~~l~~~~~~~P~~~i~~~~~~~-------~~~~~~l~~g~~D~~i~~~~~~~-~~~--------------------- 157 (300)
T TIGR02424 107 LMPEVVKRFLARAPRLRVRIMTGPN-------AYLLDQLRVGALDLVVGRLGAPE-TMQ--------------------- 157 (300)
T ss_pred hhHHHHHHHHHhCCCcEEEEEeCch-------HHHHHHHHCCCCCEEEEecCCcc-ccc---------------------
Confidence 3456677777766 44555554221 26888999999999987543211 112
Q ss_pred ccEEEeceeeccceeEEEEeCCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.+.+ .|+.....++++++.++.
T Consensus 158 --~~~~-~~l~~~~~~~~~~~~hpl 179 (300)
T TIGR02424 158 --GLSF-EHLYNEPVVFVVRAGHPL 179 (300)
T ss_pred --ceee-eeecCCceEEEEcCCCcc
Confidence 3332 378888889998876543
No 124
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=22.64 E-value=1.5e+02 Score=27.31 Aligned_cols=65 Identities=14% Similarity=0.217 Sum_probs=41.2
Q ss_pred HHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhccccEE
Q psy936 93 EILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAMKW 172 (344)
Q Consensus 93 ~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~v 172 (344)
.++..+.++.+..+++...+. ..+.+.+.+|++|+++...... .. .+
T Consensus 107 ~~l~~~~~~~~i~i~l~~~~~-------~~~~~~l~~g~~d~~i~~~~~~---~~-----------------------~l 153 (292)
T TIGR03298 107 PALAPVLAQEGVLLDLVVEDQ-------DHTAELLRSGEVLGAVTTQAKP---VQ-----------------------GC 153 (292)
T ss_pred HHHHHHHhCCCceEEEEeCcc-------hhHHHHHhCCCceEEEecCCCC---CC-----------------------Cc
Confidence 456667666555555544221 2478899999999998654322 12 33
Q ss_pred EeceeeccceeEEEEeCCC
Q psy936 173 KWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 173 ~fs~p~~~~~~~~~v~~~~ 191 (344)
. +.++....++++++++.
T Consensus 154 ~-~~~l~~~~~~~v~~~~~ 171 (292)
T TIGR03298 154 R-VVPLGAMRYLAVASPAF 171 (292)
T ss_pred e-EEecCCceEEEEECchh
Confidence 3 34778888888887653
No 125
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=22.42 E-value=1.8e+02 Score=27.25 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=31.8
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+..+++..+.+++ +.++++...+. ..+...+.+|++|+++...
T Consensus 107 ~~l~~~l~~~~~~~P~v~i~i~~~~~-------~~~~~~l~~~~~Dl~i~~~ 151 (309)
T PRK11013 107 SLLPGLCQPFLARYPDVSLNIVPQES-------PLLEEWLSAQRHDLGLTET 151 (309)
T ss_pred hhHHHHHHHHHHHCCCCeEEEEeCCH-------HHHHHHHHcCCCCEEEEcC
Confidence 34567888888776 67777665332 2577899999999998644
No 126
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=22.35 E-value=1.2e+02 Score=28.03 Aligned_cols=41 Identities=24% Similarity=0.200 Sum_probs=32.5
Q ss_pred eeeeecCCCCCCCCCHHHHhCC-CCcEEEEcCchhhHhhhhc
Q psy936 290 TAFLTLSQFTLPIHSVEDIANP-TNTWCAEAGGAVEYSIKLY 330 (344)
Q Consensus 290 ~s~Lt~~~~~~~I~TledL~~s-~~~~g~~~~~~~e~~l~~~ 330 (344)
.++++.......+++++||.+. +.++|+..|+..+.++++.
T Consensus 121 ~~~~~~~~~~~~i~~~~dl~~~~g~~Igv~~g~~~~~~l~~~ 162 (275)
T TIGR02995 121 EALLVKKGNPKGLKSYKDIAKNPDAKIAAPGGGTEEKLAREA 162 (275)
T ss_pred eeEEEECCCCCCCCCHHHhccCCCceEEEeCCcHHHHHHHHc
Confidence 4566766544568999999764 6899999999999998874
No 127
>KOG1545|consensus
Probab=22.26 E-value=17 Score=36.18 Aligned_cols=76 Identities=18% Similarity=0.222 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccCCCCCCc-CchhHHHHHHHHHHcCC-CCCCCCCcchhHHHHHHHHHHHHHHhhc
Q psy936 209 FLILISLVLIGPIMHAIMRVRRWLSGTQSELY-PISACTWFVYGALMKQG-STLNPRTDSTRIMFASWWIFIMILTAFY 285 (344)
Q Consensus 209 l~il~~~i~~~~vl~~i~r~~~~~~~~~~~~~-~i~~~~~~~~~~ll~qg-~~~~p~s~s~Ril~~~w~l~~lil~~~Y 285 (344)
+++++.+++++++++.-. .+-.+..+++..+ ++-+++|+..-++...| +++.|.+..++++-....+.+++.++.=
T Consensus 361 lgLLIFFlfIgviLFsSa-vYFAEade~~S~F~SIPdaFWwavVTMTTVGYGDm~P~TvgGKIVGslCAiaGVLTiALP 438 (507)
T KOG1545|consen 361 LGLLIFFLFIGVILFSSA-VYFAEADEPESHFSSIPDAFWWAVVTMTTVGYGDMVPVTVGGKIVGSLCAIAGVLTIALP 438 (507)
T ss_pred HHHHHHHHHHHHHHHhce-eeeeecCCCccCCCcCcccceEEEEEEEeeccccceecccCceehhhHHhhhhheEeccc
Confidence 345555555666654433 2223334444444 68999999877777777 5689999999999877777766555543
No 128
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=21.69 E-value=1.6e+02 Score=27.04 Aligned_cols=71 Identities=13% Similarity=0.032 Sum_probs=44.4
Q ss_pred ehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcc
Q psy936 90 IAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEE 168 (344)
Q Consensus 90 ~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~ 168 (344)
+-.+++..+.++. +.++++...+. ..+..++.+|++|+++..... .....
T Consensus 111 ~l~~~l~~f~~~~p~i~l~i~~~~~-------~~~~~~l~~g~~D~~i~~~~~-~~~~~--------------------- 161 (294)
T PRK09986 111 RLRPAMRHFLKENPNVEWLLRELSP-------SMQMAALERRELDAGIWRMAD-LEPNP--------------------- 161 (294)
T ss_pred HHHHHHHHHHHhCCCeEEEEEeCCH-------HHHHHHHHcCCCCEEEecCCc-cCCCC---------------------
Confidence 3456677777766 45666543221 257899999999999853210 01112
Q ss_pred ccEEEeceeeccceeEEEEeCCCC
Q psy936 169 AMKWKWGIELGQSQYVVMMKRPHE 192 (344)
Q Consensus 169 ~~~v~fs~p~~~~~~~~~v~~~~~ 192 (344)
.+.+ .++....+++++++.++
T Consensus 162 --~l~~-~~l~~~~~~~v~~~~~~ 182 (294)
T PRK09986 162 --GFTS-RRLHESAFAVAVPEEHP 182 (294)
T ss_pred --CeEE-EEeecccEEEEEcCCCC
Confidence 3444 47778889899887664
No 129
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=21.56 E-value=1.7e+02 Score=27.46 Aligned_cols=72 Identities=14% Similarity=0.161 Sum_probs=46.6
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.+++ +.++++..... ..+.+.+.+|++|+++....... ..
T Consensus 106 ~~l~~~l~~~~~~~P~i~i~i~~~~~-------~~~~~~l~~g~~D~~i~~~~~~~--~~-------------------- 156 (309)
T PRK12682 106 YVLPRVVAAFRKRYPKVNLSLHQGSP-------DEIARMVISGEADIGIATESLAD--DP-------------------- 156 (309)
T ss_pred HHHHHHHHHHHHhCCCeEEEEecCCH-------HHHHHHHHcCCccEEEecCcccC--CC--------------------
Confidence 45567788887776 55666654221 25788999999999986432111 11
Q ss_pred cccEEEeceeeccceeEEEEeCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHES 193 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~ 193 (344)
.++. .++.....+++++..++.
T Consensus 157 ---~l~~-~~l~~~~~~~~~~~~~pl 178 (309)
T PRK12682 157 ---DLAT-LPCYDWQHAVIVPPDHPL 178 (309)
T ss_pred ---cceE-EEeeeeeEEEEecCCCcc
Confidence 2332 477888888888876643
No 130
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=21.06 E-value=1.8e+02 Score=27.05 Aligned_cols=67 Identities=15% Similarity=0.195 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHCCCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhcccc
Q psy936 91 AFEILNTLSAKYEFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQEEAM 170 (344)
Q Consensus 91 ~~~ll~~la~~lnft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~ 170 (344)
-..++..+.++.|.++++..... ..+.+.+.+|++|+++...... ..
T Consensus 105 l~~~l~~f~~~~~i~i~l~~~~~-------~~~~~~l~~~~~d~~i~~~~~~---~~----------------------- 151 (294)
T PRK03635 105 FLPALAPVLARSGVLLDLVVEDQ-------DHTAELLRRGEVVGAVTTEPQP---VQ----------------------- 151 (294)
T ss_pred HHHHHHHHHhCCCcEEEEEecCc-------HHHHHHHhCCCceEEEeccCCC---CC-----------------------
Confidence 34567777777666666654321 2588999999999998643221 12
Q ss_pred EEEeceeeccceeEEEEeCCC
Q psy936 171 KWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 171 ~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.+ ...++.....+++++..+
T Consensus 152 ~l-~~~~l~~~~~~lv~~~~~ 171 (294)
T PRK03635 152 GC-RVDPLGAMRYLAVASPAF 171 (294)
T ss_pred Cc-eeeecccceEEEEEcchH
Confidence 22 245788888888887653
No 131
>PHA02650 hypothetical protein; Provisional
Probab=20.65 E-value=2.4e+02 Score=21.83 Aligned_cols=31 Identities=10% Similarity=0.289 Sum_probs=19.4
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHhh
Q psy936 200 LAPFEIEVWFLILISLVLIGPIMHAIMRVRR 230 (344)
Q Consensus 200 l~PF~~~vWl~il~~~i~~~~vl~~i~r~~~ 230 (344)
..++.|..|+.++++++++.++.++..+..+
T Consensus 44 ~~~~~~~~~ii~i~~v~i~~l~~flYLK~~~ 74 (81)
T PHA02650 44 VSWFNGQNFIFLIFSLIIVALFSFFVFKGYT 74 (81)
T ss_pred cCCchHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4567788887776666665555555544444
No 132
>cd08478 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene wh
Probab=20.46 E-value=1.7e+02 Score=24.21 Aligned_cols=66 Identities=11% Similarity=0.184 Sum_probs=40.9
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
++-.+++..+.+++ +.++++... .....+.+|++|+++...... ..
T Consensus 16 ~~l~~~l~~f~~~~P~v~i~~~~~----------~~~~~l~~~~~D~~i~~~~~~---~~-------------------- 62 (199)
T cd08478 16 HLLAPLIAKFRERYPDIELELVSN----------EGIIDLIERKTDVAIRIGELT---DS-------------------- 62 (199)
T ss_pred HHHHHHHHHHHHHCCCeEEEEEec----------cccccchhccccEEEEecCCC---CC--------------------
Confidence 34557788888876 566666421 123347789999998643321 12
Q ss_pred cccEEEeceeeccceeEEEEeCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPH 191 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~ 191 (344)
.+. +.++.....++++++.+
T Consensus 63 ---~l~-~~~l~~~~~~~v~~~~~ 82 (199)
T cd08478 63 ---TLH-ARPLGKSRLRILASPDY 82 (199)
T ss_pred ---Cce-EEEcccccEEEEECHHH
Confidence 222 34777888888887654
No 133
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=20.42 E-value=2.2e+02 Score=24.35 Aligned_cols=44 Identities=18% Similarity=0.083 Sum_probs=31.5
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeec
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFV 139 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~ 139 (344)
.+-.+++..+.+++ +.++++.... ...+++.|.+|++|+++...
T Consensus 13 ~~l~~~l~~f~~~~P~v~l~i~~~~-------~~~~~~~L~~~~~D~~i~~~ 57 (204)
T cd08429 13 SIAYRLLEPAMDLHEPIRLVCREGK-------LEQLLADLALHRLDMVLADR 57 (204)
T ss_pred HHHHHHHHHHHHhCCCcEEEEEeCC-------HHHHHHHHHcCCccEEEecC
Confidence 45567888888876 5666665522 12688999999999998544
No 134
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=20.39 E-value=2.6e+02 Score=25.95 Aligned_cols=74 Identities=15% Similarity=0.215 Sum_probs=46.0
Q ss_pred eehHHHHHHHHHHC-CCcEEEEeeCCCCCCCCchhhhhhcccceecEEEeeccchhhhhHHHhhhhhhHHHHHHHHhhhc
Q psy936 89 GIAFEILNTLSAKY-EFSYEIILPSRKTLLDQDGSIMNILKTGEVDMVAAFVPVLNIKKNKMAALVKSEEEELKLQLQQE 167 (344)
Q Consensus 89 G~~~~ll~~la~~l-nft~~~~~~~~~~~G~~~~g~~~~l~~g~~Di~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~ 167 (344)
.+-.+++..+.++. +.++++...+ ...+...+.+|++|+++....... ...
T Consensus 108 ~~l~~~l~~~~~~~p~i~~~~~~~~-------~~~~~~~l~~g~~Di~i~~~~~~~-~~~-------------------- 159 (302)
T PRK09791 108 SLMPAVISRFHQQHPQVKVRIMEGQ-------LVSMINELRQGELDFTINTYYQGP-YDH-------------------- 159 (302)
T ss_pred hhhHHHHHHHHHHCCCeEEEEEeCC-------hHHHHHHHHCCCccEEEEecCCcc-ccc--------------------
Confidence 34456777777766 3445544311 236889999999999986431111 112
Q ss_pred cccEEEeceeeccceeEEEEeCCCCCC
Q psy936 168 EAMKWKWGIELGQSQYVVMMKRPHESA 194 (344)
Q Consensus 168 ~~~~v~fs~p~~~~~~~~~v~~~~~~~ 194 (344)
.+.+ .++....+++++++.+...
T Consensus 160 ---~~~~-~~l~~~~~~l~~~~~~~~~ 182 (302)
T PRK09791 160 ---EFTF-EKLLEKQFAVFCRPGHPAI 182 (302)
T ss_pred ---ceeE-EEeccceEEEEEcCCCCcC
Confidence 3333 5888889999988776543
Done!